Biology subjects

Yuan, M.

Publications and source records attributed to Yuan, M..

132 records · Page 8Linked to original sources

bioRxiv2019

Effects of active dry yeast on growth performance, rumen fermentation characteristics and slaughter performance in beef cattle

This study aimed to investigate the effects of active dry yeast (ADY) on rumen microbial composition and slaughter performance of beef cattle. Thirty-two finishing beef cattle (simmental crossbred cattle [male] x cattle-yaks [female]), with an average body weight of 110 {+/-} 12.85 kg, were randomly assigned to one of four treatments: the low plane of nutrition group (Control), low plane of nutrition group + ADY 2 g/head/d (ADY2), low plane of nutrition group + ADY 4 g/head/d (ADY4) and high plane of nutrition group (HPN). ADY supplementation increased average daily gain (P<0.001), and the carcass weight of ADY4 group had no significant difference with HPN group (P>0.05). The serum glutamic-pyruvic transaminase activity in control and ADY4 group was higher than HPN group (P=0.001). The neutral detergent fiber (P=0.022) and acid detergent fiber (P=0.043) digestibility in HPN group was greater than control, but no difference was obtained among ADY2, ADY4 and HPN group (P>0.05). The rumen ammonium nitrogen content in control was greater than ADY2 and ADY4 group (P=0.003), and no difference was obtained ADY2, ADY4 and HPN group (P>0.05). The propionic acid content in the rumen in ADY2, ADY4, and HPN group were greater than control group (P<0.001). The simpson (P=0.014) and shannon (P=0.045) indexes in control and HPN group were greater than ADY4 group. At the phylum level, the relative abundance of Firmicutes in the HPN group was higher than ADY4 group (P=0.015). At the genus level, HPN and ADY4 were clustered together, and the relative abundance of Ruminococcaceae UCG-002 in ADY4 group was higher than control and HPN group (P=0.004). In conclusion, supplementation ADY 4 g/head/d shift the rumen microbial composition of beef cattle fed low plane of nutrition to a more similar level with cattle fed with HPN diet, produced comparable carcass weight with HPN diet.

zoology↗

bioRxiv2019

uORFlight: a vehicle towards uORF-mediated translational regulation mechanisms in eukaryotes

Upstream open reading frames (uORFs) are prevalent in eukaryotic mRNAs. They act as a translational control element for precisely tuning the expression of the downstream major open reading frame (mORF) with essential cellular functionalities. uORF variation has been clearly associated with several human diseases. In contrast, natural uORF variants in plants have not ever been identified or linked with any phenotypic changes. The paucity of such evidence encouraged us to generate this database-uORFlight (http://uorflight.whu.edu.cn). It facilitates the exploration of uORF variation among different splicing models of Arabidopsis and rice genes. Most importantly, users can evaluate uORF frequency among different accessions at the population scale and find out the causal single nucleotide polymorphism (SNP) or insertion/deletion (INDEL) which can be associated with phenotypic variation through database mining or simple experiments. Such information will help to make hypotheses of uORF function in plant development or adaption to changing environments on the basis of the cognate mORF function. This database also curates plant uORF relevant literature into distinct groups. To be broadly interesting, our database expands uORF annotation into more species of fungi (Botrytis cinerea), plant (Brassica napus, Glycine max, Gossypium raimondii, Medicago truncatula, Solanum lycopersicum, Solanum tuberosum, Triticum aestivum and Zea mays), metazoan (Caenorhabditis elegans and Drosophila melanogaster) and vertebrate (Homo sapiens, Mus musculus and Danio rerio). Therefore, uORFlight will light up the runway toward how uORF genetic variation determines phenotypic diversity and advance our understanding of translational control mechanisms.

genomics↗

bioRxiv2019

Numerical simulation for behind armor blunt trauma of human torso under non-penetrating ballistic impact

A human torso finite element model with high bio-fidelity was developed to study the behind armor blunt trauma (BABT) of pistol cartridge on human torso with bulletproof composite structure (BCS) and the effect of buffer layer (expandable polyethylene, EPE) on BABT. The bulletproof structure was made of multilayered composite of aluminum alloy (AlSi10Mg) and thermoplastic polyurethanes (TPU), and the ANSYS/LS-DYNA software was used to simulate the blunt ballistic impact process of pistol cartridge on human torso. Results indicated that the BCS could resist the shooting speed of 515 m/s without being broken. During the process of pistol cartridge shooting the BCS, the energy of pistol cartridge was transmitted to the human organs through the BCS, thereby causing human injury. Moreover, the mechanical response parameters of various organs were determined by the distance between the human organs and the impact point. The sternal fracture and liver rupture were not produced based on the threshold stress of sternum and liver injury, no matter whether the buffer layer was added or not. According to the Axelsson injury model, a slight to moderate injury was created when there was no buffer layer, but the injury level was trace to slight caused by the buffer layer with thickness of 1.0 mm, and the buffer layer with thickness of 2.5 mm and 5.0 mm caused subtle BABT. It was concluded that the buffer layer could effectively reduce the BABT, and the reduction was related to the thickness of the buffer layer. This study reveals the mechanism of the BABT, which can provide a theoretical basis for the design of the bulletproof structure and the evaluation of structural bulletproof performance and protection performance.

