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Wang C, Zhang Y, Gong W, Wang S. Highly selective detection of deoxyribonucleic acid in living cells using RecA-green fluorescent protein-single-stranded deoxyribonucleic acid filament fluorescence resonance energy transfer probe. LUMINESCENCE 2024; 39:e4716. [PMID: 38497410 DOI: 10.1002/bio.4716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024]
Abstract
A fluorescence resonance energy transfer (FRET) method was developed for double-stranded deoxyribonucleic acid (dsDNA) detection in living cells using the RecA-GFP (green fluorescent protein) fusion protein filament. In brief, the thiol-modified single-stranded DNA (ssDNA) was attached to gold nanoparticles (AuNPs); on the contrary, the prepared RecA-GFP fusion protein interacted with ssDNA. Due to the FRET between AuNPs and RecA-GFP, fluorescence of RecA-GFP fusion protein was quenched. In the presence of homologous dsDNA, homologous recombination occurred to release RecA-GFP fusion protein. Thus, the fluorescence of RecA-GFP was recovered. The dsDNA concentration was detected using fluorescence intensity of RecA-GFP. Under optimal conditions, this method could detect dsDNA activity as low as 0.015 optical density (OD) Escherichia coli cells, with a wide linear range from 0.05 to 0.9 OD cells, and the regression equation was ΔF = 342.7c + 78.9, with a linear relationship coefficient of 0.9920. Therefore, it provided a promising approach for the selective detection of dsDNA in living cells for early clinical diagnosis of genetic diseases.
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Affiliation(s)
- Chunlei Wang
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Yuanfu Zhang
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Wenyue Gong
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
| | - Shuhao Wang
- Key Laboratory of Food Safety and Life Analysis in Universities of Shandong, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China
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2
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O'Connor EC, Kambara K, Bertrand D. Advancements in the use of xenopus oocytes for modelling neurological disease for novel drug discovery. Expert Opin Drug Discov 2024; 19:173-187. [PMID: 37850233 DOI: 10.1080/17460441.2023.2270902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023]
Abstract
INTRODUCTION Introduced about 50 years ago, the model of Xenopus oocytes for the expression of recombinant proteins has gained a broad spectrum of applications. The authors herein review the benefits brought from using this model system, with a focus on modeling neurological disease mechanisms and application to drug discovery. AREAS COVERED Using multiple examples spanning from ligand gated ion channels to transporters, this review presents, in the light of the latest publications, the benefits offered from using Xenopus oocytes. Studies range from the characterization of gene mutations to the discovery of novel treatments for disorders of the central nervous system (CNS). EXPERT OPINION Development of new drugs targeting CNS disorders has been marked by failures in the translation from preclinical to clinical studies. As progress in genetics and molecular biology highlights large functional differences arising from a single to a few amino acid exchanges, the need for drug screening and functional testing against human proteins is increasing. The use of Xenopus oocytes to enable precise modeling and characterization of clinically relevant genetic variants constitutes a powerful model system that can be used to inform various aspects of CNS drug discovery and development.
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Affiliation(s)
- Eoin C O'Connor
- Roche Pharma Research and Early Development, Neuroscience & Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
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3
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Miller RG. Forensic odontology in disaster victim identification. J Forensic Sci 2024. [PMID: 38291611 DOI: 10.1111/1556-4029.15471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
This paper reviews MFI's from a historical perspective commencing with DVI in the late 20th century. For this paper, this era, 1970-90s is designated as the early modern period. As DVI by DNA analysis is introduced into the process, in the beginning of the mid-1990s, or late modern period, a shift in ID modality usage is noted. A statistical analysis of the primary identification (ID) methods established that dental identification was the majority identifier, or gold standard, in the early modern era. Although primarily viewed from a United States (US) perspective, referenced international incidents parallel the incidents investigated by US authorities. The introduction of DNA demarcated the early from the late modern era. Through research, development, and application this highly discriminating ID method would effectively, surpass dental ID as the gold standard into the late modern era. DNA ID would eventually overcome early criticism regarding cost and time consumption. In the MFI's discussed, the discriminating accuracy of DNA, when referenced against the dental identifications, validated the reliability of dental ID. Errors will be significantly minimized through confirmatory reconciliation by more than one ID method. In conclusion despite increased usage of DNA, dental ID has not been eliminated and remains a major contributor to DVI. Dental ID continues to develop through increased application of advanced imaging technology. Despite DNA's rapid advancement and application to DVI, the multidisciplinary approach to scientific identification should remain in the near future. Therefore, comparative dental ID will remain an important and reliable contributor to DVI.
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Affiliation(s)
- Raymond G Miller
- SUNY at Buffalo, School of Dental Medicine - Oral Diagnostic Sciences, Buffalo, New York, USA
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Wojtara MS, Kang J, Zaman M. Congenital Telangiectatic Erythema: Scoping Review. JMIR Dermatol 2023; 6:e48413. [PMID: 37796556 PMCID: PMC10587801 DOI: 10.2196/48413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/19/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Congenital telangiectatic erythema (CTE), also known as Bloom syndrome, is a rare autosomal recessive disorder characterized by below-average height, a narrow face, a red skin rash occurring on sun-exposed areas of the body, and an increased risk of cancer. CTE is one of many genodermatoses and photodermatoses associated with defects in DNA repair. CTE is caused by a mutation occurring in the BLM gene, which causes abnormal breaks in chromosomes. OBJECTIVE We aimed to analyze the existing literature on CTE to provide additional insight into its heredity, the spectrum of clinical presentations, and the management of this disorder. In addition, the gaps in current research and the use of artificial intelligence to streamline clinical diagnosis and the management of CTE are outlined. METHODS A literature search was conducted on PubMed, DOAJ, and Scopus using search terms such as "congenital telangiectatic erythema," "bloom syndrome," and "bloom-torre-machacek." Due to limited current literature, studies published from January 2000 to January 2023 were considered for this review. A total of 49 sources from the literature were analyzed. RESULTS Through this scoping review, the researchers were able to identify several publications focusing on Bloom syndrome. Some common subject areas included the heredity of CTE, clinical presentations of CTE, and management of CTE. In addition, the literature on rare diseases shows the potential advancements in understanding and treatment with artificial intelligence. Future studies should address the causes of heterogeneity in presentation and examine potential therapeutic candidates for CTE and similarly presenting syndromes. CONCLUSIONS This review illuminated current advances in potential molecular targets or causative pathways in the development of CTE as well as clinical features including erythema, increased cancer risk, and growth abnormalities. Future studies should continue to explore innovations in this space, especially in regard to the use of artificial intelligence, including machine learning and deep learning, for the diagnosis and clinical management of rare diseases such as CTE.
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Affiliation(s)
- Magda Sara Wojtara
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jayne Kang
- Department of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Mohammed Zaman
- Department of Biology, Stony Brook University, Stony Brook, NY, United States
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5
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Corzo HH, Hillers-Bendtsen AE, Barnes A, Zamani AY, Pawłowski F, Olsen J, Jørgensen P, Mikkelsen KV, Bykov D. Corrigendum: Coupled cluster theory on modern heterogeneous supercomputers. Front Chem 2023; 11:1256510. [PMID: 37654900 PMCID: PMC10466216 DOI: 10.3389/fchem.2023.1256510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 09/02/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fchem.2023.1154526.].
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Affiliation(s)
| | | | | | - Abdulrahman Y. Zamani
- Department of Chemistry and Biochemistry and Center for Chemical Computation and Theory, University of California, Merced, CA, United States
| | - Filip Pawłowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, United States
| | - Jeppe Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Poul Jørgensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Dmytro Bykov
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
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6
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Corzo HH, Hillers-Bendtsen AE, Barnes A, Zamani AY, Pawłowski F, Olsen J, Jørgensen P, Mikkelsen KV, Bykov D. Coupled cluster theory on modern heterogeneous supercomputers. Front Chem 2023; 11:1154526. [PMID: 37388945 PMCID: PMC10303140 DOI: 10.3389/fchem.2023.1154526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/11/2023] [Indexed: 07/01/2023] Open
Abstract
This study examines the computational challenges in elucidating intricate chemical systems, particularly through ab-initio methodologies. This work highlights the Divide-Expand-Consolidate (DEC) approach for coupled cluster (CC) theory-a linear-scaling, massively parallel framework-as a viable solution. Detailed scrutiny of the DEC framework reveals its extensive applicability for large chemical systems, yet it also acknowledges inherent limitations. To mitigate these constraints, the cluster perturbation theory is presented as an effective remedy. Attention is then directed towards the CPS (D-3) model, explicitly derived from a CC singles parent and a doubles auxiliary excitation space, for computing excitation energies. The reviewed new algorithms for the CPS (D-3) method efficiently capitalize on multiple nodes and graphical processing units, expediting heavy tensor contractions. As a result, CPS (D-3) emerges as a scalable, rapid, and precise solution for computing molecular properties in large molecular systems, marking it an efficient contender to conventional CC models.
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Affiliation(s)
| | | | | | - Abdulrahman Y. Zamani
- Department of Chemistry and Biochemistry and Center for Chemical Computation and Theory, University of California, Merced, CA, United States
| | - Filip Pawłowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, United States
| | - Jeppe Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Poul Jørgensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Dmytro Bykov
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Oane M, Mihailescu CN, Trefilov AMI. On the Thermal Behavior during Spatial Anisotropic Femtoseconds Laser-DNA Interaction: The Crucial Role of Hermite Polynomials. Materials (Basel) 2023; 16:ma16093334. [PMID: 37176217 PMCID: PMC10179366 DOI: 10.3390/ma16093334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
A novel analytical formalism based on the quantum heat transport equation is proposed for the interaction of fs-laser pulses with deoxyribonucleic acid (DNA) strands. The formalism has the intensity of the laser beam and the interaction time between the laser and the DNA as input parameters. To this end, the thermal distribution generated in the irradiated DNA strands was introduced by splitting the laser beam into transverse Hermite-Gauss modes. To achieve this goal, a new powerful mathematical model was developed and applied. Fluctuations in laser intensity were taken into account by modeling them as superpositions of Hermite-Gauss laser modes. These analyses were carried out for a laser pulse duration of 100 fs, where a tiny heat-affected zone is expected, with positive predicted effects on the stability and repeatability of this technology. The main conclusion is that the laser beam spatial distribution intensity plays an essential role in the generation of the shape and magnitude of the thermal field at the junction of the irradiated DNA strands. The model may prove useful in modeling laser beam processing under significant intensity fluctuations. There are at least two main areas of application for the present model of heat transfer from laser to DNA: (i) the study of DNA elongation without destroying the target information (for a sample temperature variation lower than 10 K; in the case of H[1,y]); and (ii) cancer treatment (especially of skin tissue), where we should obtain a temperature variation higher than 10 K (but lower than 30 K; in the case of H[2,y], H[4,y]), in order to eradicate the diseased cells.
