Automated Identification of Germline de novo Mutations in Family Trios: A Consensus-Based Informatic Approach

Accurate identification of germline de novo variants (DNVs) remains a challenging problem despite rapid advances in sequencing technologies as well as methods for the analysis of the data they generate, with putative solutions often involving ad hoc filters and visual inspection of identified variants. Here, we present a purely informatic method for the identification of DNVs by analyzing short-read genome sequencing data from proband-parent trios. Our method evaluates variant calls generated by three genome sequence analysis pipelines utilizing different algorithms-GATK HaplotypeCaller, DeepTrio and Velsera GRAF-exploring the assumption that a requirement of consensus can serve as an effective filter for high-quality DNVs. We assessed the efficacy of our method by testing DNVs identified using a previously established, highly accurate classification procedure that partially relied on manual inspection and used Sanger sequencing to validate a DNV subset comprising less confident calls. The results show that our method is highly precise and that applying a force-calling procedure to putative variants further removes false-positive calls, increasing precision of the workflow to 99.6%. Our method also identified novel DNVs, 87% of which were validated, indicating it offers a higher recall rate without compromising accuracy. We have implemented this method as an automated bioinformatics workflow suitable for large-scale analyses without need for manual intervention.

Metabolomic analysis of seminal fluids in infertile individuals

OBJECTIVE

Infertility impacts a substantial number of couples worldwide, and about 50% of cases are linked to male factors. The analysis of seminal fluid composition can improve diagnostic accuracy and offer deeper insights into the pathophysiology of male factor infertility. This study seeks to identify novel markers for diagnosing and treating male infertility by comparing organic acid profiles in the seminal fluid of individuals with normospermia, oligospermia, and azoospermia.

PATIENTS AND METHODS

Semen samples were collected from men with normospermia, oligospermia, and azoospermia. The organic acid profile in the seminal fluid was analyzed using liquid chromatography-mass spectrometry/mass spectrometry (LC/MS-MS). Data analysis was performed using SPSS and MetaboAnalyst.

RESULTS

The study revealed significant differences in metabolite levels among normospermic, oligospermic, and azoospermic individuals. In groups with oligospermia, there were significant decreases in the levels of 2-OH-Isovaleric Acid, 3-Methyl-2-Oxovaleric Acid, Ethyl-Malonic Acid, Citric Acid, Oxoproline, Malic Acid, N-Acetyl-Aspartic Acid, Suberic Acid, Glutaconic Acid, and Succinic Acid. Similarly, individuals with azoospermia exhibited a notable reduction in the levels of Citric Acid, Malic Acid, and Suberic Acid. Furthermore, according to the Variable Importance in the Projection (VIP) score analysis, Ethyl-Malonic Acid, Glycolic Acid, and 3-Methyl-2-Oxovaleric Acid were identified as crucial factors for diagnosis and potential treatment strategies.

CONCLUSIONS

The data obtained from the study highlights the significant potential of metabolites in assessing infertility and gaining a more in-depth understanding of the underlying pathological mechanisms.

Comparison of sperm carnitine profiles of normospermic, oligospermic and azospermic individuals

OBJECTIVE

The World Health Organization recognizes infertility as a public health issue. An estimated 48.5 million couples worldwide grapple with infertility. Infertility and spermatogenesis dysfunction arise from diverse genetic factors, including single-gene mutations and chromosomal abnormalities. Current research continues to explore other potential causes of infertility, leveraging both proteomic and metabolomic analyses. The primary aim of this study is to underscore the significance of investigating male infertility from a metabolomic perspective.

PATIENTS AND METHODS

This study aimed to identify new markers for diagnosing and treating male infertility by examining the carnitine profiles in seminal fluids of individuals diagnosed with the normospermic group, oligospermic group, and azospermic group, employing the LC/MS-MS method.

RESULTS

The first three L-carnitines C2 (Acetylcarnitine), C8:1 (Octenoylcarnitine), and C16:1 (Palmitoleylcarnitine), emerged as potential novel markers for diagnosis and treatment.

CONCLUSIONS

Based on these findings, we posit that the results obtained in this study will aid in diagnosing, treating, and monitoring systemic diseases, and provide a foundation for more comprehensive future molecular studies aimed at enhancing prevention and treatment strategies for infertility.

