scholarly journals Comparative Transcriptomic Signature of the Simulated Microgravity Response in Caenorhabditis elegans

2019 ◽  
Author(s):  
İrem Çelen ◽  
Aroshan Jayasinghe ◽  
Jung H. Doh ◽  
Chandran R. Sabanayagam
Keyword(s):  
Caenorhabditis Elegans ◽  
Simulated Microgravity ◽  
Space Station ◽  
Integrative Approach ◽  
Biological Processes ◽  
Rna Seq ◽  
Transcriptomic Response ◽  
Transcriptomic Signature ◽  
Ground Conditions ◽  
The Impact

AbstractBackgroundGiven the growing interest in human exploration of space, it is crucial to identify the effect of space conditions on biological processes. The International Space Station (ISS) greatly helps researchers determine these effects. However, the impact of the ISS-introduced potential confounders (e.g., the combination of radiation and microgravity exposures) on the biological processes are often neglected, and separate investigations are needed to uncover the impact of individual conditions.ResultsHere, we analyze the transcriptomic response of Caenorhabditis elegans to simulated microgravity and observe the maintained transcriptomic response after return to ground conditions for four, eight, and twelve days. Through the integration of our data with those in NASA GeneLab, we identify the gravitome, which we define as microgravity-responsive transcriptomic signatures. We show that 75% of the simulated microgravity-induced changes on gene expression persist after return to ground conditions for four days while most of these changes are reverted after twelve days return to ground conditions. Our results from integrative RNA-seq and mass spectrometry analyses suggest that simulated microgravity affects longevity regulating insulin/IGF-1 and sphingolipid signaling pathways.ConclusionsOur results address the sole impact of simulated microgravity on transcriptome by controlling for the other space-introduced conditions and utilizing RNA-seq. Using an integrative approach, we identify a conserved transcriptomic signature to microgravity and its sustained impact after return to the ground. Moreover, we present the effect of simulated microgravity on distinct ceramide profiles. Overall, this work can provide insights into the sole effect of microgravity on biological systems.

scholarly journals Spaceflight Induces Novel Regulatory Responses in Arabidopsis Seedling as Revealed by Combined Proteomic and Transcriptomic Analyses

2020 ◽  
Author(s):  
Colin Peter Singer Kruse ◽  
Alexander D Meyers ◽  
Proma Basu ◽  
Sarahann Hutchinson ◽  
Darron R Luesse ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Membrane Proteins ◽  
Plant Growth ◽  
Gene Transcription ◽  
Space Station ◽  
Growth Efficiency ◽  
Rna Seq ◽  
Plastid Gene ◽  
The Impact

Abstract Background: Understanding of gravity sensing and response is critical to long-term human habitation in space and can provide new advantages for terrestrial agriculture. To this end, the altered gene expression profile induced by microgravity has been repeatedly queried by microarray and RNA-seq experiments to understand gravitropism. However, the quantification of altered protein abundance in space has been minimally investigated. Results: Proteomic (iTRAQ-labelled LC-MS/MS) and transcriptomic (RNA-seq) analyses simultaneously quantified protein and transcript differential expression of three-day old, etiolated Arabidopsis thaliana seedlings grown aboard the International Space Station along with their ground control counterparts. Protein extracts were fractionated to isolate soluble and membrane proteins and analyzed to detect differentially phosphorylated peptides. In total, 968 RNAs, 107 soluble proteins, and 103 membrane proteins were identified as differentially expressed. In addition, the proteomic analyses identified 16 differential phosphorylation events. Proteomic data delivered novel insights and simultaneously provided new context to previously made observations of gene expression in microgravity. There is a sweeping shift in post-transcriptional mechanisms of gene regulation including RNA-decapping protein DCP5, the splicing factors GRP7 and GRP8, and AGO4,. These data also indicate AHA2 and FERONIA as well as CESA1 and SHOU4 as central to the cell wall adaptations seen in spaceflight. Patterns of tubulin-a 1, 3,4 and 6 phosphorylation further reveal an interaction of microtubule and redox homeostasis that mirrors osmotic response signaling elements. The absence of gravity also results in a seemingly wasteful dysregulation of plastid gene transcription. Conclusions: The datasets gathered from Arabidopsis seedlings exposed to microgravity revealed marked impacts on post-transcriptional regulation, cell wall synthesis, redox/microtubule dynamics, and plastid gene transcription. The impact of post-transcriptional regulatory alterations represents an unstudied element of the plant microgravity response with the potential to significantly impact plant growth efficiency and beyond. What’s more, addressing the effects of microgravity on AHA2, CESA1, and alpha tubulins has the potential to enhance cytoskeletal organization and cell wall composition, thereby enhancing biomass production and growth in microgravity. Finally, understanding and manipulating the dysregulation of plastid gene transcription has further potential to address the goal of enhancing plant growth in the stressful conditions of microgravity.