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Affiliation(s)
- Mihai Oane
- National Institute for Laser, Plasma and Radiation Physics, 077125 Măgurele, Romania
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8
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Khatun M, Jana GC, Nayim S, Dhal A, Patra A, Hossain M. Evaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding. J Biomol Struct Dyn 2023; 41:14299-14307. [PMID: 38073529 DOI: 10.1080/07391102.2023.2180436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
The interaction of deoxyribonucleic acid (DNA) with medicinally significant small molecules has long piqued the interest of researchers because its applications are directly related to the discovery of new classes of drugs. Keeping this in mind, here we report berberine derivatives and their interaction with calf thymus DNA (CT-DNA). In this report we discussed on the structural perspectives and thermodynamic characteristics of the interaction of four 9-O-substituted berberines (BRDR1 to BRDR4) with CT-DNA. The binding affinity of BRDR-DNA complexes increased with increasing the cycloalkane ring size of the substitution except BRDR2. The binding constant value obtained from UV-Visible spectral analysis was 1.12 × 106 for BRDR1, 0.37 × 106 for BRDR2, 1.72 × 106 for BRDR3 and 3.20 × 106 for BRDR4. Ferrocyanide quenching experiments revealed unequivocally that the analogues except BRDR2 had a partly intercalative binding to DNA. From the ITC experiment it was found that the bindings of BRDR1, BRDR3 and BRDR4 to DNA was favoured by negative enthalpy and positive entropy while BRDR2 was driven by positive enthalpy and positive entropy. In all cases the hydrophobic interaction plays a crucial role. Thus, the complete multispectroscopic and thermodynamic binding studies may be useful for new drug design and development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Munira Khatun
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Gopal Chandra Jana
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Sk Nayim
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Asima Dhal
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Anirudha Patra
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Maidul Hossain
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
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9
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Azeem MM, Shafa M, Aamir M, Zubair M, Souayeh B, Alam MW. Nucleotide detection mechanism and comparison based on low-dimensional materials: A review. Front Bioeng Biotechnol 2023; 11:1117871. [PMID: 36937765 PMCID: PMC10018150 DOI: 10.3389/fbioe.2023.1117871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.
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Affiliation(s)
- M. Mustafa Azeem
- Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology, Rolla, MO, United States
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Shafa
- Yunnan Key Laboratory of Metal-Organic Molecular Materials and Devices, Kunming University, Kunming, Yunnan, China
| | - Muhammad Aamir
- Department of Basic Science, Deanship of Preparatory Year, King Faisal University, Hofuf, Saudi Arabia
- *Correspondence: M. Mustafa Azeem, ; Muhammad Aamir,
| | - Muhammad Zubair
- Mechanical and Nuclear Engineering Department, University of Sharjah, Sharjah, United Arab Emirates
| | - Basma Souayeh
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
| | - Mir Waqas Alam
- Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
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10
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Bhatkalkar SG, Kumar D, Ali A, Sachar S. Influence of surfactants on biomolecular conjugation of magnetic nanoparticles. J Biomol Struct Dyn 2022; 40:12895-12907. [PMID: 34542389 DOI: 10.1080/07391102.2021.1977701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here, we report the physicochemical interaction among iron oxide nanoparticles (MNPs) and essential biomolecules, namely, serum albumin (BSA, HSA), collagen and deoxyribonucleic acid (DNA) in the presence of various cationic, anionic and non-ionic surfactants. Iron oxide nanoparticles are synthesized by the wet chemical process and are characterized by X-ray powder diffraction analysis (XRD), Fourier transform infrared spectroscopic, UV-Vis spectroscopy, scanning electron microscopy and energy-dispersive X-ray spectroscopy mapping studies . The conjugation of MNPs protein was analyzed using UV-Vis spectroscopy, fluorescence spectroscopy, circular dichroism technique and gel electrophoresis. The spectroscopic investigation illustrates the surfactant-dependent binding between MNPs and protein. Gel electrophoresis in the absence and presence of MNPs-surfactant systems has been used to study the impact on DNA structure. It was found that Tween 80 imparts better stability as well as biocompatibility to the synthesized MNPs. The findings offer extensive information on the influence of various surfactant coatings on MNP surfaces and their influence on vital biomolecules, making it useful for designing MNPs for biological applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Dinesh Kumar
- Department of Life Sciences, University of Mumbai, Vidyanagari, Mumbai, India
| | - Ahmad Ali
- Department of Life Sciences, University of Mumbai, Vidyanagari, Mumbai, India
| | - Shilpee Sachar
- Department of Chemistry, University of Mumbai, Vidyanagari, Mumbai, India
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11
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Szczuka A, Horton J, Evans KJ, DiPietri VT, Sivey JD, Wigginton KR. Chloride Enhances DNA Reactivity with Chlorine under Conditions Relevant to Water Treatment. Environ Sci Technol 2022; 56:13347-13356. [PMID: 36027047 PMCID: PMC9494735 DOI: 10.1021/acs.est.2c03267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Free available chlorine (FAC) is widely used to inactivate viruses by oxidizing viral components, including genomes. It is commonly assumed that hypochlorous acid (HOCl) is the chlorinating agent responsible for virus inactivation; however, recent studies have underscored that minor constituents of FAC existing in equilibrium with HOCl, such as molecular chlorine (Cl2), can influence FAC reactivity toward select organic compounds. This study measures the FAC reaction kinetics with dsDNA and ssDNA extracted from representative bacteriophages (T3 and ϕX174) in samples augmented with chloride. Herein, chloride enhances FAC reactivity toward dsDNA and, to a lesser extent, toward ssDNA, especially at pH < 7.5. The enhanced reactivity can be attributed to the formation of Cl2. Second-order rate constants were determined for reactions of ssDNA and dsDNA with HOCl and Cl2. DNA chlorination kinetics followed the reactivity-selectivity principle, where the more-reactive nucleophilic species (ssDNA, ∼100× more reactive than dsDNA) reacted less selectively with electrophilic FAC species. The addition of chloride was also shown to enhance the inactivation of bacteriophage T3 (dsDNA genome) by FAC but did not enhance the inactivation of bacteriophage ϕX174 (ssDNA genome). Overall, the results suggest that Cl2 is an important chlorinating agent of nucleic acids and viruses.
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Affiliation(s)
- Aleksandra Szczuka
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jordon Horton
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kelsey J. Evans
- Department
of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - Vincent T. DiPietri
- Department
of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - John D. Sivey
- Department
of Chemistry, Towson University, Towson, Maryland 21252, United States
| | - Krista R. Wigginton
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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12
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Hussain A, Jiang W, Wang X, Shahid S, Saba N, Ahmad M, Dar A, Masood SU, Imran M, Mustafa A. Mechanistic Impact of Zinc Deficiency in Human Development. Front Nutr 2022; 9:717064. [PMID: 35356730 PMCID: PMC8959901 DOI: 10.3389/fnut.2022.717064] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
Zinc (Zn) deficiency in humans is an emerging global health issue affecting approximately two billion people across the globe. The situation prevails due to the intake of Zn deficient grains and vegetables worldwide. Clinical identification of Zn deficiency in humans remains problematic because the symptoms do not appear until impair the vital organs, such as the gastrointestinal track, central nervous system, immune system, skeletal, and nervous system. Lower Zn body levels are also responsible for multiple physiological disorders, such as apoptosis, organs destruction, DNA injuries, and oxidative damage to the cellular components through reactive oxygen species (ROS). The oxidative damage causes chronic inflammation lead toward several chronic diseases, such as heart diseases, cancers, alcohol-related malady, muscular contraction, and neuro-pathogenesis. The present review focused on the physiological and growth-related changes in humans under Zn deficient conditions, mechanisms adopted by the human body under Zn deficiency for the proper functioning of the body systems, and the importance of nutritional and nutraceutical approaches to overcome Zn deficiency in humans and concluded that the biofortified food is the best source of Zn as compared to the chemical supplementation to avoid their negative impacts on human.
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Affiliation(s)
- Azhar Hussain
- Department of Soil Science, The Islamia Diversity of Bahawalpur, Bahawalpur, Pakistan
| | - Wenting Jiang
- College of Life Sciences, Yan'an University, Yan'an, China
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, China
| | - Shumaila Shahid
- Department of Soil Science, The Islamia Diversity of Bahawalpur, Bahawalpur, Pakistan
| | - Noreena Saba
- Qaid-e-Azam Medical College, Bahawal Victoria Hospital, Bahawalpur, Pakistan
| | - Maqshoof Ahmad
- Department of Soil Science, The Islamia Diversity of Bahawalpur, Bahawalpur, Pakistan
| | - Abubakar Dar
- Department of Soil Science, The Islamia Diversity of Bahawalpur, Bahawalpur, Pakistan
| | - Syed Usama Masood
- Clinical Fellow Pediatric Nephrology, Children Hospital and Institute of Child Health Multan, Multan, Pakistan
| | | | - Adnan Mustafa
- Faculty of Chemistry, Institute of Chemistry and Technology of Environmental Protection, Brno University of Technology, Brno, Czechia
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition (FA), Mendel University, Brno, Czechia
- Institute of Environmental Studies, Charles University Prague, Prague, Czechia
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13
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Qiao Z, Ye Y, Szczuka A, Harrison KR, Dodd MC, Wigginton KR. Reactivity of Viral Nucleic Acids with Chlorine and the Impact of Virus Encapsidation. Environ Sci Technol 2022; 56:218-227. [PMID: 34905340 DOI: 10.1021/acs.est.1c04239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Free chlorine disinfection is widely applied to inactivate viruses by reacting with their biomolecules, which include nucleic acids, proteins, and lipids. Knowing the reactivities of viral genomes with free chlorine and the protection that encapsidation provides would ultimately help predict virus susceptibility to the disinfectant. The relative reactivities of different viral genome types and the impact of viral higher order structure with free chlorine are poorly characterized. Here, we studied the reactivity of viral genomes representing four genome types from virus particles with diverse structures, namely, (+)ssRNA (MS2), dsRNA (φ6), ssDNA (φX174), and dsDNA (T3) with free chlorine. We compared the reactivities of these viral nucleic acids when they were suspended in phosphate buffer solutions (naked forms) and when they were in the native virus particles (encapsidated forms). The reactivities of nucleic acids were tracked by polymerase chain reaction (PCR)-based assays. The naked dsDNA of T3 was the least reactive with free chlorine, with an average second order rate constant normalized by the number of bases in the measured regions (in M-1 s-1 b-1) that was 34×, 65×, and 189× lower than those of the dsRNA of φ6, ssRNA of MS2, and ssDNA of φX174, respectively. Moreover, different regions in the ssRNA genome of MS2 and the dsRNA genome of φ6 exhibited statistically different reaction kinetics. The genomes within virus particles reacted slower than the naked genomes overall, but the extent of these differences varied among the four viruses. The results on viral nucleic acid reactivity help explain different susceptibilities of viruses to inactivation by free chlorine and also provide a valuable comparison of the susceptibilities of different nucleic acids to oxidants.
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Affiliation(s)
- Zhong Qiao
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yinyin Ye
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Civil, Structural, and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States
| | - Aleksandra Szczuka
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katherine R Harrison
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michael C Dodd
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Bukyya JL, Tejasvi MLA, Avinash A, P CH, Talwade P, Afroz MM, Pokala A, Neela PK, Shyamilee TK, Srisha V. DNA Profiling in Forensic Science: A Review. Glob Med Genet 2021; 8:135-143. [PMID: 34877570 PMCID: PMC8635824 DOI: 10.1055/s-0041-1728689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/28/2021] [Indexed: 11/26/2022] Open
Abstract
DNA is present in most of the cells in our body, which is unique in each and every individual, and we leave a trail of it everywhere we go. This has become an advantage for forensic investigators who use DNA to draw conclusion in identification of victim and accused in crime scenes. This review described the use of genetic markers in forensic investigation and their limitations.
