bioRxiv Science⌕ Search

Biology subjects

Feng, C.

Publications and source records attributed to Feng, C..

99 records · Page 6Linked to original sources

Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project

With more than 30,000 species, fish are the largest and most ancient vertebrate group. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Here, we announce the Fish10K project, an international collaborative project or initiative? aiming to sequence 10,000 representative fish genomes under a systematic context within ten years, and officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, and sequencing and assembly strategies. To illustrate, we present the genomes of ten fish species from a cohort of 93 species chosen for technology development.

genomics↗

Neuroprotective effects of crocin I and II in an ischemia-reperfusion injury model

BackgroundCrocin I and II are derived from the medicinal plant Crocus sativus L. (Saffron), and their neuroprotective effects have been attracting more and more attention. However, their protective effect against cerebral apoplexy induced by hypoxia has not been reported. In this study, we aimed to clarify the roles of crocin I and II in protecting against ischemic injury.\n\nMaterials/MethodsWe generated a rat cerebral ischemia-reperfusion injury model using a reversible cerebral artery occlusion suture method and found changes in amino acid neurotransmitters in the frontal cortex after drug administration. We also identified changes in mRNA expression of Bcl2, Bax, Casp3, P38, and NFkb1 in the frontal cortex and changes in antioxidant indices in the brain.\n\nResultsCrocin I and II both had protective effects on ischemic/anoxic injury in vivo by downregulating the expression of Casp3 and Nfkb1 mRNA and the steady-state levels of excitatory amino acids/inhibitory amino acids during ischemia and reperfusion and by improving the total antioxidant capacity and total superoxide dismutase activities during ischemia. We also found that crocin I and II had synergistic effects when used together.\n\nConclusionsThese findings displayed that crocin I and II could protect animal model against ischemic and anoxic injury and provided new evidence for both molecules potential medicinal value.

neuroscience↗

A high-throughput segregation analysis identifies the sex chromosomes of Cannabis sativa

Cannabis sativa-derived tetrahydrocannabinol (THC) production is increasing very fast worldwide. C. sativa is a dioecious plant with XY chromosomes, and only females (XX) are useful for THC production. The C. sativa sex chromosomes sequence would improve early sexing and better management of this crop; however, the C. sativa genome projects failed to identify the sex chromosomes so far. Moreover, dioecy in the Cannabaceae family is ancestral, C. sativa sex chromosomes are potentially old and thus very interesting to study as little is known about the last steps of sex chromosome evolution in plants. Here we RNA-sequenced a C. sativa family (2 parents and 10 male and female offspring) and performed a segregation analysis for all C. sativa genes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to a C. sativa genome assembly identified a single chromosome pair with a large non-recombining region. Further analysis of the >500 sex-linked genes revealed that C. sativa has a strongly degenerated Y chromosome and represents the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large non-recombining regions and be very differentiated and still be of similar size (homomorphic).

genomics↗

Age dependence of modern clinical risk groups for localized prostate cancer -- a population-based study

BackgroundOptimal prostate cancer (PCa) screening strategies will focus on men most likely to have potentially-lethal, localized disease. Age-specific incidence rates (ASIRs) for clinical risk groups could guide risk-stratified screening.\n\nObjectiveDetermine ASIRs and proportions of PCa diagnoses in Norway for modern risk-group and Gleason score categories.\n\nDesign, Setting, and ParticipantsAll men diagnosed with PCa in Norway in 2014-2017 (n=20,356).\n\nOutcome Measurements and Statistical AnalysisPatients were assigned to clinical risk groups: low, favorable-intermediate, unfavorable-intermediate, high, regional, and metastatic, using Gleason score and clinical stage. Associations were assessed between age and (1) Gleason score (including Gleason 3+4 and 4+3) and (2) PCa risk group. Risk-group ASIRs were calculated by multiplying the overall Norwegian ASIR by the proportions observed for each category.\n\nResultsOlder age was significantly associated with higher Gleason score and more advanced disease. For example, among men aged 55-59, 65-69, 75-79, and 85-89 years, the percentage with Gleason 8-10 disease was 16.5%, 23.4%, 37.2%, and 59.9%, respectively (p<0.001); the percentage with at least high-risk disease was 29.3%, 39.1%, 60.4%, and 90.6%, respectively. Corresponding percentages for low-risk PCa were 24.0%, 17.9%, 10.2%, and 4.1% (p<0.001). The respective maximum ASIRs (per 100,000 men) for low-risk, favorable-intermediate-risk, unfavorable-intermediate-risk, high-risk, regional, and metastatic disease were: 157.1, 183.8, 194.8, 408.3, 172.3, and 330.0; incidence for low-risk and favorable-intermediate-risk PCa peaked before age 70, while more advanced categories peaked after 70. At age 75-79 years, the ASIR of high-risk disease was approximately 6 times greater than at 55-59 years.\n\nConclusionsRisk of clinically-significant, localized PCa increases with age. Healthy older men may be among those most likely to benefit from PCa screening.

epidemiology↗

Oxytocin effects on the resting-state mentalizing brain network

Oxytocin(OT) has effects in both human behavior and in the brain, which is not limited in the specific brain area but also with the potential effect on connectivity with other brain regions. Evidence indicate that the effects of OT on human behavior are multifaceted, such as trust behavior, decrease anxiety, empathy and bonding behavior. Since the vital role of mentalizing in understanding others, here we proposed and tested that whether OT has a general effect on theory of mind brain network which is associated to the effect of related social behavioral and personality traits. Used a randomized, double-blind placebo-controlled group design, we investigated the resting-state functional magnetic resonance imaging after intranasal OT or placebo. The functional connectivity (FC) maps with seed in left temporoparietal junction (lTPJ) and right TPJ showed that OT significantly increased connectivity between rTPJ and default attention network (DAN), while decreased the FC between lTPJ and medial prefrontal network (MPN). With implementing machine learning approach, we further reported satisfactory classification accuracy that Identified altered FCs of TPJ can classify OT and PL group. Moreover, individuals empathy trait can modulate the FC between left TPJ and right RECT, which was positively correlated with empathic concern in PL group whereas lTPJ-rRECT negatively correlated in OT group. These results demonstrate that OT has significant effect on FC with lTPJ and rTPJ, brain regions critical for mentalizing, and the empathy concern can modulate the FC. These findings add to our understanding of the neural mechanisms by which OT modulates social behaviors, especially in social interaction involving mentalizing.

