scholarly journals Gene expression analysis provides insight into the physiology of the important staple food crop cassava

2016 ◽  
Author(s):  
Mark C. Wilson ◽  
Andrew M. Mutka ◽  
Aaron W. Hummel ◽  
Jeffrey Berry ◽  
Raj Deepika Chauhan ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Tissue Expression ◽  
Soil Conditions ◽  
List Type ◽  
Target Tissue ◽  
Storage Roots ◽  
High Productivity ◽  
Friable Embryogenic Callus ◽  
Improvement Programs ◽  
Insight Into

SummaryCassava (Manihot esculenta) feeds approximately 800 million people worldwide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest deterioration and the roots contain low nutritional content.Here, we provide molecular identities for eleven cassava tissue types through RNA-sequencing and develop an open access, web-based interface for further interrogation of the data.Through this dataset, we report novel insight into the physiology of cassava and identify promoters able to drive specified tissue expression profiles. Specifically, we focus on identification of the transcriptional signatures that define the massive, underground storage roots used as a food source and the favored target tissue for transgene integration and genome editing, friable embryogenic callus (FEC).The information gained from this study is of value for both conventional and biotechnological improvement programs.

scholarly journals Type II Collagen-Conjugated Mesenchymal Stem Cells Micromass for Articular Tissue Targeting

Biomedicines ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 880
Author(s):  
Shamsul Bin Sulaiman ◽  
Shiplu Roy Chowdhury ◽  
Mohd Fauzi Bin Mh Busra ◽  
Rizal Bin Abdul Rani ◽  
Nor Hamdan Bin Mohamad Yahaya ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Targeted Delivery ◽  
Expression Profiles ◽  
3D Culture ◽  
Type Ii Collagen ◽  
Cartilage Defects ◽  
Target Tissue ◽  
Type Ii ◽  
Antibody Conjugation

The tissue engineering approach in osteoarthritic cell therapy often requires the delivery of a substantially high cell number due to the low engraftment efficiency as a result of low affinity binding of implanted cells to the targeted tissue. A modification towards the cell membrane that provides specific epitope for antibody binding to a target tissue may be a plausible solution to increase engraftment. In this study, we intercalated palmitated protein G (PPG) with mesenchymal stem cells (MSCs) and antibody, and evaluated their effects on the properties of MSCs either in monolayer state or in a 3D culture state (gelatin microsphere, GM). Bone marrow MSCs were intercalated with PPG (PPG-MSCs), followed by coating with type II collagen antibody (PPG-MSC-Ab). The effect of PPG and antibody conjugation on the MSC proliferation and multilineage differentiation capabilities both in monolayer and GM cultures was evaluated. PPG did not affect MSC proliferation and differentiation either in monolayer or 3D culture. The PPG-MSCs were successfully conjugated with the type II collagen antibody. Both PPG-MSCs with and without antibody conjugation did not alter MSC proliferation, stemness, and the collagen, aggrecan, and sGAG expression profiles. Assessment of the osteochondral defect explant revealed that the PPG-MSC-Ab micromass was able to attach within 48 h onto the osteochondral surface. Antibody-conjugated MSCs in GM culture is a potential method for targeted delivery of MSCs in future therapy of cartilage defects and osteoarthritis.

Fluorescent protein expression in temperature tolerant and susceptible reef-building corals

2021 ◽  
pp. 1-10
Author(s):  
Exequiel Gabriel S. Dizon ◽  
Jeric P. Da-Anoy ◽  
Melissa S. Roth ◽  
Cecilia Conaco
Keyword(s):  
Spectral Properties ◽  
Coral Species ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Antioxidant Properties ◽  
Variable Expression ◽  
Acropora Digitifera ◽  
Insight Into

