journal
https://read.qxmd.com/read/35291551/potential-impact-of-serpin-peptidase-inhibitor-clade-a-member-4-serpina4-rs2093266-and-serpina5-rs1955656-genetic-variants-on-covid-19-induced-acute-kidney-injury
#1
JOURNAL ARTICLE
Sally M El-Hefnawy, Zeinab A Kasemy, Hanaa A Eid, Ibrahim Elmadbouh, Rasha G Mostafa, Thoria A Omar, Heba E Kasem, Eman M Ghonaim, Mohamed M Ghonaim, Amany A Saleh
Background: SARS-CoV-2 has a number of targets, including the kidneys. Acute Kidney Injury (AKI) might develop in up to a quarter of SARS-CoV-2 patients. In the clinical environment, AKI is linked to a high rate of death and leads to the progression of AKI to chronic renal disease. Aim: We aimed to investigate rs2093266 and rs1955656 polymorphisms in SERPINA4 and SERPINA5 genes, respectively, as risk factors for COVID-19 induced AKI. Subjects and methods: A case-control study included 227 participants who were divided into three groups: 81 healthy volunteers who served as controls, 76 COVID-19 patients without AKI and 70 COVID -19 patients with AKI...
March 11, 2022: Meta Gene
https://read.qxmd.com/read/34729360/interleukin-37-gene-polymorphism-and-susceptibility-to-coronavirus-disease-19-among-iraqi-patients
#2
JOURNAL ARTICLE
Aeshah A Ahmed, Ali H Ad'hiah
Coronavirus disease 19 (COVID-19) is a highly contagious respiratory viral infection. Dysregulated immune response is an important feature of disease, and cytokines are among the most important mediators of dysregulated immunity. Interleukin-37 (IL-37) is one such cytokine and studies have indicated its role in pathogenesis of COVID-19. However, IL37 gene polymorphisms have not been identified in patients with COVID-19. Therefore, this case-control study (100 patients and 100 controls) was performed to understand the role six single nucleotide polymorphisms of IL37 gene (SNPs: rs3811042, rs3811043, rs2466449, rs3811045, rs3811046 and rs3811047) in susceptibility to COVID-19 among cases with severe disease...
February 2022: Meta Gene
https://read.qxmd.com/read/34722158/micrornas-based-regulation-of-cytokine-regulating-immune-expressed-genes-and-their-transcription-factors-in-covid-19
#3
JOURNAL ARTICLE
Manoj Khokhar, Sojit Tomo, Purvi Purohit
Background: Coronavirus disease 2019 is characterized by the elevation of a broad spectrum of inflammatory mediators associated with poor disease outcomes. We aimed at an in-silico analysis of regulatory microRNA and their transcription factors (TF) for these inflammatory genes that may help to devise potential therapeutic strategies in the future. Methods: The cytokine regulating immune-expressed genes (CRIEG) were sorted from literature and the GEO microarray dataset...
February 2022: Meta Gene
https://read.qxmd.com/read/35036327/severity-of-coronavirus-disease-19-profile-of-inflammatory-markers-and-ace-rs4646994-and-ace2-rs2285666-gene-polymorphisms-in-iraqi-patients
#4
JOURNAL ARTICLE
Zainab S Mahmood, Hula Y Fadhil, Thaer A Abdul Hussein, Ali H Ad'hiah
Susceptibility to coronavirus disease 2019 (COVID-19) and disease severity has recently been associated with inflammatory markers and genetic polymorphisms of ACE (angiotensin-converting enzyme) and ACE2 genes, but the evidence has been inconclusive. This case-control study (99 COVID-19 patients and 96 controls) sought to assess the significance of age, C-reactive protein (CRP), neutrophil-to-lymphocyte ratio (NLR) and SARS-CoV-2 RT-PCR cycle threshold (Ct) in severity of COVID-19. Besides, two variants of ACE and ACE2 genes (rs4646994 and rs2285666, respectively) were analyzed to determine their role in COVID-19 susceptibility and/or disease severity...
January 10, 2022: Meta Gene
https://read.qxmd.com/read/34540591/study-of-rare-genetic-variants-in-tm4sf20-nfxl1-cntnap2-and-atp2c2-in-pakistani-probands-and-families-with-language-impairment
#5
JOURNAL ARTICLE
Erin M Andres, Heather L Neely, Huma Hafeez, Tahira Yasmin, Farzana Kausar, M Asim Raza Basra, Muhammad Hashim Raza
Language impairment (LI) is highly heritable and aggregates in families. Genetic investigation of LI has revealed many chromosomal regions and genes of interest, though very few studies have focused on rare variant analysis in non-English speaking or non-European samples. We selected four candidate genes ( TM4SF20, NFXL1, CNTNAP2 and ATP2C2 ) strongly suggested for specific language impairment (SLI), a subtype of LI, and investigated rare protein coding variants through Sanger sequencing of probands with LI ascertained from Pakistan...
