Effects of high‑grain diet feeding on fatty acid profiles in milk,blood,muscle,and adipose tissue,and transcriptional expression of lipid‑related genes in muscle and adipose tissue of dairy cows

Background High-grain(HG)diets affect lipid metabolism in the liver and mammary tissue of dairy cows,but its effects on muscle and adipose tissue have not been wide evaluated.Thus,the aim of this study is to clarify this issue.Methods Twelve Holstein cows were randomly divided into two groups:conventional diet group(CON,n=6)and the HG diet group(n=6).On day 7 of week 4,rumen fluid was sampled to measure pH,milk was sampled to meas-ure components,and blood was sampled to measure biochemical parameters and fatty acid composition.After the experiment,cows were slaughtered to collect muscle and adipose tissue for fatty acid composition and transcriptome analysis.Results HG feeding decreased the ruminal pH,milk’s fat content and long-chain fatty acid proportion(P<0.05)and increased the proportion of short-and medium-chain fatty acids in the milk(P<0.05)as compared with CON diets.The concentrations of blood cholesterol,low-density lipoprotein,and polyunsaturated fatty acids in the HG cows were lower than those in CON cows(P<0.05).In muscle tissue,HG feeding tended to increase the triacylglycerol(TG)concentration(P<0.10).Transcriptome analysis revealed changes in the biosynthesis of the unsaturated fatty acids pathway,the regulation of lipolysis in the adipocytes pathway,and the PPAR signalling pathway.In adipose tissue,HG feeding increased the concentration of TG and decreased the concentration of C18:1 cis9(P<0.05).At the transcrip-tome level,the fatty acid biosynthesis pathway,linoleic acid metabolism pathway,and PPAR signalling pathway were activated.Conclusion HG feeding leads to subacute rumen acidosis and a decreased milk fat content.The fatty acid profiles in the milk and plasma of dairy cows were changed by HG feeding.In muscle and adipose tissue,HG feeding increased TG concentration and up-regulated the expression of genes related to adipogenesis,while down-regulated the expression of genes related to lipid transport.These results complement our knowledge of the fatty acid composi-tion of muscle and adipose tissue in dairy cows and expand our understanding of the mechanisms by which HG diets affect lipid metabolism in muscle and adipose tissue.

Identification of epididymis-specific transcripts in the mouse and rat by transcriptional profiling

As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77 transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction （RT-PCR） analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis. Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 （E3 epididymal protein） was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics （MRG） Database （http：//mrg. genetics.washington.edu/）. （Asian J Androl 2007July; 9： 522-527）

Transcriptomic and physiological analyses identifying Lanzhou lily(Lilium davidii var.unicolor)drought adaptation strategies

Drought stress is the main limiting plant growth factor in arid and semiarid regions.The Lanzhou lily(Lilium davidii var.unicolor)is the only sweet-tasting lily grown in these regions of China that offers highly edible,medicinal,health,and ornamental value.The Tresor lily is an ornamental flower known for its strong resistance.Plants were grown under three different drought intensity treatments,namely,being watered at intervals of 5,15,and 25 d(either throughout the study or during specific growth stages).We measured the biomass,leaf area,photosynthetic response,chlorophyll content(SPAD value),and osmoregulation of both the Lanzhou lily and the Tresor lily(Lilium‘Tresor’).Additionally,we employed RNA sequencing(RNA-Seq)and qRT-PCR to investigate transcriptomic changes of the Lanzhou lily in response to drought stress.Results showed that under drought stress,the decreasing rate in the Lanzhou lily bulb weight was lower than the corresponding Tresor lily bulb rate;the net photosynthetic rate,transpiration rate,and stomatal conductance of the Lanzhou lily were all higher compared to the Tresor lily;osmoregulation constituents,such as glucose,fructose,sucrose,trehalose,and soluble sugar,in the Lanzhou lily were comparatively higher;PYL,NCED,and ERS genes were significantly expressed in the Lanzhou lily.Under moderate drought,the biosynthesis of flavonoids,circadian rhythms,and the tryptophan metabolism pathway of the Lanzhou lily were all significant.Under severe drought stress,fatty acid elongation,photosynthetic antenna protein,plant hormone signal transduction,flavone and flavonol biosynthesis,and the carotenoid biosynthesis pathway were all significant.The Lanzhou lily adapted to drought stress by coordinating its organs and the unique role of its bulb,regulating photosynthesis,increasing osmolyte content,activating circadian rhythms,signal transduction,fatty acid elongation metabolism,and phenylalanine and flavonoid metabolic pathways,which may collectively be the main adaptation strategy and mechanisms used by the Lanzhou lily under drought stress.