Expression of Human β-defensin 2 (hBD-2) in Pichia Pastoris and Investigation of Its Binding Efficiency with ACE-2

COVID-19 is a disease that have affected the entire world, and it continues to spread with new variants. A patient's innate immune system plays a critical role in the mild and severe transition of COVID-19. Antimicrobial peptides (AMPs), which are important components of the innate immune system, are potential molecules to fight pathogenic bacteria, fungi, and viruses. Human β-defensin 2 (hBD-2), a 41-amino-acid antimicrobial peptide, is one of the defensins inducibly expressed in the skin, lungs, and trachea in humans. In this study, it was aimed to investigate the interaction of hBD-2 produced recombinantly in Pichia pastoris with the human angiotensin-converting enzyme 2 (ACE-2) under in vitro conditions. First, hBD-2 was cloned in P. pastoris X-33 via the pPICZαA vector, a yeast expression platform, and its expression was confirmed by SDS-PAGE, western blotting, and qRT-PCR. Then, the interaction between recombinant hBD-2 and ACE-2 proteins was revealed by a pull-down assay. In light of these preliminary experiments, we suggest that the recombinantly produced hBD-2 may be protective against SARS-CoV-2 and be used as a supplement in treatment. However, current findings need to be supported by cell culture studies, toxicity analyses, and in vivo experiments.

Effects of Four Antibiotics on Pseudomonas aeruginosa Motility, Biofilm Formation, and Biofilm-Specific Antibiotic Resistance Genes Expression

The aim of this study was to determine the effects of 4 antibiotics (tobramycin, fosfomycin, ciprofloxacin, and piperacillin/tazobactam) against Pseudomonas aeruginosa motility, biofilm formation, and biofilm resistance gene expression changes using different methods including microscopy, microdilution, crystal violet staining, and qRT-PCR. Although the antibiotics reduced swarming motility, they inhibited biofilm formation to a greater extent than the minimum inhibitory concentration (MIC) value. The qRT-PCR results showed that the antibiotics, other than fosfomycin, decreased the expression levels of the selected biofilm resistance genes (ndvB, tssC1, PA5033 and PA2070) in the biofilm structure compared to planktonic cells. Furthermore, it was found that there was an increase in the expression levels of biofilm resistance genes in the antibiotic application groups compared to the biofilm structure that was not treated with antibiotics. These results showed for the first time that the treatment of antibiotics at sub-MIC concentrations increases the expression levels of biofilm-specific resistance genes and contributes to resistance and motility.

Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis

Graph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference to represent the diverse genetic information from different human populations and its inability to maintain the same level of accuracy for non-European ancestries. While there have been many efforts to develop computationally efficient graph-based toolkits for NGS read alignment and variant calling, methods to curate genomic variants and subsequently construct genome graphs remain an understudied problem that inevitably determines the effectiveness of the overall bioinformatics pipeline. In this study, we discuss obstacles encountered during graph construction and propose methods for sample selection based on population diversity, graph augmentation with structural variants and resolution of graph reference ambiguity caused by information overload. Moreover, we present the case for iteratively augmenting tailored genome graphs for targeted populations and demonstrate this approach on the whole-genome samples of African ancestry. Our results show that population-specific graphs, as more representative alternatives to linear or generic graph references, can achieve significantly lower read mapping errors and enhanced variant calling sensitivity, in addition to providing the improvements of joint variant calling without the need of computationally intensive post-processing steps.

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

In vitro transcriptome response to propolis in differentiated SH-SY5Y neurons

Propolis is the extract of a resinous compound that protects plants from both cold and microorganism attack and has gained a strong and sticky property because it is transformed after being collected by honey bees. Up to date, many studies have shown that propolis exhibited various beneficial biological activities, such as antifungal, antibacterial, antiviral, antioxidant, antimutagenic, and antitumor effects. Recent reports propounded the in vitro and in vivo neuroprotective effect of propolis; however, the exact molecular genetic mechanisms are still unclear. Therefore, we aimed to investigate the toxicogenomic and beneficial properties, including cytotoxic, antioxidant, apoptotic/necrotic as well as genotoxic effects of propolis (1.56-200 µg/ml) on differentiated SH-SY5Y neuronal cells. Additionally, microarray analysis was conducted on cell cultures following propolis application to explore gene differentiation. Differentially expressed genes were further analyzed using string software to characterize protein-protein interactions between gene pathways. Our results revealed that propolis applications could not have a prominent effect on cell viability even at concentrations up to 200 µg/ml. The highest propolis concentration induced apoptotic rather than necrotic cell death. The alterations in gene expression profiles, including CYP26A1, DHRS2, DHRS3, DYNC1I1, IGF2, ITGA4, SVIL, TGFβ1, and TGM2 could participate in the neuroprotective effects of propolis. In conclusion, propolis supplementation exerted remarkable advantageous; thus, it may offer great potential as a natural component in the prevention and treatment of neurodegenerative disorders. Whole-genome gene expression pattern following propolis application was investigated for the first time in neuronal cell culture to fill a gap in the literature about propolis toxicogenomics. PRACTICAL APPLICATIONS: Propolis is a very rich product in terms of benefits. In addition to its antibacterial, antiviral, antifungal, and anti-inflammatory content, it is known to have preventive and therapeutic properties for many different ailments. On the other hand, molecular mechanisms of propolis on gene expression differentiations haven't been investigated until now. Moreover, gene expression pattern is vital for all living organisms to maintain homeostasis. Thus, we conduct an experiment series for analyzing gene expression differentiation effects on neuronal cells to understand beneficial properties of propolis. Hence, it could be possible to comment on the use of propolis as a nutritional factor and beneficial diet.