Abstract Fluorescent proteins (FPs) are reported to play an important role as photoprotectants and antioxidants in corals subjected to stressful conditions. Identifying the various FP genes expressed and FP gene expression patterns under stress in diverse coral species can provide insight into FP function. In this study, we identified 16 putative FP homologues from the transcriptomes of corals with varying susceptibility to elevated temperature, including Acropora digitifera, Favites colemani, Montipora digitata and Seriatopora caliendrum. Each coral expressed a different complement of FP transcripts, which were predicted to have distinct spectral properties. The most diverse and abundant repertoire of FP transcripts, including at least 6 green FPs, were expressed in the temperature-tolerant coral, F. colemani. In comparison, the other corals expressed fewer FP types. Specific FP transcripts exhibited variable expression profiles in coral fragments subjected to 32 ± 1 °C (treatment) or 28 ± 1 °C (control) for up to 72 h, suggesting that distinct FPs may have different roles. Further studies on the expression of the proteins encoded by these FP transcripts, their fluorescence activity, tissue localization, and possible antioxidant properties, are needed to reveal their contribution to thermal stress tolerance in certain species of corals.

scholarly journals Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

2020 ◽  
Author(s):  
Feng Tian ◽  
Fan Zhou ◽  
Xiang Li ◽  
Wenping Ma ◽  
Honggui Wu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Human Cell ◽  
Expression Profiles ◽  
Single Cells ◽  
Cell Types ◽  
List Type ◽  
Cell Type ◽  
Genomic Architecture ◽  
Gene Modules

SummaryBy circumventing cellular heterogeneity, single cell omics have now been widely utilized for cell typing in human tissues, culminating with the undertaking of human cell atlas aimed at characterizing all human cell types. However, more important are the probing of gene regulatory networks, underlying chromatin architecture and critical transcription factors for each cell type. Here we report the Genomic Architecture of Cells in Tissues (GeACT), a comprehensive genomic data base that collectively address the above needs with the goal of understanding the functional genome in action. GeACT was made possible by our novel single-cell RNA-seq (MALBAC-DT) and ATAC-seq (METATAC) methods of high detectability and precision. We exemplified GeACT by first studying representative organs in human mid-gestation fetus. In particular, correlated gene modules (CGMs) are observed and found to be cell-type-dependent. We linked gene expression profiles to the underlying chromatin states, and found the key transcription factors for representative CGMs.HighlightsGenomic Architecture of Cells in Tissues (GeACT) data for human mid-gestation fetusDetermining correlated gene modules (CGMs) in different cell types by MALBAC-DTMeasuring chromatin open regions in single cells with high detectability by METATACIntegrating transcriptomics and chromatin accessibility to reveal key TFs for a CGM

scholarly journals Development and Validation of a Prognostic Nomogram Based on DNA Methylation-Driven Genes for Patients With Ovarian Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Min Zhou ◽  
Shasha Hong ◽  
Bingshu Li ◽  
Cheng Liu ◽  
Ming Hu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Dna Methylation ◽  
Mrna Expression ◽  
Risk Score ◽  
Cox Regression ◽  
Expression Profiles ◽  
Figo Stage ◽  
Prognostic Indicator ◽  
Tissue Expression ◽  
The Cancer Genome Atlas

Background: DNA methylation affects the development, progression, and prognosis of various cancers. This study aimed to identify DNA methylated-differentially expressed genes (DEGs) and develop a methylation-driven gene model to evaluate the prognosis of ovarian cancer (OC).Methods: DNA methylation and mRNA expression profiles of OC patients were downloaded from The Cancer Genome Atlas, Genotype-Tissue Expression, and Gene Expression Omnibus databases. We used the R package MethylMix to identify DNA methylation-regulated DEGs and built a prognostic signature using LASSO Cox regression. A quantitative nomogram was then drawn based on the risk score and clinicopathological features.Results: We identified 56 methylation-related DEGs and constructed a prognostic risk signature with four genes according to the LASSO Cox regression algorithm. A higher risk score not only predicted poor prognosis, but also was an independent poor prognostic indicator, which was validated by receiver operating characteristic (ROC) curves and the validation cohort. A nomogram consisting of the risk score, age, FIGO stage, and tumor status was generated to predict 3- and 5-year overall survival (OS) in the training cohort. The joint survival analysis of DNA methylation and mRNA expression demonstrated that the two genes may serve as independent prognostic biomarkers for OS in OC.Conclusion: The established qualitative risk score model was found to be robust for evaluating individualized prognosis of OC and in guiding therapy.

scholarly journals Clinical Characteristics and Outcomes of Diabetic COVID-19 patients in Kuwait