scholarly journals Spaceflight Induces Novel Regulatory Responses in Arabidopsis Seedling as Revealed by Combined Proteomic and Transcriptomic Analyses

2020 ◽  
Author(s):  
Colin Peter Singer Kruse ◽  
Alexander D Meyers ◽  
Proma Basu ◽  
Sarahann Hutchinson ◽  
Darron R Luesse ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Membrane Proteins ◽  
Plant Growth ◽  
Gene Transcription ◽  
Space Station ◽  
Growth Efficiency ◽  
Rna Seq ◽  
Plastid Gene ◽  
The Impact

Abstract Background: Understanding of gravity sensing and response is critical to long-term human habitation in space and can provide new advantages for terrestrial agriculture. To this end, the altered gene expression profile induced by microgravity has been repeatedly queried by microarray and RNA-seq experiments to understand gravitropism. However, the quantification of altered protein abundance in space has been minimally investigated.Results: Proteomic (iTRAQ-labelled LC-MS/MS) and transcriptomic (RNA-seq) analyses simultaneously quantified protein and transcript differential expression of three-day old, etiolated Arabidopsis thaliana seedlings grown aboard the International Space Station along with their ground control counterparts. Protein extracts were fractionated to isolate soluble and membrane proteins and analyzed to detect differentially phosphorylated peptides. In total, 968 RNAs, 107 soluble proteins, and 103 membrane proteins were identified as differentially expressed. In addition, the proteomic analyses identified 16 differential phosphorylation events. Proteomic data delivered novel insights and simultaneously provided new context to previously made observations of gene expression in microgravity. There is a sweeping shift in post-transcriptional mechanisms of gene regulation including RNA-decapping protein DCP5, the splicing factors GRP7 and GRP8, and AGO4. These data also indicate AHA2 and FERONIA as well as CESA1 and SHOU4 as central to the cell wall adaptations seen in spaceflight. Patterns of tubulin-a 1, 3,4 and 6 phosphorylation further reveal an interaction of microtubule and redox homeostasis that mirrors osmotic response signaling elements. The absence of gravity also results in a seemingly wasteful dysregulation of plastid gene transcription. Conclusions: The datasets gathered from Arabidopsis seedlings exposed to microgravity revealed marked impacts on post-transcriptional regulation, cell wall synthesis, redox/microtubule dynamics, and plastid gene transcription. The impact of post-transcriptional regulatory alterations represents an unstudied element of the plant microgravity response with the potential to significantly impact plant growth efficiency and beyond. What’s more, addressing the effects of microgravity on AHA2, CESA1, and alpha tubulins has the potential to enhance cytoskeletal organization and cell wall composition, thereby enhancing biomass production and growth in microgravity. Finally, understanding and manipulating the dysregulation of plastid gene transcription has further potential to address the goal of enhancing plant growth in the stressful conditions of microgravity.