Maternal serum fructosamine levels and stillbirth: a case-control study of the Stillbirth Collaborative Research Network

OBJECTIVE

To evaluate the association between maternal fructosamine levels at the time of delivery and stillbirth.

DESIGN

Secondary analysis of a case-control study.

SETTING

Multicentre study of five geographic catchment areas in the USA.

POPULATION

All singleton stillbirths with known diabetes status and fructosamine measurement, and representative live birth controls.

MAIN OUTCOME MEASURES

Fructosamine levels in stillbirths and live births among groups were adjusted for potential confounding factors, including diabetes. Optimal thresholds of fructosamine to discriminate stillbirth and live birth.

RESULTS

A total of 529 women with a stillbirth and 1499 women with a live birth were included in the analysis. Mean fructosamine levels were significantly higher in women with a stillbirth than in women with a live birth after adjustment (177 ± 3.05 versus 165 ± 2.89 μmol/L, P < 0.001). The difference in fructosamine levels between stillbirths and live births was greater among women with diabetes (194 ± 8.54 versus 162 ± 3.21 μmol/L), compared with women without diabetes (171 ± 2.50 versus 162 ± 2.56 μmol/L). The area under the curve (AUC) for fructosamine level and stillbirth was 0.634 (0.605-0.663) overall, 0.713 (0.624-0.802) with diabetes and 0.625 (0.595-0.656) with no diabetes.

CONCLUSIONS

Maternal fructosamine levels at the time of delivery were higher in women with stillbirth compared with women with live birth. Differences were substantial in women with diabetes, suggesting a potential benefit of glycaemic control in women with diabetes during pregnancy. The small differences noted in women without diabetes are not likely to justify routine screening in all cases of stillbirth.

TWEETABLE ABSTRACT

Maternal serum fructosamine levels are higher in women with stillbirth than in women with live birth, especially in women with diabetes.

Early Endoscopy Decrease the Length of Hospital Stay and the Costs in Patients with Upper Gastrointestinal Bleeding

Background

Acute gastrointestinal (GI) bleeding is a common cause of hospitalization. There are conflicting results regarding the effectiveness of early endoscopy in patients with upper GI bleeding.

Objective

The study aimed to determine the benefit of early endoscopy and the epidemiological characteristics of patients presenting to the emergency department with non-variceal acute upper GI bleeding.

Methods

Patients over 18 years of age who presented to the emergency department with upper GI between 2015 and 2016 and underwent endoscopy were included in the study. The patients were divided into two groups: early endoscopy group (endoscopy within the 24 h) and late endoscopy group (endoscopy after 24 h).

Results

Of 104 patients, 57.7% were man, and the mean age was 66.27 ± 17.64 years. Of the patients who underwent endoscopy, 80 (76.9%) were in the early endoscopy group. There was no difference in blood transfusion needs (P = 0.388), re-bleeding (P = 0.137), the need for surgery, and mortality rates with regard to the timing of endoscopy. The results of the receiver-operating characteristics curve analysis revealed patients with a GBS ≥ 9 were taken as high-risk, and a prognosis analysis was performed accordingly. However, in patients undergoing early endoscopy, a difference was detected with respect to the length of hospital stay (P = 0.011) and treatment costs (P = 0.030). In the comparison with the admission time (working/non-working h) and variables, there were no significant differences in the length of hospital stay (P = 0.230), transfusion needs (P = 0.348), re-bleeding frequency (P = 0.905), and treatment costs (P = 0.094).

Conclusion

Endoscopy within 24 h in the setting of acute upper non-variceal GI bleeding is associated with an increase in the length of hospital stay and treatment costs, but is not associated with re-bleeding, transfusion needs, need for surgery, and mortality.

