Search bioRxiv⌕ Search

Biology subjects

Ma, H.

Publications and source records attributed to Ma, H..

At least 235 records · Page 13Linked to original sources

Degree and site of chromosomal instability define its oncogenic potential

Most human cancers are aneuploid, due to a chromosomal instability (CIN) phenotype. Despite being hallmarks of cancer, however, the roles of CIN and aneuploidy in tumor formation have not unequivocally emerged from animal studies and are thus still unclear. CIN can both promote and suppress tumorigenesis, but variances in mechanisms and timings of CIN induction in different oncogenic backgrounds and associated tissues limit interpretation of the contributions of CIN. Using a novel conditional mouse model for diverse degrees of CIN, we find that a particular range is sufficient to drive very early onset spontaneous adenoma formation in the intestine, showing that CIN can act as a much more potent oncogenic driver than was previously reported. In mice predisposed to intestinal cancer (ApcMin/+), moderate but not low CIN causes a remarkable increase in adenoma burden in the entire intestinal tract, especially in the distal colon, more closely modelling human disease. Strikingly, high levels of CIN promote adenoma formation in the distal colon even more than moderate CIN does, but have no effect in the small intestine. Our results thus show that CIN can be potently oncogenic, but that certain levels of CIN can have contrasting effects in distinct tissues.

cancer biology↗

Longevity of growth-arrested bacteria requires protein synthesis and a stringent response

Gram-negative bacteria in infections, biofilms and industrial settings often stop growing due to nutrient depletion, immune responses or environmental stresses. Bacteria in this state tend to be tolerant to antibiotics and are often referred to as dormant. Rhodopseudomonas palustris, a phototrophic -proteobacterium, can remain fully viable for more than four months when growth is arrested. Here, we show that protein synthesis, specific proteins involved in translation and a stringent response are required for this remarkable longevity. Because it can generate ATP from light during growth arrest, R. palustris is an extreme example of a bacterial species that will stay alive for long periods of time as a relatively homogeneous population of cells and it is thus an excellent model organism for studies of bacterial longevity. There is evidence that other Gram-negative species also continue to synthesize proteins during growth arrest and that a stringent response is required for their longevity as well. Our observations challenge the notion that growth-arrested cells are necessarily dormant and metabolically inactive, and suggest that such bacteria may have a level of metabolic activity that is higher than many would have assumed. Our results also expand our mechanistic understanding of a crucial but understudied phase of the bacterial life cycle.\n\nIMPORTANCEWe are surrounded by bacteria; but they do not completely dominate our planet despite the ability of many to grow extremely rapidly in the laboratory. This has been interpreted to mean that bacteria in nature are often in a dormant state. We investigated life in growth arrest of Rhodopseudomonas palustris, a proteobacterium that stays alive for months when it is not growing. We found that cells were metabolically active; they continued to synthesize proteins and mounted a stringent response, both of which were required for their longevity. Our results suggest that long-lived bacteria are not necessarily inactive but have an active metabolism that is well adjusted to life without growth.

microbiology↗

Meiosis related cancer-testis genes correlate with tumor aneuploidy and immune infiltration in 21 cancer types

The meiosis stage of spermatogenesis and the aneuploidy generation in tumorigenesis are highly linked. Cancer-testis genes (CT genes) were specifically expressed in testis and cancers and may serve as the molecular basis of the shared features between spermatogenesis and tumorigenesis. In the present study, we integrated multi-omics data from bulk samples and cell lines, and single cell RNA-Seq data from testis and two tumors to systematically investigate the association between CT genes and aneuploidy. After ranking genes according to their association with aneuploidy level, we found that CT genes, especially CT genes specifically expressed in meiosis, showed a consistently positive correlation with aneuploidy and homologous recombination deficiency (HRD) level. Similar results were also found in the CT non-coding genes. Then, we constructed a regulatory network based on the single cell RNA-seq data and revealed that the gain of accelerator transcriptional factors (TFs) E2F7 and E2F8 and the loss of the stabilizer TFs RFX2 and NFYA aberrantly activated CT genes in the cancers and were associated with the increase of HRD level. Finally, we found that the association between CT genes and cytotoxic infiltrating lymphocytes can be influenced by the HRD level. In sum, our results revealed the evidence of pseudomeiotic functions of CT genes in the aneuploidy generation process in the cancer cells. The results may help illuminate the origin of aneuploidy in cancers and guide future immunotherapy targeting CT antigens.