scholarly journals Unique transcriptomic signature of omental adipose tissue in Ossabaw swine: a model of childhood obesity

2014 ◽  
Vol 46 (10) ◽  
pp. 362-375 ◽  
Author(s):  
Ryan G. Toedebusch ◽  
Michael D. Roberts ◽  
Kevin D. Wells ◽  
Joseph M. Company ◽  
Kayla M. Kanosky ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Childhood Obesity ◽  
Caloric Intake ◽  
Rna Seq ◽  
Omental Adipose Tissue ◽  
Body Fat Content ◽  
Transcriptomic Signature ◽  
And Function ◽  
Visceral Adipose ◽  
The Impact

To better understand the impact of childhood obesity on intra-abdominal adipose tissue phenotype, a complete transcriptomic analysis using deep RNA-sequencing (RNA-seq) was performed on omental adipose tissue (OMAT) obtained from lean and Western diet-induced obese juvenile Ossabaw swine. Obese animals had 88% greater body mass, 49% greater body fat content, and a 60% increase in OMAT adipocyte area (all P < 0.05) compared with lean pigs. RNA-seq revealed a 37% increase in the total transcript number in the OMAT of obese pigs. Ingenuity Pathway Analysis showed transcripts in obese OMAT were primarily enriched in the following categories: 1) development, 2) cellular function and maintenance, and 3) connective tissue development and function, while transcripts associated with RNA posttranslational modification, lipid metabolism, and small molecule biochemistry were reduced. DAVID and Gene Ontology analyses showed that many of the classically recognized gene pathways associated with adipose tissue dysfunction in obese adults including hypoxia, inflammation, angiogenesis were not altered in OMAT in our model. The current study indicates that obesity in juvenile Ossabaw swine is characterized by increases in overall OMAT transcript number and provides novel data describing early transcriptomic alterations that occur in response to excess caloric intake in visceral adipose tissue in a pig model of childhood obesity.

Fluorescent potentiometric dyes for membrane-potential imaging

1994 ◽  
Vol 52 ◽  
pp. 166-167
Author(s):  
Leslie M. Loew
Keyword(s):  
Membrane Potential ◽  
Single Cells ◽  
Quantitative Imaging ◽  
Optical Recording ◽  
Biological Processes ◽  
Major Focus ◽  
The Past ◽  
Excitable Systems ◽  
Major Application ◽  
The Impact

A major application of potentiometric dyes has been the multisite optical recording of electrical activity in excitable systems. After being championed by L.B. Cohen and his colleagues for the past 20 years, the impact of this technology is rapidly being felt and is spreading to an increasing number of neuroscience laboratories. A second class of experiments involves using dyes to image membrane potential distributions in single cells by digital imaging microscopy - a major focus of this lab. These studies usually do not require the temporal resolution of multisite optical recording, being primarily focussed on slow cell biological processes, and therefore can achieve much higher spatial resolution. We have developed 2 methods for quantitative imaging of membrane potential. One method uses dual wavelength imaging of membrane-staining dyes and the other uses quantitative 3D imaging of a fluorescent lipophilic cation; the dyes used in each case were synthesized for this purpose in this laboratory.

THE LANDSCAPE INVESTIGATIONS AS NECESSARY PART OF BIOLOGICAL STUDY IN THE COASTAL ZONE TO THE QUESTION OF THE IMPACT OF CLIMATE CHANGE ON THE ECOLOGICAL STATE OF ARTIFICAL

2017 ◽  
Author(s):  
Artem Lapenkov ◽  
Artem Lapenkov ◽  
Yury Zuyev ◽  
Yury Zuyev ◽  
Nadezhda Zuyeva ◽  
...  
Keyword(s):  
Coastal Zone ◽  
Benthic Communities ◽  
Great Depth ◽  
Research Strategy ◽  
Biological Study ◽  
Lake Ladoga ◽  
Coastal Zones ◽  
Investigation Methods ◽  
Ground Conditions ◽  
The Impact

