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Silveira KC, Fonseca IC, Oborn C, Wengryn P, Ghafoor S, Beke A, Dreseris ES, Wong C, Iacovone A, Soltys CL, Babul-Hirji R, Artigalas O, Antolini-Tavares A, Gingras AC, Campos E, Cavalcanti DP, Kannu P. CYP26B1-related disorder: expanding the ends of the spectrum through clinical and molecular evidence. Hum Genet 2023; 142:1571-1586. [PMID: 37755482 PMCID: PMC10602971 DOI: 10.1007/s00439-023-02598-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
CYP26B1 metabolizes retinoic acid in the developing embryo to regulate its levels. A limited number of individuals with pathogenic variants in CYP26B1 have been documented with a varied phenotypic spectrum, spanning from a severe manifestation involving skull anomalies, craniosynostosis, encephalocele, radio-humeral fusion, oligodactyly, and a narrow thorax, to a milder presentation characterized by craniosynostosis, restricted radio-humeral joint mobility, hearing loss, and intellectual disability. Here, we report two families with CYP26B1-related phenotypes and describe the data obtained from functional studies of the variants. Exome and Sanger sequencing were used for variant identification in family 1 and family 2, respectively. Family 1 reflects a mild phenotype, which includes craniofacial dysmorphism with brachycephaly (without craniosynostosis), arachnodactyly, reduced radioulnar joint movement, conductive hearing loss, learning disability-and compound heterozygous CYP26B1 variants: (p.[(Pro118Leu)];[(Arg234Gln)]) were found. In family 2, a stillborn fetus presented a lethal phenotype with spina bifida occulta, hydrocephalus, poor skeletal mineralization, synostosis, limb defects, and a synonymous homozygous variant in CYP26B1: c.1083C > A. A minigene assay revealed that the synonymous variant created a new splice site, removing part of exon 5 (p.Val361_Asp382del). Enzymatic activity was assessed using a luciferase assay, demonstrating a notable reduction in exogenous retinoic acid metabolism for the variant p.Val361_Asp382del. (~ 3.5 × decrease compared to wild-type); comparatively, the variants p.(Pro118Leu) and p.(Arg234Gln) demonstrated a partial loss of metabolism (1.7× and 2.3× reduction, respectively). A proximity-dependent biotin identification assay reaffirmed previously reported ER-resident protein interactions. Additional work into these interactions is critical to determine if CYP26B1 is involved with other biological events on the ER. Immunofluorescence assay suggests that mutant CYP26B1 is still localized in the endoplasmic reticulum. These results indicate that novel pathogenic variants in CYP26B1 result in varying levels of enzymatic activity that impact retinoic acid metabolism and relate to the distinct phenotypes observed.
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Affiliation(s)
- Karina C Silveira
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Inara Chacon Fonseca
- Clinical Genetics, Durham Region Cancer Centre, Lakeridge Health Oshawa, Oshawa, ON, L1G 2B9, Canada
| | - Connor Oborn
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Parker Wengryn
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Saima Ghafoor
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Alexander Beke
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Ema S Dreseris
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Aline Iacovone
- Skeletal Dysplasia Group, Medical Genetics Area, Translational Medicine Department, FCM, University of Campinas (UNICAMP), R. Tessália V de Camargo, 126, Campinas, SP, 13083-887, Brazil
| | - Carrie-Lynn Soltys
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Riyana Babul-Hirji
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Osvaldo Artigalas
- Clinical Genetics Unit, Children's Hospital, Grupo Hospitalar Conceicao, Porto Alegre, Brazil
| | | | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Eric Campos
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Denise P Cavalcanti
- Skeletal Dysplasia Group, Medical Genetics Area, Translational Medicine Department, FCM, University of Campinas (UNICAMP), R. Tessália V de Camargo, 126, Campinas, SP, 13083-887, Brazil.
