Biology subjects

Huang, N.

Publications and source records attributed to Huang, N..

At least 73 records · Page 4Linked to original sources

bioRxiv2020

Quantify the requirements to achieve grain Zn biofortification of high-yield wheat on calcareous soils

The solution to address global human Zn deficiency is Zn biofortification of staple food crops, aimed at high grain Zn concentration as well as high yield. However, the desired high grain Zn concentration above 40 mg kg-1 is rarely observed for high-yield wheat on worldwide calcareous soils, due to inadequate Zn uptake or Zn distribution to grain. The present study aims to investigate how much Zn uptake or distribution is adequate to achieve the Zn.t of high-yield wheat on calcareous soils with low available Zn ([~] 0.5 mg kg-1). Of the 123 cultivars tested in a three-year field experiment, 19 high-yield cultivars were identified with similar yields around 7.0 t ha-1 and various grain Zn concentrations from 9.3 to 26.7 mg kg-1. The adequate Zn distribution to grain was defined from the view of Zn biofortification, as the situation where the Zn distribution to grain (Zn harvest index) increased to the observed maximum of [~] 91.0% and the Zn concentration of vegetative parts (straw Zn concentration) decreased to the observed minimum of [~] 1.5 mg kg-1 (Zn.m). Under the assumed condition of adequate Zn distribution to grain ([~] 91.0%), all the extra Zn above Zn.m was remobilized from straw to grain and the grain Zn concentration would be increased to its highest attainable level, which was 14.5 [~] 31.3 mg kg-1 for the 19 high-yield cultivars but still lower than 40 mg kg-1. Thus, even with the adequate Zn distribution to grain, the current Zn uptake is still not adequate and needs to be increased to 308 g ha-1 or higher to achieve Zn.t for high-yield wheat (7.0 t ha-1) on low-Zn calcareous soils. Besides, the established method here can also provide the priority measures and quantitative guidelines to achieve Zn biofortification in other wheat production regions.

plant biology↗

bioRxiv2020

User-friendly, scalable tools and workflows for single-cell analysis

Single-cell RNA-Seq (scRNA-Seq) data analysis requires expertise in command-line tools, programming languages and scaling on compute infrastructure. As scRNA-Seq becomes widespread, computational pipelines need to be more accessible, simpler and scalable. We introduce an interactive analysis environment for scRNA-Seq, based on Galaxy, with ~70 functions from major single-cell analysis tools, which can be run on compute clusters, cloud providers or single machines, to bring compute to the data in scRNA-Seq.

bioinformatics↗

bioRxiv2020

Single cell transcriptional characterization of human megakaryocyte lineage commitment and maturation

In the current understanding of adult bone marrow hematopoiesis, megakaryocytes (MKs) originate from cells immuno-phenotypically indistinguishable from hematopoietic stem cells (HSCs), bypassing intermediate progenitors. Here, we use single cell RNA sequencing to characterize HSCs and MKs from human bone marrow, to investigate MK lineage commitment and maturation. We identify two MK primed HSC clusters exhibiting unique differentiation kinetics, at least one of which is used in steady state and stress thrombopoiesis. By analyzing transcriptional signatures we show that human bone marrow MKs originate from MK primed HSC subpopulations, supporting the notion that these display exclusive priming for MK differentiation. We show that transcriptional programs change with increasing MK ploidy, where genes upregulated in high ploidy states may have functional relevance in platelet production. Finally, we highlight the presence of a specific transcriptional signature in MKs from individuals with myocardial infarction, supporting the aberration of MK differentiation in this thrombotic state.

cell biology↗

bioRxiv2020

Comparison of visualisation tools for single-cell RNAseq data

In the last decade, single cell RNAseq (scRNAseq) datasets have grown from a single cell to millions of cells. Due to its high dimensionality, the scRNAseq data contains a lot of valuable information, however, it is not always feasible to visualise and share it in a scientific report or an article publication format. Recently, a lot of interactive analysis and visualisation tools have been developed to address this issue and facilitate knowledge transfer in the scientific community. In this study, we review and compare several of the currently available analysis and visualisation tools and benchmark those that allow to visualize the scRNAseq data on the web and share it with others. To address the problem of format compatibility for most visualisation tools, we have also developed a user-friendly R package, sceasy, which allows users to convert their own scRNAseq datasets into a specific data format for visualisation.

bioinformatics↗

bioRxiv2019

Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders

De novo mutations (DNMs) in protein-coding genes are a well-established cause of developmental disorders (DD). However, known DD-associated genes only account for a minority of the observed excess of such DNMs. To identify novel DD-associated genes, we integrated healthcare and research exome sequences on 31,058 DD parent-offspring trios, and developed a simulation-based statistical test to identify gene-specific enrichments of DNMs. We identified 285 significantly DD-associated genes, including 28 not previously robustly associated with DDs. Despite detecting more DD-associated genes than in any previous study, much of the excess of DNMs of protein-coding genes remains unaccounted for. Modelling suggests that over 1,000 novel DD-associated genes await discovery, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of dominant DDs.

