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Feb 2025 DOI 10.14302/issn.2326-0793.jpgr-25-5405
Ho Ming-FenCorresponding author
Alcohol use disorder (AUD) is the most prevalent substance use disorder. Excessive alcohol consumption leads to a range of health issues. We set out to identify inflammatory markers linked to alcohol consumption, which might ultimately offer novel insight into genetic underpinnings and have implications for alcohol-associated disease. Alcohol consumption and blood-based multi-omics data were collected by The Mayo Clinic Center for Individualized Treatment of Alcohol Dependence study. Plasma samples from patients with AUD were used for proteomics analysis using the OLINK “Explore Inflammation” panel (n=410). Liver enzymes were also measured. A genome-wide association study (GWAS) was performed to explore the relationship between genetic variants and plasma TREM2 levels. Our findings show thatplasma triggering receptor expressed on myeloid cells 2 (TREM2), a key gene associated with neurodegenerative disease, was the most significant signal correlated with alcohol consumption, and has also been associated with liver enzyme levels in patients with AUD. We identified the rs7232 single nucleotide polymorphism (SNP) in MS4A6A as a key genetic variant associated with plasma TREM2 levels, with the minor allele (A) linked to higher TREM2 levels and increased alcohol consumption, particularly in men. Furthermore, MA4A6A is an ethanol-responsive gene in a SNP-dependent manner, and the variant genotype of the rs7232 SNP was associated with lower expression for MA4A6A due to proteasome-mediated protein degradation. In summary, this study provides insight into the relationship between plasma TREM2 levels, alcohol consumption, and liver function in AUD patients, shedding light on genetic factors underlying alcohol-related diseases.
Mar 2024 DOI 10.14302/issn.2689-4602.jes-24-4956
Chadov B.F.Corresponding author
A new type of mutations-dominant lethals with a facultative manifestation -were discovered in D. melanogaster in 2000. These mutations were named conditional mutations. Under restrictive genetic conditions, the mutations manifest themselves as dominant lethals, whereas dominant lethality disappears under permissive conditions, displaying a set of other manifestations. The genes responsible for the emergence of conditional mutations were named ontogenes. The experiments with mutations in ontogenes have revealed the following processes: (1) genome editing in germline cells; (2) induction of high mutagenesis rates in germline cells of the mutants for ontogenes; (3) zygotic selection; (4) isolation of mutants; and (5) alterations in the lethality of mutants with time. The specific features in the manifestation of ontogenes together with the listed processes formed the background for construction of the model of speciation named the regeneration model. The event of speciation is represented as the regeneration of the working state of a genetic system disturbed by the emergence of a mutation in an ontogene. According to the model, it is ontogenes that are in charge of speciation and, eventually, the structure of living matter in the form of individual species. The significance of Mendelian protein-coding genes and Darwinian selection of the fittest according to these genes are doubtless but not paramount.
Mar 2022 DOI 10.14302/issn.2692-1537.ijcv-22-4117
Wu JianqingCorresponding author
Healthier World (Independent researcher for cause), P. O. Box 689, Beltsville, MD 20704. USA
Several mRNA vaccines are used on the population in the U.S. I started predicting the dangers of mRNA vaccines before March 2021 and update my findings periodically. My prior model study enabled me to identify many flaws in clinical trials, side-effect evaluation methods and mechanism studies, and I also considered consistent failure in predicting drug side effects in the past and systematic failure of FDA in keeping out dangerous drugs from market. I found that the risks of vaccination cannot be determined by experiments alone and must be determined by using a combination of methods. By studying mRNA expression dynamics and kinetics, I predict that vaccination with mRNA vaccines may increase cancer risks, multiple organ failure risks, earlier death risks, genome alteration speeds by one or more mechanisms, alter the normal selection process for viral evolution resulting in more virulent viruses, and aggravate chronic diseases or cause healed diseases to relapse. Two root problems are practical inability to control expression sites and severe adverse reactions from repeated vaccination. Based on mRNA bio-distribution, the mRNA mainly strikes the liver and other vital organs, and poses grave dangers to persons whose vascular functional reserves are relatively small, or whose vascular systems are temporarily burdened by other causes such as viral infections or life activities. If an mRNA vaccine is administered on a pregnant woman by second or booster shots, spike protein synthesis in fetus brain disrupts the highly regulated protein synthesis processes, resulting in potential brain damages. In less than a year, most of my early predicted damages are being materialized or are on the track to hit the population. In this update, I present a benefits-and-risks map to show how the number of deaths caused by mRNA vaccines is grossly underestimated and why claimed benefits like 95% effectiveness rate and 90% death rate reduction are meaningless and misleading.
