Characterization,Imprinting Status and Tissue Distribution of Porcine GTL2 Gene

The callipyge （CLPG） phenotype, exhibiting polar overdominance （POD）, is an inherited skeletal muscle hypertrophy described in sheep. The callipyge locus maps to the distal portion of ovine chromosome 18 within the DLKI-GTL2 region and corresponds to human chromosome 14 and mouse chromosome 12. The POD phenomenon is confirmed to the homologous region of swine chromosome 7. In order to clone and investigate the expression of porcine GTL2 gene, DNA and RNA samples from 60-day-old F1 animals, generated with reciprocal crosses between Large White and Meishan breeds and their parents, were used. The authors showed that porcine GTL2 acted as a uoncoding RNA. cDNA samples exhibited maternal expression of the gene in the heart, liver, spleen, lung, kidney, stomach, small intestine, skeletal muscle, and fat in pigs, and a unique tissue-specific expression different from that of humans and mice. These results indicated that the gene was conserved in the pig, human, mouse, and bovine. It will be of interest to further study the gene functions in muscle growth and fat deposition.

Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.

Tissue-specific trace elements concentration and human health risk assessment in three marine fish species from Visakhapatnam to Kakinada coasts

Purpose The current study was aimed to evaluate the bioaccumulation of elements(As,Cd,Cu,Fe,Mn,Se and Zn)in the gills,liver and muscle of three distinct marine fish species,namely Nemipterus japonicas,Upeneus vittatus and Pampus argenteus species were collected from Visakhapatnam to Kakinada coastal waters.Methods The fish tissues were analyzed for trace metals using energy-dispersive X-ray fluorescence(EDXRF).To ensure the quality control,reliability of the experimental validation,two certified reference materials(CRMs)procured from National Institute of Standards and Testing(NIST SRM 1577c-Bovine Liver)and European Commission-Joint Research Centre,Institute for Reference Materials and Measurements(ERMBB422-Fish muscle)were analyzed using EDXRF.Results The evaluated estimated daily intake(EDI)values for each metal are below the reference dose levels established by World Health Organisation(WHO).The target hazard quotient(THQ)values of both the locations of the present study are lower than one(<1)except for arsenic and the combined target hazard quotient(CTHQ)values are higher than one(>1)showing the presence of health risk.The cancer risk(CR)factor value for arsenic was below the acceptable lifetime carcinogenic risk(10^(–5)).The levels of heavy metals varied significantly among three fish species and organs.The mean concentrations of As,Cd,Cu,Fe,Mn,Se and Zn were slightly higher than the Ministry of Agriculture,Fisheries and Food(MAFF),Food and Agriculture Organization(FAO),Turkish food codex and Brazilian Legislation standard levels.The findings of this study revealed that muscles possessed the lowest concentrations mostly of all the metals when compared with liver and gills.Conclusion The study concluded that consumption of the muscle tissue may not pose severe health risk to human health but should be consumed moderately to prevent bioaccumulation of the metals especially As.

Decellularized Disc Hydrogels for hBMSCs tissue-specific differentiation and tissue regeneration

Tissue specificity,a key factor in the decellularized tissue matrix(DTM),has shown bioactive functionalities in tuning cell fate-e.g.,the differentiation of mesenchymal stem cells.Notably,cell fate is also determined by the living microenvironment,including material composition and spatial characteristics.Herein,two neighboring tissues within intervertebral discs,the nucleus pulposus(NP)and annulus fibrosus(AF),were carefully processed into DTM hydrogels(abbreviated DNP-G and DAF-G,respectively)to determine the tissue-specific effects on stem cell fate,such as specific components and different culturing methods,as well as in vivo regeneration.Distinct differences in their protein compositions were identified by proteomic analysis.Interestingly,the fate of human bone marrow mesenchymal stem cells(hBMSCs)also responds to both culturing methods and composition.Generally,hBMSCs cultured with DNP-G(3D)differentiated into NP-like cells,while hBMSCs cultured with DAF-G(2D)underwent AF-like differentiation,indicating a close correlation with the native microenvironments of NP and AF cells,respectively.Furthermore,we found that the integrin-mediated RhoA/LATS/YAP1 signaling pathway was activated in DAF-G(2D)-induced AF-specific differentiation.Additionally,the activation of YAP1 determined the tendency of NP-or AF-specific differentiation and played opposite regulatory effects.Finally,DNP-G and DAF-G specifically promoted tissue regeneration in NP degeneration and AF defect rat models,respectively.In conclusion,DNP-G and DAF-G can specifically determine the fate of stem cells through the integrin-mediated RhoA/LATS/YAP1 signaling pathway,and this tissue specificity is both compositional and spatial,supporting the utilization of tissue-specific DTM in advanced treatments of intervertebral disc degeneration.