genomics↗

bioRxiv2019

Differential serological diagnostics of different Rabbit Haemorrhagic Disease Viruses co-circulating in Australia

The lagovirus Rabbit Haemorrhagic Disease Virus (RHDV) has been circulating in Australia since the mid-1990s when it was deliberately released to control overabundant rabbit populations. In recent years, the viral diversity of different RHDVs in Australia has increased, and currently four different types of RHDV are known to be circulating. To allow for ongoing epidemiological studies and impact assessments of these viruses on Australian wild rabbit populations, it is essential that serological tools are updated. To this end, Reference sera were produced against all four virulent RHDVs (including RHDV2) known to be present in Australia and tested in a series of available immunological assays originally developed for the prototype RHDV, to assess patterns of cross reactivity and the usefulness of these assays to detect lagovirus antibodies, either in a generic or specific manner. Enzyme Linked Immuno Sorbent Assays (ELISAs) developed to detect antibody isotypes IgM, IgA and IgG were sufficiently cross reactive to detect antibodies raised against all four virulent lagoviruses. For the more specific detection of antibodies to the antigenically more different RHDV2, a competition ELISA was adapted using RHDV2 specific monoclonal antibodies in combination with Australian viral antigen. Archival serum banks from a long term rabbit monitoring site where rabbits were sampled quarterly over a period of six years were re-screened using this assay, and revealed serological evidence for the arrival of RHDV2 in this population at least six months prior to its initial detection in Australia in a deceased rabbit in May 2015. The serological methods and reference reagents described here will provide valuable tools to study presence, prevalence and impact of RHDV2 on Australian rabbit populations; however the discrimination of different antigenic variants of RHDVs as well as mixed infections at the serological level remains challenging.

epidemiology↗

bioRxiv2019

Carrion flies as sentinels for monitoring rabbit calicivirus activity in Australia

Rabbit caliciviruses are an essential tool for managing wild rabbit populations in Australia. Our understanding of rabbit calicivirus epidemiology in Australia currently depends on members of the public submitting liver samples from dead rabbits through a monitoring program called Rabbitscan. However, many wild rabbits die in inaccessible locations or are scavenged before sampling can occur, leading to considerable sampling bias. In this study we screened field-caught carrion flies for the presence of rabbit caliciviruses to monitor virus circulation patterns in the landscape, with an aim to establish a less biased epidemiological surveillance tool. Carrion flies were collected from two study sites over a 22 month period and these samples were used to optimise and validate molecular testing methods in this sample type for the currently circulating rabbit calicivirus variants. Virus was clearly detectable in field-caught carrion flies using optimised SYBR-green RT-qPCR and RT-PCR assays. However, variant identification was frequently hindered by the low virus loads present in carrion fly samples and spurious RT-PCR amplification. This was overcome by frequent sampling, which effectively acts as replicate sampling to verify inconclusive results. There was good correlation between virus detections in carrion flies and in samples recovered from wild rabbits, both temporally and for virus variant identification. The methods reported here provide a robust and efficient additional surveillance tool to monitor rabbit calicivirus activity at a landscape scale, which in turn can help to guide more effective rabbit management programs.

microbiology↗

bioRxiv2019

Structural insight into the mechanism of 4-aminoquinolines selectivity for the alpha2A-adrenoceptor

2A-adrenoceptor (AR) is a potential target for the treatment of degenerative diseases of the central nervous system, and 2A-AR agonists are one of the most effective drugs for this condition. However, the lack of high selectivity for 2A-AR subtype of traditional drugs greatly limits their clinic usage. In this study, a series of homobivalent 4-aminoquinolines conjugated by two 4-aminoquinoline moieties via varying alkane linker length (C2-C12) were characterized for their affinities for each 2-AR subtype. Subsequently, docking, molecular dynamics and mutagenesis were applied to uncover the molecular mechanism. Most 4-aminoquinolines (4-aminoquinoline monomer, C2-C6, C8-C10) were selective for the 2A-AR over 2B- and 2C-ARs. Besides, the affinities are of similar linker length-dependence for each 2-AR subtype. Among all the compounds tested, C10 has the highest affinity for the 2A-AR (pKi=-7.45{+/-}0.62), which is 12-fold and 60-fold selective over 2B-AR and 2C-AR, respectively. Docking and molecular dynamics studies suggest that C10 simultaneously interacts with an orthosteric and an "allosteric site" of the 2A-AR. The mutation of F205, which is situated at the orthosteric binding pocket decreases the affinity by 2-fold. The potential allosteric residues include Ser90, Asn93, Glu94 and W99. The specificity of C10 for the 2A-AR and the potential orthosteric and allosteric binding sites proposed in this study provide valuable guidance for the development of novel 2A-AR subtype selective compounds.