Oct 2021 DOI 10.14302/issn.2641-5526.jmid-21-3900
Perez Jean-claudeCorresponding author
Phd Maths Computer Science Bordeaux University, RETIRED Interdisciplinary Researcher (IBM Emeritus, IBM European Research Center On Artificial Intelligence Montpellier) Bordeaux Metropole, France.
In this theoretical discovery of a law of Life, there is MATHEMATICS (Geometry, Bits and Numbers) that UNIFY 3 universes as complementary as ATOMIC MASS, WAVES, and INFORMATION (DNA, RNA and Amino Acids). The discovery of a simple numerical formula for the projection of all the atomic mass of life-sustaining CONHSP bioatoms leads to the emergence of a set of Nested CODES unifying all the biological, genetic and genomic components by unifying them from bioatoms up to 'to whole genomes. In particular, we demonstrate the existence of a digital meta-code common to the three languages of biology that are RNA, DNA and amino acid sequences. Through this meta-code, genomic and proteomic images appear almost analogous and correlated. The analysis of the textures of these images then reveals a binary code as well as an undulatory code whose analysis on the human genome makes it possible to predict the alternating bands constituting the cariotypes of the chromosomes. The application of these codes to perspectives in astrobiology, cancer, and specifically in INFORMATION THEORY with the emergence of binary codes and regions of local stability (voting process), whose fractal nature we demonstrate, is illustrated. PREFACE by Professor Luc Montagnier Addendum by Robert Friedman M.D After the discovery of the DNA double helix structure allowing both the stable storage of genetic information and its transfer through messenger RNA to protein synthesis organelles themselves structured by RNA most abundant in cells, the ribosomal. This wonder of nature exists in ALL living beings from the virus to humans and is based on two codes, the linear sequence of nucleotides and that derived from codons where three nucleotides allow with a certain flexibility - synonymous codons - the choice in the twenty amino acids. But we are missing a third CODE the one governing at multicellular beings from the rotifer to human, the stabilized modulation of gene expression in a nutshell the differentiation of cells from the single cell of the fertilized egg. It is logical to think that this program which begins as soon as fertilization is written in the DNA. We are also prone to associate it with non-coding DNA sequences although they control gene expression. I introduce here the notion developed by Jean-Claude Pérez of mathematical harmony, a higher order present in all living beings and whose existence it finds in genomes, including those of viruses. Thus the natural evolution of variants of the genome of coronavirus Covid 19 tends towards increasingly long Fibonacci series. It remains to determine the Who, the How and the Why of such developments. I will bet with my mathematician colleague that waves and fractals play a role. Luc Montagnier ADDENDUM Jean-claude has given scientists a strong new direction for research. He has identified a unified field of science guided by the Golden Ratio and Fibonacci Sequence. By identifying an overall guiding principle that makes possible fractal-like nesting at all levels of biological manifestation, future researchers can begin with the "whole" instead of the "parts". If we know that complex systems are organized at varying levels by the Golden Ratio and Fibonacci Sequence, we can look for those universal patterns first and then fill in the gaps with small details to complete the picture. It's like having an overall view of a crossword puzzle before beginning to assemble the individual pieces. Without an overarching vision and guiding principle, completing the puzzle is infinitely more difficult. Once scientists and researchers realize and begin using this "SECRET IN HIDDEN IN PLAIN SIGHT," their discoveries will be orders of magnitude more fruitful. Robert Friedman M.D
Mar 2020 DOI 10.14302/issn.2575-1212.jvhc-20-3234
di Virgilio FabrizioCorresponding author
DVM, Clinique Vétérinaire Vet24 – 59700 – Marcq en Baroeul, France
