Systematic review of the old and new concepts in the epithelial-mesenchymal transition of colorectal cancer

Epithelial-to-mesenchymal transition(EMT) is defined as the transformation of an epithelial cell into a spindle cell with the loss of membrane E-cadherin expression and the gain of mesenchymal markers positivity. In the field of colorectal cancer(CRC), first data about EMT was published in 1995 and more than 400 papers had been written up to March 2016. Most of them are focused on the molecular pathways and experimentally-proved chemoresistance. In the present article, an update in the field of EMT in CRC based on the review of the literature and personal experience of the authors is presented. The information about the molecular and immunohistochemical(IHC) particularities of these processes and their possible role in the prognosis of CRC were also up-dated. This article focuses on the IHC quantification of the EMT, the immunoprofile of tumor buds and on the relation between EMT, angiogenesis, and stem cells activation. The EMT-induced chemoresistance vs chemotherapyor radiotherapy-induced EMT and cellular senescence was also synthesized for both conventional and targeted therapy. As a future perspective, the EMTangiogenesis-stemness link could be used as a possible valuable parameter for clinical follow-up and targeted therapeutic oncologic management of patients with CRC. Association of dexamethasone and angiotensin converting enzyme inhibitors combined with conventional chemotherapies could have clinical benefits in patients with CRC. The main conclusion is that, although many studies have been published, the EMT features are still incompletely elucidated and newly discovered EMT markers provide confusing data in understanding this complicated process, which might have significant clinical impact.

A study on the pathogen species and physiological races of tomato Fusarium wilt in Shanxi,China

In order to clarify the main pathogens of tomato Fusarium wilt in Shanxi Province, China, morphological identification, elongation factor 1 alpha （EF-1α） sequence analysis, specific primer amplification and pathogenicity tests were applied to study the isolates which were recovered from diseased plants collected from 17 different districts of Shanxi Province. The results were as follows： 1） Through morphological and molecular identification, the following 7 species of Fusarium were identified： F. oxysporum, F. solani, F. verticillioides, F. subglutinans, F. chlamydosporum, F. sporotrichioides, and F. semitectum; 2） 56 isolates of F. oxysporum were identified using specific primer amplification, among which, 29, 5 and 6 isolates were respectively identified as F. oxysporum f. sp. lycopersici physiological race 1, race 2, and race 3; 3） pathogenicity test indicated the significant pathogenicity of F. oxysporum, F. solani, F. verticillioides, and F. subglutinans to tomato plant. Therefore, among these 4 species confirmed as pathogenic to tomato in Shanxi, the highest isolation rate （53.3％） corresponded to F. oxysporum. Three physiological species, race 1, race 2, and race 3 of F. oxysporum f. sp. lycopersici are detected in Shanxi, among which race 1 is the most widespread pathogen and is also considered as the predominant race.

Integrated analysis of transcriptomic and proteomic data from tree peony(P.ostii)seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism

Tree peony(Paeonia section Moutan DC.)seeds are an excellent source of beneficial natural compounds that promote health,and they contain high levels of alpha-linolenic acid(ALA).In recent years,tree peony has been emerging as an oil crop.Therefore,combined analysis of the transcriptome and proteome of tree peony(P.ostii)seeds at 25,32,39,53,67,81,88,95,and 109 days after pollination(DAP)was conducted to better understand the transcriptional and translational regulation of seed development and oil biosynthesis.A total of 38,482 unigenes and 2841 proteins were identified.A total of 26,912 differentially expressed genes(DEGs)and 592 differentially expressed proteins(DEPs)were clustered into three groups corresponding to the rapid growth,seed inclusion enrichment and conversion,and late dehydration and mature stages of seed development.Fifteen lipid metabolism pathways were identified at both the transcriptome and proteome levels.Pathway enrichment analysis revealed that a period of rapid fatty acid biosynthesis occurred at 53–88 DAP.Furthermore,211 genes and 35 proteins associated with the fatty acid metabolism pathway,63 genes and 11 proteins associated with the biosynthesis of unsaturated fatty acids(UFAs),and 115 genes and 24 proteins associated with ALA metabolism were identified.Phylogenetic analysis revealed that 16 putative fatty acid desaturase(FAD)-encoding genes clustered into four FAD groups,eight of which exhibited the highest expression at 53 DAP,suggesting that they play an important role in ALA accumulation.RT-qPCR analysis indicated that the temporal expression patterns of oil biosynthesis genes were largely similar to the RNA-seq results.The expression patterns of fatty acid metabolism-and seed development-related proteins determined by MRM were also highly consistent with the results obtained in the proteomic analysis.Correlation analysis indicated significant differences in the number and abundance of DEGs and DEPs but a high level of consistency in expression patterns and metabolic pathways.The results of the present study represent the first combined transcriptomic and proteomic analysis of tree peony seeds and provide insight into tree peony seed development and oil accumulation.