pharmacology and toxicology↗

bioRxiv2018

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs

Fusion transcripts are used as biomarkers in companion diagnoses. Although more than 15,000 fusion RNAs have been identified from diverse cancer types, few common feature has been reported. Here, we compared 16,410 fusion transcripts detected in cancer (from a published cohort of 9,966 tumor samples of 33 cancer types) with genome-wide RNA-DNA interactions mapped in two normal, non-cancerous cell types (using iMARGI, an enhanced version of the MARGI [Mapping RNA-Genome Interactions assay]). Among the top 10 most significant RNA-DNA interactions in normal cells, 5 co-localized with the gene pairs that formed fusion RNAs in cancer. Furthermore, throughout the genome, the frequency of a gene pair to exhibit RNA-DNA interactions is positively correlated with the probability of this gene pair to present documented fusion transcripts in cancer. To test whether RNA-DNA interactions in normal cells are predictive of fusion RNAs, we analyzed in a validation cohort of 96 lung cancer samples using RNA-seq. We found 34 out of 42 fusion transcripts in the validation cohort exhibited RNA-DNA interactions in normal cells. Finally, combining RNA-seq, single-molecule RNA FISH, and DNA FISH, we detected a cancer sample with Eml4-Alk fusion RNA without forming the Eml4-Alk fusion gene. Collectively, these data suggest a novel RNA-poise model, where spatial proximity of RNA and DNA could poise for creation of fusion transcripts.

systems biology↗

bioRxiv2018

High-resolution mapping of regulatory element interactions and genome architecture using ARC-C

Interactions between cis-regulatory elements such as promoters and enhancers are important for transcription but global identification of these interactions remains a major challenge. Leveraging the chromatin accessiblity of regulatory elements, we developed ARC-C (accessible region chromosome conformation capture), which profiles chromatin regulatory interactions genome-wide at high resolution. Applying ARC-C to C. elegans, we identify ~15,000 significant interactions at 500bp resolution. Regions bound by transcription factors and chromatin regulators such as cohesin and condensin II are enriched for interactions, and we use ARC-C to show that the BLMP-1 transcription factor mediates interactions between its targets. Investigating domain level architecture, we find that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) and that these domains interact to form A/B (active/inactive) compartment structure. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.

genomics↗

bioRxiv2018

The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus

Our knowledge of mammalian viruses has been strongly skewed toward those that cause disease in humans and animals. However, recent metagenomic studies indicate that most apparently healthy organisms carry viruses, and that these seemingly benign viruses may comprise the bulk of virus diversity. The bias toward studying viruses associated with overt disease is apparent in the lagoviruses (family Caliciviridae) that infect rabbits and hares: although most attention has been directed toward the highly pathogenic members of this genus - the rabbit haemorrhagic disease virus and European brown hare syndrome virus - a number of benign lagoviruses have also been identified. To determine whether wild European brown hares in Australia might also carry undetected benign viruses, we used a meta-transcriptomics approach to explore the gut and liver RNA viromes of these invasive animals. This led to the discovery of three new lagoviruses. While one of the three viruses was only detected in a single hare, the other two viruses were detected in 20% of all hares tested. All three viruses were most closely related to other hare lagoviruses, but were highly distinct from both known viruses and each other. We also found evidence for complex recombination events in these viruses, which, combined with their phylogenetic distribution, suggests that there is likely extensive unsampled diversity in this genus. Additional metagenomic studies of hares and other species are clearly needed to fill gaps in the lagovirus phylogeny and hence better understand the evolutionary history of this important group of mammalian viruses.

microbiology↗

bioRxiv2018

Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3 HDAC complex

The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Ly4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss depend on chromatin context, so it is important to understand the relationship between CFP1 and other chromatin factors. Using a proteomics approach, we identified an unexpected link between C. elegans CFP-1 and a Rpd3/Sin3 histone deacetylase complex. We find that mutants of CFP-1, SIN-3, and the catalytic subunit SET-2/SET1 have similar phenotypes and misregulate common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3 HDAC complex at promoters and uncover coordinate regulation of gene expression by chromatin complexes having distinct activities.

genomics↗

bioRxiv2018

Neural underpinnnings of auditory salience in natural soundscapes

Salience is the mechanism whereby attention is automatically directed towards critical stimuli. Measuring the salience of a stimulus using behavioral methods risks confounds with top-down attention, particularly in the case of natural soundscapes. A distraction paradigm is employed here to measure physiological effects of salient auditory stimuli using electroencephalography. Several such effects are presented. In particular, a stimulus entrainment response is reduced by the presentation of distractor salient sounds. A reduction in oscillatory neural responses in the gamma frequency band is also observed following salient stimuli. These measures are used to identify salient portions of the natural scene. Finally, envelope decoding methods also indicate that salient stimuli attract attention away from other, task-related sounds.

