Biology subjects

Kaul, A.

Publications and source records attributed to Kaul, A..

8 recordsLinked to original sources

bioRxiv2026

Novel genes arise from genomic deletions across the bacterial tree of life

Bacteria are hosts to enormous genic diversity. How new genes emerge, functionalize, and spread remain longstanding questions. Here, we explore a mechanism by which adaptive deletions fuse distant gene fragments. Unlike other gene birth mechanisms that begin with rare, neutral mutations, these "deletion-born fusions" reach high frequency by hitch-hiking on the deletion. The deletion-driven proliferation of the fusion prolongs the mutational supply within these genes before loss, providing additional opportunities for neofunctionalization. We document one such gene fixing and expressing in a long-term E. coli evolution experiment, and identify additional fusion events in the Mycobacterium tuberculosis-bovis split. Finally, we develop a scalable systematic screen to detect these genes in all 2.4 million public single-isolate genomes and identify deletion-born fusions across the bacterial tree of life. These findings challenge the notion that deletions are solely destructive and highlight their role as potential catalysts for evolutionary innovation.

evolutionary biology↗

bioRxiv2025

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics

Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determine, as isolates could not have been tested for resistance before an antibiotic was discovered. Historical collections, like the British National Collection of Type Cultures (NCTC), stretching back to 1885, provide a window into this history. Here we match 1,817 sequenced high-quality genomes from the NCTC collection to their respective year of isolation to study resistance genes before and concurrent with the age of antibiotics. Concordant with previous work, we find resistance genes in both pathogens and environmental samples before the age of antibiotics. While generally rare before the introduction of an antibiotic, we find an associated increase in frequency with antibiotic introduction. Finally, we observe a trend of resistance elements becoming both increasingly mobile and nested within multiple mobile elements as time goes on. More broadly, our findings suggest that likely-functional antibiotic resistance genes were circulating in clinically relevant isolates before the age of antibiotics, but human usage is associated with increasing both their overall prevalence and mobility. DATA SUMMARYGenome assemblies downloaded and analyzed are in Supplementary Table 1, and computational tools used are found in the Methods. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact statementHistorical collections of microbial isolates enable researchers to both investigate the past and identify interesting trends over time. In this study, we queried over 1,800 isolate genomes in one such collection for genomic variation linked to antibiotic resistance. We show that numerous isolates cultured before the introduction of a given antibiotic contain genomic variation linked to antibiotic resistance; however, this phenomenon remained relatively rare. We demonstrate a strong association between the year a given antibiotic was clinically introduced and a rise in prevalence of genomic resistance to that antibiotic. Finally, we show that while mobile elements are common throughout the isolates and timeframe analyzed, genomic resistance has become increasingly mobile as time has gone on. This study shows that as expected, the clinical introduction of a given antibiotic is correlated with an increase in resistance to that antibiotic but also was linked with increased mobility of genes and alleles conferring resistance. However, we note that the effect of deposition bias in the collection cannot be excluded. Our work also indicates that numerous microbial pangenomes of pathogens naturally contained genomic resistance to a given antibiotic even before anthropogenic use of that antibiotic. Taken together, we demonstrate that although human use may affect the prevalence and mobility of genomic resistance in clinical isolates; for most antibiotics, genomic resistance existed within the pangenomes of sampled pathogens prior to clinical introduction. Quantifying and understanding the impact of antibiotic introduction in the past helps us understand how the introduction of novel antibiotics can impact bacteria; allowing better reaction to novel resistant infections as they arise.

microbiology↗

bioRxiv2023

Genomic and Proteomic Analysis of Patients with Reoccurring Discrete Subaortic Stenosis

Discrete subaortic stenosis (DSS) is a pediatric condition in which a fibrotic membrane forms within the left ventricular outflow track. The fibrotic membrane is removed surgically; however, there is a high rate of reoccurrence which requires a second surgery. There are currently no tools available to predict the risk of reoccurrence in DSS patients, a limitation addressed by this study. In this study, we analyzed resected fibrotic membranes for DSS patients at the time of first surgery for non-recurrent and recurrent patients, and at the time of second surgery for recurrent patients. RNA-sequencing was conducted to obtain a global screen of changes in RNA expression while mass spectrometry was used to obtain a global screen of changes in protein expression. The results from the RNA-sequencing and mass spectrometry provide valuable insight into genes and the proteins that are differentially regulated in recurrent vs non-recurrent DSS patients.