Defining the‘HoneySweet’insertion event utilizing NextGen sequencing and a de novo genome assembly of plum(Prunus domestica)

HoneySweet’plum(Prunus domestica)is resistant to Plum pox potyvirus,through an RNAi-triggered mechanism.Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum.DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event.To confirm the transgene arrangement of the insertion event,‘HoneySweet’DNA was subjected to whole genome sequencing using Illumina short-read technology.Results indicated two different insertion events,one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side,flanked by plum DNA.To determine the locations of the two transgene insertions,a phased plum genome assembly was developed from the commercial plum‘Improved French’.A subset of the scaffolds(2447)that were>10 kb in length and representing,>95%of the genome were annotated and used for alignment against the‘HoneySweet’transgene reads.Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart,however we were unable to identify which scaffold(s)represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars.Regardless,there was no evidence of any gene(s)being interrupted as a result of the insertions.Furthermore,RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.

MicroRNA396-mediated alteration in plant development and salinity stress response in creeping bentgrass

The conserved microRNA396(miR396)is involved in plant growth,development,and abiotic stress response in multiple plant species through regulating its targets,Growth Regulating Factor(GRF)transcription factor genes.However,the role of miR396 has not yet been characterized in perennial monocot species.In addition,the molecular mechanism of miR396-mediated abiotic stress response remains unclear.To elucidate the role of miR396 in perennial monocot species,we generated transgenic creeping bentgrass(Agrostis stolonifera)overexpressing Osa-miR396c,a rice miRNA396 gene.Transgenic plants exhibited altered development,including less shoot and root biomass,shorter internodes,smaller leaf area,fewer leaf veins,and epidermis cells per unit area than those of WT controls.In addition,transgenics showed enhanced salt tolerance associated with improved water retention,increased chlorophyll content,cell membrane integrity,and Na^(+)exclusion during high salinity exposure.Four potential targets of miR396 were identified in creeping bentgrass and up-regulated in response to salt stress.RNA-seq analysis indicates that miR396-mediated salt stress tolerance requires the coordination of stress-related functional proteins(antioxidant enzymes and Na+/H+antiporter)and regulatory proteins(transcription factors and protein kinases).This study establishes a miR396-associated molecular pathway to connect the upstream regulatory and downstream functional elements,and provides insight into the miRNA-mediated regulatory networks.

MiR396 is involved in plant response to vernalization and flower development in Agrostis stolonifera

MicroRNA396(miR396)has been demonstrated to regulate flower development by targeting growth-regulating factors(GRFs)in annual species.However,its role in perennial grasses and its potential involvement in flowering time control remain unexplored.Here we report that overexpression of miR396 in a perennial species,creeping bentgrass(Agrostis stolonifera L.),alters flower development.Most significantly,transgenic(TG)plants bypass the vernalization requirement for flowering.Gene expression analysis reveals that miR396 is induced by long-day(LD)photoperiod and vernalization.Further study identifies VRN1,VRN2,and VRN3 homologs whose expression patterns in wild-type(WT)plants are similar to those observed in wheat and barley during transition from short-day(SD)to LD,and SD to cold conditions.However,compared to WT controls,TG plants overexpressing miR396 exhibit significantly enhanced VRN1 and VRN3 expression,but repressed VRN2 expression under SD to LD conditions without vernalization,which might be associated with modified expression of methyltransferase genes.Collectively,our results unveil a potentially novel mechanism by which miR396 suppresses the vernalization requirement for flowering which might be related to the epigenetic regulation of VRN genes and provide important new insight into critical roles of a miRNA in regulating vernalization-mediated transition from vegetative to reproductive growth in monocots.