genomics↗

Survey of severe fever with thrombocytopenia syndrome virus covert infection for healthy people in Henan Province, China

BackgroundSevere fever with thrombocytopenia syndrome (SFTS) is a severe emerging disease, and its incidence has been increasing in recent years. A cross-sectional study was conducted for healthy people in high SFTS endemic areas of Henan province in 2016. MethodsThis study used stratified random sampling method and finally 14 natural villages were selected as the investigation site. The questionnaire survey and serum collection were carried out from April to May in 2016. All the serum samples were detected by SFTSV IgM and IgG antibodies by ELISA. Only positive samples of SFTSV IgM antibody need be tested SFTSV RNA and virus cultured. A month after the specimen collection, all persons positive for IgM antibody were followed up one by one to confirm whether he or she was recessive infection. Results1463 healthy persons were investigated in total. The average seropositive rates of SFTS virus specific IgG and IgM antibodies were 10.46% (153/1463) and 0.82% (12/1463), respectively. IgM antibody was positive in 12 individuals, and 6 of them SFTS virus RNA were also detected. In addition, 5 SFTS virus were isolated from the 6 SFTS virus RNA (+) individuals. By genomic sequencing and phylogenetic analysis, 5 new isolates from healthy crowd all belonged to groups A, which were similar to other isolates from SFTS patients. After one month, all people with SFTS virus IgM antibody had no illness or symptoms. ConclusionsThis study confirmed there is SFTS recessive infection in human, and it is the first report about SFTS virus isolation in healthy people. Author SummarySevere fever with thrombocytopenia syndrome (SFTS), a severe emerging infectious disease, was discovered in rural areas of China. The first SFTS case was found in Henan province, which has had the largest number of SFTS cases in China every year since the disease was discovered. However, as a high incidence area of SFTS in Henan province, the serum prevalence rate of the virus in healthy people is still not clear. Therefore, a cross-sectional survey was performed in high endemic areas and epidemic seasons in 2016. The results showed that the level of specific SFTS seroprevlence was relatively higher and possibility increasing. SFTS RNA were positive and SFTS virus was isolated from the specimens of healthy people. This study confirmed there is SFTS recessive infection in human, and it is the first report about SFTS virus isolation in healthy people.

epidemiology↗

Characterization of the workplace chemical exposome using untargeted LC-MS/MS: a case study

Western people now spend close to 90% of their time indoors, one-quarter of which occurs at their place of employment. As such, interactions between employees and the workplace built environment have significant potential impact on employee health and safety. However, the range of workers daily chemical exposures is still poorly understood. Likewise, the influence of workers themselves and of worker behavior on the chemical composition of the workplace is still unknown. In this case study, we used untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) to compare the chemical signatures of three different types of workplaces: scientific research buildings, office buildings, and one mixed-purpose building. Our results identified differential signatures of public building surfaces based on building purpose, sampling location and surface materials. Overall, these results are helping define the influence of human behavior on the workplace chemical environment and identify the chemical hazards to which people are exposed throughout their workday. HighlightsO_LIImplementation of untargeted liquid chromatography-tandem mass spectrometry to study workplace chemical exposures. C_LIO_LIShared chemical signatures were identified based on building purpose. C_LIO_LIDifferential chemical signatures were identified based on surface material and sampling location. C_LIO_LIAnnotated molecules include pharmaceuticals, illicit drugs, food chemicals, constituents of paints and stains, and cleaning products. C_LI

biochemistry↗

Genetic diversity analysis of an isolate of microsporidia infesting Athetis lepigone