Aim of the Research The aim of this study is to analyze a group of dogs of different breeds affected by osteosarcoma (OSA), to document any prevalence of this primary bone neoplasia in breeds that are phylogenetically close and to help with further research human medicine, as a model of study for prevalence and epidemiology of human OSA in multiple populations. Study Design Pilot study from two canine surgery databases between 2002 and 2013. Materials and Methods Breeds were classified in groups based on their phylogenetical proximity. Differences in prevalence of OSA between breeds and groups were evaluated with a permutation test. For each breed and each group, a ranking was made by calculating 95 % confidence intervals and counting the no-overlapping between breeds and groups. The relation between the dogs’ heights and the prevalence of OSA was analyzed using a logistic regression between the disease status and dog size. Results A total of 67 dogs with OSA, in 26 different breeds were included. Ten breeds were overrepresented and, the majority of these, were classified in 2 predisposed groups phylogenetically close to each other. The prevalence of OSA was associated with the dogs’ height within predisposed breeds, but, in general, taller breeds were not the most affected. Conclusions and Clinical Relevance In this study, despite the small number of dogs, we observed that the most commonly affected breeds with OSA are phylogenetically closely related. This highlights the importance of genetics in the aetiology of canine OSA . In this preliminary study, indications are given on breeds, samples and genome locations to be further investigated. This could allow identification of pathogenic alleles in dogs, and potentially in humans. Furthermore this pilot research can represent a model of epidemiologic study of human OSA.
Oct 2019 DOI 10.14302/issn.2372-6601.jhor-19-2986
Riede IsoldeCorresponding author
Independent Cancer Research, Im Amann 7, Ueberlingen D-88662.
With the definition of four gene classes, all differences between tumor cells and normal cells can be explained. Proliferative mutations induce a shortcut, forcing the cell to divide. They allow replication without control, induce somatic pairing defects of chromosomes and genome instability. Intact Tumor Supressors or mutant Switch Functions can inhibit this process. Oncogene mutations optimize the growth of the cells.
Sep 2019 DOI 10.14302/issn.2574-450X.jom-19-3001
Hayat Khan SikandarCorresponding author
Department of pathology PNS HAFEEZ
Gene therapy has entered a new era with the dawn of CRISPR/Cas9 technology which though were always available in nature but rediscovered to tame into a real-tlife genome editing tool. With the modernization upsurge and changes in ways the “homo sapiens” survived on this planet from hunger to current era of exuberance has led to multiple metabolic issues like type-2 diabetes. Notwithstanding the rapid emergence of medication to suppress the hyperglycemia and insulin resistance associated with this menace, need has definitely emerge to find more personalized and curative dimensions to therapeutics of type-2 diabetes mellitus. Gene therapy is one more addition to Type-2 Diabetes Mellitus (T2DM) therapy, where multiple options have emerged in the shape of microRNA, direct knocking out of cellular structures like proteins and enzymes and very recently the precision nucleases associated with CRISPR technologies. This mini-review attempt to summarize some of the recent examples of gene therapy with major focus on CRISPR/Cas technologies.
Feb 2019 DOI 10.14302/issn.2689-4602.jes-18-2431
F Chadov BorisCorresponding author
Institute of Cytology and Genetics, Siberian Department of Russian Academy of Sciences, Novosibirsk 630090, Russian Federation.
The existing hypotheses on speciation rely on Mendelian genes and mutations in them. However, genome-wide sequencing demonstrates that the Mendelian genes account less than one-tenth of the entire genome DNA. This means that a greater part of the genome has not yet been subject to large-scale evolutionary consideration. This paper deals with the conditional mutations in drosophila, which are mutations of the genes belonging to a special category (ontogenes) controlling the program of individual development. The ontogenes presumably reside in the DNA of intergenic spaces and introns. Conditional mutations display a number of properties absent in the mutations of Mendelian genes. These specific properties allow three key problems in speciation to be solved: (1) the possibility of emergence of new traits as a result of sequential mutagenesis; (2) selection of mutants; and (3) establishment of isolation. We have shown that (1) the mutations in ontogenes are able to form new multigenic regulatory blocks that escape selection during their creation; (2) mutations in ontogenes allow for existence of constantly acting zygotic selection, which is by no means less important for speciation than Darwinian selection; and (3) owing to their conditionally lethal effect, the mutations in ontogenes are able to create biological isolation barrier. This gives the grounds for assuming that the emergence of mutations in ontogenes is a necessary condition for speciation.
