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Jul 2024 DOI 10.14302/oap.jc-23-4781
S. Kadandale JayaramaCorresponding author
As a first step towards clarifying the basis of the cooperation and conflict seen in chimeric binary mixes of Dictyostelium giganteum, we examined the karyotype of six natural isolates. All six had 5 haploid chromosomes. No meiotic figures were seen. Fluorescence in-situ hybridization was carried out using conserved D. discoideum centromeric DNA sequences as probes. From it, we infer that two chromosomes are sub-metacentric, one is metacentric and two are telocentric.
Apr 2022 DOI 10.14302/issn.2372-6601.jhor-22-4133
Qing XinCorresponding author
Department of Pathology, Harbor-UCLA Medical Center, 1000 West Carson Street, Torrance, CA 90502, USA.
Background Monoclonal gammopathy of undetermined significance (MGUS) and chronic myeloid leukemia (CML) are diseases of different lineages. The diagnosis of both MGUS and CML in the same patient is a rare occurrence and has not been reported in much literature. Case Presentation We describe a 56-year-old man with a history of rheumatoid arthritis incidentally found to have an increase in IgA paraprotein. With less than 10% monoclonal plasma cells on the bone marrow biopsy and absence of hypercalcemia, renal failure, anemia and bone lesions, MGUS was diagnosed. The conventional cytogenetics at the time showed the presence of the Philadelphia chromosome in 30% of metaphases. However, there was no morphologic evidence of CML in the peripheral blood or bone marrow. Patient received no treatment and lost follow-up until 3 years later when a routine CBC showed leukocytosis and thrombocytosis. CML, chronic phase was diagnosed following a bone marrow aspiration and biopsy with Philadelphia chromosome observed in 100% of metaphases. Patient was treated with imatinib and later switched to dasatinib and complete molecular remission was continued to be achieved. Discussion and Conclusion Here we report a case of pre-leukemic CML as an incidental finding during the diagnosis of MGUS. The possible underlying mechanisms of the association are discussed although the exact cause of the coexistence is unclear.
Jun 2019 DOI 10.14302/issn.2640-690X.jfm-19-2767
Venkateshwari AnanthapurCorresponding author
Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Hyderabad, Telangana, India
Recurrent pregnancy loss is an important reproductive issue with a heterogeneous etiology where two or more consecutive abortions occur before 20 weeks of gestation. Approximately 15% of all clinically recognized pregnancies result in miscarriage with an incidence of 1 in 300 cases. Couples, who experience repeated pregnancy loss before three months of gestation, mostly have fetuses with chromosomal aneuploids. A non-consanguineous couple with a married life of 4 years was referred to the Institute with a clinical history of three first trimester abortions. Karyotype analysis revealed a balanced autosomal translocation between chromosomes 4 and 6 with 46, XX, t (4;6)(q35; q22) karyotype in the female and normal 46, XY in the male partner. Therefore, the siblings and the couple were suggested for extended genetic counseling. Interestingly, similar translocation was seen in her father and three sisters, whereas her mother and elder sister showed a normal chromosomal constitution, indicating the paternal inheritance.
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.
Dec 2017 DOI 10.14302/issn.2641-9181.ijnr-17-1859
Vasei MohammadCorresponding author
Department of Pathology and Cell therapy based research center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
Pericentric inversions in chromosome 10 are regarded as both common and rare conditions, based on breakage and rearrangement within each specific segment. We present phenotypic and cytogenetic characterizations of a rare recombinant chromosome 10, namely inv(10)(p11q26), in a 13-month-old flabby girl associated with a maternal pericentric inversion. A review of the literature on the different aspects of this condition is also provided.
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.
Jul 2024
Abdelhak KiouahCorresponding author
Vitamin D deficiency is known to affect bone healing 1. In this case report, the potential link between vitamin D, calcium, and phosphorus deficiency and periapical lesions is explored, offering fresh insights into the complex relationship between systemic health and dental pathology. This pathology is caused by a mutation in the PHEX gene on chromosome X, which encodes a protein necessary for vitamin D synthesis and phosphate reabsorption, which are essential for the mineralization of bone and teeth 23. A 25-year-old man with rickets and vitamin D deficiency presented to our clinic with recurrent abscesses in multiple teeth. Radiographic imaging revealed periapical lesions on multiple teeth with advanced endo-perio lesions on teeth 26 and 16, and a negative cold test on all his teeth. Despite successful endodontic treatment, the patient’s compromised metabolic healing raised concerns about the prognosis. This case report highlights the intricate interplay between vitamin and mineral deficiencies and dental health, emphasizing the need for cautious management and long-term follow-up.