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Affiliation(s)
- Jaya Lakshmi Bukyya
- Department of Oral Medicine and Radiology, Tirumala Institute of Dental Sciences, Nizamabad, Telangana, India
| | - M L Avinash Tejasvi
- Department of Oral Medicine and Radiology, Kamineni Institute of Dental Sciences, Narketpally, Telangana, India
| | - Anulekha Avinash
- Department of Prosthodontics, Kamineni Institute of Dental Sciences, Narketpally, Telangana, India
| | - Chanchala H P
- Department of Pedodontics and Preventive Dentistry, JSS Dental College, Mysore, Karnataka, India
| | - Priyanka Talwade
- Department of Pedodontics and Preventive Dentistry, JSS Dental College, Mysore, Karnataka, India
| | - Mohammed Malik Afroz
- Department of Oral Surgery and Diagnostic Sciences, Oral Medicine, College of Dentistry, Dar Al Uloom University, Riyadh, Kingdom of Saudi Arabia
| | - Archana Pokala
- Department of Oral Medicine and Radiology, Kamineni Institute of Dental Sciences, Narketpally, Telangana, India
| | - Praveen Kumar Neela
- Department of Orthodontics, Kamineni Institute of Dental Sciences, Narketpally, Telangana, India
| | - T K Shyamilee
- Department of Oral Pathology, Private Practice, Hyderabad, Telangana, India
| | - Vammi Srisha
- Department of Oral Medicine and Radiology, Private Practice, Bangalore, Karnataka, India
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15
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Tsutsui M, Yokota K, Arima A, Washio T, Baba Y, Kawai T. Detecting Single Molecule Deoxyribonucleic Acid in a Cell Using a Three-Dimensionally Integrated Nanopore. Small Methods 2021; 5:e2100542. [PMID: 34928053 DOI: 10.1002/smtd.202100542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/11/2021] [Indexed: 06/14/2023]
Abstract
Amplification-free genome analysis can revolutionize biology and medicine by uncovering genetic variations among individuals. Here, the authors report on a 3D-integrated nanopore for electrolysis to in situ detection of single-molecule DNA in a cell by ionic current measurements. It consists of a SiO2 multipore sheet and a SiNx nanopore membrane stacked vertically on a Si wafer. Single cell lysis is demonstrated by 106 V m-1 -level electrostatic field focused at the multinanopore. The intracellular molecules are then directly detected as they move through a sensing zone, wherein the authors find telegraphic current signatures reflecting folding degrees of freedom of the millimeter-long polynucleotides threaded through the SiNx nanopore. The present device concept may enable on-chip single-molecule sequencing to multi-omics analyses at a single-cell level.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa, 761-0395, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Institute of Nano-Life-Systems, Nagoya, Aichi, 464-8603, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Institute of Nano-Life-Systems, Nagoya, Aichi, 464-8603, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Institute of Nano-Life-Systems, Nagoya, Aichi, 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba, 263-8555, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
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16
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Suni II. Substrate Materials for Biomolecular Immobilization within Electrochemical Biosensors. Biosensors (Basel) 2021; 11:239. [PMID: 34356710 PMCID: PMC8301891 DOI: 10.3390/bios11070239] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 01/17/2023]
Abstract
Electrochemical biosensors have potential applications for agriculture, food safety, environmental monitoring, sports medicine, biomedicine, and other fields. One of the primary challenges in this field is the immobilization of biomolecular probes atop a solid substrate material with adequate stability, storage lifetime, and reproducibility. This review summarizes the current state of the art for covalent bonding of biomolecules onto solid substrate materials. Early research focused on the use of Au electrodes, with immobilization of biomolecules through ω-functionalized Au-thiol self-assembled monolayers (SAMs), but stability is usually inadequate due to the weak Au-S bond strength. Other noble substrates such as C, Pt, and Si have also been studied. While their nobility has the advantage of ensuring biocompatibility, it also has the disadvantage of making them relatively unreactive towards covalent bond formation. With the exception of Sn-doped In2O3 (indium tin oxide, ITO), most metal oxides are not electrically conductive enough for use within electrochemical biosensors. Recent research has focused on transition metal dichalcogenides (TMDs) such as MoS2 and on electrically conductive polymers such as polyaniline, polypyrrole, and polythiophene. In addition, the deposition of functionalized thin films from aryldiazonium cations has attracted significant attention as a substrate-independent method for biofunctionalization.
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Affiliation(s)
- Ian Ivar Suni
- Materials Technology Center, Southern Illinois University, Carbondale, IL 62901, USA; ; Tel.: +1-618-453-7822
- School of Chemistry and Biomolecular Sciences, Southern Illinois University, Carbondale, IL 62901, USA
- School of Mechanical, Aerospace and Materials Engineering, Southern Illinois University, Carbondale, IL 62901, USA
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17
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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18
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Lô G, Ndiaye AJS, Sow A, Fall A, Sow A, Barry O, Diop NM, Ndiaye HD, Kâne NCT, Mboup S. Comparison of Amplix® hepatitis B virus and Roche COBAS AmpliPrep/COBAS Taqman hepatitis B virus assay in quantifying HBV DNA in plasma of chronic hepatitis B in Senegal. Pan Afr Med J 2021; 38:294. [PMID: 34178213 PMCID: PMC8197065 DOI: 10.11604/pamj.2021.38.294.24819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 03/06/2021] [Indexed: 11/11/2022] Open
Abstract
Introduction quantification of hepatitis B virus DNA, a key element in the management of chronic hepatitis B, allows a more direct and reliable measurement of viral replication and monitoring of the virological response to therapy. Polymerase chain reaction (PCR) platforms performing this quantification and adaptable to intermediate laboratories have been developed. Thus, this study was conducted to evaluate the on-site performance of the AMPLIX® hepatitis B virus (HBV) real-time PCR technique in comparison with the COBAS AmpliPrep™ technique. Methods performance of the AMPLIX® HBV real-time PCR technique was evaluated with repeatability and intermediate precision (reproducibility) determined. The comparison with COBAS Taqman was performed by testing, in parallel, 42 plasma samples. The statistical analysis using Meth Val® software was focused on correlation and concordance determination. Results AMPLIX® real-time PCR assay showed good reproducibility for the low (CV=6.65%) and high (CV=3.15%) control levels but also good repeatability for both the low (CV=2.12%) and high (CV=1.60%) concentration levels. Accuracy obtained in our study were less than acceptability limit fixed to 5%. Viral load measurements between Amplix and COBAS Taqman correlated strongly with a correlation coefficient of 0.97%. Concordance analysis gave an average of the differences of 0.54 log IU/L between the viral load measurements of the 2 techniques. Conclusion based on these results, the Amplix real-time PCR platform for the quantification of HBV DNA can be considered as a reliable system for the monitoring of chronic hepatitis B and also a system adapted to intermediate laboratories.
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Affiliation(s)
- Gora Lô
- Centre Médical Inter Armées Lemonier, Dakar, Sénégal.,Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Sénégal
| | | | - Amina Sow
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Sénégal
| | - Amina Fall
- Centre Médical Inter Armées Lemonier, Dakar, Sénégal
| | - Aissatou Sow
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Sénégal
| | - Oumar Barry
- Centre Médical Inter Armées Lemonier, Dakar, Sénégal
| | | | - Halimatou Diop Ndiaye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Sénégal.,Laboratoire de Bactériologie Virologie de l´Hôpital Aristide Le Dantec, Dakar, Sénégal
| | - Ndèye Coumba Touré Kâne
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Sénégal.,Hôpital Dalal Jaam, Dakar, Sénégal
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Sénégal
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19
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Abstract
The SARS-CoV-2 virus which originated in Wuhan, China has since spread throughout the world and is affecting millions of people. When there is a novel virus outbreak, it is crucial to quickly determine if the epidemic is a result of the novel virus or a well-known virus. We propose a deep learning algorithm that uses a convolutional neural network (CNN) as well as a bi-directional long short-term memory (Bi-LSTM) neural network, for the classification of the severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) amongst Coronaviruses. Besides, we classify whether a genome sequence contains candidate regulatory motifs or otherwise. Regulatory motifs bind to transcription factors. Transcription factors are responsible for the expression of genes. The experimental results show that at peak performance, the proposed convolutional neural network bi-directional long short-term memory (CNN-Bi-LSTM) model achieves a classification accuracy of 99.95%, area under curve receiver operating characteristic (AUC ROC) of 100.00%, a specificity of 99.97%, the sensitivity of 99.97%, Cohen's Kappa equal to 0.9978, Mathews Correlation Coefficient (MCC) equal to 0.9978 for the classification of SARS CoV-2 amongst Coronaviruses. Also, the CNN-Bi-LSTM correctly detects whether a sequence has candidate regulatory motifs or binding-sites with a classification accuracy of 99.76%, AUC ROC of 100.00%, a specificity of 99.76%, a sensitivity of 99.76%, MCC equal to 0.9980, and Cohen's Kappa of 0.9970 at peak performance. These results are encouraging enough to recognise deep learning algorithms as alternative avenues for detecting SARS CoV-2 as well as detecting regulatory motifs in the SARS CoV-2 genes.
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Affiliation(s)
- Albert Whata
- School of Natural and Applied SciencesSol Plaatje University Kimberley 8301 South Africa
| | - Charles Chimedza
- School of Statistics and Actuarial ScienceUniversity of the Witwatersrand Johannesburg 2050 South Africa
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20
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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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21
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Abstract
Quantum dots (QDs) are semiconductor nanoparticles that exhibit photoluminescent properties useful for applications in the field of diagnostics and medicine. Successful implementation of these QDs for bio-imaging and bio/chemical sensing typically involves conjugation to biologically active molecules for recognition and signal generation. Unfortunately, traditional and widely studied QDs are based upon heavy metals and other toxic elements (e.g., Cd- and Pb-based QDs), which precludes their safe use in actual biological systems. Silicon quantum dots (SiQDs) offer the same advantages as these heavy-metal-based QDs with the added benefits of nontoxicity and abundance. The preparation of functional bio-inorganic hybrids from SiQDs and biomolecules has lagged significantly compared to their traditional toxic counterparts because of the challenges associated with the synthesis of water-soluble SiQDs and their relative instability in aqueous environments. Advances in SiQD synthesis and surface functionalization, however, have made possible the preparation of functional bio-inorganic hybrids from SiQDs and biological molecules through different bioconjugation reactions. In this contribution, we review the various bioconjugate reactions by which SiQDs have been linked to biomolecules and implemented as platforms for bio-imaging and bio/chemical sensing. We also highlight the challenges that need to be addressed and overcome for these materials to reach their full potential. Lastly, we give prospective applications where this unique class of nontoxic and biocompatible materials can be of great utility in the future.