Gene expression profile of Sox1,Sox2,p53,Bax and Nestin in neural stem cells and adult mouse brain tissues

Histone deacetylation is a key modulator involved in cell proliferation,apoptosis,and mRNA transcription.However,the effects of histone deacetylation on C17.2 neural stem cells(NSCs)remain unclear.Here,the histone deacetylase inhibitors nicotinamide and trichostatin A(TSA)were used to determine the role of histone deacetylation on gene transcription in NSCs.The results showed that the mRNA expression of p53,Sox1,Sox2,and Bax were significantly higher in E14.5 NSCs than in C17.2 NSCs.Nestin,a marker gene of neuronal differentiation,did not differ significantly between E14.5 NSCs and C17.2 NSCs.The transcription levels of p53 and Nestin were significantly higher in C17.2 NSCs than in differentiated brain tissues,and the expression of Bax,Sox1,and Sox2 was higher in the olfactory bulb than in other brain tissues.Nicotinamide and TSA treatment decreased the transcription of Sox2,p53,Nestin,and Bax in C17.2 NSCs,although the difference was statistically significant only for Sox2 and Nestin,Sox1 transcription was not detected.These results demonstrated that mRNA expression profiles differ between C17.2 NSCs,E14.5 NSCs,and adult mouse brain tissues,and HDAC inhibitors regulate gene expression by modulating histone acetylation.

Advances in single-cell sequencing:insights from organ transplantation

Single-cell RNA sequencing(scRNA-seq)is a comprehensive technical tool to analyze intracellular and intercellular interaction data by whole transcriptional profile analysis.Here,we describe the application in biomedical research,focusing on the immune system during organ transplantation and rejection.Unlike conventional transcriptome analysis,this method provides a full map of multiple cell populations in one specific tissue and presents a dynamic and transient unbiased method to explore the progression of allograft dysfunction,starting from the stress response to final graft failure.This promising sequencing technology remarkably improves individualized organ rejection treatment by identifying decisive cellular subgroups and cell-specific interactions.

Flor Revisited(Again):eQTL and Mutational Analysis of NB-LRR Mediated Immunity to Powdery Mildew in Barley

Genes encoding early signaling events in pathogen defense often are identified only by their phenotype. Such genes involved in barley-powdery mildew interactions include Mla, specifying race-specific resistance; Rarl （Required for Mla12-specified resistance1）, and Roml （Restoration of Mla-specified resistancel）. The HSP90-SGT1-RAR1 complex appears to function as chaperone in MLA-specified resistance, however, much remains to be discovered regarding the precise signaling underlying plant immunity. Genetic analyses of fast-neutron mutants derived from CI 16151 （Mla6） uncovered a novel locus, designated Rar3 （R_equired for Mla6-specified resitance3）. Rar3 segregates independent of Mla6 and Rarl, and rar3 mutants are susceptible to Blumeria graminis f. sp. hordei （Bgh） isolate 5874 （A VRar）, whereas, wild-type progenitor plants are resistant. Comparative expression analyses of the rar3 mutant vs. its wild-type progenitor were conducted via Barleyl GeneChip and GAIIx paired-end RNA-Seq. Whereas Rarl affects transcription of relatively few genes; Rar3 appears to influence thousands, notably in genes controlling ATP binding, catalytic activity, transcription, and phosphorylation; possibly membrane bound or in the nucleus, eQTL analysis of a segregating doubled haploid population identified over two-thousand genes as being regulated by Mla （q value/FDR=0.00001）, a subset of which are significant in Rar3 interactions. The intersection of datasets derived from mla-loss-of-function mutants, Mla-associated eQTL, and rar3-mediated transcriptome reprogramming are narrowing the focus on essential genes required for Mla-specified immunity.