December 2021: Meta Gene
https://read.qxmd.com/read/34466389/phylogenicity-of-b-1-1-7-surface-glycoprotein-novel-distance-function-and-first-report-of-v90t-missense-mutation-in-sars-cov-2-surface-glycoprotein
#6
JOURNAL ARTICLE
Done Stojanov
Phylogenicity of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 surface glycoproteins reported from Europe to the National Center for Biotechnology Information (NCBI) virus database by the mid of April 2021 is analyzed. Novel function for computing phylogenetic distance is proposed for that purpose. Proposed distance function resulted in better-fitted clusters than Jaccard and Sorensen-Dice and accurate evolutionary links were predicted for B.1.1.7 spike variants. Most B.1.1.7 spike variants were linked to their likely direct predecessors at single amino acid change, that in many cases resulted in loss of the key mutations that are associated to the higher B...
December 2021: Meta Gene
https://read.qxmd.com/read/34307051/rapid-inexpensive-methods-for-exploring-sars-cov-2-d614g-mutation
#7
JOURNAL ARTICLE
Sirwan M A Al-Jaf, Sherko S Niranji, Zana H Mahmood
A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). There are discrepancies in the impact of this mutation on the virus's infectivity. Also, the whole genome sequencings are expensive and time-consuming. This study aims to develop three fast economical assays for prompt identifications of the D614G mutation including Taqman probe-based real-time reverse transcriptase polymerase chain reaction (rRT PCR), an amplification refractory mutation system (ARMS) RT and restriction fragment length polymorphism (RFLP), in nasopharyngeal swab samples...
December 2021: Meta Gene
https://read.qxmd.com/read/34778004/is-there-any-relationship-between-serum-zinc-levels-and-angiotensin-converting-enzyme-2-gene-expression-in-patients-with-coronavirus-disease-2019
#8
JOURNAL ARTICLE
Zahra Bagheri-Hosseinabadi, Ali Pirsadeghi, Amir Rahnama, Fatemeh Bahrehmand, Mitra Abbasifard
Background: The level of angiotensin-converting enzyme 2 (ACE2) expression in different tissues is essential in the sensitivity, symptoms and consequences of COVID-19 infection. It seems that zinc is involved in the structure of the ACE2 enzyme has been identified; nonetheless, the relationship between ACE2 expression and zinc serum levels in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients is still unclear. This study aimed to evaluate the expression of ACE2 in peripheral blood-derived immune cells of COVID-19 patients and its relationship with serum zinc levels...
November 6, 2021: Meta Gene
https://read.qxmd.com/read/33996501/design-of-advanced-sirna-therapeutics-for-the-treatment-of-covid-19
#9
JOURNAL ARTICLE
Iman Niktab, Maryam Haghparast, Mohammad-Hossein Beigi, Timothy L Megraw, Amirkianoosh Kiani, Kamran Ghaedi
COVID-19 is a newly emerged viral disease that is currently affecting the whole globe. A variety of therapeutic approaches are underway to block the SARS-CoV-2 virus. Among these methods, siRNAs could be a safe and specific option, as they have been tested against other viruses. siRNAs are a class of inhibitor RNAs that act promisingly as mRNA expression blockers and they can be designed to interfere with viral mRNA to block virus replication. In order to do this, we designed and evaluated the efficacy of six highly specific siRNAs, which target essential viral mRNAs with no predicted human genome off-targets...
September 2021: Meta Gene
https://read.qxmd.com/read/33816122/elevated-expression-of-plasminogen-activator-inhibitor-pai-1-serpine1-is-independent-from-rs1799889-genotypes-in-arthrofibrosis
#10
JOURNAL ARTICLE
Banu Bayram, Aaron R Owen, Amel Dudakovic, Jacob W Bettencourt, Afton K Limberg, Mark E Morrey, Joaquin Sanchez-Sotelo, Daniel J Berry, Jean-Pierre Kocher, Andre J van Wijnen, Matthew P Abdel
Arthrofibrosis is characterized by excessive extracellular matrix deposition in patients with total knee arthroplasties (TKAs) and causes undesirable joint stiffness. The pathogenesis of arthrofibrosis remains elusive and currently there are no diagnostic biomarkers for the pathological formation of this connective tissue. Fibrotic soft tissues are known to have elevated levels of plasminogen activator inhibitor-1 (PAI-1) (encoded by SERPINE1 ), a secreted serine protease inhibitor that moderates extracellular matrix remodeling and tissue homeostasis...
