Biology subjects

Yan, W.

Publications and source records attributed to Yan, W..

8 recordsLinked to original sources

bioRxiv2018

Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina

High acuity vision in primates, including humans, is mediated by a small central retinal region called the fovea. As more accessible model organisms lack a fovea, its specialized function and dysfunction in ocular diseases remain poorly understood. We used 165,000 single-cell RNA-seq profiles to generate and validate comprehensive cellular taxonomies of macaque fovea and peripheral retina. More than 80% of >65 cell types match between the two regions, but exhibit substantial differences in proportions and gene expression, some of which we relate to functional differences. Comparison of macaque retinal types with those of mice reveals that interneuron types are tightly conserved, but that projection neuron types and programs diverge, despite conserved transcription factor codes. Key macaque types are conserved in humans, allowing mapping of cell-type and region-specific expression of >190 genes associated with 6 human retinal diseases. Our work provides a framework for comparative single-cell analysis across tissue regions and species.

neuroscience↗

bioRxiv2018

Active information maintenance in working memory by a sensory cortex

Working memory is a critical function of the brain to maintain and manipulate information over delay periods of seconds. Sensory areas have been implicated in working memory; however, it is debated whether the delay-period activity of sensory regions is actively maintaining information or passively reflecting top-down inputs. We hereby examined the anterior piriform cortex, an olfactory cortex, in head-fixed mice performing a series of olfactory working memory tasks. Information maintenance is necessary in these tasks, especially in a dual-task paradigm in which mice are required to perform another distracting task while actively maintaining information during the delay period. Optogenetic suppression of the piriform cortex activity during the delay period impaired performance in all the tasks.Furthermore, electrophysiological recordings revealed that the delay-period activity of the anterior piriform cortex encoded odor information with or without the distracting task.Thus, this sensory cortex is critical for active information maintenance in working memory.

neuroscience↗

bioRxiv2018

Epidemiology, Microbiology and Therapeutic Consequences of Chronic Osteomyelitis in Northern China: A Retrospective Analysis of 255 Patients

The study aimed to explore the epidemiology and clinical characteristics of chronic osteomyelitis observed in a northern China hospital. Clinical data of 255 patients with chronic osteomyelitis from January 2007 to January 2014 were collected and analyzed, including general information, disease data, treatment and follow-up data. Chronic osteomyelitis is more common in males and in the age group from 41-50 years of age. Common infection sites are the femur, tibiofibular, and hip joint. More g+ than g- bacterial infections were observed, with S. aureus the most commonly observed pathogenic organism. The positive detection rate from debridement bacterial culture is 75.6%. The detection rate when five samples are sent for bacterial culture is 90.6%, with pathogenic bacteria identified in 82.8% of cases. The two-stage debridement method (87.0%) has higher first curative rate than the one-stage debridement method (71.2%). To improve detection rate using bacterial culture, at least five samples are recommended. Treatment of chronic osteomyelitis with two-stage debridement, plus antibiotic-loaded polymethylmethacrylate (PMMA) beads provided good clinical results in this study and is therefore recommended.

microbiology↗

bioRxiv2018

Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota

BackgroundDespite the convenience and noninvasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum and feces samples, for 16S rRNA amplicon sequencing analyses.\n\nResultsIn this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11 - 87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples ({rho} = 0.54 - 0.71 and 0.71 - 0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the 4 gut segments, and these correlations were not high ({rho} = -0.2 - 0.4, P < 0.05) for most genera.\n\nConclusionsOur results provide evidence that the good potential of feces to identify most taxa in chicken guts, but it should be interpreted with caution by using feces as a proxy for gut in microbial structure analyses. This work provides insights and future directions regarding the usage of fecal samples in studies of the gut microbiome.

microbiology↗

bioRxiv2018

Template switching causes artificial junction formation and false identification of circular RNAs

Hundreds of thousands of putative circular RNAs have been identified through deep sequencing and bioinformatic analyses. However, the circularity of these putative RNA circles has not been experimentally validated due to limited methodologies currently available. We reported here that the template-switching capability of commonly used reverse transcriptases (e.g., SuperScript II) leads to the formation of artificial junction sequences, and consequently misclassification of large linear RNAs as RNA circles. Use of reverse transcriptases without terminal transferase activity (e.g., MonsterScript) for cDNA synthesis is critical for the identification of physiological circular RNAs. We also report two methods, MonsterScript junction PCR and high-resolution melting curve analyses, which can reliably distinguish circular RNAs from their linear forms and thus, can be used to discover and validate true circular RNAs.\n\nSignificance StatementThe vast majority of circular RNAs were identified through computational detection of junction sequences in the deep sequencing reads because these unique fusion sequences represent back-splicing events. We found that artificial junction sequences could be formed through template switching (TS) when MMLV-derived reverse transcriptases, e.g., SuperScript II, are used to synthesize cDNAs. Thus, many of the reported circular RNAs may not be RNA circles, but rather experimental artifacts. Fake circular RNAs can be avoided by using reverse transcriptases without terminal transferase activity (e.g., MonsterScript) for cDNA synthesis. We developed two novel methods, MonsterScript junction PCR and high-resolution melting curve analyses, for distinguishing circular RNAs from their linear form.