Identification of tumorigenic risk genes in human placenta-derived mesenchymal stem cells treated with 3-methylcholanthrene

Mesenchymal stem cells(MSCs)capable of tumour topotaxis have been served as cellular vehicles to deliver anti-tumour agents.As cellular components of the tumour microenvironment,MSCs also affect tumour progression.However,the tumour transformation-related genes of MSCs remain unclear since either tumorigenic or tumour suppressor effects within these cells have been researched.Hence,we aimed to identify potential biomarkers indicative of tumorigenic risk by RNA-seq analysis of human placenta tissue-derived MSCs(hPTMSCs)exposed to the carcinogenic agent,3-methylcholanthrene(3-MC).Twenty-nine tumour transformation-related genes and three pluripotency-related genes were appraised as differentially expressed genes(DEGs)in hPTMSCs.Overexpression of sfrp1 led to reduced cell viability,migration,and colony formation in A549.In contrast,the overexpression of ptgs2 exerted the opposite effect.These results indicate that A549 cells with high ptgs2 expression but low sfrp1 expression may have a more potential tumorigenic capacity.Taken together,this study suggests that ptgs2 and sfrp1 may be tumorigenic risk genes.

Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F1 super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression （SAGE） revealed 1183 differentially expressed genes （DGs）, among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F1 hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F1 hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci （QTL）, a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice.

Sodium Stress in the Halophyte Thellungiella halophila and Transcriptional Changes in a thsos1-RNA Interference Line

The plasma membrane Na＋/H＋-antiporter salt overly sensitive1 （SOS1） from the halophytic Arabidopsis-relative Thellungiella halophila （ThSOS1） shows conserved sequence and domain structure with the orthologous genes from Arabidopsis thaliana and other plants. When expression of ThSOSt was reduced by RNA interference （RNAi）, pronounced characteristics of salt-sensitivity were observed. We were interested in monitoring altered transcriptional responses between Thellungiella wild type and thsost-4, a representative RNAi line with particular emphasis on root responses to salt stress at 350 mmol/L NaCI, a concentration that is only moderately stressful for mature wild type plants. Transcript profiling revealed several functional categories of genes that were differently affected in wild-type and RNAi plants. Down-regulation of SOS1 resulted in different gene expression even in the absence of stress. The pattern of gene induction in the RNAi plant under salt stress was similar to that of glycophytic Arabidopsis rather than that of wild type Thellungiella. The RNAi plants failed to down-regulate functions that are normally reduced in wild type Thellungiella upon stress and did not up-regulate functions that characterize the Thellungiella salt stress response. Metabolite changes observed in wild type Thellungiella after salt stress were less pronounced or absent in RNAi plants. Transcript and metabolite behavior suggested SOS1 functions including but also extending its established function as a sodium transporter. The down-regulation of ThSOS1 converted the halophyte Thellungiella into a salt-sensitive plant.

DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery

Transcriptional phenotypic drug discovery has achieved great success,and various compound perturbation-based data resources,such as connectivity map(CMap)and library of integrated network-based cellular signatures(LINCS),have been presented.Computational strategies fully mining these resources for phenotypic drug discovery have been proposed.Among them,the fundamental issue is to define the proper similarity between transcriptional profiles.Traditionally,such similarity has been defined in an unsupervised way.However,due to the high dimensionality and the existence of high noise in high-throughput data,similarity defined in the traditional way lacks robustness and has limited performance.To this end,we present Dr Sim,which is a learning-based framework that automatically infers similarity rather than defining it.We evaluated Dr Sim on publicly available in vitro and in vivo datasets in drug annotation and repositioning.The results indicated that Dr Sim outperforms the existing methods.In conclusion,by learning transcriptional similarity,Dr Sim facilitates the broad utility of high-throughput transcriptional perturbation data for phenotypic drug discovery.The source code and manual of Dr Sim are available at https://github.com/bm2-lab/Dr Sim/.