Tribological, biocompatibility, and antibiofilm properties of tungsten-germanium coating using magnetron sputtering

In this study, borosilicate glass and 316 L stainless steel were coated with germanium (Ge) and tungsten (W) metals using the Magnetron Sputtering System. Surface structural, mechanical, and tribological properties of uncoated and coated samples were examined using SEM, X-ray diffraction (XRD), energy-dispersive spectroscopy, and tribometer. The XRD results showed that WGe2 chemical compound observed in (110) crystalline phase and exhibited a dense structure. According to the tribological analyses, the adhesion strength of the coated deposition on 316 L was obtained 32.8 N, and the mean coefficient of friction was around 0.3. Biocompatibility studies of coated metallic biomaterials were analyzed on fibroblast cell culture (Primary Dermal Fibroblast; Normal, Human, Adult (HDFa)) in vitro. Hoescht 33258 fluorescent staining was performed to investigate the cellular density and chromosomal abnormalities of the HDFa cell line on the borosilicate glasses coated with germanium-tungsten (W-Ge). Cell viabilities of HDFa cell line on each surface (W-Ge coated borosilicate glass, uncoated borosilicate glass, and cell culture plate surface) were analyzed by using (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) cytotoxicity assay. The antibiofilm activity of W-Ge coated borosilicate glass showed a significant reduction effect on Staphylococcus aureus (ATCC 25923) and Pseudomonas aeruginosa (ATCC 27853) adherence compared to control groups. In the light of findings, tungsten and germanium, which are some of the most common industrial materials, were investigated as biocompatible and antimicrobial surface coatings and recommended as bio-implant materials for the first time.

Is ceftriaxone effective in experimental brain ischemia/reperfusion injury?

OBJECTIVE

The aim of the present study was to investigate the neuroprotective effect of ceftriaxone in a rat brain ischemia/reperfusion injury model.

METHODS

The oxidative stress parameter, malondialdehyde (MDA) levels with or without ceftriaxone treatment in brain ischemia/reperfusion injured rats as well as in controls were measured in serum and brain tissue. Motor examinations of the rats were also performed. One-way Analysis of Variance (ANOVA) test was used for analysis. Duncan's Multiple Range Test was performed in multiple comparisons. p < 0.05 were considered statistically significant.  RESULTS: The data of this study showed that ceftriaxone treatment reduced the MDA levels in brain tissues in ischemia/reperfusion injured rats. Moreover, Bederson motor scores were higher in the ceftriaxone treated group as compared to the ischemia group (p = 0.092).

CONCLUSION

These results suggest that ceftriaxone could be beneficial for the prevention of brain ischemia/reperfusion injury caused by acute arterial occlusion through reducing the tissue MDA level (Tab. 2, Fig. 5, Ref. 24).

The investigation of the antitumoral effect of Cornus mas L in mice with ehrlich solid tumor

AIM

Cornus mas L is commonly used due to its anti-inflammatory, anti-carcinogenic and anti-oxidant properties. In the study, the effects of C. mas L extract on a solid tumor were examined in the Ehrlich solid tumor model developed in Balb/C type mice.

METHODS

Ehrlich acid tumor (EAT) cells (1x106 EAT cell) from the stock animal were injected subcutaneously (s.c.) through the nape of the mice. Treatment groups of solid tumor-induced animals received 100 mg/kg and 200 mg/kg of C. mas L extract intraperitoneally (i.p.) for 14 days.

RESULTS

Tumor volumes and animal weights were found to be statistically significant compared to the control group (p < 0.05). AgNOR staining was performed in tumor tissues. Statistically significant differences were observed between the groups in terms of TAA/NA ratio (p < 0.05). Immunohistochemical and biochemical parameters were also evaluated. An estimation of tumor proliferation of the lung, liver, brain, kidney, testis and tumor antioxidant parameters viz. lipid peroxidation, reduced glutathione (GSH), glutathione S-transferase (GST), superoxide dismutase (SOD) and catalase (CAT) was made.

CONCLUSIONS

Our study showed that the anti-tumor effect of C. mas L in assisted tumor development with EAT cells, was mediated by the enhancement of oxidative stress with multiple mechanisms (Tab. 6, Fig. 12, Ref. 38).

Diagnostic impact of 18F-FDG PET/CT on the management of rare breast carcinomas: Apocrine and neuroendocrine carcinomas

OBJECTIVE

We aimed to evaluate the diagnostic impact of ¹⁸F-FDG PET/CT in staging apocrine breast carcinoma (ABC) and primary breast neuroendocrine carcinoma (PBNEC) and to demonstrate possible alterations of the ¹⁸F-FDG uptake in these histopathologic subtypes. In addition, we aimed to compare ¹⁸F-FDG PET/CT findings between ABC, PBNEC and invasive ductal carcinoma.

MATERIAL AND METHODS

A total of 570 patients and 585 breast lesions were retrospectively included in this study. After patients were classified into molecular subtypes according to the histopathological analysis, ¹⁸F-FDG PET/CT imaging was performed. The SUVmax findings of primary tumors obtained from ¹⁸F-FDG PET/CT were compared between the groups.

