Biology subjects

Pal, K.

Publications and source records attributed to Pal, K..

26 records · Page 2Linked to original sources

bioRxiv2020

Vascular Endothelial Growth Factor as an Immediate-Early Activator of UV-induced Skin Injury

The negative health consequences of acute ultraviolet (UV) exposure are evident, with reports of 30,000 emergency room visits annually to treat the effects of sunburn in the United States alone. Acute effects of sunburn include erythema, edema, and severe pain, and chronic overexposure to UV radiation can lead to skin cancer. While the pain associated with the acute effects of sunburn may be relieved by current interventions, existing post-sunburn treatments are not capable of reversing the cumulative and long-term pathological effects of UV exposure, an unmet clinical need. Here we show that activation of the vascular endothelial growth factor (VEGF) pathway is a direct and immediate consequence of acute UV exposure, and activation of VEGF signaling is necessary for the initiating the acute pathological effects of sunburn. In UV-exposed human subjects, VEGF signaling is activated within hours. Topical delivery of VEGF pathway inhibitors, targeted against the ligand VEGF-A (gold nanoparticles conjugated with anti-VEGF antibodies) and small molecule antagonists of VEGF receptor signaling, prevent the development of erythema and edema in UV-exposed mice. Collectively, these findings suggest targeting VEGF signaling may reduce the subsequent inflammation and pathology associated with UV-induced skin damage, which reveals a new post-exposure therapeutic window to potentially inhibit the known detrimental effects of UV on human skin.

molecular biology↗

bioRxiv2020

Optimizing nucleic acid extraction and transcriptome evaluation from low-input, fixed clinical samples

Tumor biopsies are commonly formalin-fixed and paraffin-embedded (FFPE) for long-term and efficient storage. However, FFPE preservation can greatly compromise the quality of samples, the extraction of nucleic acids, and feasibility of downstream studies, including RNA sequencing. These challenges are especially evident in the studies of clinical trial samples, where the sizes of biopsies often limit the amount of material available for study. Here, we evaluate two nucleic acid extraction kits (Covaris truXTRAC FFPE tNA Plus, QIAGEN miRNeasy FFPE) and three hybridized-capture-based RNA sequencing library preparations (Agilent SureSelect XT RNA Direct, Agilent SureSelect XT HS, and Illumina TruSeq RNA Exome) to evaluate the impact of these sample processing steps on transcriptome evaluation in a melanoma biopsy procured in a clinical setting and preserved by FFPE. While there exist many options for extraction and library preparation that are appropriate for RNA sequencing from FFPE samples, we observed that combinations of experimental approaches may have subtle impacts on downstream analysis, including gene expression quantification and fusion detection.

genomics↗

bioRxiv2020

Fluorogenic DNase Sensor Reveals Ubiquitous DNase Activity in Podosomes and Invadopodia

Podosomes and invadopodia, collectively termed invadosomes, are important adhesive and degradative units formed in macrophages, osteoclasts, dendritic cells, cancer cells, and many other cell types. Invadosomes are well known for recruiting proteases that degrade matrix proteins and facilitate cell invasion. In contrast to the extensively studied proteases, another important class of degradative enzymes, DNase, remains uninvestigated and in fact, unknown in invadosomes. Using surface nuclease sensor (SNS), which reports deoxyribonuclease (DNase) activity on the cell membrane by fluorescence signal, we revealed that invadosomes, regardless of cell types or species, universally recruit DNase and readily degrade extracellular double-stranded DNA (dsDNA). We identified the recruited DNase as GPI-anchored membrane protein DNase X which functions locally at the cell-substrate interface and is co-localized with the actin cores of the invadosomes. DNase recruitment is highly consistent and rapid in invadosomes. Co-imaging of F-actin and DNase activity shows that 46-86% invadosomes (dependent on cell types) have associated DNase activities. Time series imaging shows that DNase becomes active within a minute after the actin nucleation, functioning concomitantly with protease activity in podosomes but preceding it in invadopodia. Overall, this discovery suggests a richer arsenal of degradative enzymes in invadosomes at the cell-substrate interface. This work would likely prompt more studies to investigate DNase in invadosomes, in particular, to understand the physiological role of invadosome-associated membrane DNase in cell functions such as immune response, cell migration, matrix remodeling, etc.

cell biology↗

bioRxiv2020

A ChIC solution for ChIP-seq quality assessment

Despite the widespread adoption of the ChIP-seq technique, there is still no consensus on quality assessment procedures. Quantitative metrics previously proposed in literature are not always effective in discriminating the success or failure of an experiment, thus hampering objectivity and reproducibility of quality control. Here we introduce ChIC, a new framework for ChIP-seq data quality assessment that overcomes the limitations of previous solutions. ChIC is the first method for ChIP-seq quality control directly considering the enrichment profile shape, thus achieving good performances on ChIP targets yielding sharp and broad peaks alike. We integrate a comprehensive set of quality control metrics into one single score reliably summarizing the sample quality. The ChIC score is based on a machine learning classifier trained on a compendium with thousands of ChIP-seq profiles, which can also be used as a reference for easier evaluation of new datasets. ChIC is implemented as a user-friendly R/Bioconductor package.