Jan 2019 DOI 10.14302/issn.2572-3030.jcgb-18-2527
Zhang XiCorresponding author
Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States
As remarkable advances have been made in immunotherapies, the overall goal of immunotherapy has become the selection of patients and evaluating the benefits of treatment. One of the major obstacles to develop immunotherapies is the lack of effective immune monitoring. Monitoring of key changes in the immune system during immunotherapy (immunomonitoring) provides important insights into efficacy as well as the immune mechanisms of response at the molecular and cellular levels. Immunomonitoring techniques include traditional immunoassays that use specific antibodies to recognize the analytes of interest, new high-throughput immunoassays that target immune cells and nucleic acids, and less classical immunogenomic approaches that rely on genome-wide profiling and computational analysis on various types of clinical samples. Substantial progress has been made in the application of immunomonitoring strategies to pre-clinical and clinical studies, especially for patients with cancer and infectious diseases. Current and emerging immunoassays performed in clinical practice will be examined herein, and immunogenomic approaches that complement these techniques will be highlighted and compared with traditional methods. Finally, we will discuss several new computational methods for analyzing gene signatures for immunomonitoring, including gene expression data profiling by microarray, the nCounter technique, regular RNA-seq, and single-cell RNA-seq. Novel immunomonitoring techniques, especially immunogenomic approaches, will continue to be developed to facilitate assessment of immunotherapeutic response and predict patient outcomes in cancer and infectious disease.
Sep 2018 DOI 10.14302/issn.2641-9467.jgrc-18-2270
Li YuanCorresponding author
Department of Astronomy and Theoretical Physics
Rice, as one of the most important crops in the world, is facing an ever-accelerating challenge from climate change. Epigenetic modification with its substantially high epimutation rate and the possibility for some epigenetic variation to act as a heritable contributor to crop environmental adaptability may hold great potentials for rapid crop breeding. Epigenetic modification is controlled by epigenetic pathways, and mutations disturbing the epigenetic pathways may lead to significant epigenetic and/or genetic changes. This is especially true for rice, whose genome is rich in epigenetic modifications and transposable elements (TEs) that are generally epigenetically silenced. Here, in this paper, we first reviewed the pathways that establish, maintain and remove rice DNA methylation, which is the most well studied epigenetic marker, as well as the genes that are involved. We then discussed how TEs amplify the phenotypic impact of epigenetic changes that could be a result of epigenetic pathway disturbances. At last, we presented the enormous amount of rice genome data that are publically available, within which great genetic variation in the genes that are involved within the epigenetic pathways is embedded. This genetic variation awaits to be exploited for their potentials in generating a heritable source of variation for rapid environmental adaptation, which may hold tremendous importance for rice breeding in the face of climate change.
Aug 2018 DOI 10.14302/issn.2576-6694.jbbs-18-2173
Tabassum Khan NidaCorresponding author
Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology Engineering and Management Sciences,(BUITEMS),Quetta, Pakistan
Bioinformatic tools is widely used to manage the enormous genomic and proteomic data involving DNA/protein sequences management, drug designing, homology modelling, motif/domain prediction ,docking, annotation and dynamic simulation etc. Bioinformatics offers a wide range of applications in numerous disciplines such as genomics. Proteomics, comparative genomics, nutrigenomics, microbial genome, biodefense, forensics etc. Thus it offers promising future to accelerate scientific research in biotechnology
May 2018
Alatsathianos IoannisCorresponding author
Laboratory of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
Genetics alone cannot thoroughly expound the environmental impact on the molecular complexity of the endocrine system. Epigenetic-induced alteration in gene expression has emerged as a way in which environmental compounds may exert endocrine effects. The environmental compounds that interfere with normal endocrine signaling are one of the largest classes of toxicants we are exposed to, on a daily basis. Epigenetic mechanisms, mainly the methylation of DNA and the modification of histones, lead to differentiated activation and deactivation of genome domains creating phenotype plasticity and divergent endocrine function among populations and individuals, as well. The issues examined in the present review are related to environmental epigenetics, and more precisely, the epigenetic-mediated modulation and relevance of endocrine disrupting chemicals, focusing on three broad aspects: 1) persistence of EDs, 2) their major hormonal effects and 3) the potential of compounds previously considered as endocrine disruptors to induce epigenetic effects. Evidence suggests that environmental exposures notably impact expression of endocrine-related genes and, thus, affect clinical endocrine outcomes.