bioengineering↗

bioRxiv2019

Computational comparison of developmental cell lineage trees by alignments

The developmental cell lineage tree, which records every cell division event and the terminal developmental state of each single cell, is one of the most important traits of multicellular organisms, as well as key to many significant unresolved questions in biology. Recent technological breakthroughs are paving the way for direct determination of cell lineage trees, yet a general framework for the computational analysis of lineage trees, in particular an algorithm to compare two lineage trees, is still lacking. Based on previous findings that the same developmental program can be invoked by different cells on the lineage tree to produce highly similar subtrees, we designed Developmental Cell Lineage Tree Alignment (DELTA), an algorithm that exhaustively searches for lineage trees with phenotypic resemblance in lineal organization of terminal cells, meanwhile resolving detailed correspondence between individual cells. Using simulated and nematode lineage trees, we demonstrated DELTAs capability of revealing similarities of developmental programs by lineal resemblances. Moreover, DELTA successfully identifies gene deletion-triggered homeotic cell fate transformations, reveals functional relationship between mutants by quantifying their lineal similarities, and finds the evolutionary correspondence between cell types defined non-uniformly for different species. DELTA establishes novel foundation for comparative study of lineage trees, much like sequence alignment algorithm for biological sequences, and along with the increase of lineage tree data, will likely bring unique insights for the myriads of important questions surrounding cell lineage trees.

bioinformatics↗

bioRxiv2018

The splicing regulator Prp31 prevents retinal degeneration in Drosophila by regulating Rhodopsin levels

Retinitis pigmentosa (RP) is a clinically heterogeneous disease affecting 1.6 million people worldwide. The second-largest group of genes causing autosomal dominant RP in human encodes regulators of the splicing machinery, but the molecular consequences that link defects in splicing factor genes to the aetiology of the disease remain to be elucidated. Mutations in PRPF31, one of the splicing factors, are linked to RP11. To get insight into the mechanisms by which mutations in this gene lead to retinal degeneration, we induced mutations in the Drosophila orthologue Prp31. Flies heterozygous mutant for Prp31 are viable and develop normal eyes and retina. However, photoreceptors degenerate under light stress, thus resembling the human disease phenotype. Prp31 mutant flies show a high degree of phenotypic variability, similar as reported for human RP11 patients. Degeneration is associated with increased accumulation of rhodopsin 1, both in the rhabdomere and in the cell body. In fact, reducing rhodopsin levels by raising animals in a carotenoid-free medium not only suppressed rhodopsin accumulation, but also retinal degeneration. In addition, our results underscore the relevance of eye color mutations on phenotypic traits, in particular whilst studying a complex process such as retinal degeneration.\n\nArticle SummaryRetinitis pigmentosa (RP) is a human disease affecting 1.6 million people worldwide. So far >50 genes have been identified that are causally related to RP. Mutations in the splicing factor PRPF31 are linked to RP11. We induced mutations in the Drosophila orthologue Prp31 and show that flies heterozygous for Prp31 undergo light-dependent retinal degeneration. Degeneration is associated with increased accumulation of the light-sensitive molecule, rhodopsin 1. In fact, reducing rhodopsin levels by dietary intervention suppressed retinal degeneration. We believe that this model will help to better understand the aetiology of the human disease.

genetics↗

bioRxiv2018

Yap regulates glucose utilization and sustains nucleotide synthesis to enable organ growth

The Hippo pathway and its nuclear effector Yap regulate organ size and cancer formation. While many modulators of Hippo activity have been identified, little is known about the Yap target genes that mediate these growth effects. Here, we show that yap-/- mutant zebrafish exhibit defects in hepatic progenitor potential and liver growth due to impaired glucose transport and nucleotide biosynthesis: transcriptomic and metabolomic analyses reveal that Yap regulates expression of glucose transporter glut1, causing decreased glucose uptake and use for nucleotide biosynthesis in yap-/- mutants, and impaired glucose tolerance in adults. Nucleotide supplementation improved Yap-deficiency phenotypes, indicating functional importance of glucose-fuelled nucleotide biosynthesis. Yap-regulated Glut1 expression and glucose uptake are conserved in mammals, suggesting that stimulation of anabolic glucose metabolism is an evolutionarily conserved mechanism by which the Hippo pathway controls organ growth. Together, our results reveal a central role for Hippo signalling in metabolic homeostasis.

developmental biology↗