In this study, PCR amplification, cloning and sequencing analysis were adopted to explore genetic diversity of microsporidia (LEP9557) infecting Athetis lepigone. The small subunit ribosomal DNA (SSU rDNA), internal transcribed spacer (ITS) and intergenic spacers (IGS) of ribosomal RNA (rRNA) were cloned from the strain and sequenced. By means of multiple sequence alignment, we found that the three gene regions had different levels of polymorphism. There was greater polymorphism in ITS (74 variable sites) and IGS (55.59%) regions than in the SSU rDNA (17 variable sites). Phylogenetic analysis was performed using Kimura 2-parameter with neighbor joining and the results showed that LEP9557 had a close relationship with Nosema bombycis. Sequences of each clone were submitted to Genbank (Accession number: MF150254-MF150258). All of the results indicated the presence of genetic diversity in LEP9557, which established the foundation for identifying the phylogeny and relationships with other microsporidian strains, and had significant biological meaning for maintaining the survival and population continuity of the strain.

microbiology↗

Development of Human Neuroblastomas in Mouse-Human Neural Crest Chimeras

Neuroblastoma (NB), derived from the neural crest (NC), is the most common pediatric extracranial solid tumor. Here we establish a platform that allows studying human NBs in mouse-human NC chimeras. Chimeric mice were produced by injecting human NC cells carrying NB relevant oncogenes in-utero into gastrulating mouse embryos. The mice developed tumors composed of a heterogenous cell population that closely resembled that seen in primary NBs of patients but were significantly different from homogenous tumors formed in xenotransplantation models. The human tumors emerged in immunocompetent hosts and were extensively infiltrated by mouse cytotoxic T cells reflecting a vigorous host anti-tumor immune response. However, the tumors blunted the immune response by inducing infiltration of regulatory T cells and expression of immune checkpoints similar to escape mechanisms seen in human cancer patients. Thus, this experimental platform allows studying human tumor initiation, progression, manifestation and tumor - immune-system interactions in an animal model system.

cancer biology↗

The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells

Overexpression of anti-apoptotic proteins MCL1 and Bcl-xL is a frequent event in blood and solid cancers. Inhibitors targeting MCL1 are in clinical development, however many cancer models are intrinsically resistant to this approach. To discover mechanisms underlying resistance to MCL1 inhibition, we performed multiple flow-cytometry based genome-wide CRISPR screens that interrogate two drugs directly or indirectly targeting MCL1. Remarkably, both screens identified three components (CUL5, RNF7 and UBE2F) of a cullin-RING ubiquitin ligase complex (CRL5) that resensitized cells to MCL1 inhibition. We find that levels of the BH3-only pro-apoptotic proteins Bim and Noxa are proteasomally regulated by the CRL5 complex. Accumulation of Noxa caused by depletion of CRL5 components particularly skewed the balance in favor of apoptosis when cells were challenged with an MCL1 inhibitor. Discovery of a novel role of CRL5 in apoptosis and resistance to MCL1 inhibitors exposes new drug targets and the potential to improve combination treatments.

cancer biology↗

Cities of the future, visualizing climate change to inspire actions

Combating against climate change requires unified action across all sectors of society. However, this collective action is precluded by the consensus gap between scientific knowledge and public opinion. A growing body of evidence suggests that facts do not persuade people to act. Instead, it is visualization - the ability to simulate relatable scenarios - is the most effective approach for motivating behavior change. Here, we exemplify this approach, using current climate projections to enable people to visualize cities of the future, rather than describing intangible climate variables. Analyzing city pairs for 520 major cities of the world, we characterize which cities will most closely resemble the climate conditions of which other major cities by 2050. On average, most cities will resemble cities that are over 1000km south, and 22% of cities will experience climate conditions that are not currently experienced by any existing major cities. We predict that Londons climate in 2050 will resemble Barcelonas climate today, Madrid will resemble to Marrakesh, Moscow to Sofia, Seattle to San Francisco, Stockholm to Budapest, Tokyo to Changsha, etc. Our approach illustrates how complex climate data can be packaged to provide tangible information. By allowing people to visualize their own climate futures, we hope to empower citizens, policy makers and scientists to visualize expected climate impacts and adapt decision making accordingly.