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Affiliation(s)
- Christopher Jay T Robidillo
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Physical Sciences and Mathematics, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Jonathan G C Veinot
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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22
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Persano L, Szukalski A, Gaio M, Moffa M, Salvadori G, Sznitko L, Camposeo A, Mysliwiec J, Sapienza R, Mennucci B, Pisignano D. Dye Stabilization and Wavelength Tunability in Lasing Fibers Based on DNA. Adv Opt Mater 2020; 8:2001039. [PMID: 33365226 PMCID: PMC7745753 DOI: 10.1002/adom.202001039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/31/2020] [Indexed: 05/22/2023]
Abstract
Lasers based on biological materials are attracting an increasing interest in view of their use in integrated and transient photonics. Deoxyribonucleic acid (DNA) as optical biopolymer in combination with highly emissive dyes has been reported to have excellent potential in this respect. However, achieving miniaturized lasing systems based on solid-state DNA shaped in different geometries to confine and enhance emission is still a challenge, and the physicochemical mechanisms originating fluorescence enhancement are not fully understood. Herein, a class of wavelength-tunable lasers based on DNA nanofibers is demonstrated, for which optical properties are highly controlled through the system morphology. A synergistic effect is highlighted at the basis of lasing action. Through a quantum chemical investigation, it is shown that the interaction of DNA with the encapsulated dye leads to hindered twisting and suppressed channels for the nonradiative decay. This is combined with effective waveguiding, optical gain, and tailored mode confinement to promote morphologically controlled lasing in DNA-based nanofibers. The results establish design rules for the development of bright and tunable nanolasers and optical networks based on DNA nanostructures.
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Affiliation(s)
- Luana Persano
- NESTIstituto Nanoscienze‐CNR and Scuola Normale SuperiorePiazza S. Silvestro 12PisaI‐56127Italy
| | - Adam Szukalski
- Faculty of ChemistryWroclaw University of Science and TechnologyWybrzeze Wyspianskiego 27Wroclaw50‐370Poland
| | - Michele Gaio
- The Blackett LaboratoryDepartment of PhysicsImperial College LondonLondonSW7 2AZUK
| | - Maria Moffa
- NESTIstituto Nanoscienze‐CNR and Scuola Normale SuperiorePiazza S. Silvestro 12PisaI‐56127Italy
| | - Giacomo Salvadori
- Department of ChemistryUniversity of PisaVia G. Moruzzi 13PisaI‐56124Italy
| | - Lech Sznitko
- Faculty of ChemistryWroclaw University of Science and TechnologyWybrzeze Wyspianskiego 27Wroclaw50‐370Poland
| | - Andrea Camposeo
- NESTIstituto Nanoscienze‐CNR and Scuola Normale SuperiorePiazza S. Silvestro 12PisaI‐56127Italy
| | - Jaroslaw Mysliwiec
- Faculty of ChemistryWroclaw University of Science and TechnologyWybrzeze Wyspianskiego 27Wroclaw50‐370Poland
| | - Riccardo Sapienza
- The Blackett LaboratoryDepartment of PhysicsImperial College LondonLondonSW7 2AZUK
| | - Benedetta Mennucci
- Department of ChemistryUniversity of PisaVia G. Moruzzi 13PisaI‐56124Italy
| | - Dario Pisignano
- NESTIstituto Nanoscienze‐CNR and Scuola Normale SuperiorePiazza S. Silvestro 12PisaI‐56127Italy
- Dipartimento di FisicaUniversità di PisaLargo B. Pontecorvo 3PisaI‐56127Italy
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23
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Abstract
To investigate the molecular mechanisms of later metabolic health changes in large for gestational age (LGA) newborns by analyzing deoxyribonucleic acid (DNA) methylation patterns in the placenta of LGA and appropriate for gestational age (AGA) newborns.A total of 6 placentas of LGA and 6 placentas of AGA newborns were enrolled as LGA group and AGA group. DNA methylation was analyzed using the Illumina Infinium Human MethylationEPIC BeadChip microarrays and verified via pyrosequencing and reverse transcription-quantitative real-time polymerase chain reaction. Functional enrichment analysis were constructed by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis based on the differentially methylated regions between LGA and AGA groups.Clinical investigation showed that LGA newborns had significantly lower hemoglobin and blood glucose compared to AGA newborns. Birth weight was negatively correlated to hemoglobin and blood glucose. Genome-wide DNA methylation analysis identified 17 244 methylation variable positions achieving genome-wide significance (adjusted P < .05). 34% methylation variable positions were located in the gene promoter region. A total of 117 differentially methylated regions were revealed by bump hunting analysis, which mapped to 107 genes. Function analysis showed 13 genes enriched in "adhesion and infection process, endocrine and other factor-regulated calcium reabsorption, calcium signaling pathway and transmembrane transport". Four genes linked to type II diabetes mellitus. Among the 13 genes, we selected GNAS and calcium voltage-gated channel subunit alpha1 G for independent verification of pyrosequencing, and the messenger ribonucleic acid levels of guanine nucleotide binding protein, calcium voltage-gated channel subunit alpha1 G, DECR1, and FK506 binding protein 11 were verified by reverse transcription-quantitative real-time polymerase chain reaction.DNA methylation variation and gene expression differences in placental samples were associated with LGA newborns, which linking the effect of intrauterine environment to regulation of the offspring's gene expression. Furthermore, pathway analysis suggested that intrauterine environment affecting fetal growth might had a functional impact on multiple signaling pathways involved in fetal growth, metabolism, and inflammation. Further studies were required to understand the differences of methylation patterns.
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Affiliation(s)
- Zheng Shen
- Department of Clinical laboratory, Zhejiang University School of Medicine Children's Hospital
- National Clinical Research Center for Child Health
| | - Yanfei Tang
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
- Second Hospital of Jiaxing
| | - Yemei Song
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
- Huzhou Central Hospital
| | - Wenxia Shen
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
- Women and Children's Hospital of Shaoxin
| | - Chaochun Zou
- National Clinical Research Center for Child Health
- Department of Endocrinology, Zhejiang University School of Medicine Children's Hospital
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24
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Li Y, Zhang J, Zhang H, Liu B, Wang G, Cao M, Fu B, Li H, Jiang Q, Yu L, Xian Y, Su B, Jiang X. Importance and safety of autologous sperm cryopreservation for fertility preservation in young male patients with cancer. Medicine (Baltimore) 2020; 99:e19589. [PMID: 32282708 PMCID: PMC7440101 DOI: 10.1097/md.0000000000019589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
With development of tumor treatment, survival time of patients with cancer is significantly prolonged. Therefore, the current emphasis is not only the survival, but also the quality of life, especially, it is crucial for young male cancer patients who are unmarried and maintaining fertility. However, the awareness of fertility preservation for these patients is currently insufficient.To give physician and cancer patients more clear understanding of the importance and safety of sperm cryopreservation, so that achieve patient fertility benefits.First, the knowledge level and attitudes about fertility preservation were investigated by surveying 332 cancer patients and 103 medical staff with questionnaires. Second, 30 male cancer patients (experimental group) and 30 normal donors (control group) were selected and their sperm samples were cryopreserved. The sperm quality was compared between cancer patients and normal donors, before and after antitumor treatment in the cancer patients, and before and after sperm cryopreservation in both groups.In the questionnaire survey, we found that there were 70% to 80% of medical staffs and cancer patients lacked knowledge of fertility preservation, and 27.7% of patients worried that tumor and sperm cryopreservation might affect their offspring. In the sperm preservative experiment, we found that sperm quality in cancer patients was further damaged after radiotherapy/chemotherapy in addition to tumor itself had a negative effect. However, sperm deoxyribonucleic acid fragments were not affected by sperm cryopreservation although there were significant differences in sperm quality before and after sperm preservation in both groups.Radiotherapy/chemotherapy would further damage sperm quality of young male cancer patients. Medical staff should be aware of importance of sperm cryopreservation for fertility preservation for these patients. It is also necessary that medical staff should inform the patient about the safety of sperm freezing and guide the patient to participate in sperm cryopreservation.
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Affiliation(s)
- Yinfeng Li
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China
| | - Jian Zhang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China
| | - Hanfeng Zhang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China
| | - Bo Liu
- Department of Human Sperm Bank, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Guorong Wang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China
| | - Maoqiu Cao
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China
| | - Bencui Fu
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China
| | - Hui Li
- Department of Human Sperm Bank, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Qinghua Jiang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China
| | - Lin Yu
- Department of Human Sperm Bank, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yang Xian
- Department of Human Sperm Bank, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Bizhen Su
- Department of Human Sperm Bank, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaohui Jiang
- Department of Human Sperm Bank, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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Takahashi T, Fukagawa M, Sakurai T, Hoshino H. Non-hybridization single nucleotide polymorphism detection and genotyping assay through direct discrimination of single base mutation by capillary electrophoretic separation of single-stranded DNA. J Sep Sci 2019; 43:657-662. [PMID: 31707747 DOI: 10.1002/jssc.201900897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022]
Abstract
The significant demands for single nucleotide polymorphism detection and genotyping assays have grown. Most common assays are based on the recognition of the target sequence by the hybridization with its specific probe having the complementary sequence of the target. Herein, a simple, label-free, and economical non-hybridization assay was developed for single nucleotide polymorphism detection and genotyping, based on the direct discrimination of single base mutation by simple capillary electrophoresis separation for single-stranded DNA in an acidic electrophoretic buffer solution containing urea. Capillary electrophoresis separation of single-base sequential isomers of DNA was achieved due to charge differences resulting from the different protonation properties of the DNA bases. Single nucleotide polymorphism detection and genotyping were achieved by discriminating the electropherogram pattern change, that is, peak number in the electropherogram, obtained by the proposed method. The successful practical application of the proposed method was demonstrated through single nucleotide polymorphism detection and genotyping on a known gene region of 84-mer, in which guanine to adenine single-base mutation is commonly observed, using a human hair sample in combination with genomic DNA extraction, polymerase chain reaction amplification, DNA purification from polymerase chain reaction products, and capillary electrophoresis separation.
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Affiliation(s)
- Toru Takahashi
- Department of applied chemistry and biotechnology, Graduate school of engineering, University of Fukui, Fukui, Japan
| | - Mayu Fukagawa
- Department of applied chemistry and biotechnology, Faculty of engineering, University of Fukui, Fukui, Japan
| | - Takao Sakurai
- Department of Environmental Benign Systems, Graduate school of environmental studies, Tohoku University, Sendai, Japan
| | - Hitoshi Hoshino
- Department of Environmental Benign Systems, Graduate school of environmental studies, Tohoku University, Sendai, Japan
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Rutagwera DG, Molès JP, Kankasa C, Mwiya M, Tuaillon E, Peries M, Nagot N, Van de Perre P, Tylleskär T. Prevalence and determinants of HIV shedding in breast milk during continued breastfeeding among Zambian mothers not on antiretroviral treatment (ART): A cross-sectional study. Medicine (Baltimore) 2019; 98:e17383. [PMID: 31689745 PMCID: PMC6946397 DOI: 10.1097/md.0000000000017383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The risk of postnatal HIV transmission exists throughout the breastfeeding period. HIV shedding in breast milk beyond six months has not been studied extensively. The aim of this study was to determine prevalence and determinants of HIV shedding in breast milk during continued breastfeedingA cross-sectional study was nested in the PROMISE-PEP trial in Lusaka, Zambia to analyze breast milk samples collected from both breasts at week 38 post-partum (mid-way during continued breastfeeding). We measured concurrent HIV deoxyribonucleic acid (DNA) and HIV ribonucleic acid (RNA) as proxies for cell-associated HIV (CAV) and cell-free HIV (CFV) shedding in breast milk respectively. Participants' socio-demographic date, concurrent blood test results, sub clinical mastitis test results and contraceptive use data were available. Logistic regression models were used to identify determinants of HIV shedding in breast milk (detecting either CAV or CFV).The prevalence of HIV shedding in breast milk at 9 months post-partum was 79.4% (95%CI: 74.0 - 84.0). CAV only, CFV only and both CAV and CFV were detectable in 13.7%, 17.3% and 48.4% mothers, respectively. The odds of shedding HIV in breast milk decreased significantly with current use of combined oral contraceptives (AOR: 0.37; 95%CI: 0.17 - 0.83) and increased significantly with low CD4 count (AOR: 3.47; 95%CI: 1.23 - 9.80), unsuppressed plasma viral load (AOR: 6.27; 95%CI: 2.47 - 15.96) and severe sub-clinical mastitis (AOR: 12.56; 95%CI: 2.48 - 63.58).This study estimated that about 80% of HIV infected mothers not on ART shed HIV in breast milk during continued breastfeeding. Major factors driving this shedding were low CD4 count, unsuppressed plasma viral load and severe sub-clinical mastitis. The inverse relationship between breast milk HIV and use of combined oral contraceptives needs further clarification. Continued shedding of CAV may contribute to residual postnatal transmission of HIV in mothers on successful ART.