2020 ◽  
Author(s):  
Abdullah Alshukry ◽  
Mohammad Bu Abbas ◽  
Yaseen Ali ◽  
Barrak Alahmad ◽  
Abdullah A. Al-Shammari ◽  
...  
Keyword(s):  
Clinical Characteristics ◽  
Clinical Laboratory ◽  
Fasting Blood Glucose ◽  
List Type ◽  
Laboratory Findings ◽  
Reactive Protein ◽  
Patients With Diabetes ◽  
Laboratory Investigations ◽  
Insight Into ◽  
Variable Clinical Presentation

AbstractBackgroundCOVID-19 has a highly variable clinical presentation, ranging from asymptomatic to severe respiratory symptoms and death. Diabetes seems to be one of the main comorbidities contributing to a worse COVID-19 outcome.ObjectiveIn here we analyze the clinical characteristics and outcomes of diabetic COVID-19 patients.MethodsIn this single-center, retrospective study of 417 consecutive COVID-19 patients, we analyze and compare disease severity, outcome, associated complications, and clinical laboratory findings between diabetic and non-diabetic COVID-19 patients.ResultsCOVID-19 patients with diabetes had more severe outcomes and higher mortality than non-diabetic COVID-19 patients. Diabetic COVID-19 patients had significantly higher prevalence of comorbidities, such as hypertension. Laboratory investigations also highlighted notably higher levels of C-reactive protein in diabetic COVID019 patients and lower estimated glomerular filtration rate. They also showed a higher incidence of complications.ConclusionDiabetes could be a major contributor to worsening outcomes in COVID-19 patients. Understanding the pathophysiology underlining these findings could provide insight into better management and improved outcome of such cases.Highlights of the StudyA significantly higher proportion of Diabetic COVID-19 patients required admission to the ICU.Higher fasting blood glucose was associated with higher risk of COVID-19 associated mortality.Diabetic COVID-19 patients had significantly higher incidence of complications including sepsis, ARDS, cardiac failure and renal failure.

scholarly journals Asparagine accumulation in chicory storage roots is controlled by translocation and feedback regulation of asparagine biosynthesis in leaves

2020 ◽  
Author(s):  
Emanoella Soares ◽  
Leonard Shumbe ◽  
Nicholas Dauchot ◽  
Christine Notté ◽  
Claire Prouin ◽  
...  
Keyword(s):  
Public Health ◽  
High Temperature ◽  
Feedback Loop ◽  
Reducing Sugars ◽  
Feedback Regulation ◽  
Negative Feedback Loop ◽  
List Type ◽  
Storage Roots ◽  
Crop Species ◽  
Selection Of

SummaryThe presence of acrylamide (AA), a potentially carcinogenic and neurotoxic compound, in food has become a major concern for public health. AA in plant-derived food mainly arises from the reaction of the amino acid asparagine (Asn) and reducing sugars during processing of foodstuffs at high temperature.Using a selection of genotypes from the chicory germplasm we performed Asn measurements in storage roots and leaves to identify genotypes contrasting for Asn accumulation. We combined molecular analysis and grafting experiments to show that leaf to root translocation controls asparagine biosynthesis and accumulation in chicory storage roots.We could demonstrate that Asn accumulation in storage roots depends on Asn biosynthesis and transport from the leaf, and that a negative feedback loop by Asn on CiASN1 expression impacts Asn biosynthesis in leaves.Our results provide a new model for asparagine biosynthesis in root crop species and highlight the importance of characterizing and manipulating asparagine transport to reduce AA content in processed plant-based foodstuffs.

Reality in depression

2011 ◽  
Vol 26 (S2) ◽  
pp. 2065-2065
Author(s):  
J. Cutting
Keyword(s):  
External World ◽  
Depressive Illness ◽  
List Type ◽  
Type Number ◽  
Depressive Realism ◽  
Descriptive Account ◽  
Insight Into

The presentation will cover 3 aspects of reality: 1)Reality as resistance;2)Reality as actuality;3)Reality as correct insight.A brief consideration of the nature of these in normals will be given. A descriptive account of the psychopathology of each aspect will be then discussed, with particular emphasis on: a)undue resistance in depressive illness;b)qualitative differences in actuality, i.e experience of external world and body in schizophrenia;c)so-called “depressive realism” as a more correct insight into ones owen actions than is possessed in normals.