Evolutionary Lineages and Functional Diversification of Plant Hexokinases

Sequencing data from 10 species show that a plant hexokinase （HXK） family contains 5-11 genes. Functionally, a given family can include metabolic catalysts, glucose signaling proteins, and non-catalytic, apparent regulatory enzyme homologs. This study has two goals. The first aim is to develop a predictive method to determine which HXK proteins within a species have which type of function. The second aim is to determine whether HXK-dependent glucose signaling proteins occur among more primitive plants, as well as among angiosperms. Using a molecular phylogeny ap- proach, combined with selective experimental testing, we found that non-catalytic HXK homologs might occur in all plants, including the relatively primitive Selaginella moellendorffi. We also found that different lineages of angiosperm HXKs have apparent conserved features for catalytic activity and for sub-cellular targeting. Most higher-plant HXKs are expressed predominantly at mitochondria, with HXKs of one lineage occurring in the plastid, and HXKs of one monocot lineage occurring in the cytosol. Using protoplast transient expression assays, we found that HXK glucose signaling pro- teins occur likely in all higher plants and in S. moellendorffi as well. Thus, the use of glucose by plant HXK isoforms in metabolism and/or as a regulatory metabolite occurs as widespread, conserved processes.

A new lignan from Gynostemma pentaphyllum

A new lignan ligballinone 1 with the know ligbaUinol 2 were isolated from plant Gynostemma pentaphyllum. Their structures were determined through spectroscopic methods including ESI-MS, 1D and 2D NMR （^1H, ^13C, DEPT, ^1H-^1H COSY, HMQC, HMBC） and X-ray diffraction experiment for 2.

Cotton Marker Database(CMD) as an Enhanced Resource for Cotton Research Community

Recently,thousands of SSR and now SNP markers have been discovered in cotton.Each of these markers provides a valuable molecular tool applying genetic and genomic research to cotton improvement.Cotton DNA marker database(CMD) continues to serve as a molecular marker resource for

OsSIDP366,a DUF1644 gene,positively regulates responses to drought and salt stresses in rice

Domain of unknown function 1644 （DUF1644） is a highly conserved amino acid sequence motif present only in plants. Analysis of expression data of the family of DUF1644- containing genes indicated that they may regulate responses to abiotic stress in rice. Here we present our discovery of the role of Os.SIDP366, a member of the DUF1644 gene family, in response to drought and salinity stresses in rice. Transgenic rice plants overexpressing OsSIDP366 showed enhanced drought and salinity tolerance and reduced water loss as compared to that in the control, whereas plants with downregulated OsSIDP366 expression levels using RNA interference （RNAi） were more sensitive to salinity and drought treatments. The sensitivity to abscisic acid （ABA） treatment was not changed in OsStDP366-overexpressing plants, and OsSIDP366 expression was not affected in ABA- deficient mutants. Subcellular localization analysis revealed that OsSIDP366 is presented in the cytoplasmic foci that colocalized with protein markers for both processing bodies （PBs） and stress granules （SGs） in rice protoplasts. Digital gene expression （DGE） profile analysis indicated that stress-related genes such as SNACl, OsHAK5 and PRs were upregulated in OsSIDP366-overexpressing plants. These results suggest that OsSIDP366 may function as a regulator of the PBs/SGs and positively regulate salt and drought resistance in rice.

A Genome-Wide Scenario of Terpene Pathways in Self-pollinated Artemisia annua

Scenarios of genes to metabolites in Artemisia annua remain uninvestigated. Here, we report the use of an integrated approach combining metabolomics, transcriptomics, and gene function analyses to charac- terize gene-to-terpene and terpene pathway scenarios in a self-pollinating variety of this species. Eightyeight metabolites including 22 sesquiterpenes （e.g., artemisinin）, 26 monoterpenes, two triterpenes, one diterpene and 38 other non-polar metabolites were identified from 14 tissues. These metabolites were differentially produced by leaves and flowers at lower to higher positions. Sequences from cDNA libraries of six tissues were assembled into 18 871 contigs and genome-wide gene expression profiles in tissues were strongly associated with developmental stages and spatial specificities. Sequence mining identified 47 genes that mapped to the artemisinin, non-amorphadiene sesquiterpene, monoterpene, triterpene, 2-C- methyl-D-erythritol 4-phosphate and mevalonate pathways. Pearson correlation analysis resulted in network integration that characterized significant correlations of gene-to-gene expression patterns and gene expression-to-metabolite levels in six tissues simultaneously. More importantly, manipulations of amorpha-4,11-diene synthase gene expression not only affected the activity of this pathway toward artemisinin, artemisinic acid, and arteannuin b but also altered non-amorphadiene sesquiterpene and genome-wide volatile profiles. Such gene-to-terpene landscapes associated with different tissues are fundamental to the metabolic engineering of artemisinin.