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Affiliation(s)
- David Gatsinzi Rutagwera
- Centre for International Health, University of Bergen, Bergen, Norway
- Department of Pediatrics and Child Health, University Teaching Hospitals, School of Medicine University of Zambia, Lusaka, Zambia
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic Infections, INSERM, Université de Montpellier, Etablissement français du Sang
| | - Chipepo Kankasa
- Department of Pediatrics and Child Health, University Teaching Hospitals, School of Medicine University of Zambia, Lusaka, Zambia
| | - Mwiya Mwiya
- Department of Pediatrics and Child Health, University Teaching Hospitals, School of Medicine University of Zambia, Lusaka, Zambia
| | - Edouard Tuaillon
- Pathogenesis and Control of Chronic Infections, INSERM, Université de Montpellier, Etablissement français du Sang
- University Hospital of Montpellier, Montpellier, France
| | - Marianne Peries
- Pathogenesis and Control of Chronic Infections, INSERM, Université de Montpellier, Etablissement français du Sang
| | - Nicolas Nagot
- Pathogenesis and Control of Chronic Infections, INSERM, Université de Montpellier, Etablissement français du Sang
- University Hospital of Montpellier, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic Infections, INSERM, Université de Montpellier, Etablissement français du Sang
- University Hospital of Montpellier, Montpellier, France
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Malucelli G. Biomacromolecules and Bio-Sourced Products for the Design of Flame Retarded Fabrics: Current State of the Art and Future Perspectives. Molecules 2019; 24:E3774. [PMID: 31635143 DOI: 10.3390/molecules24203774] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/12/2019] [Accepted: 10/19/2019] [Indexed: 11/26/2022] Open
Abstract
The search for possible alternatives to traditional flame retardants (FRs) is pushing the academic and industrial communities towards the design of new products that exhibit low environmental impact and toxicity, notwithstanding high performances, when put in contact with a flame or exposed to an irradiative heat flux. In this context, in the last five to ten years, the suitability and effectiveness of some biomacromolecules and bio-sourced products with a specific chemical structure and composition as effective flame retardants for natural or synthetic textiles has been thoroughly explored at the lab-scale level. In particular, different proteins (such as whey proteins, caseins, and hydrophobins), nucleic acids and extracts from natural sources, even wastes and crops, have been selected and exploited for designing flame retardant finishing treatments for several fibers and fabrics. It was found that these biomacromolecules and bio-sourced products, which usually bear key elements (i.e., nitrogen, phosphorus, and sulphur) can be easily applied to textiles using standard impregnation/exhaustion methods or even the layer-by-layer technique; moreover, these “green” products are mostly responsible for the formation of a stable protective char (i.e., a carbonaceous residue), as a result of the exposure of the textile substrate to a heat flux or a flame. This review is aimed at summarizing the development and the recent progress concerning the utilization of biomacromolecules/bio-sourced products as effective flame retardants for different textile materials. Furthermore, the existing drawbacks and limitations of the proposed finishing approaches as well as some possible further advances will be considered.
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Kumar N, Singh AK. Cell-Free Fetal DNA: A Novel Biomarker for Early Prediction of Pre-eclampsia and Other Obstetric Complications. Curr Hypertens Rev 2019; 15:57-63. [PMID: 29766818 DOI: 10.2174/1573402114666180516131832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/06/2018] [Accepted: 05/11/2018] [Indexed: 11/22/2022]
Abstract
Hypertensive disorder of pregnancy, especially Pre-eclampsia is one of the major causes of increased maternal and perinatal morbidity and mortality all over the world. Early prediction of pre-eclampsia is the need of modern obstetrics, as this can timely prevent the progress of disease as well as related fetal and maternal morbidity and mortality. In addition to the screening of fetal aneuploidies, Rhesus-D status, fetal sex, single gene disorders, the cell-free fetal Deoxyribonucleic acid (DNA) quantification has emerged as a promising biomarker for the prediction of pre-eclampsia. Hence, its use can help in the early prediction of hypertensive disorders of pregnancy, especially pre-eclampsia even before the appearance of symptoms. Furthermore, in future, it can also help in the determination of the complete DNA sequence of every gene of the fetus. The present review focuses on recent literature concerning the use of cell-free fetal DNA in early prediction of preeclampsia as well as for non-invasive prenatal genetic screening of fetus for various disorders. Methods: The recent literature related to cell-free fetal DNA was searched from numerous English language journals and published peer-reviewed articles on Pubmed, Google Scholar, MEDLINE and various government agencies till 2016.
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Affiliation(s)
- Naina Kumar
- Department of Obstetrics and Gynecology, Maharishi Markandeshwar Institute of Medical Sciences and Research, Mullana-133207, Ambala, Haryana, India, Postal address: House Number 2, "F" Block, MMIMSR Campus, Mullana- 133207, Ambala, Haryana, India
| | - Amit Kant Singh
- Department of Physiology, U.P. University of Medical Sciences, Saifai, Etawah, Uttar Pradesh, India, Postal Address: House No. 168, Kaveri Kunj, Phase II, Kamla Nagar-282005, Agra, Uttar Pradesh, India
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29
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Shintani Y, Ibori S, Kawarada H. Deoxyribonucleic-acid-sensitive Polycrystalline Diamond Solution-gate Field-effect Transistor with a Carboxyl-terminated Boron-doped Channel. ANAL SCI 2019; 35:923-927. [PMID: 31061238 DOI: 10.2116/analsci.18p520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper describes a deoxyribonucleic-acid-sensitive electrolyte solution-gate field-effect transistor (SGFET) sensor utilizing a partial carboxyl-terminated boron-doped polycrystalline diamond surface as a linker to connect a deoxyribonucleic acid (DNA) probe. A high density of carboxyl termination on the polycrystalline diamond surface that was employed as a FET channel was achieved using a vacuum ultraviolet system with oxygen gas. A single-stranded DNA probe was immobilized on the polycrystalline diamond channel via amino coupling. The current-voltage characteristics of the polycrystalline diamond SGFET sensor was examined with bias voltages within its potential voltage window. The characteristics of the drain-source current verses the drain-source voltage showed a pinch-off, a shift voltage of up to 40 mV with a coefficient of variation of 4 - 11% was obtained between hybridization and denaturation. In addition, a single nucleotide mutation of DNA sequence was selectively recognized by the shift voltage up to ca. 10 mV.
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Affiliation(s)
| | - Shoji Ibori
- School of Science and Engineering, Waseda University
| | - Hiroshi Kawarada
- School of Science and Engineering, Waseda University.,Kagami Memorial Laboratory for Materials Science and Technology, Waseda University
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30
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Rouschop SH, Karl T, Risch A, van Ewijk PA, Schrauwen-Hinderling VB, Opperhuizen A, van Schooten FJ, Godschalk RW. Gene expression and DNA methylation as mechanisms of disturbed metabolism in offspring after exposure to a prenatal HF diet. J Lipid Res 2019; 60:1250-1259. [PMID: 31064776 PMCID: PMC6602131 DOI: 10.1194/jlr.m092593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/03/2019] [Indexed: 12/17/2022] Open
Abstract
Exposure to a prenatal high-fat (HF) diet leads to an impaired metabolic phenotype in mouse offspring. The underlying mechanisms, however, are not yet fully understood. Therefore, this study investigated whether the impaired metabolic phenotype may be mediated through altered hepatic DNA methylation and gene expression. We showed that exposure to a prenatal HF diet altered the offspring’s hepatic gene expression of pathways involved in lipid synthesis and uptake (SREBP), oxidative stress response [nuclear factor (erythroid-derived 2)-like 2 (Nrf2)], and cell proliferation. The downregulation of the SREBP pathway related to previously reported decreased hepatic lipid uptake and postprandial hypertriglyceridemia in the offspring exposed to the prenatal HF diet. The upregulation of the Nrf2 pathway was associated with increased oxidative stress levels in offspring livers. The prenatal HF diet also induced hypermethylation of transcription factor (TF) binding sites upstream of lipin 1 (Lpin1), a gene involved in lipid metabolism. Furthermore, DNA methylation of Lpin1 TF binding sites correlated with mRNA expression of Lpin1. These findings suggest that the effect of a prenatal HF diet on the adult offspring’s metabolic phenotype are regulated by changes in hepatic gene expression and DNA methylation.
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Affiliation(s)
- Sven H Rouschop
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Tanja Karl
- Department of Biosciences University of Salzburg, Salzburg, Austria
| | - Angela Risch
- Department of Biosciences University of Salzburg, Salzburg, Austria
| | - Petronella A van Ewijk
- Department of Radiology and Nuclear Medicine Maastricht University Medical Center, Maastricht, The Netherlands
| | - Vera B Schrauwen-Hinderling
- Department of Radiology and Nuclear Medicine Maastricht University Medical Center, Maastricht, The Netherlands
| | - Antoon Opperhuizen
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.,Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, The Netherlands
| | - Frederik J van Schooten
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Roger W Godschalk
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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31
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Howell SC, Qiu X, Curtis JE. Monte Carlo simulation algorithm for B-DNA. J Comput Chem 2018; 37:2553-63. [PMID: 27671358 DOI: 10.1002/jcc.24474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/12/2016] [Accepted: 07/23/2016] [Indexed: 01/12/2023]
Abstract
Understanding the structure-function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small-angle X-ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all-atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub-ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B-DNA is represented using a wormlike bead-rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse-grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Steven C Howell
- Neutron Condensed Matter Science Group, NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-8562
| | - Xiangyun Qiu
- Department of Physics, The George Washington University, Washington, District of Columbia, 20052
| | - Joseph E Curtis
- Neutron Condensed Matter Science Group, NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899-8562.
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32
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Okafor MT, Nwagha TU, Anusiem C, Okoli UA, Nubila NI, Al-Alloosh F, Udenyia IJ. Cancer prevention, the need to preserve the integrity of the genome at all cost. Niger J Clin Pract 2018; 21:539-545. [PMID: 29735851 DOI: 10.4103/njcp.njcp_272_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Introduction The entire genetic information carried by an organism makes up its genome. Genes have a diverse number of functions. They code different proteins for normal proliferation of cells. However, changes in the base sequence of genes affect their protein by-products which act as messengers for normal cellular functions such as proliferation and repairs. Salient processes for maintaining the integrity of the genome are hinged on intricate mechanisms put in place for the evolution to tackle genomic stresses. Aim To discuss how cells sense and repair damage to their deoxyribonucleic acid (DNA) as well as to highlight how defects in the genes involved in DNA repair contribute to cancer development. Methodology: Online searches on the following databases such as Google Scholar, PubMed, Biomed Central, and SciELO were done. Attempt was made to review articles with keywords such as cancer, cell cycle, tumor suppressor genes, and DNA repair. Results The cell cycle, tumor suppression genes, DNA repair mechanism, as well as their contribution to cancer development, were discussed and reviewed. Conclusion Knowledge on how cells detect and repair DNA damage through an array of mechanisms should allay our anxiety as regards cancer development. More studies on DNA damage detection and repair processes are important toward a holistic approach to cancer treatment.