neuroscience↗

SIP: An Interchangeable Pipeline for scRNA-seq Data Processing

Multiple steps of bioinformatics processing are needed to convert the raw scRNA-seq data to information that can be used in downstream analyses and in building cell atlases. Dozens of software packages have been developed and different labs tend to have different preferences on choices of the workflow. Such diversity can cause difficulties in future efforts of aggregating data from multiple labs, and also difficulties for new labs to start in this field. A few pipelines have been developed to help integrating multiple steps into a whole, but the fixed software architecture makes it hard for developers to add new features or exchange parts in the pipeline.\n\nWe presented SIP, a Single-cell Interchangeable Pipeline. It is a one-stop platform for the processing of scRNA-seq data from multiple platforms, and will also support for other types of data like scATAC-seq data. SIP utilizes container technology to solve the deployment dilemma when handling multiple packages and provides an easy-to-use interface for users to conduct the complicated multi-step process from raw data to final results with a single command. It also allows advanced users to assemble different versions of the pipeline by interchanging parts or adding new modules. SIP is available at https://github.com/XuegongLab/SIP under the GPL-3.0 license.

bioinformatics↗

Genome-wide identification of functional tRNA-derived fragments in Senescence-accelerated mouse prone 8 brain

tRNA-derived fragments (tRFs) have been linked previously to the development of various diseases, such as cancer and viral infection. However, tRFs seem also related to brain aging and related diseases, especially Alzheimer and Parkinson disease. RNA sequencing, a state-of-the-art technology, has allowed for investigation of tRFs in this field. In this study, we investigated the changes of tRFs in the brains of a senescence-accelerated mouse model, senescence-accelerated mouse prone 8 (SAMP8), that show age-dependent deficits in learning and memory; and a control model, senescence-accelerated mouse resistant 1 (SAMR1), with normal aging, both at 7 months of age. A total of 570 tRF transcripts were discovered. Among these transcripts, 8, including 3 upregulated and 5 downregulated transcripts, were differentially expressed in the SAMP8 mice. Then, we obtained 110 potential target genes in a miRNA-like pattern. GO survey implicated these target genes in the function of various aspects, e.g. postsynaptic density (GO: 0014069). Furthermore, we assessed in detail those tRFs whose miRNA-like pattern was most likely to affect the progression of either Alzheimer and Parkinson disease, such as AS-tDR-011775 acting on Mobp and Park2. In fact, we found the tRFs to be involved in the regulation of gene expression by means other than the miRNA-like pattern. Therefore, these 8 dysregulated tRFs may hold consequences far into the future and can be attractive biomarkers and valid targets. In brief, our study is the first to provide a comprehensive analysis on tRFs in SAMP8 mouse brain, and this breakthrough identified promising new targets for preventing the age-related changes of brain and the therapeutic intervention of Alzheimers and Parkinsons.

neuroscience↗

Activity-induced Ca2+ signaling in perisynaptic Schwann cells is mediated by P2Y1 receptors and regulates muscle fatigue

Perisynaptic glial cells respond to neural activity by increasing cytosolic levels of calcium, but the functional significance of this pathway is unclear. Terminal/persiynaptic Schwann cells (TPSCs) are a perisynaptic glial cell at the neuromuscular junction. Here, we provide genetic evidence that neural activity-induced intracellular calcium accumulation in neonatal TPSCs is mediated exclusively by P2Y1 receptors. In P2ry1 mutant mice lacking these responses, postsynaptic, rather than presynaptic, function was altered in response to nerve stimulation. This impairment was correlated with a greater susceptibility to activity-induced muscle fatigue. Interestingly, fatigue in P2ry1 mutants was exacerbated by exposure to high potassium to a greater degree than in control mice. High potassium itself increased cytosolic levels of calcium in TPSCs, a response which was also reduced P2ry1 mutants. These results suggest that activity-induced calcium responses in perisynaptic glia at the NMJ regulate postsynaptic function and muscle fatigue by influencing the levels of perisynaptic potassium.

neuroscience↗

Moderate Nucleotide Diversity In The Atlantic Herring Is Associated With A Low Mutation Rate

The Atlantic herring (Clupea harengus) is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate ({pi}=0.3%), only three-fold higher than in human. The expected nucleotide diversity for selectively neutral alleles is a function of population size and the mutation rate, and it is strongly affected by demographic history. Here, we present a pedigree-based estimation of the mutation rate in the Atlantic herring. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 1.7 x 10-9 per base per generation. There was no significant difference in the frequency of paternal and maternal mutations (8 and 7, respectively). Furthermore, we observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development when we do not expect a strong gender effect. The now estimated mutation rate - the lowest among vertebrates analyzed to date - partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size (>1011). But our analysis indicates that a species like the herring will never reach its expected nucleotide diversity for selectively neutral alleles primarily because of fluctuations in population size due to climate variation during the millions of years it takes to build up a high nucleotide diversity. In addition, background selection and selective sweeps lead to reductions in nucleotide diversity at linked neutral sites.

genomics↗