| | - Peter Kannu
- Department of Medical Genetics, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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Ghafoor S, Tognella A, Stocker D, Hötker AM, Kaniewska M, Sartoretti T, Euler A, Vonlanthen R, Bueter M, Alkadhi H. Diagnostic performance of CT with Valsalva maneuver for the diagnosis and characterization of inguinal hernias. Hernia 2023; 27:1253-1261. [PMID: 37410196 PMCID: PMC10533612 DOI: 10.1007/s10029-023-02830-y] [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: 04/10/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE Inguinal hernias are mainly diagnosed clinically, but imaging can aid in equivocal cases or for treatment planning. The purpose of this study was to evaluate the diagnostic performance of CT with Valsalva maneuver for the diagnosis and characterization of inguinal hernias. METHODS This single-center retrospective study reviewed all consecutive Valsalva-CT studies between 2018 and 2019. A composite clinical reference standard including surgery was used. Three blinded, independent readers (readers 1-3) reviewed the CT images and scored the presence and type of inguinal hernia. A fourth reader measured hernia size. Interreader agreement was quantified with Krippendorff's α coefficients. Sensitivity, specificity, and accuracy of Valsalva-CT for the detection of inguinal hernias was computed for each reader. RESULTS The final study population included 351 patients (99 women) with median age 52.2 years (interquartile range (IQR), 47.2, 68.9). A total of 381 inguinal hernias were present in 221 patients. Sensitivity, specificity, and accuracy were 85.8%, 98.1%, and 91.5% for reader 1, 72.7%, 92.5%, and 81.8% for reader 2, and 68.2%, 96.3%, and 81.1% for reader 3. Hernia neck size was significantly larger in cases correctly detected by all three readers (19.0 mm, IQR 13, 25), compared to those missed by all readers (7.0 mm, IQR, 5, 9; p < 0.001). Interreader agreement was substantial (α = 0.723) for the diagnosis of hernia and moderate (α = 0.522) for the type of hernia. CONCLUSION Valsalva-CT shows very high specificity and high accuracy for the diagnosis of inguinal hernia. Sensitivity is only moderate which is associated with missed smaller hernias.
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Affiliation(s)
- S Ghafoor
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - A Tognella
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - D Stocker
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - A M Hötker
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - M Kaniewska
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - T Sartoretti
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - A Euler
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - R Vonlanthen
- Department of Visceral and Transplantation Surgery, University Hospital of Zurich, Zurich, Switzerland
| | - M Bueter
- Department of Visceral and Transplantation Surgery, University Hospital of Zurich, Zurich, Switzerland
| | - H Alkadhi
- Diagnostic and Interventional Radiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Ghafoor S, Alkadhi H. Comment to: Diagnostic performance of CT with Valsalva maneuver for the diagnosis and characterization of inguinal hernias. Author's reply. Hernia 2023; 27:1335-1336. [PMID: 37642772 DOI: 10.1007/s10029-023-02867-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023]
Affiliation(s)
- S Ghafoor
- Diagnostic and Interventional Radiology, University Hospital Zurich, University Zurich, Zurich, Switzerland.
| | - H Alkadhi
- Diagnostic and Interventional Radiology, University Hospital Zurich, University Zurich, Zurich, Switzerland
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4
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Jonas JP, Rössler F, Ghafoor S, Kobe A, Pfammatter T, Schlag C, Gutschow CA, Petrowsky H, Müller PC, Oberkofler CE. Surgical therapy of celiac axis and superior mesenteric artery syndrome. Langenbecks Arch Surg 2023; 408:59. [PMID: 36690823 PMCID: PMC9870837 DOI: 10.1007/s00423-023-02803-w] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/20/2022] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Compression syndromes of the celiac artery (CAS) or superior mesenteric artery (SMAS) are rare conditions that are difficult to diagnose; optimal treatment remains complex, and symptoms often persist after surgery. We aim to review the literature on surgical treatment and postoperative outcome in CAS and SMAS syndrome. METHODS A systematic literature review of medical literature databases on the surgical treatment of CAS and SMAS syndrome was performed from 2000 to 2022. Articles were included according to PROSPERO guidelines. The primary endpoint was the failure-to-treat rate, defined as persistence of symptoms at first follow-up. RESULTS Twenty-three studies on CAS (n = 548) and 11 on SMAS (n = 168) undergoing surgery were included. Failure-to-treat rate was 28% for CAS and 21% for SMAS. Intraoperative blood loss was 95 ml (0-217) and 31 ml (21-50), respectively, and conversion rate was 4% in CAS patients and 0% for SMAS. Major postoperative morbidity was 2% for each group, and mortality was described in 0% of CAS and 0.4% of SMAS patients. Median length of stay was 3 days (1-12) for CAS and 5 days (1-10) for SMAS patients. Consequently, 47% of CAS and 5% of SMAS patients underwent subsequent interventions for persisting symptoms. CONCLUSION Failure of surgical treatment was observed in up to every forth patient with a high rate of subsequent interventions. A thorough preoperative work-up with a careful patient selection is of paramount importance. Nevertheless, the surgical procedure was associated with a beneficial risk profile and can be performed minimally invasive.