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Affiliation(s)
- M T Okafor
- Department of Pharmacology and Therapeutics, College of Medicine, University of Nigeria Enugu Campus, Nigeria
| | - T U Nwagha
- Department of Haematology and Immunology, College of Medicine, University of Nigeria, Nsukka, Nigeria
| | - C Anusiem
- Department of Pharmacology and Therapeutics, College of Medicine, University of Nigeria Enugu Campus, Nigeria
| | - U A Okoli
- Department of Biochemistry College of Medicine, University of Nigeria, Nsukka, Nigeria
| | - N I Nubila
- Department of Pharmacology and Therapeutics, College of Medicine, University of Nigeria Enugu Campus, Nigeria
| | - F Al-Alloosh
- Department of Surgical Oncology, Al-Amal National Hospital for Cancer Management, Iraq, Baghdad
| | - I J Udenyia
- Department of Pharmacology and Therapeutics, College of Medicine, University of Nigeria Enugu Campus, Nigeria
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Maiese K. Novel Treatment Strategies for the Nervous System: Circadian Clock Genes, Non-coding RNAs, and Forkhead Transcription Factors. Curr Neurovasc Res 2018; 15:81-91. [PMID: 29557749 PMCID: PMC6021214 DOI: 10.2174/1567202615666180319151244] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/23/2018] [Accepted: 02/07/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND With the global increase in lifespan expectancy, neurodegenerative disorders continue to affect an ever-increasing number of individuals throughout the world. New treatment strategies for neurodegenerative diseases are desperately required given the lack of current treatment modalities. METHODS Here, we examine novel strategies for neurodegenerative disorders that include circadian clock genes, non-coding Ribonucleic Acids (RNAs), and the mammalian forkhead transcription factors of the O class (FoxOs). RESULTS Circadian clock genes, non-coding RNAs, and FoxOs offer exciting prospects to potentially limit or remove the significant disability and death associated with neurodegenerative disorders. Each of these pathways has an intimate relationship with the programmed death pathways of autophagy and apoptosis and share a common link to the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1) and the mechanistic target of rapamycin (mTOR). Circadian clock genes are necessary to modulate autophagy, limit cognitive loss, and prevent neuronal injury. Non-coding RNAs can control neuronal stem cell development and neuronal differentiation and offer protection against vascular disease such as atherosclerosis. FoxOs provide exciting prospects to block neuronal apoptotic death and to activate pathways of autophagy to remove toxic accumulations in neurons that can lead to neurodegenerative disorders. CONCLUSION Continued work with circadian clock genes, non-coding RNAs, and FoxOs can offer new prospects and hope for the development of vital strategies for the treatment of neurodegenerative diseases. These innovative investigative avenues have the potential to significantly limit disability and death from these devastating disorders.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, Newark, New Jersey 07101
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Abstract
BACKGROUND With almost 47 million individuals worldwide suffering from some aspect of dementia, it is clear that cognitive loss impacts a significant proportion of the global population. Unfortunately, definitive treatments to resolve or prevent the onset of cognitive loss are limited. In most cases such care is currently non-existent prompting the need for novel treatment strategies. METHODS Mammalian forkhead transcription factors of the O class (FoxO) are one such avenue of investigation that offer an exciting potential to bring new treatments forward for disorders that involve cognitive loss. Here we examine the background, structure, expression, and function of FoxO transcription factors and their role in cognitive loss, programmed cell death in the nervous system with apoptosis and autophagy, and areas to target FoxOs for dementia and specific disorders such as Alzheimer's disease. RESULTS FoxO proteins work in concert with a number of other cell survival pathways that involve growth factors, such as erythropoietin and neurotrophins, silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), Wnt1 inducible signaling pathway protein 1 (WISP1), Wnt signaling, and cancer-related pathways. FoxO transcription factors oversee proinflammatory pathways, affect nervous system amyloid (Aβ) production and toxicity, lead to mitochondrial dysfunction, foster neuronal apoptotic cell death, and accelerate the progression of degenerative disease. However, under some scenarios such as those involving autophagy, FoxOs also can offer protection in the nervous system and reduce toxic intracellular protein accumulations and potentially limit Aβ toxicity. CONCLUSION Given the ability of FoxOs to not only promote apoptotic cell death in the nervous system, but also through the induction of autophagy offer protection against degenerative disease that can lead to dementia, a fine balance in the activity of FoxOs may be required to target cognitive loss in individuals. Future work should yield exciting new prospects for FoxO proteins as new targets to treat the onset and progression of cognitive loss and dementia.
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Affiliation(s)
- Kenneth Maiese
- Cellular and Molecular Signaling, Newark, New Jersey 07101
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35
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Hou L, Vierra-Green C, Lazaro A, Brady C, Haagenson M, Spellman S, Hurley CK. Limited HLA sequence variation outside of antigen recognition domain exons of 360 10 of 10 matched unrelated hematopoietic stem cell transplant donor-recipient pairs. HLA 2016; 89:39-46. [PMID: 27976839 DOI: 10.1111/tan.12942] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/24/2016] [Accepted: 11/17/2016] [Indexed: 12/27/2022]
Abstract
Traditional DNA-based typing focuses primarily on interrogating the exons of human leukocyte antigen (HLA) genes that form the antigen recognition domain (ARD). The relevance of mismatching donor and recipient for HLA variation outside the ARD on hematopoietic stem cell transplantation (HSCT) outcomes is unknown. This study was designed to evaluate the frequency of variation outside the ARD in 10 of 10 (HLA-A, -B, -C, -DRB1, -DQB1) matched unrelated donor transplant pairs (n = 360). Next-generation DNA sequencing was used to characterize both HLA exons and introns for HLA-A, -B, -C alleles; exons 2, 3 and the intervening intron for HLA-DRB1 and exons only for HLA-DQA1 and -DQB1. Over 97% of alleles at each locus were matched for their nucleotide sequence outside of the ARD exons. Of the 4320 allele comparisons overall, only 17 allele pairs were mismatched for non-ARD exons, 41 for noncoding regions and 9 for ARD exons. The observed variation between donor and recipient usually involved a single nucleotide difference (88% of mismatches); 88% of the non-ARD exon variants impacted the amino acid sequence. The impact of amino acid sequence variation caused by substitutions in exons outside ARD regions in D-R pairs will be difficult to assess in HSCT outcome studies because these mismatches do not occur very frequently.
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Affiliation(s)
- L Hou
- Department of Pediatrics, Georgetown University, Washington, DC, USA
| | - C Vierra-Green
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - A Lazaro
- Department of Pediatrics, Georgetown University, Washington, DC, USA
| | - C Brady
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - M Haagenson
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - S Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - C K Hurley
- Department of Pediatrics, Georgetown University, Washington, DC, USA.,Department of Oncology, Georgetown University, Washington, DC, USA
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36
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Love-Gregory L, Kraja AT, Allum F, Aslibekyan S, Hedman ÅK, Duan Y, Borecki IB, Arnett DK, McCarthy MI, Deloukas P, Ordovas JM, Hopkins PN, Grundberg E, Abumrad NA. Higher chylomicron remnants and LDL particle numbers associate with CD36 SNPs and DNA methylation sites that reduce CD36. J Lipid Res 2016; 57:2176-2184. [PMID: 27729386 DOI: 10.1194/jlr.p065250] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 09/28/2016] [Indexed: 12/18/2022] Open
Abstract
Cluster of differentiation 36 (CD36) variants influence fasting lipids and risk of metabolic syndrome, but their impact on postprandial lipids, an independent risk factor for cardiovascular disease, is unclear. We determined the effects of SNPs within a ∼410 kb region encompassing CD36 and its proximal and distal promoters on chylomicron (CM) remnants and LDL particles at fasting and at 3.5 and 6 h following a high-fat meal (Genetics of Lipid Lowering Drugs and Diet Network study, n = 1,117). Five promoter variants associated with CMs, four with delayed TG clearance and five with LDL particle number. To assess mechanisms underlying the associations, we queried expression quantitative trait loci, DNA methylation, and ChIP-seq datasets for adipose and heart tissues that function in postprandial lipid clearance. Several SNPs that associated with higher serum lipids correlated with lower adipose and heart CD36 mRNA and aligned to active motifs for PPARγ, a major CD36 regulator. The SNPs also associated with DNA methylation sites that related to reduced CD36 mRNA and higher serum lipids, but mixed-model analyses indicated that the SNPs and methylation independently influence CD36 mRNA. The findings support contributions of CD36 SNPs that reduce adipose and heart CD36 RNA expression to inter-individual variability of postprandial lipid metabolism and document changes in CD36 DNA methylation that influence both CD36 expression and lipids.
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Affiliation(s)
- Latisha Love-Gregory
- Department of Medicine, Center for Human Nutrition Washington University School of Medicine, St. Louis, MO 63110
| | - Aldi T Kraja
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110
| | - Fiona Allum
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama, Birmingham, AL 35294
| | - Åsa K Hedman
- Departments of Medical Sciences and Molecular Epidemiology, and Science for Life Laboratory, Uppsala University, Uppsala 75185, Sweden
| | - Yanan Duan
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110
| | - Ingrid B Borecki
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63110
| | - Donna K Arnett
- Department of Epidemiology, University of Alabama, Birmingham, AL 35294
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK, and Oxford Centre for Diabetes, Endocrinology, and Metabolism and Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford OX3 7JU, UK
| | - Panos Deloukas
- William Harvey Research Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Jose M Ordovas
- JM-USDA-Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111
| | - Paul N Hopkins
- Cardiovascular Genetics Research, University of Utah, Salt Lake City, UT 84132
| | - Elin Grundberg
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Québec, Canada H3A 0G1
| | - Nada A Abumrad
- Department of Medicine, Center for Human Nutrition Washington University School of Medicine, St. Louis, MO 63110
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37
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Gary R, Carbone G, Petriashvili G, De Santo MP, Barberi R. Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy. Sensors (Basel) 2016; 16:258. [PMID: 26907286 DOI: 10.3390/s16020258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/17/2016] [Accepted: 02/16/2016] [Indexed: 11/19/2022]
Abstract
The gold nanoparticle (GNP) aggregation growth induced by deoxyribonucleic acid (DNA) is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA.
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38
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Puddu M, Mikutis G, Stark WJ, Grass RN. Submicrometer-Sized Thermometer Particles Exploiting Selective Nucleic Acid Stability. Small 2016; 12:452-456. [PMID: 26670705 DOI: 10.1002/smll.201502883] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/05/2015] [Indexed: 06/05/2023]
Abstract
Encapsulated nucleic acid selective damage quantification by real-time polymerase chain reaction is used as sensing mechanism to build a novel class of submicrometer size thermometer. Thanks to the high thermal and chemical stability, and the capability of storing the read accumulated thermal history, the sensor overcomes some of current limitations in small scale thermometry.