June 2021: Meta Gene
https://read.qxmd.com/read/34075330/a-variant-in-tmprss2-is-associated-with-decreased-disease-severity-in-covid-19
#11
JOURNAL ARTICLE
Vishnubhotla Ravikanth, Mitnala Sasikala, Vankadari Naveen, Sabbu Sai Latha, Kishore Venkata Laxmi Parsa, Ketavarapu Vijayasarathy, Ramars Amanchy, Steffie Avanthi, Bale Govardhan, Kalapala Rakesh, Daram Sarala Kumari, Bojja Srikaran, Guduru Venkat Rao, D Nageshwar Reddy
Background: Mortality due to COVID-19 caused by SARS-CoV-2 infection varies among populations. Functional relevance of genetic variations in Angiotensin-converting enzyme 2 ( ACE2 ) and Transmembrane serine protease 2 ( TMPRSS2 ), two crucial host factors for viral entry, might explain some of this variation. Methods: In this comparative study in Indian subjects, we recruited 510 COVID-19 patients and retrieved DNA from 520 controls from a repository. Associations between variants in ACE2 and TMPRSS2 with disease severity were identified by whole exome sequencing (WES, n  = 20) and targeted genotyping ( n  = 1010)...
May 28, 2021: Meta Gene
https://read.qxmd.com/read/33619452/rare-mutations-in-the-accessory-proteins-orf6-orf7b-and-orf10-of-the-sars-cov-2-genomes
#12
JOURNAL ARTICLE
S K Sarif Hassan, Pabitra Pal Choudhury, Bidyut Roy
A total number of 3080 SARS-CoV-2 genomes from all continents are considered from the NCBI database. Every accessory protein ORF6, ORF7b, and ORF10 of SARS-CoV-2 possess a single missense mutation in less than 1.5% of the 3080 genomes. It has now been observed that different non-synonymous mutations occurred in these three accessory proteins. Most of these rare mutations are changing the amino acids such as hydrophilic to hydrophobic, acidic or basic to hydrophobic, and vice versa etc. So these highly conserved proteins might play an essential role in virus pathogenicity...
February 18, 2021: Meta Gene
https://read.qxmd.com/read/33349792/essential-interpretations-of-bioinformatics-in-covid-19-pandemic
#13
REVIEW
Manisha Ray, Mukund Namdev Sable, Saurav Sarkar, Vinay Kumar Hallur
The currently emerging pathogen SARS-CoV-2 has produced the global pandemic crisis by causing COVID-19. The unique and novel genetic makeup of SARS-CoV-2 has been created puzzle in biological research, due to which the potential drug/vaccine candidates have not yet been discovered by the scientific community. Meanwhile, the advantages of bioinformatics in viral research had created a milestone since last few decades. The exploitation of bioinformatics tools and techniques has successfully interpreted this viral genomics architecture...
December 17, 2020: Meta Gene
https://read.qxmd.com/read/32835005/methods-for-making-multiple-alignment-of-genomic-sequences-for-severe-acute-respiratory-syndrome-coronavirus-2
#14
JOURNAL ARTICLE
Yoshiyuki Suzuki
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 and caused a pandemic. To monitor the global transmission pattern of SARS-CoV-2, it is required to constantly update the phylogenetic tree of genomic sequences with 29.9 kb, which may be time consuming. Phylogenetic analysis of SARS-CoV-2 may be accelerated by making a multiple alignment of nucleotide sequences using the CPA (combining pairwise alignments) method, in which a pairwise alignment is made for a reference and each of other sequences, and the pairwise alignments are combined into a multiple alignment...
December 2020: Meta Gene
https://read.qxmd.com/read/33224734/therapeutic-potential-of-mirnas-targeting-sars-cov-2-host-cell-receptor-ace2
#15
JOURNAL ARTICLE
Ibrahim Bozgeyik
In late December 2019, several cases of pneumonia of unknown etiology (COVID-19) were reported in Wuhan, Hubei province, China. Based on clinical findings, blood tests and chest radiographs, this disease was diagnosed as a virus-associated pneumonia. Sequence analysis revealed a novel coronavirus, called SARS-CoV-2 (formerly called 2019-nCoV), as the causative agent of pneumonia of unknown etiology. So far, the SARS-CoV-2 infection continues to spread, and this virus poses a serious public health threat. In this study, it was aimed to reveal potential miRNA targets for the regulation of SARS-CoV-2 host cell receptor ACE2...