Apr 2018
PEREZ Jean-claudeCorresponding author
Maths and Computer Science, retired interdisciplinary researcher (IBM Emeritus),7 avenue de terre-rouge F33127 Martignas Bordeaux metropole France, phone 33 0781181112,
The global analysis of 3 human genomes of increasing levels of evolution (neanderthal / sapiens build34 of 2003 / sapiens hg38 of 2013) reveals 2 levels of numerical constraints controlling, structuring and optimizing the DNA sequences of these genomes. A global constraint - which we will call "HGO" for "Human Genome Optimum" - optimizes the genome at its global scale of 3.5 billion base pairs. This same operator when applied to each of the 24 individual chromosomes reveals a hierarchical structure of these 24 chromosomes according to a numerical spectrum of amplitude ½ Phi extending from chromosome 4 to chromosome 19. This first level of comparison reveals a very Great analogy between these 3 genomes. Then we introduce a global analysis method of roughness or fractal texture of the DNA sequences at the level of each chromosome. After having demonstrated that the chromosome4 seems to play a privileged role in the human genome, radically differentiating it from the 23 other chromosomes, we limit the study to the exhaustive analysis of different whole chromosomes4 relative to the 6 primates Homosapiens, Neanderthal, Chimpanzee, Orang-outan, Gorilla and Macaque. There are then remarkable resonances and periods - based on the sequences of Fibonacci and Lucas - totally differentiating the chromosomes 4 of these different primate species: 21 base pairs period for the chimpanzee and the urang-outan, 34 bases pairs period for Man, and 55 base pairs period for the gorilla. Finally, the major result is that the comparative analysis of the respective chromosomes4 of sapiens and neanderthal shows for the first time major differences in long-range fractal structures between the DNA sequences of these two genomes. Thus, while the chromosome4 of sapiens has an obvious resonance of 34 nucleotides, that of Neanderthal seems "torn" between two attractors of fractal textures, one on this same resonance 34, but with a roughness radically different from that of sapiens, While the other resonance is tuned to the number of Lucas 123. Finally, on a more theoretical level, this method reveals properties of "discrete digital standing waves" such as periods, resonances, phase shifts or phase positions. To conclude, we suggest that this chromosome4 could possibly play a role as a "referential" with respect to each of the 23 other chromosomes of the nuclear genome and possibly also with respect to the mitochondrial mtDNA genome.
Apr 2018 DOI 10.14302/issn.2326-0793.jpgr-18-2004
Anwar PervezCorresponding author
Department of Biochemistry and molecular Biology, University of Gujrat Sialkot subcampus, Pakistan
Human proteome project was revolutionized about 40 years ago with purpose of summarizing whole proteomic data at one place. It was launched after human genome project to map and observe all proteins. The goal related proteomic study is to draft the entire human proteome in disease diagnosis by using bioinformatics tools. Pillars of human proteome project provide different databases related to proteins at transcriptional and translational level. Human proteome organization(HUPO) published biology disease HUPO whose aim is to measure protein and proteome by life and processes related to human diseases. Different human organ like plasma, liver, brain and diabetic base project are used to characterize human disease and health. Major data resources accumulated in databases like peptides Atlas, GPMDB and neXtProt for proteins. Matrices of human proteome project identify and characterize the protein products as Post translational modification (PTM), splice various isoforms from 20,300 proteins. Matrices related to different years make proteomes counterpart by magnify the research biomedical community with high output of instruments and specimen pre-analytical protocols. CALIPHO multidisciplinary group provides information about protein complexities, interactions, function and structure complexities after Uniport and Swissprot. Different bioinformatics tools are used for structural and functional annotations of protein, disease diagnosis and mutations due to protein. Extensive study of human proteome project has been proved helpful in disease treatment at translational and post- translational levels. In future, human proteome project along with bioinformatics will include protein profiling, biomarkers, Mass spectrophotometer technique and cross analysis of different proteome projects.
