Biology subjects

Omer, D.

Publications and source records attributed to Omer, D..

6 recordsLinked to original sources

bioRxiv2024

Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-matched Sample with Nanopore Sequencing and Optical Genome Mapping

Carcinogenesis often involves significant alterations in the cancer genome architecture, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping and nanopore sequencing are attractive technologies that bridge this resolution gap and offer enhanced performance for cytogenetic applications. These methods profile native, individual DNA molecules, thus capturing epigenetic information. We applied both techniques to characterize a clear cell renal cell carcinoma (ccRCC) tumors structural and copy number landscape, highlighting the relative strengths of each method in the context of variant size and average read length. Additionally, we assessed their utility for methylome and hydroxymethylome profiling, emphasizing differences in epigenetic analysis applicability.

genomics↗

bioRxiv2023

Six novel nsSNPs affect RUNX1 gene may leading to Acute Myeloid Leukemia (AML) using Bioinformatics approach

BackgroundRUNX1 is one of the most frequently mutated genes in human AMLs, most of RUNX1 mutations in acute myeloid leukemia (AML) are missense or deletion-truncation and behave as loss-of-function mutations. The molecular consequences of cancer associated mutations in Acute myeloid leukemia (AML) linked factors are not very well understood. Here, we recognize possible pathogenic SNPs in the RUNX1 gene as Functional differences caused by SNPs might have harmful effects on protein structure and function using various computational tools. MethodologyData gained from NCBI database and various tools used to study nsSNPs which they are: SIFT, Polyphen-2, Provean, SNAP2, I-Mutant, Project Hope, Raptor X, PolymiRTS and Gene MANIA. ResultOur study reveals six novel SNPs observed to be the most damaging SNPs that affect structure and function of RUNX1 gene using various bioinformatics tools. ConclusionThis study revealed 7 damaging SNPs, 6 novel nsSNP out of them in the RUNX1 gene that leads to AML, by using different bioinformatics tools. Also, 23 functional classes were predicted in 8 SNPs in the 3UTR, among them, 6 alleles disrupted a conserved miRNA site and 16 derived alleles created a new site of miRNA. This might result in the de regulation of the gene function. Hopefully, these results will help in genetic studying and diagnosis of AML improvement.

bioinformatics↗

bioRxiv2023

Twenty novel nsSNPs may affect FLT3 gene leading to Acute Myeloid Leukemia (AML) using in silico analysis

Background: Mutations within the FMS-like tyrosine kinase 3 (FLT3) gene represent one of the most common genetic alteration that disturb intracellular signaling networks with a key role in leukemia pathogenesis. laboratory studies considerable obstacle to identify functional SNPs in a specific gene. Thus, the "in silico" technique is possible now to carry out research investigations without the need for extensive lab work. Methodology: data retrieved from NCBI database and different algorithm used to analyse nsSNPs which they are: SIFT, Polyphen-2, Provean, SNAP2, P-Mut, I-Mutant, Project Hope, Raptor X, PolymiRTS and Gene MANIA. Result: Our study reveals twenty novel SNPs regarded to be the most damaging SNPs that affect structure and function of FLT3 gene using different bioinformatics algorithm. Conclusion: This study revealed 20 damaging SNPs considered to be novel nsSNP in FLT3 gene that leads to AML, by using different algorithms. Additionally, 69 functional classes were predicted in 12 SNPs in the 3UTR, among them, 31 alleles disrupted a conserved miRNA site and 37 derived alleles created a new site of miRNA. This might result in the de regulation of the gene function. These results could be valuable for molecular studying, diagnosis and treatment of AML patients.

bioinformatics↗

bioRxiv2022

Entorhinal grid-like codes and time-locked network dynamics track others navigating through space

Navigating through crowded, dynamically changing social environments requires the ability to keep track of other individuals. Grid cells in the entorhinal cortex are a central component of self-related navigation but whether they also track others movement is unclear. Here, we propose that entorhinal grid-like codes make an essential contribution to socio-spatial navigation. Sixty human participants underwent functional magnetic resonance imaging (fMRI) while observing and re-tracing different paths of a demonstrator that navigated a virtual reality environment. Results revealed that grid-like codes in the entorhinal cortex tracked the other individual navigating through space. Further, the activity of grid-like codes was time-locked to increases in co-activation and entorhinal-cortical connectivity that included the striatum, the hippocampus, parahippocampal and right posterior parietal cortices, altogether modulated by accuracy when subsequently re-tracing the paths. This suggests that network dynamics time-locked to entorhinal grid-cell-related activity might serve to distribute information about the socio-spatial map throughout the brain.

neuroscience↗

bioRxiv2020

Molecular characterization of clonal human renal forming cells

The adult kidney replaces its parenchyma in vivo in steady state and during regeneration by segment-specific clonal cell proliferation. To understand human adult kidney clonal cell growth, we derived tissue from human nephrectomies and performed limiting dilution to establish genuine clonal cultures from one single cell. Clonal efficiency of the human kidney was x%. Remarkably, a single renal cell could give rise to up to 3.3*10(6) cells. Phenotypically, two types of clonal cultures were apparent; a stably proliferating cuboidal epithelial-like appearing (EL) and a rapidly proliferating fibroblast-like appearing (FL). RNA sequencing of all clonal cultures separated FL from EL cultures according to proximal-distal/collecting renal epithelial tubular identity, respectively. Moreover, distinct molecular features in respect to cell-cycle, epithelial-mesenchymal transition, oxidative phosphorylation, BMP signaling pathway and cell surface markers were observed for each clone type. Surprisingly, clonal expansion (>3 months) was sustained in EL clones harboring markers of mature kidney epithelia (high CD24, CDH1, EpCAM, EMA) in contrast to de-differentiated FL clones (high NCAM1, serpine1), which showed fast lineage amplification and exhausted in a few weeks. Thus, the human adult kidney harbors progenitor cell function in which segment identity and the level of epithelial differentiation dictate clonal characteristics.

cell biology↗

bioRxiv2019

Local network determinants of spontaneously emerging cortical maps

Spontaneously emerging cortical maps related to the functional architecture of visual cortex have been observed initially in anesthetized cats and, subsequently, in monkey, albeit only under certain anesthetic regimes, and not in the awake state. Here we propose a network model that can accommodate these diverse findings. The model identifies two crucial determinants for the emergence of spontaneous map-like activity - local balance between excitatory and inhibitory activity, and the strength of feature-specific synaptic connections (e.g. orientation, ocularity). Our model further shows that dynamically, map-like activity patterns could be triggered either by standing or travelling waves, a mode of operation which is determined by the spatial extent of lateral connections within a given network. Our results suggest that careful pharmacological intervention can unveil the prevalence of maps - recurring spatial patterns of inhomogeneous lateral connectivity - in cortex without the need to explicitly identify area specific optimal features.

neuroscience↗