Biology subjects

Abraham, S.

Publications and source records attributed to Abraham, S..

24 records · Page 2Linked to original sources

bioRxiv2020

Bursting out: linking changes in nano-topography and biomechanical properties of biofilm-forming Escherichia coli to T4 lytic cycle

Bacteriophage infection cycle has been extensively studied, yet little is known on the structural and mechanical changes that lead to bacterial lysis. Here, bio-atomic force microscopy was used to study in real-time and in-situ the impact of the canonical phage T4 on the nano-topography and biomechanics of irreversibly attached, biofilm-forming E. coli cells. The results show that in contrast to the lytic cycle in planktonic cells, which ends explosively, anchored cells that are in the process of forming biofilms undergo gradual lysis, developing distinct sub-micron lesions ([~]300 nm in diameter) within the cell envelope. Furthermore, it is shown that the envelope rigidity and cell elasticity decrease (>50% and >40%, respectively) following T4 infection. These new insights show that the well-established lytic pathway of planktonic cells may be significantly different from that of biofilm-forming cells. Elucidating the lysis paradigm of these cells may advance biofilm removal and phage therapeutic. There is no conflict of interest and all co-authors have seen and approved the current version for submission.

microbiology↗

bioRxiv2020

STX18-AS1 is a Long Noncoding RNA predisposing to Atrial Septal Defect via downregulation of NKX2-5 in differentiating cardiomyocytes

Previous genome-wide association studies (GWAS) have identified a region of chromosome 4p16 associated with the risk of Atrial Septal Defect (ASD), which is among the commonest Congenital Heart Disease (CHD) phenotypes. Here, we identify the responsible gene in the region and elucidate disease mechanisms. Linkage disequilibrium in the region, eQTL analyses in human atrial tissues, and spatio-temporal gene expression studies in human embryonic hearts concordantly suggested the long noncoding RNA (lncRNA) STX18-AS1 as the causative gene in the region. Using CRISPR/Cas9 knockdown in HepG2 cells, STX18-AS1 was shown to regulate the expression of the key cardiac transcription factor NKX2-5 via a trans-acting effect on promoter histone methylation. Furthermore, STX18-AS1 knockdown depleted the potential of human embryonic stem cells (H9) to differentiate into cardiomyocytes, without affecting their viability and pluripotency, providing a mechanistic explanation for the clinical association.

genetics↗

bioRxiv2019

Ultrastructural details of mammalian chromosome architecture

Over the past decade, 3C-related methods, complemented by increasingly detailed microscopic views of the nucleus, have provided unprecedented insights into chromosome folding in vivo. Here, to overcome the resolution limits inherent to the majority of genome-wide chromosome architecture mapping studies, we extend a recently-developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human embryonic stem cells and fibroblasts. Micro-C maps robustly capture well-described features of mammalian chromosome folding including A/B compartment organization, topologically associating domains (TADs), and cis interaction peaks anchored at CTCF binding sites, while also providing a detailed 1-dimensional map of nucleosome positioning and phasing genome-wide. Compared to high-resolution in situ Hi-C, Micro-C exhibits substantially improved signal-to-noise with an order of magnitude greater dynamic range, enabling not only localization of domain boundaries with single-nucleosome accuracy, but also resolving more than 20,000 additional looping interaction peaks in each cell type. Intriguingly, many of these newly-identified peaks are localized along stripe patterns and form transitive grids, consistent with their anchors being pause sites impeding the process of cohesin-dependent loop extrusion. Together, our analyses provide the highest resolution maps of chromosome folding in human cells to date, and provide a valuable resource for studies of chromosome folding mechanisms.

genomics↗

bioRxiv2019

Challenges and Strategies for Recruiting Type 1 Diabetes Families in Kuwait with Strong Beliefs in Familism