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Affiliation(s)
- J P Jonas
- Department of Surgery and Transplantation, Swiss HPB & Transplant Center Zurich, University Hospital Zurich, Zurich, Switzerland
| | - F Rössler
- Department of Surgery and Transplantation, Swiss HPB & Transplant Center Zurich, University Hospital Zurich, Zurich, Switzerland
| | - S Ghafoor
- Department of Diagnostic and Interventional Radiology, University Hospital Zurich, Zurich, Switzerland
| | - A Kobe
- Department of Diagnostic and Interventional Radiology, University Hospital Zurich, Zurich, Switzerland
| | - T Pfammatter
- Department of Diagnostic and Interventional Radiology, University Hospital Zurich, Zurich, Switzerland
| | - C Schlag
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - C A Gutschow
- Department of Surgery and Transplantation, Swiss HPB & Transplant Center Zurich, University Hospital Zurich, Zurich, Switzerland
| | - H Petrowsky
- Department of Surgery and Transplantation, Swiss HPB & Transplant Center Zurich, University Hospital Zurich, Zurich, Switzerland
| | - P C Müller
- Department of Surgery and Transplantation, Swiss HPB & Transplant Center Zurich, University Hospital Zurich, Zurich, Switzerland
| | - C E Oberkofler
- Department of Surgery and Transplantation, Swiss HPB & Transplant Center Zurich, University Hospital Zurich, Zurich, Switzerland.
- Vivévis AG-Visceral, Tumor, Robotic Surgery, Clinic Hirslanden, Zurich, Switzerland.
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Ghafoor S, Rafiq MA, Shah STA, Ansar M, Paton T, Ajmal M, Agha Z, Qamar R, Azam M. KIF1A novel frameshift variant p.(Ser887Profs*64) exhibits clinical heterogeneity in a Pakistani family with Hereditary Sensory and Autonomic Neuropathy Type IIC. Int J Neurosci 2022:1-11. [DOI: 10.1080/00207454.2022.2140428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Saima Ghafoor
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Muhammad Arshad Rafiq
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Muhammad Ansar
- Jules-Gonin Eye Hospital, Ophthalmology Department of the University of Lausanne
| | - Tara Paton
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Muhmmad Ajmal
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Zehra Agha
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Raheel Qamar
- Pakistan Academy of Sciences, Islamabad, Pakistan
- Science and Technology Sector, ICESCO, Rabat, Morocco
| | - Maleeha Azam
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
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Ghafoor S, Silveira KDC, Qamar R, Azam M, Kannu P. Exome Sequencing Identifies a Biallelic GALNS Variant (p.Asp233Asn) Causing Mucopolysaccharidosis Type IVA in a Pakistani Consanguineous Family. Genes (Basel) 2022; 13:genes13101743. [PMID: 36292628 PMCID: PMC9602411 DOI: 10.3390/genes13101743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 01/02/2023] Open
Abstract
Mucopolysaccharidoses (MPS) type IVA is a lysosomal storage disease that mainly affects the skeletal system and is caused by a deficiency of the enzyme N-acetylgalactosamine-6-sulfatase (GALNS). The condition can mistakenly be diagnosed as a primary skeletal dysplasia such as spondylo-epiphyseal dysplasia, which shares many similar phenotypic features. Here, we utilised whole exome sequencing to make the diagnosis of MPS IVA in a resource poor country. We report for the first time the identification of a biallelic GALNS missense variant (c.697G>A, p.Asp233Asn) in the Pakistani population and highlight the potential contribution that academic institutions can make in rare disease diagnosis in the absence of a developed clinical genetic service.