RESULTS

Invasive ductal carcinoma was the most prevalent breast carcinoma (77.7%, n=446), with a low proportion of ABC (4.1%, n=24) and PBNEC (2.4%; n=14) diagnosed. The highest mean SUVmax was calculated in HER2 subtype of ABC and ¹⁸F-FDG uptake ratio in HER2 and TN subtypes were found statistically higher than Luminal B type of ABC (p=0.038 and p=0.019, respectively). Although ¹⁸F-FDG uptake in Luminal B subtype of PBNEC was higher than Luminal A subtype, difference was not statistically significant. Additionally, the axillary metastasis rate was significantly higher in the ABC group (p=0.015).

CONCLUSIONS

The histopathological ABC subtype group showed different ¹⁸F-FDG uptake than the invasive ductal carcinoma group. Even if ¹⁸F-FDG uptake was lower in the PBNEC group than in the other groups, PET/CT showed and adequate performance in detecting primary tumors and metastases. The ¹⁸F-FDG PET/CT scan results may contribute to the initial staging and management of ABC and PBNEC patients.

Frequency of psychiatric disorders in nonemergent admissions to emergency department

Objectives

Repeated admissions of patients with undiagnosed psychiatric problems in emergency departments (ED) is a major contributor to patient unsatisfaction and overcrowding in EDs. We evaluated the presence of psychiatric disorders in non-emergent admissions in the ED of a tertiary care hospital.

Materials and Methods

This cross-sectional study was carried out in Eskisehir Osmangazi University Hospital between December 2015 and March 2016. The study group consists of 4320 non-emergent patients (31% of all admissions to non-emergent ED). Psychiatric assessments of patients were done using the Primary Care Evaluation of Mental Disorders (PRIME-MD) scale prior to their discharge from the ED. The Mann-Whitney U, Kruskal-Wallis and Chi-square tests, as well as multivariate logistic regression, were performed for statistical analysis.

Results

The mean age was 30 ± 11.7 years years ranging from 18 to 78 years. Among non-emergent cases, 44% had at least one psychiatric disorder. The most frequent psychiatric disorder was mood disorder (major and minor depression). Females with a comorbid disease and lower education level had increased risk for mood disorders, anxiety disorders, and somatoform disorders. Single males with a comorbid disease had increased risk for alcohol dependence.

Conclusions

Undiagnosed patients with psychiatric disorders appear to be frequent users of medical emergency department services. These results might be helpful in developing more effective strategies to serve the mental health needs of the undiagnosed. People's awareness of psychiatric disorders should be increased.

Protective therapeutic effects of peptide nanofiber and hyaluronic acid hybrid membrane in in vivo osteoarthritis model

Osteoarthritis (OA) is a condition where tissue function is lost through a combination of secondary inflammation and deterioration in articular cartilage. One of the most common causes of OA is age-related tissue impairment because of wear and tear due to mechanical erosion. Hyaluronic acid-based viscoelastic supplements have been widely used for the treatment of knee injuries. However, the current formulations of hyaluronic acid are unable to provide efficient healing and recovery. Here, a nanofiber-hyaluronic acid membrane system that was prepared by using a quarter of the concentration of commercially available hyaluronic acid supplement, Hyalgan®, was used for the treatment of an osteoarthritis model, and Synvisc®, which is another commercially available hyaluronic acid containing viscoelastic supplement, was used as a control. The results show that this system provides efficient protection of arthritic cartilage tissue through the preservation of cartilage morphology with reduced osteophyte formation, protection of the subchondral region from deterioration, and maintenance of cartilage specific matrix proteins in vivo. In addition, the hybrid nanofiber membrane enabled chondrocyte encapsulation and provided a suitable culturing environment for stem cell growth in vitro. Overall, our results suggest that this hybrid nanofibrous scaffold provides a potential platform the treatment of OA.

STATEMENT OF SIGNIFICANCE

Osteoarthritis is a debilitating joint disease affecting millions of people worldwide. It occurs especially in knees due to aging, sport injuries or obesity. Although hyaluronic acid-based viscoelastic supplements are widely used, there is still no effective treatment method for osteoarthritis, which necessitates surgical operation as an only choice for severe cases. Therefore, there is an urgent need for efficient therapeutics. In this study, a nanofiber-HA membrane system was developed for the efficient protection of arthritic cartilage tissue from degeneration. This hybrid nanofiber system provided superior therapeutic activity at a relatively lower concentration of hyaluronic acid than Hyalgan® and Synvisc® gels, which are currently used in clinics. This work demonstrates for the first time that this hybrid nanofiber membrane scaffold can be utilized as a potential candidate for osteoarthritis treatment.