Characterisation and Expression Analysis of Sox9 in the Multiocellated Racerunner, Eremias multiocellata

Sox9 is an important member of Sox family which is involved in a variety of developmental processes including sex determination and gonadal differentiation. The cDNA of Sox9 from multiocellated racerunner E. multiocellata was cloned using reverse transcription-polymerase chain reaction （RT-PCR） and rapid amplification of cDNA ends （RACE）. The sequence contains a 1497 bp open reading frame, which encodes a 498 amino acid protein with a predicted molecular weight of 55.45 kDa. EmSox9 displays high similarity to those of reptiles, and shows an overall amino acid identity of 〉82%. We also investigated the tissue-specific expression of EmSox9 mRNA by realtime quantitative PCR. Sox9 mRNA is present in brain, heart, liver, kidney, gonads and muscle tissues of adult E. multiocellata, with the highest expression in brain and testis. The results indicate that Sox9 may play important roles in some tissues during E. multiocellata neural and gonadal development.

Endophytic fungal diversity of endemic carnivorous plant Nepenthes khasiana in Meghalaya,India

The present investigation deals with the isolation of endophytic fungi from leaf,stem,root and pitcher cup tissue segments of the endemic carnivorous plant Nepenthes khaisana collected from its natural habitat for a period of one year at monthly intervals.Out of 576 tissue segments inoculated,a total of 39 fungal endophytes along with mycelia sterilia were isolated from the host plant.To assess the diversity of fungal endophytes,the colonization frequency(%CF)was first recorded using past software and MS excel.The fungal isolates were mainly composed of the phylum Ascomycota,followed by Zygomycota and Oomycota.The highest percentage colonization frequency on an average of three replicates were recorded in pitcher cup tissues followed by root,stem and least was recorded in leaf of the host plant.Among the isolates,Globisporangium irregulare(83.33%)showed high%CF in leaf,Juxtiphoma eupyrena(83.33%)reported to have maximum%CF in the stem,Talaromyces ruber(66.66%)was recorded high%CF in root and mycelia sterilia(white)were showed the highest%CF in the segments of leaf.The diversity index analyses of Shannon-Weiner,Simpson’s index,species richness and species evenness of diversity showed that leaf of N.Khasiana has the highest diversity than the other parts of the plant.So,with the help of the present finding,we conclude that the distribution of fungal endophytes and their%colonization frequencies vary within different tissues of the host plant and thus,this confirms tissue specificity nature of endophytic fungi.

Identification and expression of a novel human testis-specific gene by digital differential display

Background Evidence for the importance of genetic factors in male infertility is accumulating This study was designed to identify a novel testis specific gene related to spermatogenesis by a new strategy of digital differential display (DDD) Methods Based on the generation of expressed sequenced tags (ESTs), comparing the testis libraries with other tissue or cell line libraries by the DDD program, we identified a new contig of the ESTs which were derived from testis libraries and represented a novel gene Multi tissue RT PCR was performed to analyse its tissue specific expression The full length cDNA of the new gene was obtained using the BLAST program Sequencing was performed and the result was analysed Semi quantitative RT PCR and Northern blot analyseis of mRNA from differential normal tissues were performed to clarify the expression pattern of the new gene The sequence of the opening reading frame was integrated into the pQE 30 vector expressed in Escherichia coil strain M15(pREP4) With IPTG induction, the target protein was detected Results A full length cDNA sequence of the new gene named SPATA12 (GeneBank accession number AY221117) in human testis was identified SPATA12 was 2430 bp in length, located in chromosome 3p21 1 3p21 2 The sequence of the opening reading frame was 676-1248 bp, as was confirmed by RT PCR and sequencing The cDNA encodes a novel protein of 190 amino acids with a theoretical molecular weight of 20 417 8 and isoelectric point of 5 23 The sequence has no significant homology with any known protein in databases Semi quantitative RT PCR and Northern blot analyses of multiple tissues showed that SPATA12 was expressed significantly in normal human testis The expression recombinant of SPATA12 was constructed and a high level of the histidine tagged fusion protein was obtained Conclusions DDD can be confirmed by SPATA12 as a novel computational biology based approach for identification of the testis specific expression genes SPATA12 may function as a testicular germ cell associated gene that plays some roles in spermatogenesis Moreover, a great amount of SPATA12 protein could be obtained by the gene recombination technique, thus providing a reliable foundation for investigating the biological function of this new protein

Deletions are easy detectable in cochlear mitochondrial DNA of Cu/Zn superoxide dismutase gene knockout mice