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Affiliation(s)
- Saima Ghafoor
- Translational Genomics Laboratory, COMSATS University Islamabad, Islamabad 45550, Pakistan
| | | | - Raheel Qamar
- Pakistan Academy of Sciences, Islamabad 44000, Pakistan
- Science and Technology Sector, ICESCO, Rabat 10104, Morocco
| | - Maleeha Azam
- Translational Genomics Laboratory, COMSATS University Islamabad, Islamabad 45550, Pakistan
- Correspondence: or (M.A.); (P.K.); Tel.: +92-(51)-9235033 (M.A.); +1-(780)-492-9044 (P.K.)
| | - Peter Kannu
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Correspondence: or (M.A.); (P.K.); Tel.: +92-(51)-9235033 (M.A.); +1-(780)-492-9044 (P.K.)
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7
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Malik S, Rashid M, Javid A, Hussain A, Bukhari SM, Suleman S, Noor R, Husaain S, Ismat N, Hussain M, Ghafoor S, Mustafa G, Ali W. Genetic variations and phylogenetic relationship of genus Uromastyx from Punjab Pakistan. BRAZ J BIOL 2021; 84:e254253. [PMID: 34816973 DOI: 10.1590/1519-6984.254253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/24/2021] [Indexed: 11/22/2022] Open
Abstract
During the present study, specimens were collected from selected sites of Cholistan desert and Kalabagh Game Reserve, Punjab province, Pakistan. Each captured specimen was tagged with voucher number and morphometric measurements were taken. The average snout to vent length was 172.559±1.40 mm and average weight was 92.1±1.30 g. The DNA of Uromastyx hardwickii was amplified and sequenced using 16S rRNA primer set. The obtained DNA sequence has shown reliable and clear species identification. After trimming ambiguous bases, the obtained 16S rRNA fragment was 520 bp while 16S rRNA fragments aligned with closely matched sequence from NCBI comprised of 510 bp. Closely matched sequences of genus Uromastyx were retrieved from NCBI in blast searches. Neighbour-joining tree of genus Uromastyx was constructed based on p-distance using MEGA X. The mean intraspecific variation was 0.095±0.01 while intraspecific variation was ranging from 0-1%. Similarly, interspecific variation of Uromastyx hardwikii with Saara asmussi, Uromastyx alfredschmidti, Uromastyx geyri, Uromastyx thomasi, Uromastyx alfredschmidti was 0-12%, 0-19%, 0-19%, 0-20%, 12-19% respectively. The newly produced DNA was submitted to NCBI and accession number was obtained (MW052563.1). Results of current study provided information about the molecular and morphological identification of Genus Uromastyx. In our recommendation, comprehensive molecular based identification of Pakistan's reptiles is required to report any new or subspecies from country.