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Affiliation(s)
- Michela Puddu
- Institute of Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg, 8093, Zurich, Switzerland
| | - Gediminas Mikutis
- Institute of Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg, 8093, Zurich, Switzerland
| | - Wendelin J Stark
- Institute of Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg, 8093, Zurich, Switzerland
| | - Robert N Grass
- Institute of Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg, 8093, Zurich, Switzerland
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39
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Farsani MS, Sahhaf MRA, Abootalebi V. Performance Improvement of the Goertzel Algorithm in Estimating of Protein Coding Regions Using Modified Anti-notch Filter and Linear Predictive Coding Model. J Med Signals Sens 2016; 6:130-40. [PMID: 27563569 PMCID: PMC4973456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The aim of this paper is to improve the performance of the conventional Goertzel algorithm in determining the protein coding regions in deoxyribonucleic acid (DNA) sequences. First, the symbolic DNA sequences are converted into numerical signals using electron ion interaction potential method. Then by combining the modified anti-notch filter and linear predictive coding model, we proposed an efficient algorithm to achieve the performance improvement in the Goertzel algorithm for estimating genetic regions. Finally, a thresholding method is applied to precisely identify the exon and intron regions. The proposed algorithm is applied to several genes, including genes available in databases BG570 and HMR195 and the results are compared to other methods based on the nucleotide level evaluation criteria. Results demonstrate that our proposed method reduces the number of incorrect nucleotides which are estimated to be in the noncoding region. In addition, the area under the receiver operating characteristic curve has improved by the factor of 1.35 and 1.12 in HMR195 and BG570 datasets respectively, in comparison with the conventional Goertzel algorithm.
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Affiliation(s)
- Mahsa Saffari Farsani
- Department of Electrical and Computer Engineering, Yazd University, Yazd, Iran,Address for correspondence: Mahsa Saffari Farsani, Faculty of Electrical and Computer Engineering, Yazd University, Yazd, Iran. E-mail:
| | | | - Vahid Abootalebi
- Department of Electrical and Computer Engineering, Yazd University, Yazd, Iran
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40
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Saberkari H, Shamsi M, Joroughi M, Golabi F, Sedaaghi MH. Cancer Classification in Microarray Data using a Hybrid Selective Independent Component Analysis and υ-Support Vector Machine Algorithm. J Med Signals Sens 2014; 4:291-8. [PMID: 25426433 PMCID: PMC4236808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 07/31/2014] [Indexed: 11/20/2022]
Abstract
Microarray data have an important role in identification and classification of the cancer tissues. Having a few samples of microarrays in cancer researches is always one of the most concerns which lead to some problems in designing the classifiers. For this matter, preprocessing gene selection techniques should be utilized before classification to remove the noninformative genes from the microarray data. An appropriate gene selection method can significantly improve the performance of cancer classification. In this paper, we use selective independent component analysis (SICA) for decreasing the dimension of microarray data. Using this selective algorithm, we can solve the instability problem occurred in the case of employing conventional independent component analysis (ICA) methods. First, the reconstruction error and selective set are analyzed as independent components of each gene, which have a small part in making error in order to reconstruct new sample. Then, some of the modified support vector machine (υ-SVM) algorithm sub-classifiers are trained, simultaneously. Eventually, the best sub-classifier with the highest recognition rate is selected. The proposed algorithm is applied on three cancer datasets (leukemia, breast cancer and lung cancer datasets), and its results are compared with other existing methods. The results illustrate that the proposed algorithm (SICA + υ-SVM) has higher accuracy and validity in order to increase the classification accuracy. Such that, our proposed algorithm exhibits relative improvements of 3.3% in correctness rate over ICA + SVM and SVM algorithms in lung cancer dataset.
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Affiliation(s)
- Hamidreza Saberkari
- Department of Electrical Engineering, Genomic Signal Processing Laboratory, Sahand University of Technology, Tabriz, Iran
| | - Mousa Shamsi
- Department of Electrical Engineering, Genomic Signal Processing Laboratory, Sahand University of Technology, Tabriz, Iran
| | - Mahsa Joroughi
- Department of Electrical Engineering, Genomic Signal Processing Laboratory, Sahand University of Technology, Tabriz, Iran
| | - Faegheh Golabi
- Department of Electrical Engineering, Genomic Signal Processing Laboratory, Sahand University of Technology, Tabriz, Iran
| | - Mohammad Hossein Sedaaghi
- Department of Electrical Engineering, Genomic Signal Processing Laboratory, Sahand University of Technology, Tabriz, Iran
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41
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Yotapan N, Charoenpakdee C, Wathanathavorn P, Ditmangklo B, Wagenknecht HA, Vilaivan T. Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label. Beilstein J Org Chem 2014; 10:2166-74. [PMID: 25246975 PMCID: PMC4168962 DOI: 10.3762/bjoc.10.224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/19/2014] [Indexed: 12/16/2022] Open
Abstract
DNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA–DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes.
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Affiliation(s)
- Nattawut Yotapan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chayan Charoenpakdee
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Pawinee Wathanathavorn
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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42
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Li A, Meyre D. Jumping on the Train of Personalized Medicine: A Primer for Non-Geneticist Clinicians: Part 1. Fundamental Concepts in Molecular Genetics. ACTA ACUST UNITED AC 2014; 10:91-100. [PMID: 25132812 PMCID: PMC4133961 DOI: 10.2174/1573400510666140319234955] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 01/31/2014] [Accepted: 04/18/2014] [Indexed: 01/23/2023]
Abstract
With the decrease in sequencing cost and the rise of companies providing sequencing services, it is likely that personalized whole-genome sequencing will eventually become an instrument of common medical practice. We write this series of three reviews to help non-geneticist clinicians get ready for the major breakthroughs that are likely to occur in the coming years in the fast-moving field of personalized medicine. This first paper focuses on the fundamental concepts of molecular genetics. We review how recombination occurs during meiosis, how de novo genetic variations including single nucleotide polymorphisms (SNPs), insertions and deletions are generated and how they are inherited from one generation to the next. We detail how genetic variants can impact protein expression and function, and summarize the main characteristics of the human genome. We also explain how the achievements of the Human Genome Project, the HapMap Project, and more recently, the 1000 Genomes Project, have boosted the identification of genetic variants contributing to common diseases in human populations. The second and third papers will focus on genetic epidemiology and clinical applications in personalized medicine.
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Affiliation(s)
- Aihua Li
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON L8N 3Z5, Canada
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43
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Savelyev A, MacKerell AD. All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem 2014; 35:1219-39. [PMID: 24752978 PMCID: PMC4075971 DOI: 10.1002/jcc.23611] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/19/2014] [Accepted: 03/23/2014] [Indexed: 12/16/2022]
Abstract
Presented is a first generation atomistic force field (FF) for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages, and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting quantum mechanical (QM) data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude FF yields stable DNA duplexes on the 100-ns time scale and satisfactorily reproduce (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII substates of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive FF, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA.
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Affiliation(s)
- Alexey Savelyev
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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44
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Roberts JL, Hovanes K, Dasouki M, Manzardo AM, Butler MG. Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services. Gene 2014; 535:70-8. [PMID: 24188901 PMCID: PMC4423794 DOI: 10.1016/j.gene.2013.10.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/26/2013] [Accepted: 10/10/2013] [Indexed: 01/15/2023]
Abstract
Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009-2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.
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Key Words
- A2BP1
- ACADL
- ACOXL
- ADIPOQ
- ALS2 chromosome region gene 8
- ALS2CR8
- ANKRD11
- ANOVA
- ASD
- Autism spectrum disorders (ASD)
- BAC
- BCL2-like 11 gene
- BCL2L11
- CACNA1C
- CHRNA7
- CNV
- COBL
- CT
- Chromosomal microarray analysis
- Copy number variant (CNV)
- DLG1
- DLG4
- DNA
- Developmental delay
- EEF1B2
- EEG
- F-box only 45 gene
- FAM117B
- FAT tumor suppressor 1 gene
- FAT1
- FBXO45
- FISH
- FXR2
- FZD5
- GALR1
- GATA zinc finger domain-containing protein 2B gene
- GATAD2B
- GDNF-inducible zinc finger protein 1 gene
- GZF1
- HAX1
- HCLS1-associated protein X1 gene
- HDAC
- IDH1
- IL1RAPL1
- ITPR1
- KLF7
- KNG1
- LINS
- LMNA
- Learning disability
- MAP2
- MBP
- MRPL19
- MYL1
- NADH-ubiquinone oxidoreductase Fe-S protein 1 gene
- NDUFS1
- NLGN2
- NPHP1
- NRXN1
- PAK2
- PARK2
- PMP22
- POLG
- PRPF8
- PTEN
- PTH2R
- RPE
- SACS
- SD
- SH2B adaptor protein 1 gene
- SH2B1
- SH3 and multiple ankyrin repeat domains 3 gene
- SHANK3
- SHOX
- SMARCA4
- STAG2
- SUMF1
- SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member gene
- TRAPPC2
- UCSC
- USP6
- University of California, Santa Cruz
- X-linked inhibitor of apoptosis gene
- XIAP
- YWHAE
- ZNF407
- aCGH
- acyl-coA dehydrogenase, long chain gene
- acyl-coA oxidase-like gene
- adipocyte-, C1q-, and collagen domain containing gene
- analysis of variance
- ankyrin repeat domain-containing protein 11 gene
- array comparative genomic hybridization
- ataxin 2-binding protein 1 gene
- autism spectrum disorder
- bacterial artificial chromosome
- calcium channel, voltage dependent, L-type, alpha 1C subunit gene
- cholinergic receptor, neuronal nicotinic, alpha polypeptide 7 gene
- computed tomography
- copy number variant
- cordon-bleu gene
- deoxyribonucleic acid
- discs, large homolog 1 gene
- discs, large homolog 4 gene
- electroencephalogram
- eukaryotic translation elongation factor 1, beta-2 gene
- family with sequence similarity 117, member B gene
- fluorescence in situ hybridization
- fragile X mental retardation, autosomal homolog 2 gene
- frizzled 5 gene
- galanin receptor 1 gene
- histone deacetylase gene
- inositol 1,4,5-triphosphate receptor, type 1 gene
- interleukin 1 receptor accessory protein-like 1 gene
- isocitrate dehydrogenase 1 gene
- kininogen 1 gene
- kruppel-like factor 7 gene
- lamin A gene
- lines homolog gene
- microtubule-associated protein 2 gene
- mitochondrial ribosomal protein L19 gene
- myelin basic protein gene
- myosin, light peptide 1 gene
- nephrocystin 1 gene
- neurexin 1 gene
- neuroligin 2 gene
- parathyroid hormone receptor 2 gene
- parkin gene
- peripheral myelin protein 22 gene
- phosphatase and tensin homolog gene
- polymerase gamma gene
- precursor mRNA-processing factor 8 gene
- protein-activated kinase 2 gene
- ribulose 5-phosphate 3-epimerase gene
- sacsin gene
- short stature homeobox gene
- standard deviation
- stromal antigen 2 gene
- sulfatase-modifying factor 1 gene
- tracking protein particle complex, subunit 2 gene
- tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon isoform gene
- ubiquitin-specific protease 6 gene
- zinc finger protein 407 gene
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Affiliation(s)
- Jennifer L Roberts
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA
| | | | - Majed Dasouki
- Department of Neurology, The University of Kansas Medical Center, Kansas City, KS, USA; King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ann M Manzardo
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA
| | - Merlin G Butler
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA.