bioinformatics↗

bioRxiv2019

A complex structure of arrestin-2 bound to a G protein-coupled receptor

Arrestins comprise a family of signal regulators of G-protein-coupled receptors (GPCRs), which include arrestins 1 to 4. While arrestins 1 and 4 are visual arrestins dedicated to rhodopsin, arrestins 2 and 3 (Arr2 and Arr3) are {beta}-arrestins known to regulate many nonvisual GPCRs. The dynamic and promiscuous coupling of Arr2 to nonvisual GPCRs has posed technical challenges to tackle the basis of arrestin binding to GPCRs. Here we report the structure of Arr2 in complex with neurotensin receptor 1 (NTSR1), which reveals an overall assembly that is strikingly different from the visual arrestin-rhodopsin complex by a 90{degrees} rotation of Arr2 relative to the receptor. In this new configuration, intracellular loop 3 (ICL3) and transmembrane helix 6 (TM6) of the receptor are oriented toward the N-terminal domain of the arrestin, making it possible for GPCRs that lack the C-terminal tail to couple Arr2 through their ICL3. Molecular dynamics simulation and crosslinking data further support the assembly of the Arr2-NTSR1 complex. Sequence analysis and homology modeling suggest that the Arr2-NTSR1 complex structure may provide an alternative template for modeling arrestin-GPCR interactions.

biophysics↗

bioRxiv2019

Health behaviors among male and female university students in Cambodia: a cross-sectional survey

BackgroundStudents go through a transition when they enter university, which involves major individual and contextual changes in every domain of life that may lead to several behavioral and health problems. This paper describes a wide range of health behaviors among male and female university students in Cambodia.\n\nMethodsA cross-sectional survey was conducted in 2015 among students randomly selected from the Royal University of Phnom Penh and University of Battambang. Health-related behaviors in different domains were collected using a structured questionnaire. Chi-square test, Fishers exact test, or independent Students t-test was used as appropriate to describe and compare the variables among male and female students.\n\nResultsThis study included 1359 students, of whom 50.8% were male, and the mean age was 21.3 years (SD= 2.3). Of the total, 79.5% reported not having any vigorous-intensity activities, 25.9% not having moderate-intensity activities, and 33.5% not having walked continuously for 10 minutes during the past seven days. The prevalence of substance use was low with 38.3% currently drinking alcohol, 1.1% smoking tobacco, and 0.4% using an illicit drug during the past 12 months. About one in ten (10.6%) reported having sexual intercourse, with a mean number of partners of 2.1 (SD= 2.4) during the past 12 months, and 42.4% not using a condom in the last intercourse. Only 7.1% reported having been diagnosed with a sexually transmitted infection in the past 12 months; of whom, 60% sought for treatment. About one-third (33.6%) reported eating fast food once or twice, and 5.3% having it three times or more over the last week. More than half (55.6%) had one to two servings of fruits and vegetables daily, and 9.9% did not eat any fruits and vegetables over the last week.\n\nConclusionsWe found that the prevalence of sexual risk behaviors and substance use was plausibly low among university students in this study. However, the rates of inactive lifestyle and unhealthy food consumption were concerning. Public policy and universities should promote healthy behaviors among the students. The interventions may take advantage of and expend upon the good health behaviors and consider gender differences.

scientific communication and education↗

bioRxiv2019

Cellular metabolic activity marker via selective turn-ON detection of serum albumin using an NBD-based fluoroprobe

A nitrobenzoxadiazole-based fluoroprobe (NBD-Bu) is designed to probe cellular metabolic activity in cancer and normal cells. NBD-Bu shows a significant fluorescence enhancement upon selective binding to serum albumin. The site specificity of NBD-Bu has been explored through a competitive displacement assay in the presence of site-specific markers such as warfarin and ibuprofen. Subsequently, high-resolution fluorescence microscopy results consolidated the potential of NBD-Bu for cellular imaging and detection of abnormal cellular metabolic activity.

cancer biology↗

bioRxiv2016

GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data

MotivationSanger sequencing remains the reference method for sequence variant detection, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases considerable expertise. Additionally, variant reporting and nomenclature is typically left to the user, which can lead to inconsistencies.\n\nResultsWe introduce GLASS, a tool built to assist with the assessment of gene variations in Sanger sequencing data. Critically, it provides a standardized variant output as recommended by the Human Genome Variation Society.\n\nAvailabilityThe program is freely available online at http://bat.infspire.org/genomepd/glass/.\n\nContactnikos.darzentas@gmail.com, malcikova.jitka@fnbrno.cz\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