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Affiliation(s)
- S Malik
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - M Rashid
- University of Veterinary and Animal Sciences, Faculty of Fisheries and Wildlife, Lahore, Pakistan
| | - A Javid
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - A Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S M Bukhari
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Suleman
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - R Noor
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Husaain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - N Ismat
- The University of Lahore, Institue of Molecular Biology and Biotechnology - IMBB, Pakistan
| | - M Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - S Ghafoor
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - G Mustafa
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - W Ali
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
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Emery MV, Bolhofner K, Ghafoor S, Winingear S, Buikstra JE, Fulginiti LC, Stone AC. Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth. Forensic Sci Int Genet 2021; 56:102610. [PMID: 34735939 DOI: 10.1016/j.fsigen.2021.102610] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/29/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022]
Abstract
The recovery and analysis of genetic material obtained from thermally altered human bones and teeth are increasingly important to forensic investigations, especially in cases where soft-tissue identification is no longer possible. Although little is known about how these fire-related processes affect DNA degradation over time, next-generation sequencing technology in combination with traditional osteobiographical applications may provide us clues to these questions. In this study, we compare whole mitochondrial genome data generated using two different DNA extraction methods from 27 thermally altered samples obtained from fire victims (Maricopa County, Arizona) . DNA extracts were converted to double-stranded DNA libraries and enriched for whole mitochondrial DNA (mtDNA) using synthetic biotinylated RNA baits, then sequenced on an Illumina MiSeq. We processed the mitochondrial data using an in-house computational pipeline (MitoPipe1.0) composed of ancient DNA and modern genomics applications, then compared the resulting information across the two extraction types and five burn categories. Our analysis shows that DNA fragmentation increases with temperature, but that the acute insult from fire combined with the lack of water is insufficient to produce 5' and 3' terminal deamination characteristic of ancient DNA. Our data also suggest an acute and significant point of DNA degradation between 350 °C and 550 °C, and that the likelihood of generating high quality mtDNA haplogroup calls decreases significantly at temperatures > 550 °C. This research is part of a concerted effort to understand how fire affects our ability to generate genetic profiles suitable for forensic identification purposes.
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Affiliation(s)
- M V Emery
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States.
| | - K Bolhofner
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Bioarchaeology, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States; School of Life Sciences, Arizona State University, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Ghafoor
- Center for Evolution and Medicine, Arizona State University, United States; School of Life Sciences, Arizona State University, United States
| | - S Winingear
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; School of Life Sciences, Arizona State University, United States
| | - J E Buikstra
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeology, Arizona State University, United States; School of Life Sciences, Arizona State University, United States
| | - L C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States; School of Life Sciences, Arizona State University, United States
| | - A C Stone
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeology, Arizona State University, United States.
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Kim S, Wu M, Stylianou A, Ghafoor S, Lakhman Y, Park K, Leitao M, Sonoda Y, Gardner G, Broach V, Jewell E, Cohen S, Tew W, Zivanovic O, Roche KL, Mueller J, Zamarin D, Abu-Rustum N, Aghajanian C, Cadoo K, Weigelt B. Circulating cell-free DNA in patients with newly diagnosed and recurrent cervical cancer. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.06.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Ghafoor S, Akhtar T, Khawar MB, Sheikh N. Alterations in hepatic trace elements and ferritin expression in high energy diet fed rat model. J BIOL REG HOMEOS AG 2020; 34:1229-1233. [PMID: 32643354 DOI: 10.23812/18-360-l-70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- S Ghafoor
- Cell & Molecular Biology Laboratory, Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - T Akhtar
- Cell & Molecular Biology Laboratory, Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - M B Khawar
- Cell & Molecular Biology Laboratory, Department of Zoology, University of the Punjab, Lahore, Pakistan.,State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R. China.,University Chinese Academy of Sciences, Beijing, P.R. China
| | - N Sheikh
- Cell & Molecular Biology Laboratory, Department of Zoology, University of the Punjab, Lahore, Pakistan
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Nasim H, Ghafoor S, Shah A, Khan A. Synthesis of phosphate based bioactive glasses. Dent Mater 2017. [DOI: 10.1016/j.dental.2017.08.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ud-Din A, Rauf M, Ghafoor S, Khattak MNK, Hameed MW, Shah H, Jan S, Muhammad K, Rehman A, Inamullah. Efficient use of artificial micro-RNA to downregulate the expression of genes at the post-transcriptional level in Arabidopsis thaliana. Genet Mol Res 2016; 15:gmr7439. [PMID: 27173203 DOI: 10.4238/gmr.15027439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Micro-RNAs are cellular components regulating gene expression at the post-transcription level. In the present study, artificial micro-RNAs were used to decrease the transcript level of two genes, AtExpA8 (encoding an expansin) and AHL25 (encoding an AT-hook motif nuclear localized protein) in Arabidopsis thaliana. The backbone of the Arabidopsis endogenous MIR319a micro-RNA was used in a site-directed mutagenesis approach for the generation of artificial micro-RNAs targeting two genes. The recombinant cassettes were expressed under the control of the CaMV 35S promoter in individual A. thaliana plants. Transgenic lines of the third generation were tested by isolating total RNA and by subsequent cDNA synthesis using oligo-dT18 primers and mRNAs as templates. The expression of the two target genes was checked through quantitative real-time polymerase chain reaction to confirm reduced transcript levels for AtExpA8 and AHL25. Downregulation of AtExpA8 resulted in the formation of short hypocotyls compared with those of the wild-type control in response to low pH and high salt concentration. This technology could be used to prevent the expression of exogenous and invading genes posing a threat to the normal cellular physiology of the host plant.