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Petkova Z, Tchekalarova J, Pechlivanova D, Moyanova S, Kortenska L, Mitreva R, Popov D, Markova P, Lozanov V, Atanasova D, Lazarov N, Stoynev A. Treatment with melatonin after status epilepticus attenuates seizure activity and neuronal damage but does not prevent the disturbance in diurnal rhythms and behavioral alterations in spontaneously hypertensive rats in kainate model of temporal lobe epilepsy. Epilepsy Behav 2014; 31:198-208. [PMID: 24440891 DOI: 10.1016/j.yebeh.2013.12.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 11/14/2013] [Accepted: 12/15/2013] [Indexed: 11/16/2022]
Abstract
Melatonin is involved in the control of circadian and seasonal rhythmicity, possesses potent antioxidant activity, and exerts a neuroprotective and anticonvulsant effect. Spontaneously hypertensive rats (SHRs) are widely accepted as an experimental model of essential hypertension with hyperactivity, deficient sustained attention, and alterations in circadian autonomic profiles. The purpose of the present study was to determine whether melatonin treatment during epileptogenesis can prevent the deleterious consequences of status epilepticus (SE) in SHRs in the kainate (KA) model of temporal lobe of epilepsy (TLE). Spontaneous recurrent seizures (SRSs) were EEG- and video-recorded during and after the treatment protocol. Melatonin (10mg/kg diluted in drinking water, 8weeks) increased the seizure-latent period, decreased the frequency of SRSs, and attenuated the circadian rhythm of seizure activity in SHRs. However, melatonin was unable to affect the disturbed diurnal rhythms and behavioral changes associated with epilepsy, including the decreased anxiety level, depression, and impaired spatial memory. Melatonin reduced neuronal damage specifically in the CA1 area of the hippocampus and piriform cortex and decreased hippocampal serotonin (5-HT) levels both in control and epileptic SHRs. Although long-term melatonin treatment after SE shows a potential to attenuate seizure activity and neuronal loss, it is unable to restore epilepsy-associated behavioral abnormalities in SHRs.
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Affiliation(s)
- Zlatina Petkova
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Jana Tchekalarova
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
| | - Daniela Pechlivanova
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Slavianka Moyanova
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Lidia Kortenska
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Rumiana Mitreva
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Deyan Popov
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Petya Markova
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Valentin Lozanov
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Dimitrina Atanasova
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Nikolai Lazarov
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Alexander Stoynev
- Institute of Neurobiology, Acad. G. Bonchev Str., Bl. 23, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
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Roy M, Barman S. Effective gene prediction by high resolution frequency estimator based on least-norm solution technique. EURASIP J Bioinform Syst Biol 2014; 2014:2. [PMID: 24386895 PMCID: PMC3895782 DOI: 10.1186/1687-4153-2014-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/15/2013] [Indexed: 11/10/2022]
Abstract
Linear algebraic concept of subspace plays a significant role in the recent techniques of spectrum estimation. In this article, the authors have utilized the noise subspace concept for finding hidden periodicities in DNA sequence. With the vast growth of genomic sequences, the demand to identify accurately the protein-coding regions in DNA is increasingly rising. Several techniques of DNA feature extraction which involves various cross fields have come up in the recent past, among which application of digital signal processing tools is of prime importance. It is known that coding segments have a 3-base periodicity, while non-coding regions do not have this unique feature. One of the most important spectrum analysis techniques based on the concept of subspace is the least-norm method. The least-norm estimator developed in this paper shows sharp period-3 peaks in coding regions completely eliminating background noise. Comparison of proposed method with existing sliding discrete Fourier transform (SDFT) method popularly known as modified periodogram method has been drawn on several genes from various organisms and the results show that the proposed method has better as well as an effective approach towards gene prediction. Resolution, quality factor, sensitivity, specificity, miss rate, and wrong rate are used to establish superiority of least-norm gene prediction method over existing method.
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Affiliation(s)
- Manidipa Roy
- The Calcutta Technical School, Govt. of West Bengal, 110,S.N.Banerjee Road, Kolkata 700013, India
| | - Soma Barman
- Institute of Radio Physics & Electronics, University of Calcutta, 92, A.P.C. Road, Kolkata 700 009, India
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Hoei-Hansen CE, Dali CÍ, Lyngbye TJ, Duno M, Uldall P. Alternating hemiplegia of childhood in Denmark: clinical manifestations and ATP1A3 mutation status. Eur J Paediatr Neurol 2014; 18:50-4. [PMID: 24100174 DOI: 10.1016/j.ejpn.2013.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/19/2013] [Accepted: 08/22/2013] [Indexed: 11/22/2022]
Abstract
Alternating hemiplegia of childhood (AHC) is a rare neurodevelopmental disorder characterized by early-onset recurrent distinctive hemiplegic episodes commonly accompanied by other paroxysmal features and developmental impairment. De novo mutations in ATP1A3 were recently identified as a genetic cause of AHC. To describe the entire Danish cohort of paediatric AHC patients we approached neuropaediatricians nationwide. All currently acknowledged Danish patients ≤16 years with AHC were genetically tested and seen by the same child neurologist (PU). Ten patients; seven girls and three boys were identified. Mean present age was 10.0 years (range 1-16). Mean age at presentation was 7.4 months (range 1-18 months). Sequencing of ATP1A3 in all ten patients revealed a pathogenic mutation in seven. Two females with moderate psychomotor impairment were heterozygous for the known p.G947R mutation, whereas one severely retarded boy was heterozygous for the common p.E815K mutation. The prevalent p.D801N mutation was identified in two moderate to severely retarded children. Interestingly, in a set of monochorionic male twins a novel p.D801E mutation was identified, underscoring that the asparagine at position 801 is a mutation hotspot. Three girls aged 5-13 years did not reveal any ATP1A3 mutations. They were rather mildly clinically affected and displayed a normal or near-normal psychomotor development. This is the first study of AHC in the Danish paediatric population. The patients harboured a wide range of psychomotor difficulties. Patients with no mutation detected tended to be less severely affected. Prevalence was approximately 1 per 100,000 children.
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Salila Vijayalal Mohan HK, An J, Zheng L. Sequence-dependent electrical response of ssDNA-decorated carbon nanotube, field-effect transistors to dopamine. Beilstein J Nanotechnol 2014; 5:2113-21. [PMID: 25551039 PMCID: PMC4273222 DOI: 10.3762/bjnano.5.220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 10/24/2014] [Indexed: 05/08/2023]
Abstract
Single-walled carbon nanotube (SWCNT)-based field-effect transistors (FETs) have been explored for use as biological/chemical sensors. Dopamine (DA) is a biomolecule with great clinical significance for disease diagnosis, however, SWCNT FETs lack responsivity and selectivity for its detection due to the presence of interfering compounds such as uric acid (UA). Surface modification of CNTs using single-stranded deoxyribonucleic acid (ssDNA) renders the surface responsive to DA and screens the interferent. Due to the presence of different bases in ssDNA, it is necessary to investigate the effect of sequence on the FET-based molecular recognition of DA. SWCNT FETs were decorated with homo- and repeated-base ssDNA sequences, and the electrical response induced by DA in the presence and absence of UA was gauged in terms of the variation in transistor electrical parameters including conductance, transconductance, threshold voltage and hysteresis gap. Our results showed that the response of ssDNA-decorated devices to DA, irrespective of the presence or absence of UA, was DNA sequence dependent and exhibited the trend: G > A > C and GA > GT > AC > CT, for homo- and repeated-base sequences, respectively. The different response of various SWCNT-ssDNA systems to DA underlines the sequence selectivity, whereas the detection of DA in the presence of UA highlights the molecular selectivity of the ssDNA-decorated devices.
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Affiliation(s)
| | - Jianing An
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Lianxi Zheng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
- Department of Mechanical Engineering, Khalifa University of Science, Technology & Research (KUSTAR), P.O. Box 127788, Abu Dhabi, United Arab Emirates
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El Kenz H, Efira A, Le PQ, Thiry C, Valsamis J, Azerad MA, Corazza F. Transfusion support of autoimmune hemolytic anemia: how could the blood group genotyping help? Transl Res 2014; 163:36-42. [PMID: 24120494 DOI: 10.1016/j.trsl.2013.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 11/25/2022]
Abstract
Conventional pretransfusion testing based on hemagglutination assays can be challenging for patients with autoimmune hemolytic anemia (AIHA) because of the presence of auto-antibodies. It has been suggested that deoxyribonucleic acid-based methods could be more efficient in the selection of antigen-matched red blood cell units in those settings. Because of the high risk of alloimmunization of these patients and the labor-intensive nature of adsorption techniques, we decided to evaluate the feasibility of selecting antigen-matched units on the basis of RBC genotyping. We included in our routine RBC genotyping program samples from 7 patients with AIHA presenting a strongly positive direct antiglobulin test. This made the routine compatibility tests difficult. Most patients had previously received transfusions because of warm AIHA. Matched donor units were selected according to the genotype. For all but 1 patient, blood group genotyping could be done on time to allow antigen-matched transfusion. Four patients received antigen-matched red blood cell units based on RBC genotyping and for 1 patient the fact that no matched units were available led us to postpone the transfusion. After each transfusion, the recovery was recorded and considered satisfactory for all transfused patients.
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Affiliation(s)
- Hanane El Kenz
- Department of Transfusion, Hospital Blood Bank, CHU-Brugmann and Queen Fabiola Children University Hospital, Brussels, Belgium.
| | - André Efira
- Department of Hematology, CHU-Brugmann, Brussels, Belgium
| | - Phu Quoc Le
- Department of Hematology, Queen Fabiola University Children Hospital, Brussels, Belgium
| | - Claire Thiry
- Department of Transfusion, Hospital Blood Bank, CHU-Brugmann and Queen Fabiola Children University Hospital, Brussels, Belgium
| | - Joseph Valsamis
- Laboratory of Clinical Biology, CHU-Brugmann, Brussels, Belgium
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Lucas SJ, Baştaş K, Budak H. Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection. Gene 2014; 536:254-64. [PMID: 24368332 DOI: 10.1016/j.gene.2013.12.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/22/2013] [Accepted: 12/10/2013] [Indexed: 01/15/2023]
Abstract
The present study aims to investigate small RNA interactions with putative disease response genes in the model grass species Brachypodium distachyon. The fungal pathogen Fusarium culmorum (Fusarium herein) and phytohormone salicylic acid treatment were used to induce the disease response in Brachypodium. Initially, 121 different putative disease response genes were identified using bioinformatic and homology based approaches. Computational prediction was used to identify 33 candidate new miRNA coding sequences, of which 9 were verified by analysis of small RNA sequence libraries. Putative Brachypodium miRNA target sites were identified in the disease response genes, and a subset of which were screened for expression and possible miRNA interactions in 5 different Brachypodium lines infected with Fusarium. An NBS-LRR family gene, 1g34430, was polymorphic among the lines, forming two major genotypes, one of which has its miRNA target sites deleted, resulting in altered gene expression during infection. There were siRNAs putatively involved in regulation of this gene, indicating a role of small RNAs in the B. distachyon disease response.
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