Transcriptome Profiling and Analysis during Cotton Fiber Cell Development

In this project,we aim to elucidate the molecular mechanism controlling initiation and elongation of tetraploid Gossypium hirsutum fiber cells by setting up a high throughput custom-designed

An integrative approach of digital image analysis and transcriptome profiling to explore potential predictive biomarkers for TGFβblockade therapy

Increasing evidence suggests that the presence and spatial localization and distribution pattern of tumor infiltrating lymphocytes(TILs)is associate with response to immunotherapies.Recent studies have identified TGFβactivity and signaling as a determinant of T cell exclusion in the tumor microenvironment and poor response to PD-1/PD-L1 blockade.Here we coupled the artificial intelligence(AI)-powered digital image analysis and gene expression profiling as an integrative approach to quantify distribution of TILs and characterize the associated TGFβpathway activity.Analysis of T cell spatial distribution in the solid tumor biopsies revealed substantial differences in the distribution patterns.The digital image analysis approach achieves 74%concordance with the pathologist assessment for tumor-immune phenotypes.The transcriptomic profiling suggests that the TIL score was negatively correlated with TGFβpathway activation,together with elevated TGFβsignaling activity observed in excluded and desert tumor phenotypes.The present results demonstrate that the automated digital pathology algorithm for quantitative analysis of CD8 immunohistochemistry image can successfully assign the tumor into one of three infiltration phenotypes:immune desert,immune excluded or immune inflamed.The association between“cold”tumor-immune phenotypes and TGFβsignature further demonstrates their potential as predictive biomarkers to identify appropriate patients that may benefit from TGFβblockade.

Transcriptome and metabolome profiling of unheading in F1 hybrid rice

Heading date is a crucial agronomic trait.However,rice usually delays heading due to the photoperiod,temperature,hormones or age.The present research was conducted to analyze the mechanism cotrlling heading date in F,hybrid rice.We constructed two test-crossing populations using two introgression lines(ILs),P20 and P21 coming from SH527/FH838 as the male parent,respectively,and male sterile line Jin23A as the female parent.Meanwhile,the F,hybrids of H20,obtained by mating P20 with Jin23A and having no heading,and H21,from the crossing between P21 and Jin23A having normal heading,were both observed under long days.Here,we analyzed the photoperiodic response of F,hybrids by transcriptome and metabolome profiling.The greater differences displayed in the transcriptome and the metabolome were caused by photoperiod(exogenous)instead of genes(endogenous).The coping mechanism resulted from long days(LD)in H20,leading to differences in the circadian rhythm and glutathione metabolism relative to other samples.The circadian oscillator and GSH/GSSG cycle typically regulate ROS homeostasis,and both of them are responsible for modulating ROS in H20 under LD condition.Both circadian rhythm genes and the reported genes related to heading date function via the DHD1/OsMFT1-Ehd1-RFT1-OsMADS14/OsMADS18 pathway and the glutathione metabolism pathway by regulating oxidative reduction processes.Both pathways are involved in the heading process and they interacted through the oxidative reduction process which was induced by photoperiod regulation,and all of them collectively modulated the heading process.The results of this study will be helpful for unraveling the mechanism of F,hybrid responses to unheading under LD condition.

Effects of lactic acid bacteria-fermented formula milk supplementation on ileal microbiota,transcriptomic profile,and mucosal immunity in weaned piglets