Coastal zones have great diversity of resources. The shallow water zones contain the most of plant and benthic communities. A description of relief and type of ground is needed for the rigorous monitoring of biota and environmental condition of coastal zone. Generally, on the basis of these data the investigation methods of the coastal zone are selected. The shallows research strategy has been developed by us for northern part of the Lake Ladoga. If the coastal areas are characterized by great depth and flat topography, then sonar’s can be used to describe them and samples of ground can be taken by bottom grabs. In the Lake Ladoga these methods don’t operate correctly by reason of the compound bottom relief and the fact that a sizeable part of the bottom is occupied by hard ground. Therefore, our investigations base on the diving transect method of Golikov and Skarlato (1965). A diver moves along transects. He registers the depth, length to coastline, water temperature, relief and ground, edificators and records video. In the laboratory all these data are decoded and used for mapping of bays. Studies of plant communities have been performed and strategy for research of benthic communities in complex relief and hard ground conditions has been developed based on the descriptions of shallow waters. Description of the Malay Nikonovskia Bay bottom has given an opportunity to estimate changes in the bottom of the bay under the influence of the trout farm.

The Management of Post-Tonsillectomy Morbidity in Patients With Sleep Apnoea

2019 ◽  
Vol 70 (10) ◽  
pp. 3738-3740
Keyword(s):  
Day Surgery ◽  
Sleep Apnoea ◽  
Integrative Approach ◽  
Multicenter Studies ◽  
Therapeutic Modalities ◽  
Advantages And Disadvantages ◽  
Obstructive Sleep ◽  
Wide Range ◽  
The Impact ◽  
Surgery Center

The Tonsillectomy in children or adults is an intervention commonly encountered in the ENT (Ear Nose and Throat) and Head and Neck surgeon practice. The current tendency is to perform this type of surgery in major ambulatory surgery centers. Two objectives are thus pursued: first of all, the increase of the patient quality of life through the reintegration into the family as quickly as possible and secondly, the expenses associated with continuous hospitalization are reduced. Any tertiary (multidisciplinary) sleep center must ensure the complete diagnosis and treatment (including surgery) of sleep respiratory disorders. Under these conditions the selection of patients and especially the implementation of the specific protocols in order to control the postoperative complications it becomes essential. The present paper describes our experience of tonsillectomy as treatment for selected patients with chronic rhonchopathy (snoring) and mild to moderate obstructive sleep apnoea. It was presented the impact of antibiotics protocols in reducing the main morbid outcomes following tonsillectomy, in our day surgery center. The obtained results can also be a prerequisite for the integrative approach of the patients with sleep apnoea who were recommended surgical treatment. Considering the wide range of therapeutic modalities used in sleep apnoea, each with its specific advantages and disadvantages, more extensive and multicenter studies are needed. Keywords: post-tonsillectomy morbidity, day surgery center, sleep disorders

scholarly journals Endemic Juniperus Montane Species Facing Extinction Risk under Climate Change in Southwest China: Integrative Approach for Conservation Assessment and Prioritization

Biology ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 63
Author(s):  
Mohammed A. Dakhil ◽  
Marwa Waseem A. Halmy ◽  
Walaa A. Hassan ◽  
Ali El-Keblawy ◽  
Kaiwen Pan ◽  
...  
Keyword(s):  
Climate Change ◽  
Potential Distribution ◽  
Extinction Risk ◽  
In Situ Conservation ◽  
Integrative Approach ◽  
Conservation Assessment ◽  
Distribution Models ◽  
Area Of Occupancy ◽  
Annual Range ◽  
The Impact