November 18, 2020: Meta Gene
https://read.qxmd.com/read/32837914/the-duffy-t-33c-is-an-insightful-marker-of-human-history-and-admixture
#16
JOURNAL ARTICLE
Musab M Ali Albsheer, Ayman Hussien, Dominic Kwiatkowski, Muzamil Mahdi Abdel Hamid, Muntaser E Ibrahim
A contrasting genotype and allele frequency pattern between Africans and non-Africans in the Duffy (T-33C) locus is reported. Its near fixation in various populations suggest is no longer under natural selection, and that current distribution is possibly a relic of distant extreme selection combined with genetic drift during the out of Africa. We put this difference into the utility to infer the ancestral state of ambiguous loci in different populations.
August 11, 2020: Meta Gene
https://read.qxmd.com/read/37560748/adenosine-a-2a-receptor-gene-polymorphisms-adora2a-are-associated-with-maximal-concentric-contraction-pain
#17
JOURNAL ARTICLE
Patrick J O'Connor, Bryan D Loy, Jacob B Lindheimer, Sarah F Covert
OBJECTIVES: To test associations of adenosine A2A receptor gene ( ADORA2A ) polymorphisms with maximal concentric contraction pain, caffeine-induced perceptual changes, and responses to mild eccentric injury. DESIGN: Targeted candidate gene association study. METHODS: ADORA2A (rs5751876) was genotyped in 26 adults. Pain of a maximal elbow flexor contraction was assessed. Participants performed 18 eccentric actions of the elbow flexors. Arm volume was measured before and 24- and 48-h post-injury...
December 2018: Meta Gene
https://read.qxmd.com/read/29577025/a-simulations-approach-for-meta-analysis-of-genetic-association-studies-based-on-additive-genetic-model
#18
JOURNAL ARTICLE
Majnu John, Todd Lencz, Anil K Malhotra, Christoph U Correll, Jian-Ping Zhang
Meta-analysis of genetic association studies is being increasingly used to assess phenotypic differences between genotype groups. When the underlying genetic model is assumed to be dominant or recessive, assessing the phenotype differences based on summary statistics, reported for individual studies in a meta-analysis, is a valid strategy. However, when the genetic model is additive, a similar strategy based on summary statistics will lead to biased results. This fact about the additive model is one of the things that we establish in this paper, using simulations...
June 2018: Meta Gene
https://read.qxmd.com/read/28948156/short-poly-glutamine-repeat-in-the-androgen-receptor-in-new-world-monkeys
#19
JOURNAL ARTICLE
Chihiro Hiramatsu, Annika Paukner, Hika Kuroshima, Kazuo Fujita, Stephen J Suomi, Miho Inoue-Murayama
The androgen receptor mediates various physiological and developmental functions and is highly conserved in mammals. Although great intraspecific length polymorphisms in poly glutamine (poly-Q) and poly glycine (poly-G) regions of the androgen receptor in humans, apes and several Old World monkeys have been reported, little is known about the characteristics of these regions in New World monkeys. In this study, we surveyed 17 species of New World monkeys and found length polymorphisms in these regions in three species (common squirrel monkeys, tufted capuchin monkeys and owl monkeys)...
December 2017: Meta Gene
https://read.qxmd.com/read/28373962/the-influence-of-different-calorie-restriction-protocols-on-serum-pro-inflammatory-cytokines-adipokines-and-igf-i-levels-in-female-c57bl6-mice-short-term-and-long-term-diet-effects
#20
JOURNAL ARTICLE
Soner Dogan, Amitabha Ray, Margot P Cleary
Calorie restriction (CR) is an effective intervention to prevent chronic diseases including cancer. Although many factors, i.e., sex hormones, IGF-I and mTOR have been studied in response to CR, the molecular mechanisms of CR remain to be identified. Our objective was to determine the short and long-term effects of different CR protocols on pro-inflammatory cytokines. Our hypothesis was that Intermittent CR (ICR) would result in greater inhibition of pro-inflammatory serum cytokines compared to Chronic CR (CCR) as we previously found ICR to be more protective in the prevention of mammary tumor development...
June 2017: Meta Gene
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