Background:Lactic acid bacteria(LAB)participating in milk fermentation naturally release and enrich the fermented dairy product with a broad range of bioactive metabolites,which has numerous roles in the intestinal health-promot-ing of the consumer.However,information is lacking regarding the application prospect of LAB fermented milk in the animal industry.This study investigated the effects of lactic acid bacteria-fermented formula milk(LFM)on the growth performance,intestinal immunity,microbiota composition,and transcriptomic responses in weaned piglets.A total of 24 male weaned piglets were randomly divided into the control(CON)and LFM groups.Each group consisted of 6 replicates(cages)with 2 piglets per cage.Each piglet in the LFM group were supplemented with 80 mL LFM three times a day,while the CON group was treated with the same amount of drinking water.Results:LFM significantly increased the average daily gain of piglets over the entire 14 d(P<0.01)and the average daily feed intake from 7 to 14 d(P<0.05).Compared to the CON group,ileal goblet cell count,villus-crypt ratio,sIgA,and lactate concentrations in the LFM group were significantly increased(P<0.05).Transcriptomic analysis of ileal mucosa identified 487 differentially expressed genes(DEGs)between two groups.Especially,DEGs involved in the intestinal immune network for IgA production pathways,such as polymeric immunoglobulin receptor(PIGR),were significantly up-regulated(P<0.01)by LFM supplementation.Moreover,trefoil factor 2(TFF2)in the LFM group,one of the DEGs involved in the secretory function of goblet cells,was also significantly up-regulated(P<0.01).Sequenc-ing of the 16S rRNA gene of microbiota demonstrated that LFM led to selective enrichment of lactate-producing and short-chain fatty acid(SCFA)-producing bacteria in the ileum,such as an increase in the relative abundance of Entero-coccus(P=0.09)and Acetitomaculum(P<0.05).Conclusions:LFM can improve intestinal health and immune tolerance,thus enhancing the growth performance of weaned piglets.The changes in microbiota and metabolites induced by LFM might mediate the regulation of the secretory function of goblet cells.

Obesity,metabolic health and omics:Current status and future directions

The growing obesity epidemic is becoming a major public health concern,and the associated costs represent a considerable burden on societies.Among the most common complications of severe obesity are the development of hypertension,dyslipidemia,type 2 diabetes,cardiovascular disease,and various types of cancer.Interestingly,some obese individuals have a favorable metabolic profile and appear to be somehow protected from the detrimental effects of excessive adipose tissue accumulation.These individuals remain normoglycemic,insulin sensitive,and hypotensive with proper blood lipid levels,despite their high body mass index and/or waist circumference.Multiple independent observations have led to the concept of the metabolically healthy obese(MHO) phenotype,yet no consensus has been reached to date regarding a universal definition or the main mechanism behind this phenomenon.Recent technological advances and the use of high-throughput analysis techniques have revolutionized different areas of biomedical research.A multi-omics approach,which is used to investigate changes at different molecular levels in an organism or tissue,may provide valuable insights into the interplay between the molecules or pathways and the roles of different factors involved in the mechanisms underlying metabolic health deterioration.The aim of this review is to present the current status regarding the use of omics technologies to investigate the MHO phenotype,as well as the results of targeted analyses conducted in MHO individuals.

Combined intestinal microbiota and transcriptomic analysis to investigate the effect of different stocking densities on the ability of Pacific white shrimp(Litopenaeus vannamei)to utilize Chlorella sorokiniana

Aiming to investigate the impact of different stocking densities on the ability of Pacific white shrimp(Litopenaeus vannamei)to utilize Chlorella sorokiniana(CHL),a 3×2 factorial design stocking experiment was used in this study.Specifically,shrimp was fed with two dietary protein sources(fishmeal[FM]and CHL)at low(LSD;100 per m^(3)),medium(MSD;200 per m^(3))and high(HSD;300 per m^(3))stocking densities for 8 weeks.The growth performance and resistance to Vibrio parahaemolyticus(1.0×10^(7) CFU/mL)of shrimp decreased with the increase of stocking density,but dietary CHL improved this result.Differences between the CHL and FM groups for V.parahaemolyticus resistance were significant only under high-density conditions(P<0.05).Significant interactions between stocking density and protein source were found on the activities of catalase(CAT),superoxide dismutase(SOD)and phenol oxidase(PO),and the contents of malondialdehyde(MDA)in the hepatopancreas and the activities of intestinal amylase,most of which were significantly different between CHL and FM groups only at high stocking density(P<0.05).Analysis of 16S rDNA sequencing showed that dietary CHL increased the alpha diversity of intestinal microbiota,inhibited the colonization of pathogenic bacteria and enhanced the abundance of beneficial bacteria.Transcriptomic results showed that at high stocking densities,differentially expressed genes(DEGs)in the FM vs CHL group were mostly upregulated and primarily enriched in immune and metabolic related pathways including Toll,immune deficiency(Imd)and glycolysis–gluconeogenesis pathways.Pearson correlation analysis revealed significant correlation between the top ten intestinal bacteria at the genus level and markedly enriched DEGs,also more were detected under high density situations.In conclusion,CHL has great potential as a novel protein source in the intensive farming of shrimp.