scientific communication and education↗

Optical Sectioning of Live Mammal with Near-Infrared Light Sheet

Deep-tissue three-dimensional optical imaging of live mammals in vivo with high spatiotemporal resolution in non-invasive manners has been challenging due to light scattering. Here, we developed near-infrared (NIR) light sheet microscopy (LSM) with optical excitation and emission wavelengths up to ~ 1320 nm and ~ 1700 nm respectively, far into the NIR-II (1000-1700 nm) region for 3D optical sectioning through live tissues. Suppressed scattering of both excitation and emission photons allowed one-photon optical sectioning at ~ 2 mm depth in highly scattering brain tissues. NIR-II LSM enabled non-invasive in vivo imaging of live mice, revealing never-before-seen dynamic processes such as highly abnormal tumor microcirculation, and 3D molecular imaging of an important immune checkpoint protein, programmed-death ligand 1 (PD-L1) receptors at the single cell scale in tumors. In vivo two-color near-infrared light sheet sectioning enabled simultaneous volumetric imaging of tumor vasculatures and PD-L1 proteins in live mammals.

bioengineering↗

Comparative genetic architectures of schizophrenia in East Asian and European populations

Author summarySchizophrenia is a severe psychiatric disorder with a lifetime risk of about 1% world-wide. Most large schizophrenia genetic studies have studied people of primarily European ancestry, potentially missing important biological insights. Here we present a study of East Asian participants (22,778 schizophrenia cases and 35,362 controls), identifying 21 genome-wide significant schizophrenia associations in 19 genetic loci. Over the genome, the common genetic variants that confer risk for schizophrenia have highly similar effects in those of East Asian and European ancestry (rg=0.98), indicating for the first time that the genetic basis of schizophrenia and its biology are broadly shared across these world populations. A fixed-effect meta-analysis including individuals from East Asian and European ancestries revealed 208 genome-wide significant schizophrenia associations in 176 genetic loci (53 novel). Trans-ancestry fine-mapping more precisely isolated schizophrenia causal alleles in 70% of these loci. Despite consistent genetic effects across populations, polygenic risk models trained in one population have reduced performance in the other, highlighting the importance of including all major ancestral groups with sufficient sample size to ensure the findings have maximum relevance for all populations.

genetics↗

WindSTORM: Robust online image processing for high-throughput nanoscopy

High-throughput nanoscopy becomes increasingly important for unraveling complex biological processes from a large heterogeneous cell population at a nanoscale resolution. High-density emitter localization combined with a large field of view and fast imaging frame rate is commonly used to achieve a high imaging throughput, but the image processing speed in the dense emitter scenario remains a bottleneck. Here we present a simple non-iterative approach, referred to as WindSTORM, to achieve high-speed high-density emitter localization with robust performance for various image characteristics. We demonstrate that WindSTORM improves the computation speed by two orders of magnitude on CPU and three orders of magnitude upon GPU acceleration to realize online image processing, without compromising localization accuracy. Further, due to the embedded background correction, WindSTORM is highly robust in the presence of high and non-uniform background. WindSTORM paves the way for next generation of high-throughput nanoscopy.

bioinformatics↗

How Mg2+ stimulates DNA repair in prokaryotic (6-4) photolyases

Prokaryotic (6-4) photolyases branch at the base of the evolution of cryptochromes and photolyases. In the Agrobacterium (6-4) photolyase PhrB, the repair of DNA with UV-induced (6-4) pyrimidin dimers is stimulated by Mg2+. We show that Mg2+ is required for efficient lesion binding and for charge stabilization after electron transfer from the FADH- chromophore to the DNA lesion. Two highly conserved Asp residues close to the DNA binding site are essential for the Mg2+ effect. Simulations showed that two Mg2+ bind to the region around these residues. DNA repair by eukaryotic (6-4) photolyases is not increased by Mg2+. Here, the structurally overlapping region contains no Asp but positively charged Lys or Arg. During evolution, charge stabilization and DNA binding by Mg2+ was therefore replaced by a positive amino acid. We argue that this transition has evolved in a freshwater environment. Prokaryotic (6-4) photolyases usually contain an FeS cluster. DNA repair of a cyanobacterial member of this group which is missing the FeS cluster was also found to be stimulated by Mg2+.