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Affiliation(s)
- A Ud-Din
- Department of Genetics, Garden Campus, Hazara University, Mansehra, Pakistan.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Rauf
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - S Ghafoor
- Department of Genetics, Garden Campus, Hazara University, Mansehra, Pakistan
| | - M N K Khattak
- Department of Zoology, Garden Campus, Hazara University, Mansehra, Pakistan
| | - M W Hameed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karachi, Pakistan
| | - H Shah
- National Agricultural Research Centre, Islamabad, Pakistan
| | - S Jan
- Department of Genetics, Garden Campus, Hazara University, Mansehra, Pakistan
| | - K Muhammad
- Department of Genetics, Garden Campus, Hazara University, Mansehra, Pakistan
| | - A Rehman
- Department of Zoology, Garden Campus, Hazara University, Mansehra, Pakistan
| | - Inamullah
- Department of Genetics, Garden Campus, Hazara University, Mansehra, Pakistan
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Blackburn J, Kawasaki K, Porntaveetus T, Kawasaki M, Otsuka-Tanaka Y, Miake Y, Ota MS, Watanabe M, Hishinuma M, Nomoto T, Oommen S, Ghafoor S, Harada F, Nozawa-Inoue K, Maeda T, Peterková R, Lesot H, Inoue J, Akiyama T, Schmidt-Ullrich R, Liu B, Hu Y, Page A, Ramírez Á, Sharpe PT, Ohazama A. Excess NF-κB induces ectopic odontogenesis in embryonic incisor epithelium. J Dent Res 2014; 94:121-8. [PMID: 25376721 DOI: 10.1177/0022034514556707] [Citation(s) in RCA: 16] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nuclear factor kappa B (NF-κB) signaling plays critical roles in many physiological and pathological processes, including regulating organogenesis. Down-regulation of NF-κB signaling during development results in hypohidrotic ectodermal dysplasia. The roles of NF-κB signaling in tooth development, however, are not fully understood. We examined mice overexpressing IKKβ, an essential component of the NF-κB pathway, under keratin 5 promoter (K5-Ikkβ). K5-Ikkβ mice showed supernumerary incisors whose formation was accompanied by up-regulation of canonical Wnt signaling. Apoptosis that is normally observed in wild-type incisor epithelium was reduced in K5-Ikkβ mice. The supernumerary incisors in K5-Ikkβ mice were found to phenocopy extra incisors in mice with mutations of Wnt inhibitor, Wise. Excess NF-κB activity thus induces an ectopic odontogenesis program that is usually suppressed under physiological conditions.