scholarly journals Breakdown of multiple sclerosis genetics to identify an integrated disease network and potential variant mechanisms

2019 ◽  
Vol 51 (11) ◽  
pp. 562-577
Author(s):  
C. Joy Shepard ◽  
Sara G. Cline ◽  
David Hinds ◽  
Seyedehameneh Jahanbakhsh ◽  
Jeremy W. Prokop
Keyword(s):  
Multiple Sclerosis ◽  
Immune Cell ◽  
Expression Profiles ◽  
Missense Variant ◽  
Cell Types ◽  
Tissue Expression ◽  
Specific Expression ◽  
Genomic Databases ◽  
Genetic Traits ◽  
Immune System Dysfunction

Genetics of multiple sclerosis (MS) are highly polygenic with few insights into mechanistic associations with pathology. In this study, we assessed MS genetics through linkage disequilibrium and missense variant interpretation to yield a MS gene network. This network of 96 genes was taken through pathway analysis, tissue expression profiles, single cell expression segregation, expression quantitative trait loci (eQTLs), genome annotations, transcription factor (TF) binding profiles, structural genome looping, and overlap with additional associated genetic traits. This work revealed immune system dysfunction, nerve cell myelination, energetic control, transcriptional regulation, and variants that overlap multiple autoimmune disorders. Tissue-specific expression and eQTLs of MS genes implicate multiple immune cell types including macrophages, neutrophils, and T cells, while the genes in neural cell types enrich for oligodendrocyte and myelin sheath biology. There are eQTLs in linkage with lead MS variants in 25 genes including the multitissue eQTL, rs9271640, for HLA-DRB1/ DRB5. Using multiple functional genomic databases, we identified noncoding variants that disrupt TF binding for GABPA, CTCF, EGR1, YY1, SPI1, CLOCK, ARNTL, BACH1, and GFI1. Overall, this paper suggests multiple genetic mechanisms for MS associated variants while highlighting the importance of a systems biology and network approach when elucidating intersections of the immune and nervous system.

scholarly journals Overlapping protein-coding genes in human genome and their coincidental expression in tissues

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao-Hsin Chen ◽  
Chao-Yu Pan ◽  
Wen-chang Lin
Keyword(s):  
Human Genome ◽  
Expression Profiles ◽  
Tissue Expression ◽  
Human Protein ◽  
Clear Understanding ◽  
Overlapping Genes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Overlapping Gene

Abstract The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5ʹ-tandem overlapping and 3ʹ-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.

The SLC9A-C Mammalian Na+/H+Exchanger Family: Molecules, Mechanisms, and Physiology

2019 ◽  
Vol 99 (4) ◽  
pp. 2015-2113 ◽  
Author(s):  
S. F. Pedersen ◽  
L. Counillon
Keyword(s):  
State Of The Art ◽  
Expression Profiles ◽  
Tissue Expression ◽  
Gene Organization ◽  
Core Knowledge ◽  
Current State ◽  
Organ Systems ◽  
Evolutionarily Conserved ◽  
Solute Carrier ◽  
Art Research

Na+/H+exchangers play pivotal roles in the control of cell and tissue pH by mediating the electroneutral exchange of Na+and H+across cellular membranes. They belong to an ancient family of highly evolutionarily conserved proteins, and they play essential physiological roles in all phyla. In this review, we focus on the mammalian Na+/H+exchangers (NHEs), the solute carrier (SLC) 9 family. This family of electroneutral transporters constitutes three branches: SLC9A, -B, and -C. Within these, each isoform exhibits distinct tissue expression profiles, regulation, and physiological roles. Some of these transporters are highly studied, with hundreds of original articles, and some are still only rudimentarily understood. In this review, we present and discuss the pioneering original work as well as the current state-of-the-art research on mammalian NHEs. We aim to provide the reader with a comprehensive view of core knowledge and recent insights into each family member, from gene organization over protein structure and regulation to physiological and pathophysiological roles. Particular attention is given to the integrated physiology of NHEs in the main organ systems. We provide several novel analyses and useful overviews, and we pinpoint main remaining enigmas, which we hope will inspire novel research on these highly versatile proteins.

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