A5084382035- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Plant Disease Resistance and Genetics
- Neurobiology and Insect Physiology Research
- Aerogels and thermal insulation
- Plant Virus Research Studies
- Epigenetics and DNA Methylation
- Microbial bioremediation and biosurfactants
- RNA Research and Splicing
- Signaling Pathways in Disease
- Insect and Arachnid Ecology and Behavior
- Circadian rhythm and melatonin
- ZnO doping and properties
- Insect behavior and control techniques
- Microbial Metabolic Engineering and Bioproduction
- CRISPR and Genetic Engineering
- Cancer-related gene regulation
- Radiative Heat Transfer Studies
- Hydrocarbon exploration and reservoir analysis
- Transition Metal Oxide Nanomaterials
- Copper-based nanomaterials and applications
- Mesoporous Materials and Catalysis
- Insect symbiosis and bacterial influences
- Endoplasmic Reticulum Stress and Disease
Rutgers, The State University of New Jersey
2014-2025
Xi'an University of Architecture and Technology
2009
Novartis (Switzerland)
2008
Zhaotong University
2006
State Key Laboratory of Pollution Control and Resource Reuse
2006
Tongji University
2006
University of California, Berkeley
1991-1995
Lawrence Berkeley National Laboratory
1991-1995
University of California, Davis
1994
Sustained increases in life expectancy have underscored the importance of managing diseases with a high incidence late life, such as various neurodegenerative conditions. Alzheimer's disease (AD) is most common among these, and consequently significant research effort spent on studying it. Although lot known about pathology AD role beta-amyloid (Abeta) peptides, complete network interactions regulating Abeta metabolism toxicity still eludes us. To address this, we conducted genetic...
Abstract The brush border is comprised of microvilli surface protrusions on the apical epithelia. This specialized structure greatly increases absorptive area and plays crucial roles in human health. However, transcriptional regulatory networks controlling genes are not fully understood. Here, we identify that hepatocyte nuclear factor 4 (HNF4) transcription a conserved important regulator gene program multiple organs, such as intestine, kidney yolk sac. Compromised signatures impaired...
FK506 binding proteins (FKBPs), also called immunophilins, are prolyl-isomerases (PPIases) that participate in a wide variety of cellular functions including hormone signaling and protein folding. Recent studies indicate contain PPIase activity can alter the processing Alzheimer's Amyloid Precursor Protein (APP). Originally identified hematopoietic cells, FKBP52 is much more abundantly expressed neurons, hippocampus, frontal cortex, basal ganglia. Given fact high molecular weight...
Aberrant activation of transposable elements (TEs) has been a well-documented source genomic instability and disease, stemming from their insertion into genes imposition epigenetic effects on nearby loci. However, the extent to which disruptive involve concomitant or subsequent formation DNA:RNA hybrids (R-loops) remains unknown. Here we used immunoprecipitation followed by high-throughput sequencing (DRIP-seq) map R-loop profiles TEs satellites in D. melanogaster ovaries control rhino...
Silica aerogel is a network of short bonded chains silica particles, which are fused together. Particles diameters 2-5 nm and pores diameter 10-100 produce solid-gas matrix in the volume fraction solid can be less than 5 percent. The small pore size effectively limits motion gas molecules hence reduces apparent conductivity to very low level. In this paper, we establish model for determination terms sizes. We use method adsorption-desorption determine distribution aerogel. thermal measured...
Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which provided important insight into the population dynamics TEs. However, such approaches are not able to identify insertions uncharacterized TEs, nor can they assemble full sequence inserted elements. Here, we use nanopore and Hi-C scaffolding produce de novo genome assemblies two wild strains Drosophila melanogaster from Genetic Reference Panel (DGRP)....
N6-methyladenine (6mA or m6dA) is a DNA modification that has long been known to play an important role in variety of biological functions prokaryotes. This only recently described eukaryotes, where it seems have evolved species-specific ranging from nucleosome positioning transposon repression. In Drosophila, 6mA shown be for enforcing the tissue specificity neuronal genes brain and suppressing transposable element expression ovaries. this study, we analyzed raw signal data nanopore...
Topologically associating domains, or TADs, are functional units that organize chromosomes into 3D structures of interacting chromatin. TADs play an important role in regulating gene expression by constraining enhancer-promoter contacts and there is evidence deletion TAD boundaries leads to aberrant neighboring genes. While the mechanisms formation have been well-studied, current knowledge on patterns evolution across species limited. Due integral regulation, their structure organization...
Abstract Transposable elements (TEs) must replicate in germline cells to pass novel insertions offspring. In Drosophila melanogaster ovaries, TEs can exploit specific developmental windows of opportunity evade host silencing and increase their copy numbers. However, TE activity the distinct cell types testis are not well understood. Here, we reanalyze publicly available single-cell RNA-seq datasets quantify expression testis. We develop a method for identification gene modules find that...