molecular biology↗

bioRxiv2018

Whole genome sequence of an edible and potential medicinal fungus, Cordyceps guangdongensis

Cordyceps guangdongensis is an edible fungus which has been approved as a Novel Food by the Chinese Ministry of Public Health in 2013. It also has a broad application prospect in pharmaceutical industries with many medicinal activities. In this study, the whole genome of C. guangdongensis GD15, a single spore isolate from a wild strain, was sequenced and assembled with Illumina and PacBio sequencing technology. The generated genome is 29.05 Mb in size, comprising 9 scaffolds with an average GC content of 57.01%. It is predicted to contain a total of 9150 protein-coding genes. Sequence identification and comparative analysis indicated that the assembled scaffolds contained two complete chromosomes and four single-end chromosomes, showing a high level assembly. Gene annotation revealed a diversity of transporters that could contribute to the genome size and evolution. Besides, approximately 15.49% and 13.70% genes involved in metabolic processes were annotated by KEGG and COG respectively. Genes belonging to CAZymes accounted for a proportion of 2.84% of the total genes. In addition, 435 transcription factors (TFs) were identified, which were involved in various biological processes. Among the identified TFs, the fungal transcription regulatory proteins (18.39%) and fungal-specific TFs (19.77%) represented the two largest classes of TFs. These data provided a much needed genomic resource for studying C. guangdongensis, laying a solid foundation for further genetic and biological studies, especially for elucidating the genome evolution and exploring the regulatory mechanism of fruiting body development.

genomics↗

bioRxiv2017

UV-Induced Keratin 1 Proteolysis Mediates UV-Induced Skin Damage

Keratins play critical roles in intermediate filament formation, inflammatory responses and cellular signaling in epithelium. While keratins is a major epidermal fluorophore, the mechanisms underlying the autofluorescence (AF) of keratins and its biomedical implications have remained unknown. Our study used mouse skin as a model to study these topics, showing that UV dose-dependently induced increases in green AF at the spinous layer of the epidermis of mouse within 6 hr of the UV exposures, which may be used for non-invasive prediction of UV-induced skin damage. The UV-induced AF appears to be induced by cysteine protease-mediated keratin 1 proteolysis: 1) UV rapidly induced significant keratin 1 degradation; 2) administration of keratin 1 siRNA largely decreased the UV-induced AF; and 3) administration of E-64, a cysteine protease inhibitor, significantly attenuated the UV-induced AF and keratin 1 degradation. Our study has also suggested that the UV-induced keratin 1 proteolysis may be a novel crucial pathological factor in UV-induced skin damage, which is supported by both the findings that indicate critical biological roles of keratin 1 in epithelium and our observation that prevention of UV-induced keratin 1 proteolysis can lead to decreased UV-induced skin damage. Collectively, our study has suggested that UV-induced keratin 1 proteolysis may be a novel and valuable target for diagnosis, prevention and treatment of UV-induced skin damage.

pathology↗

bioRxiv2017

AASRA: An Anchor Alignment-Based Small RNA Annotation Pipeline

SncRNA-Seq has become a routine for sncRNA profiling; however, software packages currently available are either exclusively for miRNA or piRNA annotation (e.g., miRDeep, miRanalyzer, Shortstack, PIANO), or for direct mapping of the sequence reads to the genome (e.g., Bowtie 2, SOAP and BWA), which tend to generate inaccurate counting due to repetitive matches to the genome or sncRNA homologs. Moreover, novel sncRNA variants in the sequencing reads, including those bearing small overhangs or internal insertions, deletions or mutations, are totally excluded from counting by these algorithms, leading to potential quantification bias. To overcome these problems, a comprehensive software package that can annotate all known small RNA species with adjustable tolerance towards small mismatches is needed. AASRA is based on our unique anchor alignment algorithm, which not only avoids repetitive or ambiguous counting, but also distinguishes mature miRNA from precursor miRNA reads. Compared to all existing pipelines for small RNA annotation, AASRA is superior in the following aspects: 1) AASRA can annotate all known sncRNA species simultaneously with the capability of distinguishing mature and precursor miRNAs; 2) AASRA can identify and allow for inclusion of sncRNA variants with small overhangs and/or internal insertions/deletions into the final counts; 3) AASRA is the fastest among all small RNA annotation pipelines tested. AASRA represents an all-in-one sncRNA annotation pipeline, which allows for high-speed, simultaneous annotation of all known sncRNA species with the capability to distinguish mature from precursor miRNAs, and to identify novel sncRNA variants in the sncRNA-Seq sequencing reads.\n\nAvailability and ImplementationThe AASRA software is freely available at https://github.com/biogramming/AASRA.

bioinformatics↗