The effects of aflatoxin B1 on growth hormone regulated gene-1 and interaction between DNA and aflatoxin B1 in broiler chickens during hatching

Many types of aflatoxin cause problems for both public and animal health. Aflatoxin B₁ (AFB₁) is the most toxic and commonly encountered fungal toxin that appears in poultry feed and in feeds stored under unsuitable conditions. AFB₁ decreases feed quality, egg production and fertility of hatching eggs. Also, AFB₁ alters the development of embryos by infecting eggs. We investigated using sequence analysis the changes caused by different concentrations of AFB₁ on the promoter sequences of the growth hormone regulated gene-1 (GHRG-1) in chick embryo at 13, 17, 19 and 21 days incubation. DNA isolated from the liver of chick embryos treated with different concentrations of AFB₁ was separated using agarose gel electrophoresis to detect apoptosis, and DNA interaction with AFB₁ was investigated using plasmids to detect changes in electrophoretic mobility and their effects on DNA. Base changes of the promoter sequences of GHRG-1 in 5 ng/egg, 15 ng/egg and 40 ng/egg doses of AFB₁ were increased on day 19 compared to base changes of the same AFB₁ doses on day 13. We also found that AFB at different concentrations changed the mobility of DNA by binding to it, and that high doses of AFB1 destroyed DNA. The DNA interaction study using plasmid demonstrated that AFB₁ at high doses was bound to plasmid DNA, slowed its mobility and inhibited restriction cuts.

Supramolecular Peptide Nanofiber Morphology Affects Mechanotransduction of Stem Cells

Chirality and morphology are essential factors for protein function and interactions with other biomacromolecules. Extracellular matrix (ECM) proteins are also similar to other proteins in this sense; however, the complexity of the natural ECM makes it difficult to study these factors at the cellular level. The synthetic peptide nanomaterials harbor great promise in mimicking specific ECM molecules as model systems. In this work, we demonstrate that mechanosensory responses of stem cells are directly regulated by the chirality and morphology of ECM-mimetic peptide nanofibers with strictly controlled characteristics. Structural signals presented on l-amino acid containing cylindrical nanofibers (l-VV) favored the formation of integrin β1-based focal adhesion complexes, which increased the osteogenic potential of stem cells through the activation of nuclear YAP. On the other hand, twisted ribbon-like nanofibers (l-FF and d-FF) guided the cells into round shapes and decreased the formation of focal adhesion complexes, which resulted in the confinement of YAP proteins in the cytosol and a corresponding decrease in osteogenic potential. Interestingly, the d-form of twisted-ribbon like nanofibers (d-FF) increased the chondrogenic potential of stem cells more than their l-form (l-FF). Our results provide new insights into the importance and relevance of morphology and chirality of nanomaterials in their interactions with cells and reveal that precise control over the chemical and physical properties of nanostructures can affect stem cell fate even without the incorporation of specific epitopes.

REMOVED: Psychiatric social work needs of families having children with mental diseases in Turkey

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Peptide-Based Materials for Cartilage Tissue Regeneration

Cartilaginous tissue requires structural and metabolic support after traumatic or chronic injuries because of its limited capacity for regeneration. However, current techniques for cartilage regeneration are either invasive or ineffective for long-term repair. Developing alternative approaches to regenerate cartilage tissue is needed. Therefore, versatile scaffolds formed by biomaterials are promising tools for cartilage regeneration. Bioactive scaffolds further enhance the utility in a broad range of applications including the treatment of major cartilage defects. This chapter provides an overview of cartilage tissue, tissue defects, and the methods used for regeneration, with emphasis on peptide scaffold materials that can be used to supplement or replace current medical treatment options.

Glycosaminoglycan-Mimetic Signals Direct the Osteo/Chondrogenic Differentiation of Mesenchymal Stem Cells in a Three-Dimensional Peptide Nanofiber Extracellular Matrix Mimetic Environment

Recent efforts in bioactive scaffold development focus strongly on the elucidation of complex cellular responses through the use of synthetic systems. Designing synthetic extracellular matrix (ECM) materials must be based on understanding of cellular behaviors upon interaction with natural and artificial scaffolds. Hence, due to their ability to mimic both the biochemical and mechanical properties of the native tissue environment, supramolecular assemblies of bioactive peptide nanostructures are especially promising for development of bioactive ECM-mimetic scaffolds. In this study, we used glycosaminoglycan (GAG) mimetic peptide nanofiber gel as a three-dimensional (3D) platform to investigate how cell lineage commitment is altered by external factors. We observed that amount of fetal bovine serum (FBS) presented in the cell media had synergistic effects on the ability of GAG-mimetic nanofiber gel to mediate the differentiation of mesenchymal stem cells into osteogenic and chondrogenic lineages. In particular, lower FBS concentration in the culture medium was observed to enhance osteogenic differentiation while higher amount FBS promotes chondrogenic differentiation in tandem with the effects of the GAG-mimetic 3D peptide nanofiber network, even in the absence of externally administered growth factors. We therefore demonstrate that mesenchymal stem cell differentiation can be specifically controlled by the combined influence of growth medium components and a 3D peptide nanofiber environment.