Type 1 diabetes (T1D) is one of the most common endocrine and metabolic conditions in children. In fact, this disease in children and adolescents has been increasing exponentially, with Kuwait being ranked second highest in the world regarding the number of T1D incidences. Kuwait is an oil-rich country known for its strong sense of familism, affiliative obedience, and filial obligation. Therefore, a familial study of this disease may disclose certain causative agents responsible for passing the disease on to subsequent generations.\n\nTo recruit T1D patients and their family members, three different scenarios were developed. First, since Kuwaiti families are generally obedient to their doctors, the authors decided to recruit the patients through their endocrine physicians. Second, home visits were performed for meeting the families requirements. In this case, a team consisting of one nurse, two phlebotomists (a male and a female, since some refused to be seen by the opposite gender), and a driver of the institutes car was arranged. Finally, two diabetes educators were employed to resolve any issues raised during the recruitment process. Utilizing these approaches helped convince the culturally and religiously oriented Kuwaiti families to participate in this study. In this case, the doctors and educators were not only aware of the obstacles in this population but also sensitive to the families beliefs. This paper reports on our experience in recruitment and presents a roadmap for any future familial studies on culturally tailored societies i.e. Arab populations.

scientific communication and education↗

bioRxiv2018

Examination of Australian Streptococcus suis Isolates From Clinically Affected Pigs in a Global Context and the Genomic Characterisation of ST1 as a Predictor of Virulence

Streptococcus suis is a major zoonotic pathogen that causes severe disease in both humans and pigs. In this study, we investigated S. suis from 148 cases of clinical disease in pigs from 46 pig herds over a period of seven years. These isolates underwent whole genome sequencing, genome analysis and antimicrobial susceptibility testing. Genome sequence data of Australian isolates was compared at the core genome level to clinical isolates from overseas. Results demonstrated eight predominant multi-locus sequence types and two major cps gene types (cps2 and 3). At the core genome level Australian isolates clustered predominantly within one large clade consisting of isolates from the UK, Canada and North America. In particular, serotype 2 MLST25 strains were very closely associated with Canadian and North American strains. A very small proportion of Australian swine isolates (5%) were phylogenetically associated with south-east Asian and UK isolates, many of which were classified as causing systemic disease, and derived from cases of human and swine disease. In addition, we show that ST1 clones carry a constellation of putative virulence genes not present in other Australian STs, and that this is mirrored in overseas ST1 clones. Based on this dataset we provide a comprehensive outline of the current S. suis clones associated with disease in Australian pigs and their global context, and discuss the implications this has on antimicrobial therapy, potential vaccine candidates and public health.\n\nImportanceIn this study, we examine in detail, the genomic characteristics of 148 Streptococcus suis isolates from clinically diseased Australian pigs. We report the antimicrobial susceptibility profiles, virulence gene analysis and relationship to isolates from other regions of the world. We also demonstrate that ST1 clones, regardless of serotype, carry a large array of putative virulence genes while maintaining a small total gene content. This compilation of data has major ramifications for vaccine development, and refines the understanding of the distribution of various strains of this potentially-fatal zoonotic agent in the global pig industry

microbiology↗

bioRxiv2017

HNF1A is a Novel Oncogene and Central Regulator of Pancreatic Cancer Stem Cells

The biological properties of pancreatic cancer stem cells (PCSCs) remain incompletely defined and the central regulators are unknown. By bioinformatic analysis of a PCSC-enriched gene signature, we identified the transcription factor HNF1A as a putative central regulator of PCSC function. Levels of HNF1A and its target genes were found to be elevated in PCSCs and tumorspheres, and depletion of HNF1A resulted in growth inhibition, apoptosis, impaired tumorsphere formation, PCSC depletion, and downregulation of OCT4 expression. Conversely, HNF1A overexpression increased PCSC numbers and tumorsphere formation in pancreatic cancer cells and drove PDA cell growth. Importantly, depletion of HNF1A in primary tumor xenografts impaired tumor growth and depleted PCSCs in vivo. Finally, we established an HNF1A-dependent gene signature in PDA cells that significantly correlated with reduced survivability in patients. These findings identify HNF1A as a central transcriptional regulator of the PCSC state and novel oncogene in pancreatic ductal adenocarcinoma.

cancer biology↗