Climate change is an important driver of biodiversity loss and extinction of endemic montane species. In China, three endemic Juniperus spp. (Juniperuspingii var. pingii, J.tibetica, and J.komarovii) are threatened and subjected to the risk of extinction. This study aimed to predict the potential distribution of these three Juniperus species under climate change and dispersal scenarios, to identify critical drivers explaining their potential distributions, to assess the extinction risk by estimating the loss percentage in their area of occupancy (AOO), and to identify priority areas for their conservation in China. We used ensemble modeling to evaluate the impact of climate change and project AOO. Our results revealed that the projected AOOs followed a similar trend in the three Juniperus species, which predicted an entire loss of their suitable habitats under both climate and dispersal scenarios. Temperature annual range and isothermality were the most critical key variables explaining the potential distribution of these three Juniperus species; they contribute by 16–56.1% and 20.4–38.3%, respectively. Accounting for the use of different thresholds provides a balanced approach for species distribution models’ applications in conservation assessment when the goal is to assess potential climatic suitability in new geographical areas. Therefore, south Sichuan and north Yunnan could be considered important priority conservation areas for in situ conservation and search for unknown populations of these three Juniperus species.

scholarly journals The Impact of Spaceflight and Microgravity on the Human Islet-1+ Cardiovascular Progenitor Cell Transcriptome

2021 ◽  
Vol 22 (7) ◽  
pp. 3577
Author(s):  
Victor Camberos ◽  
Jonathan Baio ◽  
Ana Mandujano ◽  
Aida F. Martinez ◽  
Leonard Bailey ◽  
...  
Keyword(s):  
Early Stage ◽  
Space Station ◽  
Cardiovascular Development ◽  
Support Cell ◽  
Cell Transcriptome ◽  
Islet 1 ◽  
Life On Earth ◽  
The Impact ◽  
And Oxidative Stress ◽  
Insight Into

Understanding the transcriptomic impact of microgravity and the spaceflight environment is relevant for future missions in space and microgravity-based applications designed to benefit life on Earth. Here, we investigated the transcriptome of adult and neonatal cardiovascular progenitors following culture aboard the International Space Station for 30 days and compared it to the transcriptome of clonally identical cells cultured on Earth. Cardiovascular progenitors acquire a gene expression profile representative of an early-stage, dedifferentiated, stem-like state, regardless of age. Signaling pathways that support cell proliferation and survival were induced by spaceflight along with transcripts related to cell cycle re-entry, cardiovascular development, and oxidative stress. These findings contribute new insight into the multifaceted influence of reduced gravitational environments.

scholarly journals Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Li Tong ◽  
◽  
Po-Yen Wu ◽  
John H. Phan ◽  
Hamid R. Hassazadeh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Analysis ◽  
Disease Outcome ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Normalization Methods ◽  
The Us ◽  
Sequencing Quality ◽  
Improved Accuracy ◽  
The Impact

Abstract To use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users. The US Food and Drug Administration (FDA) has led the Sequencing Quality Control (SEQC) project to conduct a comprehensive investigation of 278 representative RNA-seq data analysis pipelines consisting of 13 sequence mapping, three quantification, and seven normalization methods. In this article, we focused on the impact of the joint effects of RNA-seq pipelines on gene expression estimation as well as the downstream prediction of disease outcomes. First, we developed and applied three metrics (i.e., accuracy, precision, and reliability) to quantitatively evaluate each pipeline’s performance on gene expression estimation. We then investigated the correlation between the proposed metrics and the downstream prediction performance using two real-world cancer datasets (i.e., SEQC neuroblastoma dataset and the NIH/NCI TCGA lung adenocarcinoma dataset). We found that RNA-seq pipeline components jointly and significantly impacted the accuracy of gene expression estimation, and its impact was extended to the downstream prediction of these cancer outcomes. Specifically, RNA-seq pipelines that produced more accurate, precise, and reliable gene expression estimation tended to perform better in the prediction of disease outcome. In the end, we provided scenarios as guidelines for users to use these three metrics to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation, which lead to the improved downstream gene expression-based prediction of disease outcome.

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