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
Feb 2020 DOI 10.14302/issn.2690-4837.ijip-20-3176
Bajaj AnubhaCorresponding author
MD. (Pathology) Panjab University, Department of Histopathology, A.B. Diagnostics, A-1, Ring Road, Rajouri Garden, New Delhi, 110027, India.
Multiple endocrine neoplasia type 1 (MEN1) is a syndrome emerging from characteristic mutations of MEN1 gene with concurrently enunciated multiple endocrine and tumours and associated non-endocrine neoplasm. Previously designated as Werner’s syndrome, MEN1 syndrome denominates genomic mutation within chromosome 11q13 or a tumour suppressor gene with a distinctive protein product nomenclated as “menin”. MEN1 syndrome demonstrates an autosomal dominant pattern of disease inheritance where genomic mutations delineate a comprehensive (100%) disease penetrance. MEN1 gene was initially identified in 1997 upon chromosome 11q13. Although twelve genetic mutations were primarily identified, currently beyond eighteen hundred genomic mutations are scripted12. MEN1 syndrome is comprised of diverse combination of twenty or more endocrine and non-endocrine tumours exemplifying a classic triad of pituitary, parathyroid and pancreatic neoplasm. Diverse non endocrine tumours enunciated with MEN1 syndrome are denominated with meningioma, ependymoma or angiofibroma12. Endocrine tumours are discerned on account of excessive hormonal secretion engendered from various neoplasm or on account of neoplastic evolution. Approximately 10% instances can occur due to a de-novo genomic variant. Offspring of an individual with MEN1 syndrome quantifies a 50% possibility of inheriting the genomic variant. Cogent prenatal diagnosis can be determined in instances where specific genomic variant of a particular family is known. Physical, psychological and social restrictions are prevalent with MEN1 syndrome. Heterozygotes with MEN1 genetic variant are denominated as carriers and manifest a two- fold possible mortality12.
Dec 2019 DOI 10.14302/issn.2694-1198.jge-19-3079
Volobuev A.N.Corresponding author
Samara State Medical University, Department of Medical Physics, Samara, Russia
The problem of natural selection against recessive homozygotes in a population is investigated. It is shown that natural selection of mutant alleles linked with the Х-chromosome in a population at women is described by the nonlinear differential equation of the third order. The order of the differential equation characterizes a power of selection. It is marked that the high order of the differential equation of natural selection allows level all mutational processes in Earth populations.
Nov 2019 DOI 10.14302/issn.2324-7339.jcrhap-19-3070
Sharma BechanCorresponding author
Department of Biochemistry, Faculty of Science, University of Allahabad, Allahabad-211002, UP, India.
The telomeres existing at the end of the eukaryotic chromosome, play an important role in localization, pairing of homologous chromosomes during cell division and synapsis formation, while telomerase is involved in maintenance of the telomere length. The application of antiHIV-1 molecules particularly NRTIs have been shown to interfere with telomerase function thereby inducing aging processes. Since the application of these molecules has already indicated production of oxidative stress and toxicity in AIDS patients, their adverse impact on telomerase function may further worsen the situation. In addition, the negative influence of antiHIV-1 regimens on certain host factors involved in telomerase function may enhance aging. HAART changes the landscape of the disease by progressively decreasing the progression of HIV-1, but exerts prolonged adverse effects on the telomerase function. Though there is no exact information available on this issue, intensive efforts are needed to explore regulation of telomerase expression in HIV infected individuals and particularly those receiving antiretrovirals.