Feb 2018 DOI 10.14302/issn.2832-5311.jpcd-18-1955
Zhu Qian-HaoCorresponding author
CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
Circular RNAs (circRNAs) are covalently closed single-stranded loop RNA molecules with or without protein coding capability. CircRNAs were previously considered to be splicing intermediates or artifacts but are now found to be pervasively expressed in all eukaryotes studied with some demonstrated to have important molecular functions in various biological processes. CircRNA is now a hot study topic of molecular biology. In this review, we summarize the progress achieved so far on plant circRNAs, including identification and functional characterization, compare the similarities and differences of circRNAs between plants and animals, and discuss the challenges for confident detection and functional investigation of plant circRNAs. Similar to what have been found in animals, plant genomes contain a large number of circRNAs that potentially regulate a wide range of biological progresses related to plant development and biotic/abiotic responses. Despite only a few plant circRNAs have been functionally characterized, novel function/mechanism that has not been reported in animals was revealed, implying more exciting findings about plant circRNAs are expected in future studies.
Nov 2017 DOI 10.14302/issn.2638-4469.japb-17-1838
Jambagi ShridharCorresponding author
School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
Strawberry powdery mildew, caused by Podosphaeraaphanis is a major fungal disease that affects strawberry yield and quality. In the model plant species Arabidopsis and the crop plants barley, tomato and pea, the Mildew resistance locus O (MLO) proteins have been found to be required for powdery mildew susceptibility. The present study, based on the sequence of a wild plum (Prunus americana) MLO protein, identified 16 MLO genes within the genome of woodland strawberry, Fragaria vesca and examined their expression pattern in response to powdery mildew infection in three diploid strawberry cultivars. Phylogenetic analysis showed that the FvMLO genes can be classified into six clades. Four FvMLO genes were grouped into clade III, which comprises MLO genes from Arabidopsis, tomato and grapevine that mediate powdery mildew susceptibility. A RNA-seq analysis of two diploid strawberry cultivars, F. vescassp. vesca accession Hawaii 4 (HW) and F. vesca f. semperflorens line “Yellow Wonder 5AF7” (YW) at 1 d (1 DAI) and 8 d (8 DAI) after infection showed the expression of 12 out of the 16 FvMLO genes. The comparison of Fragments Per Kilobase of transcript per Million mapped reads (FPKM values) detected by RNA-seq and expression values of qRT-PCR for FvMLO genes showed substantial agreement. The FvMLO3 gene, which was grouped in clade III and orthologous to the Arabidopsis,tomato and grapevine genes, was highly expressed in YW compared to other FvMLO genes across varieties. The results showed that FvMLO genes can be used as potential candidates to engineer powdery mildew resistance in strawberry based on MLO suppression or genome editing.
Oct 2017 DOI 10.14302/issn.2572-5424.jgm-17-1609
PEREZ Jean-claudeCorresponding author
7 avenue de terre-rouge F33127 Martignas Bordeaux metropole France
DUF1220 proteins regions show the largest Homo-Sapiens lineage-specific increase in copy number of any protein-coding region in the human genome and map principally to 1q21.1. DUF1220 deletions have been associated with microcephaly and macrocephaly, respectively. DUF1220 copy number has been linked to both brain size in humans and brain evolution among primates. Remarkably, dosage variations involving DUF1220 sequences have now been linked to human brain expansion, autism severity, total IQ, and cognitive and mathematical aptitude scores. We analyzed in chromosome 1q a total of 245 DUF1220 proteins. Finally the method is extended analysing the long 1q21 region from 7 other close primates like Neanderthal, great apes : chimp, gorilla, orangutan and monkeys : macaque, marmoset, vervet. This remarkable property is confirmed by comparing these primates to other mammals such as mice, rabbit, cow, dolphin and Elephant. We then show four classes of multi-periodic fractal structures for all 19 DUF1220 regions and 19 NBPF genes studied cases. The analysis of these spectra of fractal periods1 reveals a simple linear interdependence, hierarchization and unification between the numerical sequences of each of these 4 spectra and the sequences of Fibonacci and Lucas. Given the evidence of this numerical relationship, we suggest that this discovery may be one of the major causes of a cognitive development of man superior to that of the great primates. Finally the mathematical roots of this whole numbers resonance patterns is discussed.