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction

Gene Ontology(GO)has been widely used to annotate functions of genes and gene products.Here,we proposed a new method,Triplet GO,to deduce GO terms of protein-coding and noncoding genes,through the integration of four complementary pipelines built on transcript expression profile,genetic sequence alignment,protein sequence alignment,and naīve probability.Triplet GO was tested on a large set of 5754 genes from 8 species(human,mouse,Arabidopsis,rat,fly,budding yeast,fission yeast,and nematoda)and 2433 proteins with available expression data from the third Critical Assessment of Protein Function Annotation challenge(CAFA3).Experimental results show that Triplet GO achieves function annotation accuracy significantly beyond the current state-of-the-art approaches.Detailed analyses show that the major advantage of Triplet GO lies in the coupling of a new triplet network-based profiling method with the feature space mapping technique,which can accurately recognize function patterns from transcript expression profiles.Meanwhile,the combination of multiple complementary models,especially those from transcript expression and protein-level alignments,improves the coverage and accuracy of the final GO annotation results.The standalone package and an online server of Triplet GO are freely available at https://zhanggroup.org/Triplet GO/.

Low Ca diet leads to increased Ca retention by changing the gut flora and ileal pH value in laying hens

Osteoporosis is a common degenerative metabolic bone disease in caged laying hens.Intensive egg production mobilizing large amounts of Ca from bone for eggshell formation,consequently leading to Ca deficiency,has been recognized as a critical factor causing osteoporosis in commercial laying hens.The aim of this study was to examine the effect of Ca deficiency on the function of the gut microbiotaebone axis and related egg production traits and bone health in laying hens.Twenty-four 48-week-old laying hens were fed a control diet(Control,3.72%)or a low Ca diet(LC,2.04%)for 60 d(n=12).Compared to the Control hens,the LC hens had higher levels of alkaline phosphatase and tartrate resistant acid phosphatase(P<0.05)with lower bone strength,eggshell thickness,and eggshell strength(P<0.05).In addition,the LC hens had higher plasma estradiol concentrations,while having lower concentrations of interleukin-1(IL-1)and IL-6.The LC hens also had a lower pH value in the ileum with an increased Ca retention.The principal co-ordinates analysis showed significantly separate cecal microbiota populations between the Control and LC hens.The Prevotellaceae_UCG-001,Subdoligranulum,Peptococcus,and Eubacterium_hallii_group(P<0.05)were higher,while the CHKC1001 and Sutterella(P<0.05)were lower at the genus level in the LC hens.In addition,Prevotellaceae_UCG-001,Subdoligranulum and Eubacter-ium_hallii_group had a negative correlation,while Sutterella was positively correlated with ileal pH values.The transcriptome analysis revealed that the low Ca diet caused 20 and 31 genes to be signifi-cantly up-and down-regulated,respectively.The gene expressions of cystic fibrosis transmembrane conductance regulator,solute carrier family 26 member 3 of the anion exchangers,and mitogen-activated protein kinase 12 of pro-inflammatory factors were lower in the LC birds,which was corre-lated with the lower ileal pH values.These results suggest that the hens with low Ca diet-induced osteoporosis have an increased intestinal Ca retention with a decreased ileal pH value,correlated with the changes in Prevotellaceae_UCG-001,Subdoligranulum,and Eubacterium_hallii_group of beneficial genera.The results provide insights for further understanding and preventing osteoporosis in laying hens.