neuroscience↗

bioRxiv2018

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

The Oxford Nanopore sequencing enables to directly detect methylation sites in DNA from reads without extra laboratory techniques. In this study, we develop DeepSignal, a deep learning method to detect DNA methylated sites from Nanopore sequencing reads. DeepSignal construct features from both raw electrical signals and signal sequences in Nanopore reads. Testing on Nanopore reads of pUC19, E. coli and human, we show that DeepSignal can achieve both higher read level and genome level accuracy on detecting 6mA and 5mC methylation comparing to previous HMM based methods. Moreover, DeepSignal achieves similar performance cross different methylation bases and different methylation motifs. Furthermore, DeepSignal can detect 5mC and 6mA methylation states of genome sites with above 90% genome level accuracy under just 5X coverage using controlled methylation data.

bioinformatics↗

bioRxiv2018

RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome

Nuclear speckles are interchromatin structures enriched in RNA splicing factors. Determining their relative positions with respect to the folded nuclear genome could provide critical information on co-and post-transcriptional regulation of gene expression. However, it remains challenging to identify which parts of the nuclear genome are in proximity to nuclear speckles, due to physical separation between nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNAs, 7SK and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA, nuclear speckle associated RNA), may extend to sufficient proximity to the nuclear genome. Leveraging a transcriptome-genome interaction assay (MARGI), we identified nsaRNA-interacting genomic sequences, which exhibited clustering patterns (nsaPeaks) in the genome, suggesting existence of relatively stable interaction sites for nsaRNAs in nuclear genome. Posttranscriptional pre-mRNAs, which are known to be clustered to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Furthermore, CDK9 proteins that localize to the vicinity of nuclear speckles produced ChIP-seq peaks that overlapped with nsaPeaks. Our combined DNA FISH and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs locate in sufficient proximity to nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.

bioinformatics↗

bioRxiv2018

Chromatin accessibility dynamics across C. elegans development and ageing

An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, hundreds of promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements is regulated during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

genomics↗

bioRxiv2017

The complement system supports normal postnatal development and gonadal function in both sexes

Male and female infertility are clinically managed and classified as distinct diseases, and relatively little is known about mechanisms of gonadal function common to both sexes. We used genome-wide genetic analysis on 74,896 women and men to find rare genetic variants that modulate gonadal function in both sexes. This uncovered an association with variants disrupting CSMD1, a complement regulatory protein located on 8p23, in a genomic region with an exceptional evolution. We found that Csmd1 knockout mice display a diverse array of gonadal defects in both sexes, and in females, impaired mammary gland development that leads to increased offspring mortality. The complement pathway is significantly disrupted in Csmd1 mice, and further disruption of the complement pathway from joint inactivation of C3 leads to more extreme reproductive defects. Our results can explain a novel human genetic association with infertility and implicate the complement system in the normal development of postnatal tissues.

developmental biology↗

bioRxiv2017

A strain-specific multiplex RT-PCR for Australian rabbit haemorrhagic disease viruses uncovers a new recombinant virus variant in rabbits and hares

Rabbit haemorrhagic disease virus (RHDV, or GI.1), is a calicivirus in the genus Lagovirus that has been widely utilised in Australia as a biological control agent for the management of overabundant wild European rabbit (Oryctolagus cuniculus) populations since 1996. Recently, two exotic incursions of pathogenic lagoviruses have been reported in Australia; GI.1a-Aus, previously called RHDVa-Aus, is a GI.1a virus detected in January 2014, and the novel lagovirus GI.2 (previously known as RHDV2). Furthermore, an additional GI.1a strain, GI.1a-K5 (also known as 08Q712), was released nationwide in March 2017 as a supplementary tool for wild rabbit management. To discriminate between these lagoviruses, a highly sensitive strain-specific multiplex RT-PCR assay was developed, which allows fast, cost-effective, and sensitive detection of the four pathogenic lagoviruses currently known to be circulating in Australia. In addition, we developed a universal qRT-PCR assay to be used in conjunction with the multiplex assay that broadly detects all four viruses and facilitates quantification of viral RNA load in samples. These assays enable rapid detection, identification, and quantification of pathogenic lagoviruses in the Australian context. Using these assays, a novel recombinant lagovirus was detected in rabbit tissues samples, which contained the non-structural genes of GI.1a-Aus and the structural genes of GI.2. This variant was also recovered from the liver of a European brown hare (Lepus europaeus). The impact of this novel recombinant on Australian wild lagomorph populations and its competitiveness in relation to circulating field strains, particularly GI.2, requires further studies.

microbiology↗