Mar 2017 DOI 10.14302/issn.2326-0793.jpgr-17-1447
D. Howard TimothyCorresponding author
Center for Genomics & Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
Factors that contribute to the onset of atherosclerosis may be elucidated by bioinformatic techniques applied to multiple sources of genomic and proteomic data. The results of genome wide association studies, such as the CardioGramPlusC4D study, expression data, such as that available from expression quantitative trait loci (eQTL) databases, along with protein interaction and pathway data available in Ingenuity Pathway Analysis (IPA), constitute a substantial set of data amenable to bioinformatics analysis. This study used bioinformatic analyses of recent genome wide association data to identify a seed set of genes likely associated with atherosclerosis. The set was expanded to include protein interaction candidates to create a network of proteins possibly influencing the onset and progression of atherosclerosis. Local average connectivity (LAC), eigenvector centrality, and betweenness metrics were calculated for the interaction network to identify top gene and protein candidates for a better understanding of the atherosclerotic disease process. The top ranking genes included some known to be involved with cardiovascular disease (APOA1, APOA5, APOB, APOC1, APOC2, APOE, CDKN1A, CXCL12, SCARB1, SMARCA4 and TERT), and others that are less obvious and require further investigation (TP53, MYC, PPARG, YWHAQ, RB1, AR, ESR1, EGFR, UBC and YWHAZ). Collectively these data help define a more focused set of genes that likely play a pivotal role in the pathogenesis of atherosclerosis and are therefore natural targets for novel therapeutic interventions.
Jul 2016 DOI 10.14302/issn.2576-2818.jfb-16-1035
Sugimoto MayumiCorresponding author
National Livestock Breeding Center, Nishigo, Fukushima, Japan,
Female fertility is an economically important trait in the dairy industry, and the fertility selection index has been developed as a method of including female fertility in the breeding goals of this industry. This index considers a combination of factors, including days open, number of inseminations per lactation, success after first insemination, and pregnancy within 70 d, 90 d, and 110 d after parity. Based on a genome-wide association study of the fertility selection index using 442 Holsteins, we found that the index is influenced by a variation in the thioredoxin fold region of the family with the sequence similarity 213, member A (FAM213A) protein. FAM213A is a CXXC motif-containing peroxiredoxin 2-like protein that regulates cellular redox status. A replacement of isoleucine with valine in FAM213A was associated with poor fertility in cows. The overexpression of FAM213AVal in bovine endometrial epithelial cells reduced reactive oxygen species to a lesser extent relative to the overexpression of FAM213AIle and caused a decrease in cyclooxygenase-2 expression. Downregulation of cyclooxygenase-2 led to a decline in prostaglandin E2, which is critical for implantation because it protects the conceptus from the maternal immune system. Cows with FAM213AVal showed lower levels of prostaglandin E2 than did cows with FAM213AIle, suggesting that cows with FAM213AVal are less fertile than cows with FAM213AIle because of their reduced uterine environment. Thus, the present study found that FAM213A unexpectedly modulates female fertility in cattle.
Jun 2015 DOI 10.14302/issn.2470-0436.jos-14-528
Sanjay SrinivasanCorresponding author
Ophthalmology and Visual Sciences, Khoo Teck Puat Hospital, Singapore
A previously healthy 25 year old Chinese male presented with left eye blurring of vision and was diagnosed to have left eye branch retinal vein occlusion. Initial blood investigations and thrombophilia screen were negative. The patient subsequently improved with observation and conservative management, with no further events over a 2 year follow up period. The blood investigations were repeated 2 years later as part of a health check-up and he was then tested to be heterozygous for the factor V leiden mutation. This was confirmed by sequencing of his genome that identified the mutation. The laboratory was contacted to provide details regarding the testing methods and was noted to have performed the two tests via different methods. While false negative rates in genetic testing are low, we believe that there is greater need to standardize testing methods as ascertaining genetic conditions play a great role in clinical diagnosis, treatment and prognosis. Clinicians should be aware of the limitations of these tests. When clinical suspicion is high, there may be a role for repeat tests with different methods or in different laboratories.