Genomic data mining for functional annotation of human long noncoding RNAs

Life may have begun in an RNA world,which is supported by increasing evidence of the vital role that RNAs perform in biological systems.In the human genome,most genes actually do not encode proteins;they are noncoding RNA genes.The largest class of noncoding genes is known as long noncoding RNAs(lncRNAs),which are transcripts greater in length than 200 nucleotides,but with no protein-coding capacity.While some lncRNAs have been demonstrated to be key regulators of gene expression and 3D genome organization,most lncRNAs are still uncharacterized.We thus propose several data mining and machine learning approaches for the functional annotation of human lncRNAs by leveraging the vast amount of data from genetic and genomic studies.Recent results from our studies and those of other groups indicate that genomic data mining can give insights into lncRNA functions and provide valuable information for experimental studies of candidate lncRNAs associated with human disease.

Human Genetic Variants Associated with COVID-19 Severity are Enriched in Immune and Epithelium Regulatory Networks

Human genetic variants can influence the severity of symptoms infected with SARS-COV-2.Several genome-wide asso-ciation studies have identified human genomic risk single nucleotide polymorphisms(SNPs)associated with coronavirus disease 2019(COVID-19)severity.However,the causal tissues or cell types underlying COVID-19 severity are uncertain.In addition,candidate genes associated with these risk SNPs were investigated based on genomic proximity instead of their functional cellular contexts.Here,we compiled regulatory networks of 77 human contexts and revealed those risk SNPs’enriched cellular contexts and associated risk SNPs with transcription factors,regulatory elements,and target genes.Twenty-one human contexts were identified and grouped into two categories:immune cells and epithelium cells.We further aggregated the regulatory networks of immune cells and epithelium cells.These two aggregated regulatory networks were investigated to reveal their association with risk SNPs’regulation.Two genomic clusters,the chemokine receptors cluster and the oligoadenylate synthetase(OAS)cluster,showed the strongest association with COVID-19 severity,and they had different regulatory programs in immune and epithelium contexts.Our findings were supported by analysis of both SNP array and whole genome sequencing-based genome wide association study(GWAS)summary statistics.

Cold adaptation does not alter ATP homeostasis during cold exposure in Drosophila melanogaster

In insects and other ectotherms,cold temperatures cause a coma resulting from loss of neuromuscular function,during which ionic and metabolic homeostasis are progressively lost.Cold adaptation improves homeostasis during cold exposure,but the ultimate targets of selection are still an open question.Cold acclimation and adaptation remodels mitochondrial metabolism in insects,suggesting that aerobic energy production during cold exposure could be a target of selection.Here,we test the hypothesis that cold adaptation improves the ability to maintain rates of aerobic energy production during cold exposure by using^(31)P NMR on live flies.Using lines of Drosophila melanogaster artificially selected for fast and slow recovery from a cold coma,we show that cold exposure does not lower ATP levels and that cold adaptation does not alter aerobic ATP production during cold exposure.Cold-hardy and cold-susceptible lines both experienced a brief transition to anaerobic metabolism during cooling,but this was rapidly reversed during cold exposure,suggesting that oxidative phosphorylation was sufficient to meet energy demands below the critical thermal minimum,even in cold-susceptible flies.We thus reject the hypothesis that performance under mild low temperatures is set by aerobic ATP supply limitations in D.melanogaster,excluding oxygen and capacity limitation as a weak link in energy supply.This work suggests that the modulations to mitochondrial metabolism resulting from cold acclimation or adaptation may arise from selection on a biosynthetic product(s)of those pathways rather than selection on ATP supply during cold exposure.