biochemistry↗

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed.\n\nHere, we present memote (https://github.com/opencobra/memote) an open-source software containing a community-maintained, standardized set of metabolic model tests. The tests cover a range of aspects from annotations to conceptual integrity and can be extended to include experimental datasets for automatic model validation. In addition to testing a model once, memote can be configured to do so automatically, i.e., while building a GEM. A comprehensive report displays the models performance parameters, which supports informed model development and facilitates error detection.\n\nMemote provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.

systems biology↗

The synchronization and adaptation of Neurospora crassa circadian and conidiation rhythms to short light-dark cycles

Circadian clocks control the physiological and behavioral daily rhythms to adapt to the changing environment with a period of ~24 h. However, the influence and mechanism of extreme light-dark cycles on the circadian clock remain unclear. We show that, in the fungus Neurospora crassa under short LD cycles, both the growth rate and the ratio of microconidia production contributes to adaptation in LD12:12 (light for 12 h and dark for 12 h, periodically). Mathematical modeling and experiments demonstrate that in short LD cycles, the expression of the core clock protein FREQUENCY is entrained to the LD cycles when LD>3:3 while it free runs when T[≤] LD3:3. We investigated the changes in circadian/diurnal rhythms under a series of different LD conditions, and the results showed that conidial rhythmicity can be adapted to the short LD cycles. We further demonstrate that the existence of unknown blue light photoreceptor(s) and the circadian clock might promote the conidiation rhythms that resonate with the environment. A high-intensity light induced the expression of a set of downstream genes involved in various metabolic pathways. The ubiquitin E3 ligase FWD-1 and the previously described CRY-dependent oscillator system were implicated in regulating conidiation under short LD conditions.

microbiology↗

Enhanced super-resolution microscopy by extreme value based emitter recovery

Super-resolution localization microscopy allows visualization of biological structure at nanoscale resolution. However, the presence of heterogeneous background can degrade the nanoscale resolution by tens of nanometers and introduce significant image artifacts. Here we develop a new approach, referred to as extreme value based emitter recovery (EVER), to accurately recover the distorted fluorescent emitters from heterogeneous background. Through numerical simulation and biological experiments, we demonstrate that EVER significantly improves the accuracy and fidelity of the reconstructed super-resolution image for a wide variety of imaging characteristics. EVER requires no manual adjustment of parameters and is implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of super-resolution images. Our method paves the way for accurate nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.

cell biology↗

Epigenetic Drift of H3K27me3 in Aging Links Glycolysis to Healthy Longevity

Epigenetic alteration has been implicated in aging. However, the mechanism by which epigenetic change impacts aging is unclear. H3K27me3, a highly conserved histone modification signifying transcriptional repression, is marked and maintained by Polycomb Repressive Complexes (PRCs). Here, we explore the mechanism by which age-modulated increase of H3K27me3 impacts adult lifespan. Using Drosophila, we reveal that aging leads to loss of fidelity in epigenetic marking and drift of H3K27me3 and consequential reduction in the expression of glycolytic genes with negative effects on energy production and redox state. Moreover, we show that a reduction of H3K27me3 by PRCs-deficiency promotes glycolysis and healthy lifespan. While perturbing glycolysis by gene mutation diminishes the pro-lifespan benefits mediated by PRCs-deficiency, transgenic increase of glycolytic genes in wild-type animals extends longevity. Together, we propose that epigenetic drift of H3K27me3 defines a new aging mechanism and that stimulation of glycolysis promotes metabolic health and longevity.

molecular biology↗

Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions

Filamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this \"two-speed\" genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6- methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.

molecular biology↗