Jan 2015 DOI 10.14302/issn.2379-7835.ijn-14-606
Michael J. GladeCorresponding author
Telomeres are strings of DNA that are not themselves genes but that extend every chromosome beyond its last gene. Terminal telomeres are sacrificed during every mitotic event in human cells (“telomere attrition”), preserving the functional genome despite the “end replication problem.” However, the “telomeric theory of biological aging” suggests that when an individual cell has reproduced itself a sufficient number of times (the “Hayflick limit”), some the its telomeres have become critically shortened (“telomeric crisis”) and cannot completely “cap off” a chromosome, and any further attempts to replicate such a chromosome would produce damaged DNA and a dysfunctional cell (“cellular aging”). As cells enter telomeric crisis, they usually initiate intracellular signaling cascades that arrest DNA replication and mitotic activity, converting biologically active cells into inactive cells (“cellular senescence”). The progressive accumulation of senescent cells impairs the healthy functioning of tissues and produces “biological aging.” Oxidative stress damages telomeres and accelerates telomere attrition and biological aging. Premature biological aging is associated with degenerative diseases and diminished quality of life. Reducing the level of systemic oxidative stress can ease the oxidative drive toward cellular senescence and premature biological aging. Increased intakes of antioxidant-rich foods and specific antioxidant nutrients (such as fruits and vegetables, α -lipoic acid, astaxanthin, eicosapentaenoic acid, docosahexaenoic acid, trans-resveratrol, N-acetylcysteine, methylsulfonylmethane, lutein, vitamin C, vitamin D, vitamin E, and γ-tocotrienol) may decrease cellular and systemic oxidative stress and decelerate biological aging.
Oct 2014 DOI 10.14302/issn.2374-9431.jbd-13-212
Ahmad Sliem HamdyCorresponding author
Biochemistry and internal Medicine*, Basic oral and medical sciences, College of dentistry, Qassim University, Saudi Arabia
Diabetes mellitus type 2 (DMT2) is a complex polygenic disorder. DMT2 is a result of insulin resistance and destruction of pancreatic β-cell or dysfunction. Therefore, glucose builds up in the bloodstream, leading to nerve damage, blindness, organ failures and sometimes death. Recently, some recently discovered genes play a key role in regulating the sensitivity to insulin. Scientists have long known that the disease often runs in families, and other genetic links. Human genetic discoveries will keep improving our knowledge about diabetes for many years to come. Varieties of prospective diabetic researches were developed to diagnose and control DMT2. Researchers spent thousands of millions of dollars to address DMT2. Pioneers of advanced biotechnology developed bioinformatics tools that changed the course of research about the role of metabolomics in DMT2. It will facilitate the identification of possible causes of DMT2 in genome studies. The present article aimed at reviewing the research studies per training to metabolomics and bioinformatics in genome studies in relation to DMT2.
Dec 2012 DOI 10.14302/issn.2326-0793.jpgr-12-101
Han JianCorresponding author
Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
Eukaryotic Signature Proteins (ESPs) are proteins that delineate the eukaryotes from the archaea and bacteria. They have no recognisable homologues in any prokaryotic genome, but their homologues are present in all main branches of eukaryotes. ESPs are thus likely to have descended from ancient proteins that have existed since the first eukaryotic cell. The last dataset of ESPs was calculated more than a decade ago, thus with advances in technology and the rapid completion of many evolutionary important genomes, this dataset required recalculating. This study recalculated the Giardia lamblia ESP dataset and provides a procedure to calculate signature proteins beginning with any species. The G. lamblia ESP dataset contained a range of proteins including many associated with the membrane, cytoskeleton, nucleus and protein synthesis. ESP datasets have implications on current models of eukaryotic evolution, having high importance in phylogenetic analysis due to ESPs’ consistency and conservation in all eukaryotic species.