Serum chitotriosidase levels in cancer patients undergoing high dose chemotherapy and stem cell transplantation

OBJECTIVE

Human chitotriosidase (ChT) is an active chitinase expressed by activated phagocytes. Increased ChT activity has been reported in systemic Candida albicans infections and in Gram-negative and Gram-positive bacterial infections, indicating that an increase in ChT activity reflects phagocyte activation. The aim of this study was to determine the changes in serum ChT activity in patients who underwent high dose chemotherapy (HDC) and stem cell transplantation (SCT), who are at an increased risk for fungal and bacterial infections due to depression of the immune system during the neutropenic period.

PATIENTS AND METHODS

A total of 55 SCT patients were included in the study. Serum ChT activity was determined before the initiation of HDC and during the neutropenic period after hematopoietic stem cell reinfusion on post-transplant first, fifth and tenth days.

RESULTS

Chitotriosidase levels before transplantation were significantly lower than the results at first, fifth and tenth days post-hematopoietic stem cell reinfusion.

CONCLUSIONS

Although the number of neutrophils was low, ChT enzyme activity was high in newly produced granules of neutrophils. Chitotriosidase may be supplemented as a drug for preventing and treating infections in the near future.

Bioactive supramolecular peptide nanofibers for regenerative medicine

Recent advances in understanding of cell-matrix interactions and the role of the extracellular matrix (ECM) in regulation of cellular behavior have created new perspectives for regenerative medicine. Supramolecular peptide nanofiber systems have been used as synthetic scaffolds in regenerative medicine applications due to their tailorable properties and ability to mimic ECM proteins. Through designed bioactive epitopes, peptide nanofiber systems provide biomolecular recognition sites that can trigger specific interactions with cell surface receptors. The present Review covers structural and biochemical properties of the self-assembled peptide nanofibers for tissue regeneration, and highlights studies that investigate the ability of ECM mimetic peptides to alter cellular behavior including cell adhesion, proliferation, and/or differentiation.

Carinal sleeve pneumonectomy for lung cancer

BACKGROUND

Here, we present our experience of 12 lung cancer cases operated with carinal sleeve pneumonectomy (CSP) from 2001 to 2011.

METHODS

12 cases who had undergone CSP in our department from 2001 to 2011 were retrospectively evaluated and presented by taking into account their demographical and clinical features, the surgical technique that was used, the complications that developed and the latest conditions of these patients.

RESULTS

Of the 12 cases, 11 were male and 1 was female with a mean age of 58.6 years (40-71 years). 11 cases had right and 1 had left CSP. The ethiology for resection was lung cancer in all cases. 10 cases had carinal invasion of the lung cancer, 1 had bronchopleural fistula developing after right pneumonectomy, 1 had distal tracheal rupture due to intubation tube placed during pneumonectomy; these all resulted in performing CSP. Five patients developed complications during the postoperative period. Three cases developed recurrences/metastases during the follow-up. Nine patients died, 3 patients were alive and were followed-up by our department. For all the cases, the median survival was 9 months, the estimated survival rate of 2-years was 33%, and 5-year survival rate was 22%. Survival for 2-4 years was 71%.

CONCLUSIONS

We think that with increasing surgical experience better results are obtained in these technically demanding procedures.

In vitro bactericidal activity of enrofloxacin against gyrA mutant and qnr-containing Escherichia coli isolates from animals

The objective of this work was to investigate the bactericidal activity of enrofloxacin against gyrA mutant and qnr-containing Escherichia coli isolates from animals. The minimum inhibitory concentrations (MICs) of gyrA mutant and qnr-containing E coli isolates ranged from 1 µg/ml to 32 µg/ml for enrofloxacin. Time-kill experiments were performed using selected E coli isolates. For the time-kill experiments, the colony counts were determined by plating each diluted sample onto plate count agar and an integrated pharmacokinetic/pharmacodynamics area measure (log ratio area) was applied to the colony-forming units (cfu) data. In general, enrofloxacin exhibited bactericidal activity against all the gyrA mutant E coli isolates at all concentrations greater than four times the MIC. However, the bactericidal activity of enrofloxacin for all the qnr-containing E coli isolates was less dependent on concentration. The results of the present study indicated that the genetic mechanism of resistance might account for the different bactericidal activities of enrofloxacin observed for the gyrA mutant and the qnr-containing E coli isolates. Therefore, in addition to MIC assays, genetic mechanism-based pharmacodynamic models should be used to provide accurate predictions of the effects of drugs on resistant bacteria.