Abstract Objectives To investigate the tissue specificity of reactive oxygen species (ROS) damage to mitochondrial DNA (mtDNA) and to determine whether cochlear mtDNA is a sensitive target for ROS damage. Methods 10 Cu/ZnSOD gene (Cu/Zn superoxide dismutase gene, Sod1) knockout mice and 16 wild-type mice were analyzed by nested polymerase chain reaction (PCR).Results Three deletions were detected in various tissues of Sod1 knockout mice. MtDNA3867bp and mtDNA3726bp deletions were the most visible, and mtDNA4236bp deletion was barely detected in these tissues. There were obvious differences in the ratio of deleted mtDNA/total mtDNA in different tissue. Deleted mtDNA was most abundant in the liver and kidney and less in cochlea, heart and brain. The lowest was in spleen and skin. The ratio in various tissues was 3-20 times in Sod1 knockout mice over wild-type mice. In cochlea, the ratio was about 15. Conclusions Without the protection of Sod1, ROS can lead to mtDNA deletions in various tissues with significant tissue specificity. Cochlear mtDNA is a sensitive target for ROS damage.

Commentary: PROTACs make undruggable targets druggable: Challenge and opportunity

Proteostasis(protein homeostasis) ensures precise adjustment of cellular demand to proteins in the stress conditions, which is essential in the maintenance of health environment inside cells and is indispensable for the life of organisms1.

PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders

De novo variants(DNVs)are one of the most significant contributors to severe earlyonset genetic disorders such as autism spectrum disorder,intellectual disability,and other developmental and neuropsychiatric(DNP)disorders.Presently,a plethora of DNVs have been identified using next-generation sequencing,and many efforts have been made to understand their impact at the gene level.However,there has been little exploration of the effects at the isoform level.The brain contains a high level of alternative splicing and regulation,and exhibits a more divergent splicing program than other tissues.Therefore,it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP disorders.To facilitate a better usage and improve the isoform-level interpretation of variants,we developed NeuroPsychiatric Mutation Knowledge Base(PsyMuKB).It contains a comprehensive,carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoformspecific mutations.PsyMuKB allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations,such as expression,transcript genomic structures,protein interactions,and the mutation sites mapped on the protein structures.It also provides an easy-to-use web interface,allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and isoforms.PsyMuKB thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related disorders.PsyMuKB is freely accessible at http://psymukb.net.

Epigenetic modulation of DNA methylation by nutrition and its mechanisms in animals

It is well known that phenotype of animals may be modified by the nutritional modulations through epigenetic mechanisms. As a key and central component of epigenetic network, DNA methylation is labile in response to nutritional influences. Alterations in DNA methylation profiles can lead to changes in gene expression, resulting in diverse phenotypes with the potential for decreased growth and health.Here, I reviewed the biological process of DNA methylation that results in the addition of methyl groups to DNA; the possible ways including methyl donors, DNA methyltransferase(DNMT) activity and other cofactors, the critical periods including prenatal, postnatal and dietary transition periods, and tissue specific of epigenetic modulation of DNA methylation by nutrition and its mechanisms in animals.

A novel cytochrome P450 gene from Catharanthus roseus cell line C_(20)hi:cloning and characterization of expression

An expressed sequence tag(EST)obtained from a subtractive-suppression hybridization cDNA library constructed using Catharanthus roseus cell line C_(20)hi and its parental cell line C_(20)D was used to clone a ful-length cytochrome P450 cDNA of cyp71d1.The encoded polypeptide contained 507 amino acids with 39-56% identity to other CYP7ID subfamily members at the.amino acid level.Expression characteristics of cyp71d1 were determined using semi-quantitative RT-PCR.The cyp71d1 transcript was expressed in all three cell lines with the highest level in the cell line C_(20)hi.In the mature C.roseus plant,the cyp71d1 cDNA was highly expressed in petals,roots and stems,but very weakly expressed in young leaves.Its transcription level increased with the development of flowers.2,4-D could down-regulate the transcription of cyp71d1,as did KT,but only to a minor degree.Neither light nor yeast elicitor could induce the transcription of cyp71d1.

Skin cell-derived extracellular vesicles:a promising therapeutic strategy for cutaneous injury

Wound healing refers to the healing process that occurs after the skin and other tissues are separated or damaged by internal or external forces.It is a complex combination of tissue regeneration,granulation tissue hyperplasia,and scar formation,and shows the synergistic effects of these processes.After skin damage,the environment around the wound and the cells at site of the damage respond immediately,and a range of cytokines and growth factors are released.In cutaneous injury,extracellular vesicle(EV)signaling plays a vital role in the healing process via paracrine and endocrine mechanisms.EVs are natural intercellular and inter-organ communication tools that carry various bioactive substances for message exchange.Stem cells and stem cell EVs facilitate tissue repair,showing promising potential in regenerative medicine.Nevertheless,EVs derived from specific skin tissue cells,such as epidermal cells,fibroblasts,vascular endothelial cells and inflammatory cells,also play important roles in cutaneous tissue repair.Here,we describe the characteristics of wound healing,concentrating on the production and functions of EVs derived from specific skin cells,and provide new ideas for wound therapy using EVs.