Transcriptome profile of human neuroblastoma cells in the hypomagnetic field

Research has shown that the hypomagnetic field(HMF)can affect embryo development,cell proliferation,learning and memory,and in vitro tubulin assembly.In the present study,we aimed to elucidate the molecular mechanism by which the HMF exerts its effect,by comparing the transcriptome profiles of human neuroblastoma cells exposed to either the HMF or the geomagnetic field.A total of 2464 differentially expressed genes(DEGs)were identified,216 of which were up-regulated and2248 of which were down-regulated after exposure to the HMF.These DEGs were found to be significantly clustered into several key processes,namely macromolecule localization,protein transport,RNA processing,and brain function.Seventeen DEGs were verified by real-time quantitative PCR,and the expression levels of nine of these DEGs were measured every 6 h.Most notably,MAPK1 and CRY2,showed significant up-and down-regulation,respectively,during the first 6 h of HMF exposure,which suggests involvement of the MAPK pathway and cryptochrome in the early bio-HMF response.Our results provide insights into the molecular mechanisms underlying the observed biological effects of the HMF.

Transcriptome sequencing and annotation of the halophytic microalga Dunaliella salina

The unicellular green alga Dunaliella salina is well adapted to salt stress and contains compounds（including β-carotene and vitamins） with potential commercial value.A large transcriptome database of D.salina during the adjustment, exponential and stationary growth phases was generated using a high throughput sequencing platform.We characterized the metabolic processes in D.salina with a focus on valuable metabolites, with the aim of manipulating D.salina to achieve greater economic value in large-scale production through a bioengineering strategy.Gene expression profiles under salt stress verified using quantitative polymerase chain reaction（qPCR） implied that salt can regulate the expression of key genes.This study generated a substantial fraction of D.salina transcriptional sequences for the entire growth cycle, providing a basis for the discovery of novel genes.This first full-scale transcriptome study of D.salina establishes a foundation for further comparative genomic studies.

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN FRESH SHOOTS OF TEA(CAMELLIA SINENSIS)OVER THREE SEASONS

Metabolites,especially secondary metabolites,are very important in the adaption of tea plants and the quality of tea products.Here,we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level.The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring,summer,and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry.We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis.Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation.Flavonoids,amino acids,organic acids and alkaloids were the predominant metabolites.Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring.The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

Enhanced delivery of a low dose of aducanumab via FUS in 5×FAD mice,an AD model

Background:Aducanumab(Adu),which is a human IgG1 monoclonal antibody that targets oligomer and fibril forms of beta-amyloid,has been reported to reduce amyloid pathology and improve impaired cognition after administration of a high dose(10 mg/kg)of the drug in Alzheimer’s disease(AD)clinical trials.The purpose of this study was to investigate the effects of a lower dose of Adu(3 mg/kg)with enhanced delivery via focused ultrasound(FUS)in an AD mouse model.Methods:The FUS with microbubbles opened the blood-brain barrier(BBB)of the hippocampus for the delivery of Adu.The combined therapy of FUS and Adu was performed three times in total and each treatment was performed biweekly.Y-maze test,Brdu labeling,and immunohistochemical experimental methods were employed in this study.In addition,RNA sequencing and ingenuity pathway analysis were employed to investigate gene expression profiles in the hippocampi of experimental animals.Results:The FUS-mediated BBB opening markedly increased the delivery of Adu into the brain by approximately 8.1 times in the brains.The combined treatment induced significantly less cognitive decline and decreased the level of amyloid plaques in the hippocampi of the 5×FAD mice compared with Adu or FUS alone.Combined treatment with FUS and Adu activated phagocytic microglia and increased the number of astrocytes associated with amyloid plaques in the hippocampi of 5×FAD mice.Furthermore,RNA sequencing identified that 4 enriched canonical pathways including phagosome formation,neuroinflammation signaling,CREB signaling and reelin signaling were altered in the hippocami of 5×FAD mice receiving the combined treatment.Conclusion:In conclusion,the enhanced delivery of a low dose of Adu(3 mg/kg)via FUS decreases amyloid deposits and attenuates cognitive function deficits.FUS-mediated BBB opening increases adult hippocampal neurogenesis as well as drug delivery.We present an AD treatment strategy through the synergistic effect of the combined therapy of FUS and Adu.