DNA microarray technology and its application in fish biology and aquaculture

Fishery is an important industry in China as well as in the rest of the world,and it provides a human food resource containing high-quality protein.Best practice in aquaculture requires a full understanding of the genomic controls and transcriptional profiles of cultured fish species.Improvements in aquaculture can be made by regulation of the expression of functional genes.Microarray technology is a powerful tool for rapid screening of genes or transcriptional profiles in a particular fish or for a particular economic character;for example,genes that are related to growth and disease control in the fish.This review provides a brief introduction to microarray technology and its methods and applications,together with a discussion of the achievements in fish biology that have resulted from this technology.

Metabolomic Screening Applied to Rice FOX Arabidopsis Lines Leads to the Identification of a Gene-Changing Nitrogen Metabolism

Plant metabolomics developed as a powerful tool to examine gene functions and to gain deeper insight into the physiology of the plant cell. In this study, we screened Arabidopsis lines overexpressing rice full-length （FL） cDNAs （rice FOX Arabidopsis lines） using a gas chromatography-time-of-flight mass spectrometry （GC-TOF/MS）-based technique to identify rice genes that caused metabolic changes. This screening system allows fast and reliable identification of candi- date lines showing altered metabolite profiles. We performed metabolomic and transcriptomic analysis of a rice FOX Ara- bidopsis line that harbored the FL cDNA of the rice ortholog of the Lateral Organ Boundaries （LOB） Domain （LBD）/ Asymmetric Leaves2-1ike （ASL） gene of Arabidopsis, At-LBD37/ASL39. The investigated rice FOX Arabidopsis line showed prominent changes in the levels of metabolites related to nitrogen metabolism. The transcriptomic data as well as the results from the metabolite analysis of the Arabidopsis At-LBD37/ASL39-overexpressor plants were consistent with these findings. Furthermore, the metabolomic and transcriptomic analysis of the Os-LBD37/ASL39-overexpressing rice plants indicated that Os-LBD37/ASL39 is associated with processes related to nitrogen metabolism in rice. Thus, the combination of a metabolomics-based screening method and a gain-of-function approach is useful for rapid characterization of novel genes in both Arabidopsis and rice.

Developmental and Feedforward Control of the Expression of Folate Biosynthesis Genes in Tomato Fruit

Little is known about how plants regulate their folate content, including whether the expression of folate biosynthesis genes is orchestrated during development or modulated by folate levels. Nor is much known about how folate levels impact the expression of other genes. These points were addressed using wild-type tomato fruit and fruit engineered for high folate content. In wild-type fruit, the expression of genes specifying early steps in folate biosynthesis declined during development but that of other genes did not. In engineered fruit overexpressing foreign GTP cyclohy- drolase I and aminodeoxychorismate synthase genes, the expression of the respective endogenous genes did not change, but that of three downstream pathway genes--aminodeoxychorismate lyase, dihydroneopterin aldolase, and mitochondrial folylpolyglutamate synthase--respectively increased by up to 7.8-, 2.8-, and 1.7-fold, apparently in response to the build-up of specific folate pathway metabolites. These results indicate that, in fruit, certain folate pathway genes are developmentally regulated and that certain others are subject to feedforward control by pathway intermediates. Micro- array analysis showed that only 14 other transcripts （of 11 000 surveyed） increased in abundance by two-fold or more in high-folate fruit, demonstrating that the induction of folate pathway genes is relatively specific.

Novel methods for studying normal and disordered erythropoiesis

Erythropoiesis is a process during which multipotential hematopoietic stem cells proliferate, differentiate and eventually form mature erythrocytes. Interestingly, unlike most cell types, an important feature of erythropoiesis is that following each mitosis the daughter cells are morphologically and functionally different from the parent cell from which they are derived, demonstrating the need to study erythropoiesis in a stage-specific manner. This has been impossible until recently due to lack of methods for isolating erythroid cells at each distinct developmental stage. This review summarizes recent advances in the development of methods for isolating both murine and human erythroid cells and their applications. These methods provide powerful means for studying normal and impaired erythropoiesis associated with hematological disorders.