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Affiliation(s)
- J Blackburn
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK
| | - K Kawasaki
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK Department of Pediatric Dentistry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Porntaveetus
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - M Kawasaki
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK Division of Bio-Prosthodontics, Department of Oral Health Science, Course for Oral Life Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Y Otsuka-Tanaka
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK Department of Special Needs Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo, Japan
| | - Y Miake
- Department of Ultrastructural Science, Tokyo Dental College, Chiyoda-ku, Tokyo, Japan
| | - M S Ota
- Laboratory of Food Biological Science, Department of Food and Nutrition, Japan Women's University, Bunkyō, Japan
| | - M Watanabe
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Hishinuma
- Department of Special Needs Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo, Japan
| | - T Nomoto
- Department of Special Needs Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo, Japan
| | - S Oommen
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK
| | - S Ghafoor
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK
| | - F Harada
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK
| | - K Nozawa-Inoue
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK
| | - T Maeda
- Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - R Peterková
- Department of Teratology, Institute of Experimental Medicine, Academy of Sciences CR, Prague, Czech Republic
| | - H Lesot
- INSERM UMR_S1109, Team "Osteoarticular and Dental Regenerative NanoMedicine," FMTS, Faculté de Médecine, Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France
| | - J Inoue
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - T Akiyama
- Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - R Schmidt-Ullrich
- Department of Signal Transduction in Tumor Cells, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - B Liu
- Department of Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Y Hu
- Laboratory of Experimental Immunology, Inflammation and Tumorigenesis Section, National. Cancer Institute-Frederick, Frederick, MD, USA
| | - A Page
- Department of Epithelial Biomedicine, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Á Ramírez
- Department of Epithelial Biomedicine, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - P T Sharpe
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK
| | - A Ohazama
- Craniofacial Development and Stem Cell Biology and Biomedical Research Centre, Kings College London, London, UK Division of Oral Anatomy, Department of Oral Biological Science, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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14
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Ghafoor S, Shah MM, Ahmad H, Swati ZA, Shah SH, Pervez A, Farooq U. Molecular characterization of Ephedra species found in Pakistan. Genet Mol Res 2007; 6:1123-1130. [PMID: 18273806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ephedra, also known as "ma huang", is a dioecious, drought- and frost-resistant, perennial, evergreen shrub with compelling medicinal value. The genus is represented by 42 species around the world, 9 of which were provisionally reported from Pakistan. Species of the genus have a controversial taxonomy due to their overlapping morphological features. Conventional tools alone are not sufficient for characterizing the species. The objective of present study was to assess the genetic variability present in different biotypes of Ephedra growing in Pakistan using molecular markers. A total of six genotypes collected from diverse geographic zones of Pakistan were used. The DNA of all genotypes was amplified using nine randomly amplified polymorphic DNA (RAPD) primers to study genetic variability at the molecular level. The dissimilarity coefficient matrix based on the data of 9 RAPD primers was used to construct a dendrogram which was then used to group the genotypes in clusters. Based on the dendrogram and dissimilarity coefficient matrix, the RAPD markers used here revealed a moderate to high level of genetic polymorphism (6 to 49%) among the genotypes. It was found that the collection of genotype accessions from Swat Valley in northwestern Pakistan was most distantly related to the other five collections. More molecular markers including functional genes and ribosomal spacer regions are suggested to find a better estimate of the genetic diversity present in Ephedra growing in Pakistan. The information provided here is useful for identifying valuable Ephedra variants which will be used for medicinal purposes and earning foreign currency.
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Affiliation(s)
- S Ghafoor
- Department of Genetics, Hazara University, Dhodial Mansehra, Pakistan
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15
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Shah SM, Karira KA, Soomro MS, Ghafoor S. Serum lipoprotein (a) in offspring of patients with premature myocardial infarction. J PAK MED ASSOC 2001; 51:180-3. [PMID: 11467239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
OBJECTIVES To compare serum Lp(a), lipids: TC, TG and lipoproteins: HDL-C and LDL-C levels of offspring with history of paternal myocardial infarction with the serum levels in offspring without paternal history of myocardial infarction. SETTING Basic Medical Sciences Institute, Jinnah Postgraduate Medical Centre, Karachi. METHODS Thirty offspring between the ages of 8-25 years with the history of paternal myocardial infarction were randomly selected from population and were matched with offspring having no history of parental myocardial infarction. RESULTS Offspring of fathers who had a myocardial infarction tended to have a significantly raised level of Lp(a) (p < 0.001) compared with those without parental history. None of the other lipoprotein variables we examined exhibited a significant difference between the two groups of subjects. CONCLUSION The offspring of fathers with early myocardial infarction have higher mean values of Lp(a) than control subjects suggesting that this lipid variable may strongly predispose to CAD.
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Affiliation(s)
- S M Shah
- Department of Biochemistry, Kyber Medical College, Peshawar
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