molecular biology↗

bioRxiv2022

Engineering Antioxidant and Oxygen-Releasing Lignin Composites to Accelerate Wound Healing

The application of engineered biomaterials for wound healing has been pursued since the beginning of tissue engineering. Here, we attempt to apply functionalized lignin to confer antioxidation to the extracellular microenvironments of wounds and to deliver oxygen from the dissociation of calcium peroxide for enhanced vascularization and healing responses without eliciting inflammatory responses. Elemental analysis showed 17 times higher quantity of calcium in the oxygen releasing nanoparticles. Lignin composites including the oxygen releasing nanoparticles released around 500 ppm oxygen per day at least for 7 days. By modulating the concentration of the methacrylated gelatin, we were able to maintain the injectability of lignin composite precursors and the stiffness of lignin composites suitable for wound healing after photo-crosslinking. In situ formation of lignin composites with the oxygen releasing nanoparticles enhanced the rate of tissue granulation, the formation of blood vessels and the infiltration of -smooth muscle actin+ fibroblasts into the wounds over 7 days. At 30 days after surgery, the lignin composite with oxygen generating nanoparticles remodeled the collagen architecture resembling to the reticular pattern of unwounded collagen with minimal scar formation. Thus, our study shows the potential of functionalized lignin for wound healing applications requiring balanced antioxidation and controlled release of oxygen for enhanced tissue granulation, vascularization and maturation of collagens.

bioengineering↗

bioRxiv2020

Phenotypic Differences in Adult and Fetal Dermal Fibroblast Responses to Mechanical Tension

ObjectiveFetal regenerative wound healing is characterized by hyaluronan(HA)-rich microenvironment and fibroblasts that produce pericellular matrices(PCM) abundant in high molecular weight HA. Recent studies showed that while small wounds in fetal skin heal regeneratively, large wounds heal with fibrosis. We posit large wounds generate higher mechanical tension which alters HA metabolism in the fetal fibroblasts and lead to a pro-fibrotic phenotype. ApproachC57BL/6J murine fetal (FFB; E14.5) and adult (AFB; 8wk) dermal fibroblasts were subjected to +/-10% tonic strain. Changes in PCM, HA enzymes and molecular weight, and fibrotic gene expression were measured. ResultsFFB pericellular matrix reduced upon exposure to increased tension, and the HA profile shifted from high to lower molecular weight. Under static conditions, AFB had higher expression of HA synthases (HAS) 1 and 2 and degradation enzymes KIAA1199, HYAL1, and TMEM2 than FFB, suggesting more HA turnover in AFB. Tension resulted in an increase in HAS1, HAS3, KIAA1199, and HYAL2 expression and a decrease in HAS2 and TMEM2 expression in FFB. CD26, a marker associated with scar production, increased in FFB under tension, along with altered fibrotic gene expression profile and reorganized cytoskeletal f-actin and increased -SMA that resembled AFB. InnovationThis study elucidates the differences in how biomechanical tension alters HA metabolism and fibrotic phenotype of FFB vs AFB, providing further understanding of the fetal regenerative wound healing phenotype. ConclusionUnderstanding the intrinsic differences in HA metabolism and fibrotic phenotype among FFB and AFB in response to wound mechanical stimuli may yield new insights to promote regenerative wound healing.

molecular biology↗

bioRxiv2020

A non-invasive method to generate induced pluripotent stem cells from primate urine

Comparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically even impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. Here, we report the generation of primate iPSCs from urine samples. We first validate and optimize the procedure using human urine samples and show that Sendai virus transduction of reprogramming factors into urinary cells efficiently generates integration-free iPSCs, which maintain their pluripotency under feeder-free culture conditions. We demonstrate that this method is also applicable to gorilla and orangutan urinary cells isolated from a non-sterile zoo floor. We characterize the urinary cells, iPSCs and derived neural progenitor cells using karyotyping, immunohistochemistry, differentiation assays and RNA-sequencing. We show that the urine-derived human iPSCs are indistinguishable from well characterized PBMC-derived human iPSCs and that the gorilla and orangutan iPSCs are well comparable to the human iPSCs. In summary, this study introduces a novel and efficient approach to generate iPSCs non-invasively from primate urine. This will allow to extend the zoo of species available for a comparative approach to molecular and cellular phenotypes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/247619v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@127e69forg.highwire.dtl.DTLVardef@95ebfcorg.highwire.dtl.DTLVardef@b815b2org.highwire.dtl.DTLVardef@1988492_HPS_FORMAT_FIGEXP M_FIG Workflow overview for establishing iPSCs from primate urine (A) We established the protocol for human urine based on a previous description (Zhou 2012). We tested volume, storage and culture conditions for primary cells and compared reprogramming by overexpression of OCT3/4, SOX2, KLF4 and MYC (OSKM) via lipofection of episomal vectors and via transduction of a sendai virus derived vector (SeV). (B) We used the the protocol established in humans and adapted it for unsterile floor-collected samples from non-human primates by adding Normocure to the first passages of primary cell culture and reprogrammed visually healthy and uncontaminated cultures using SeV. (C) Pluripotency of established cultures was verified by marker expression, differentiation capacity and cell type classification using RNA sequencing. C_FIG

cell biology↗

bioRxiv2020

Estrogen receptors in human bladder cells regulate innate cytokine responses to differentially modulate uropathogenic E. coli colonization

The bladder epithelial cells elicit robust innate immune responses against urinary tract infections (UTIs) for preventing the bacterial colonization. Physiological fluctuations in circulating estrogen levels in women increase the susceptibility to UTI pathogenesis, often resulting in adverse health outcomes. Dr adhesin bearing Escherichia coli (Dr E. coli) cause recurrent UTIs in menopausal women and acute pyelonephritis in pregnant women. Dr E. coli bind to epithelial cells via host innate immune receptor CD55, under hormonal influence. The role of estrogens or estrogen receptors (ERs) in regulating the innate immune responses in the bladder are poorly understood. In the current study, we investigated the role of ER, ER{beta} and GPR30 in modulating the innate immune responses against Dr E. coli induced UTI using human bladder epithelial carcinoma 5637 cells (HBEC). Both ER and ER{beta} agonist treatment in bladder cells induced a protection against Dr E. coli invasion via upregulation of TNF and downregulation of CD55 and IL10, and these effects were reversed by action of ER and ER{beta} antagoinsts. In contrast, the agonist-mediated activation of GPR30 led to an increased bacterial colonization due to suppression of innate immune factors in the bladder cells, and these effects were reversed by the antagonist-mediated suppression of GPR30. Further, siRNA-mediated ER knockdown in the bladder cells reversed the protection against bacterial invasion observed in the ER positive bladder cells, by modulating the gene expression of TNF, CD55 and IL10, thus confirming the protective role of ER. We demonstrate for the first time a protective role of nuclear ERs, ER and ER{beta} but not of membrane ER, GPR30 against Dr E. coli invasion in HBEC 5637 cells. These findings have many clinical implications and suggest that ERs may serve as potential drug targets towards developing novel therapeutics for regulating local innate immunity and treating UTIs. HighlightsO_LIEstrogen receptor (ER) subtypes regulate the gene expression of innate immune molecules, CD55, TNF and IL10 in human bladder epithelial cells impacting the bacterial colonization by Dr E. coli. C_LIO_LIActivation of nuclear ER subtypes, ER and ER{beta}, upregulate the gene expression of proinflammatory cytokine, TNF, but downregulate the gene expression of anti-inflammatory cytokine, IL10, and Dr E. coli colonization receptor, CD55, thus leading to efficient bacterial clearance in human bladder cells. C_LIO_LIIn contrast, activation of the membrane ER subtype, GPR30, shows opposite effects to ER and ER{beta} that were mediated on TNF, IL10 and CD55 gene expression, thus leading to impaired bacterial clearance of Dr E. coli in human bladder cells. C_LIO_LIER subtypes can serve as potential drug candidates for designing new therapies to boost or modulate the local immunity in the human bladder preventing the establishment of E. coli infections. C_LI

immunology↗

bioRxiv2017

Measuring the reproducibility and quality of Hi-C data

Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study. Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established (e.g., ratio of intra to interchromosomal interactions) and novel (e.g., QuASAR-QC) measures to identify low quality experiments. In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community.

genomics↗