Molecular characterisation of quinolone resistance in Escherichia coli from animals in Turkey

The aim of this study were to detect the gyrA, parC and marR mutations and qnr genes (qnrA, qnrB and qnrS) in 120 strains of Escherichia coli isolated from animals. European Committee on Antimicrobial Susceptibility Testing and Clinical Laboratory Standards Institute disc diffusion and minimum inhibitory concentration (MIC) tests, respectively, were used to determine fluoroquinolone (FQ) resistance, and molecular methods were used to detect the mutations and the genes. E coli isolates with an MIC of ≥8&emsp14;mg/l had mutation at Ser-80 in parC in addition to mutations at Ser-83, Asp-87 or both in gyrA. The nucleotide change was detected in marR (Ser-3 → Asn, Ala-53 → Glu, Gly-103 → Ser, Tyr-137 → His). Only four E coli isolates (3.3 per cent) contained qnrA and qnrS, and qnrB was not detected. Two E coli isolates from healthy calves also contained qnrA and qnrS. The MICs of enrofloxacin and danofloxacin for qnr-containing E coli isolates ranged from 32&emsp14;mg/l to 256&emsp14;mg/l. The results of this study indicated that the FQ-resistant E coli isolates presented an alteration in gyrA (Ser-83 → Leu, Asp-87 → Asn) and parC (Ser-80 → Ile) with high MICs (8-256&emsp14;mg/l), and there was a low prevalence of qnr genes among E coli isolated from animals.

A registry for the collection of data in cochlear implant patients

The need to optimize the use of all the information that modern technological tools have made available to the physician ENT/audiologist has increasingly emerged within the Italian scientific community. Towards this purpose, it is necessary to create a registry of the patients using cochlear implants (CIs). This registry will include a homogeneous summary of the information deriving from multiple sources related to daily clinical practice, in order to assess auditory benefits, safety and reliability in patients with cochlear implants, and organization over the national territory. The primary objectives relative to the above-mentioned analysis are to assess the impact of the use of cochlear implants on patient health, to ensure traceability of the devices currently used, monitoring their safety and reliability over time, to guarantee access of the technique in clinical and organizational conditions that can allow the best possible benefits. The aspects concerning implementation of the registry were discussed extensively during the first meetings of the Working Group (WG). In particular, owing to the complexity and high costs related mainly to the development of the technological aspects and the need to involve technological partners external to the WG, and to respect current privacy laws, the WG members decided that the project should be limited to proposal of a paper registry to be implemented at a later stage, possibly within the framework of successive research projects. During meetings, the WG members discussed various aspects of implementation of the registry, and in particular the scientific features connected to objectives, inclusion criteria, and structure of the forms needed for data collection and organizational aspects. A registry is proposed herein.

Systematic review of the literature on the clinical effectiveness of the cochlear implant procedure in paediatric patients

The aim of this systematic review of the literature was to summarize the results of scientific publications on the clinical effectiveness of the cochlear implant (CI) procedure in children. The members of the Working Group first examined existing national and international literature and the principal international guidelines on the procedure. They considered as universally-accepted the usefulness/effectiveness of unilateral cochlear implantation in severely-profoundly deaf children. Accordingly, they focused attention on systematic reviews addressing clinical effectiveness and cost/efficacy of the CI procedure, with particular regard to the most controversial issues for which international consensus is lacking. The following aspects were evaluated: post-CI outcomes linked to precocity of CI; bilateral (simultaneous/ sequential) CI vs. unilateral CI and vs. bimodal stimulation; benefits derived from CI in deaf children with associated disabilities. With regard to the outcomes after implantation linked to precocity of intervention, there are few studies comparing post-CI outcomes in children implanted within the first year of life with those of children implanted in the second year. The selected studies suggest that children implanted within the first year of life present hearing and communicative outcomes that are better than those of children implanted after 12 months of age. Concerning children implanted after the first year of life, all studies confirm an advantage with respect to implant precocity, and many document an advantage in children who received cochlear implants under 18 months of age compared to those implanted at a later stage. With regard to bilateral CI, the studies demonstrate that compared to unilateral CI, bilateral CI offers advantages in terms of hearing in noise, sound localization and during hearing in a silent environment. There is, however, a wide range of variability. The studies also document the advantages after sequential bilateral CI. In these cases, a short interval between interventions, precocity of the first CI and precocity of the second CI are considered positive prognostic factors. In deaf children with associated disabilities, the studies analyzed evidence that the CI procedure is also suitable for children with disabilities associated with deafness, and that even these children may benefit from the procedure, even if these may be slower and inferior to those in children with isolated deafness, especially in terms of high communicative and perceptive skills.