Abstract Transposable elements are molecular parasites that persist in their host genome by generating new copies to outpace natural selection. exert a large influence on evolution, some cases providing adaptive changes. Here we measure the fitness effect of transposable element insertions fission yeast Schizosaccharomyces pombe type strain removing all its only native family, long terminal repeat retrotransposon Tf2. We show Tf2 provide positive contribution host. ablation results changes...
Cells in renewing tissues exhibit dramatic transcriptional changes as they differentiate. The contribution of chromatin looping to tissue renewal is incompletely understood. Enhancer-promoter interactions could be relatively stable cells transition from progenitor differentiated states; alternatively, dynamic the gene expression their loci. intestinal epithelium most rapidly mammalian tissue. Proliferative crypts Lieberkühn sustain a stream that are continually shed into lumen. We apply...
Abstract In recent decades forensic fingerprinting of oil-spill hydrocarbons has emerged as an important tool for correlating oils and evaluating their source character. Two long-term hydrocarbon spills, off-road diesel spill (Mandan, ND) a crude oil (Bemidji, MN) experiencing methanogenic biodegradation were previously shown to be undergoing unexpected progression homologous n-alkane n-alkylated cyclohexane loss. Both exhibited degradative losses proceeding from the high-molecular-weight...
D. melanogaster is an excellent animal model to study how the circadian (≅ 24-h) timing system and sleep regulate daily wake-sleep cycles. Splicing of a temperature-sensitive 3'-terminal intron (termed dmpi8) from clock gene period (per) regulates distribution activity in Drosophila. The role dmpi8 splicing on behavior was further evaluated by analyzing sleep. Transgenic flies same genetic background but expressing either wild-type recombinant per or one where efficiency increased were...
Similar to many diurnal animals, Drosophila melanogaster exhibits a mid-day siesta that is more robust as temperature increases, an adaptive response aims minimize the deleterious effects from exposure heat. This temperature-dependent plasticity in sleep levels partly based on thermal sensitive splicing of intron 3' untranslated region (UTR) circadian clock gene termed period (per). In this study, we evaluated possible role for serine/arginine-rich (SR) factors regulation dmpi8 efficiency...
Many diurnal animals exhibit a mid-day 'siesta', generally thought to be an adaptive response aimed at minimizing exposure heat on warm days, suggesting that in regions with cooler climates siestas might less prominent feature of animal behavior. Drosophila melanogaster exhibits thermal plasticity its siesta is partly governed by the thermosensitive splicing 3'-terminal intron (termed dmpi8) from key circadian clock gene period (per). For example, decreases temperature lead progressively...
Coevolution between transposable elements (TEs) and their hosts can be antagonistic, where TEs evolve to avoid silencing the host responds by reestablishing TE suppression, or mutualistic, are co-opted benefit host. The TART-A functions as an important component of Drosophila telomeres but has also reportedly inserted into melanogaster nuclear export factor gene nxf2 . We find that, rather than inserting , actually captured a portion sequence. show that produces abundant Piwi-interacting...
R-loops are three-stranded nucleotide structures consisting of a DNA:RNA hybrid and displaced ssDNA non-template strand. Previous work suggests that R-loop formation is primarily determined by the thermodynamics binding, which governed base composition (e.g., GC skew) transcription-induced DNA superhelicity. However, have been described at genomic locations lack these properties, suggesting they may serve other context-specific roles. To better understand genetic determinants formation, we...
Flow cytometry estimates of genome sizes among species Drosophila show a 3-fold variation, ranging from ∼127 Mb in mercatorum to ∼400 cyrtoloma. However, the assembled portion Muller F element (orthologous fourth chromosome melanogaster) shows nearly 14-fold variation size, ∼1.3 >18 Mb. Here, we present chromosome-level long-read assemblies for 4 with expanded elements size 2.3 20.5 Each is as single scaffold each assembly. These will enable new insights into evolutionary causes and...
Technical Briefs Approximate Formulation for Coupled Conduction and Radiation Through a Medium With Arbitrary Optical Thickness S. Q. Zeng, Zeng Lawrence Berkeley Laboratory, University of California, Berkeley, CA 94720; Department Mechanical Engineering, California at 94720 Search other works by this author on: This Site PubMed Google Scholar A. J. Hunt, Hunt R. Grief, Grief W. Cao Author Article Information Heat Transfer. Aug 1995, 117(3): 797-799 (3 pages)...
Nocardia sp. C-14-1, isolated from acrylic fiber wastewater, can degrade long-chain alkanes and succinonitrile efficiently. Here we report the characterization of an indigenous plasmid pC1. The overall nucleotide sequence pC1 consisted 5841 bp. five ORFs, encoding a DNA recombinase, replication protein (Rep(pC1)) three proteins unknown function, were predicted on Rep(pC1) displayed its homology with Rep Rhodococcus large p33701, suggesting theta type replication. An Escherichia coli...
Abstract Topologically associating domains (TADs) are thought to play an important role in preventing gene misexpression by spatially constraining enhancer–promoter contacts. The deleterious nature of implies that TADs should, therefore, be conserved among related species. Several early studies comparing chromosome conformation between species reported high levels TAD conservation; however, more recent have questioned these results. Furthermore, work suggests reorganization is not associated...