Biology subjects

Yao, M.

Publications and source records attributed to Yao, M..

78 records · Page 5Linked to original sources

bioRxiv2019

Time- and size-resolved bacterial aerosol dynamics in highly polluted air: new clues for haze formation mechanism

Aerosol chemistry is often studied without considering microbial involvements. Here, we have applied a high-volume (1 m3/min) aerosol sampler and the Micro-Orifice Uniform Deposit Impactor (NanoMoudi) along with molecular and microscopic methods to investigate time-and size-resolved bacterial aerosol dynamics in air. Under high particulate matter (PM) polluted episodes, bacterial aerosols were detected to have a viability up to 50-70% in the 0.56-1 m size range, at which elevated levels of SO42-, NO3- and NH4+ were concurrently observed. Engineered or acclimated for both pharmaceuticals and wastewater treatment, bacteria such as Psychrobacter spp., Massilia spp., Acinetobacter lwoffii, Exiguobacterium aurantiacum, and Bacillus megaterium were shown to have experienced massive abundance shifts in polluted air on early mornings and late afternoons, on which were previously reported to witness rapid new particle formation events. For example, Acinetobacter spp. were shown to account for > 96% abundance at a corresponding PM2.5 level of 208 ng/m3. The bacterial aerosol changes corresponded to the observed PM2.5 mass peak shift from 3.2-5.6 m to the high viability size range of 0.56-1m. Additionally, it is interesting that elevated levels of soluble Na, Ca, Mg, K, Al, Fe and P elements that are required for bacterial growth were observed to co-occur with those significant bacterial aerosol structure shifts in the air. For particular time-resolved PM2.5 pollution episodes, Acinetobacter and Massilia were shown to alternate in dominating the time-resolved aerosol community structures. The results from a HYSPLIT trajectory model simulation suggested that the role by air mass transport in affecting the observed bacterial aerosol dynamics could be minor. As an evidence, we found that Acinetobacter, Psychrobacter, Exiguobacterium, and Bacillus genera were emitted into the air with a level of > 3000 CFU/m3 from a pharmaceutical plant. In addition, high level of VOCs up to 15,030 ppbv, mainly Acetone (61%) and Acetaldehyde (11%), were also detected in the air inside the plant. All the data including size-resolved viability and time-resolved bacterial aerosol dynamics together with their growth conditions detected in the air suggested that airborne bacteria in the size range of 0.56- 1m could have played important roles for haze formation in Beijing. The results about time- and size-resolved bacterial aerosol dynamics from this work provide a fresh understanding of aerosol chemistry especially in highly polluted air. It is hoped that these findings could lend a support in future cost-effective air pollution control practices.

microbiology↗

bioRxiv2018

Mechanical Stretch Kills Transformed Cancer Cells

Transformed cancer cells differ from normal cells in several important features like anchorage independence, Warburg effect and mechanosensing. Consequently, transformed cancer cells develop an anaplastic morphology and respond aberrantly to external mechanical forces. Consistent with altered mechano-responsiveness, here we show that transformed cancer cells from many different tissues have reduced growth and become apoptotic upon cyclic stretch as do normal cells after the transformation. When matrix rigidity sensing is restored in transformed cancer cells, they survive and grow faster on soft surface upon cyclic stretch like normal cells but undergo anoikis without stretch by activation of death associated protein kinase1 (DAPK1). In contrast, stretch-dependent apoptosis (mechanoptosis) of transformed cells is driven by stretch-mediated calcium influx and calcium-dependent calpain 2 protease activation on both collagen and fibronectin matrices. Further, mechanosensitive calcium channel, Piezo1 is needed for mechanoptosis. Thus, cyclic stretching of transformed cells from different tissues activates apoptosis, whereas similar stretching of normal cells stimulates growth.

cell biology↗

bioRxiv2018

Baseline human gut microbiota profile in healthy people and standard reporting template

A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individuals microbiome to the growing knowledgebase of \"normal\" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and abundances the study also generated a list of contigs of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBIs Short Read Archive.

microbiology↗

bioRxiv2018

Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions

Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome resequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.

genomics↗

bioRxiv2018

miRNAs play important roles in aroma weakening during the shelf life of ‘Nanguo’ pear after cold storage

Cold storage is commonly employed to delay senescence in Nanguo pears after harvest. However, this technique also causes fruit aroma weakening. MicroRNAs play important roles in plant development and in eliciting responses to abiotic environmental stressors. In this study, the miRNA transcript profile of the fruit at the first day (C0, LT0) move in and out of cold storage and the optimum tasting period (COTP, LTOTP) during shelf life at room temperature were analyzed, respectively. More than 300 known miRNAs were identified in Nanguo pears; 176 and 135 miRNAs were significantly differentially expressed on the C0 vs. LT0 and on the COTP vs. LTOTP, respectively. After prediction the target genes of these miRNAs, LOX2S, LOX1_5, HPL, and ADH1 were found differentially expressed, which were the key genes during aroma formation. The expression pattern of these target genes and the related miRNAs were identified by RT-PCR. Mdm-miR172a-h, mdm-miR159a/b/c, mdm-miR160a-e, mdm-miR395a-i, mdm/ppe-miR399a, mdm/ppe-miR535a/b, and mdm-miR7120a/b negatively regulated target gene expression. These results indicate that miRNAs play key roles in aroma weakening in refrigerated Nanguo pear and provide valuable information for studying the molecular mechanisms of miRNAs in the aroma weakening of fruits due to cold storage.

molecular biology↗

bioRxiv2017

Force-Dependent Binding Of Vinculin To α-Catenin Regulates Cell-Cell Contacts Stability And Collective Cell Behavior

The shaping of a multicellular body and repair of adult tissues require fine-tuning of cell adhesion, cell mechanics and intercellular transmission of mechanical load. Adherens junctions (AJs) are the major intercellular junctions by which cells sense and exert mechanical force on each other. However, how AJs adapt to mechanical stress and how this adaptation contributes to cell-cell cohesion and eventually to tissue-scale dynamics and mechanics remains largely unknown. Here, by analyzing the tension-dependent recruitment of vinculin, -catenin and F-actin as a function of stiffness, as well as the dynamics of GFP-tagged wild-type and mutated -catenins, altered for their binding capability to vinculin, we demonstrate that the force-dependent binding of vinculin stabilizes -catenin and is responsible for AJ adaptation to force. Challenging cadherin complexes mechanical coupling with magnetic tweezers, and cell-cell cohesion during collective cell movements, further highlight that tension-dependent adaptation of AJs regulates cell-cell contact dynamics and coordinated collective cell migration. Altogether, these data demonstrate that the force-dependent -catenin/vinculin interaction, manipulated here by mutagenesis and mechanical control, is a core regulator of AJ mechanics and long-range cell-cell interactions.\n\nSummary statementCombining cell biology and biomechanical analysis, we show here that the coupling between cadherin complexes and actin trough tension-dependent -catenin/vinculin association is regulating AJ stability and dynamics as well as tissue-scale mechanics.

cell biology↗