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.2572-5424.jgm-19-3024
Hayat Khan SikandarCorresponding author
PNS HAFEEZ Hospital
Background The objective of this review is to unify the various genetic defects along with elaborating metabolic pathways in Familial Combined Hyperlipidemia(FCHL) and also to differentiate the phenotype of FCHL from metabolic syndrome. Methods PubMed and Cochrane’s library was searched for keyword “Familial combined hyperlipidemia” and latter with “Familial combined hyperlipidemia genes” to finally shortlist 23 articles. Further search with key words “molecular pathogenesis of familial combined hyperlipidemia” and “metabolic syndrome and familial combined hyperlipidemia” was carried out for finding molecular defects in FCHL, non-molecular findings distinguishing FCHL from metabolic syndrome and overlapping features between FCHL and metabolic syndrome. Results Major culprit regions identified included Chromosome-1q21-q24(USF1 and FOXA2) , Ch-11q (APOA5), Ch-16q24, Ch-20q12-q13.1, Ch.4q32.3 (rs6829588), and Ch-19q13.32 containing PVRL-2 gene (Also known as Nectin-2). The genetic and metabolic pathways linked to FCHL may involve: 1-Defective clearance of Apo-B containing lipoproteins, 2-Overproduction of Apo-B containing lipoprotein i.e., VLDL and 3-Adipose tissue dysfunction. FCHL phenotype showed close resemblance with metabolic syndrome clinical and biochemical features with slight differences. Conclusion The reviewed data suggested that FCHL phenotype is the resultant end outcome from multiple molecular defects and thus underlying genetic defect identification in the index case is important for personalized medicine and incoming gene therapy. Further research is warranted to explore specific genetic defects.
Apr 2016 DOI 10.14302/issn.2575-7881.jdrr-15-863
A. Fuertes MiguelCorresponding author
Centro de Biología Molecular ‘‘Severo Ochoa’’ (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
It was, previously, reported that the specific pattern of the compositional features of particular human-mouse orthologs defining in human two clusters, named C2 and C5, are present in different clusters in mouse. Since, thus, these orthologs can harbor a significant number of nucleotide differences a large sample of human-mouse orthologs having in human the C2 and C5 compositional features were collected in order to identify the orthologs that have been conserved or diverged during speciation. From the collection, 945 and 1051 orthologs had in human the C2 and C5 profile, respectively, while in mouse only 77 and 125, respectively, had these profiles. We further analyzed whether or not the frequency-usage of trinucleotides having the same gross composition computed from the reading of all nearest-neighbors of the DNA sequence might convey a layer of biological information in terms of chromosomal topology and function. In human, more than 50% of the C2 and C5 genes were found distributed in six chromosomes and preferentially located in GC-rich bands of chromosomes 11, 16 and 19. It was, also, found that 80% of the entire set of genes of band 19p13.3 had the C2 and C5 profile. The data shown also indicate that the proteins codified by the C5 genes have a bias towards nucleus and cytoplasm and specific post-translational modifications while the proteins codified by the C2 genes are mainly located in the cellular membrane or secreted to the external cellular milieu and particular post-transcriptional modifications
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.
Dec 2014 DOI 10.14302/issn.2326-0793.jpgr-14-598
YC Fung KimCorresponding author
CSIRO Preventative Health National Research Flagship, Australia
Colorectal cancer is one of the most commonly diagnosed cancers worldwide and its prevalence can be reduced by changes to lifestyle and diet. Fermentation of dietary fibre by the gut microbiota and formation of short chain fatty acids, in particular butyrate, is widely thought to play a role in preventing development of the disease. Despite butyrate’s known pro-apoptotic effects, a subpopulation of cancer cells is able to overcome these anti-neoplastic effects of colonic luminal butyrate to proliferate and establish tumours in vivo. In this study, a time course analysis of HT29 and HT29-BR cells treated with butyrate was conducted and global gene expression analysis was used to identify novel mechanisms associated with butyrate-induced apoptosis and in the acquisition of butyrate resistance. Bioinformatic analysis of the data identified deregulated O-GlcNAcylation activity and disruption to gene transcription by BRD4 as possible factors involved with butyrate-induced apoptosis. EGF signalling was identified as being potentially involved in the acquisition of butyrate resistance. Furthermore, the expression of the minichromosome maintenance protein family was significantly reduced in the HT29-BR cell line reflecting disruptions to the DNA replication process. Together, this may confer a unique survival advantage for cells with acquired butyrate resistance.