scholarly journals Design, challenges, and the potential of transcriptomics to understand social behavior

2020 ◽  
Vol 66 (3) ◽  
pp. 321-330 ◽  
Author(s):  
Wen Kin Lim ◽  
Ajay S Mathuru
Keyword(s):  
Social Behavior ◽  
Molecular Basis ◽  
Behavioral Plasticity ◽  
Single Cells ◽  
Rna Seq ◽  
Tissue Samples ◽  
Design Considerations ◽  
The Past ◽  
Underlying Mechanisms ◽  
Design Challenges

Abstract Rapid advances in Ribonucleic Acid sequencing (or RNA-seq) technology for analyzing entire transcriptomes of desired tissue samples, or even of single cells at scale, have revolutionized biology in the past decade. Increasing accessibility and falling costs are making it possible to address many problems in biology that were once considered intractable, including the study of various social behaviors. RNA-seq is opening new avenues to understand long-standing questions on the molecular basis of behavioral plasticity and individual variation in the expression of a behavior. As whole transcriptomes are examined, it has become possible to make unbiased discoveries of underlying mechanisms with little or no necessity to predict genes involved in advance. However, researchers need to be aware of technical limitations and have to make specific decisions when applying RNA-seq to study social behavior. Here, we provide a perspective on the applications of RNA-seq and experimental design considerations for behavioral scientists who are unfamiliar with the technology but are considering using it in their research.

scholarly journals The past determines the future: sugar source history and transcriptional memory

2020 ◽  
Vol 66 (6) ◽  
pp. 1029-1035
Author(s):  
Poonam Bheda ◽  
Antonis Kirmizis ◽  
Robert Schneider
Keyword(s):  
Gene Expression ◽  
Single Cells ◽  
Transcriptional Response ◽  
Altered Gene Expression ◽  
The Past ◽  
Transcriptional Memory ◽  
Higher Eukaryotes ◽  
Altered Gene ◽  
Underlying Mechanisms ◽  
Sugar Source

Abstract Transcriptional reinduction memory is a phenomenon whereby cells “remember” their transcriptional response to a previous stimulus such that subsequent encounters with the same stimulus can result in altered gene expression kinetics. Chromatin structure is thought to play a role in certain transcriptional memory mechanisms, leading to questions as to whether and how memory can be actively maintained and inherited to progeny through cell division. Here we summarize efforts towards dissecting chromatin-based transcriptional memory inheritance of GAL genes in Saccharomyces cerevisiae. We focus on methods and analyses of GAL (as well as MAL and INO) memory in single cells and discuss the challenges in unraveling the underlying mechanisms in yeast and higher eukaryotes.

scholarly journals Behavioral and Gene Expression Analysis of Stxbp6-Knockout Mice

2021 ◽  
Vol 11 (4) ◽  
pp. 436
Author(s):  
Cong Liu ◽  
Qian Hu ◽  
Yan Chen ◽  
Lingqian Wu ◽  
Xionghao Liu ◽  
...  
Keyword(s):  
Nervous System ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Regulatory Pathways ◽  
The Past ◽  
Protein Receptor ◽  
Normal Behavior ◽  
Sensitive Factor ◽  
The Central Nervous System ◽  
Underlying Mechanisms

Since the first report that Stxbp6, a brain-enriched protein, regulates the assembly of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes, little has been discovered about its functions over the past two decades. To determine the effects of Stxbp6 loss on nervous-system-associated phenotypes and underlying mechanisms, we constructed a global Stxbp6-knockout mouse. We found that Stxbp6-null mice survive normally, with normal behavior, but gained less weight relative to age- and sex-matched wildtype mice. RNA-seq analysis of the cerebral cortex of Stxbp6-null mice relative to wildtype controls identified 126 differentially expressed genes. Of these, 57 were upregulated and 69 were downregulated. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the most significant enriched KEGG term was “complement and coagulation cascades”. Our results suggest some potential regulatory pathways of Stxbp6 in the central nervous system, providing a remarkable new resource for understanding Stxbp6 function at the organism level.

scholarly journals Molecular Basis of Atrial Fibrillation Initiation and Maintenance

Hearts ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 170-187
Author(s):  
Kira Beneke ◽  
Cristina E. Molina
Keyword(s):  
Atrial Fibrillation ◽  
Molecular Basis ◽  
Genetic Factors ◽  
Transcriptional Regulators ◽  
Genetic Changes ◽  
Therapeutic Implications ◽  
The Past ◽  
Risk Variants ◽  
Underlying Mechanisms ◽  
And Oxidative Stress

Atrial fibrillation (AF) is the most common cardiac arrhythmia, largely associated to morbidity and mortality. Over the past decades, research in appearance and progression of this arrhythmia have turned into significant advances in its management. However, the incidence of AF continues to increase with the aging of the population and many important fundamental and translational underlaying mechanisms remain elusive. Here, we review recent advances in molecular and cellular basis for AF initiation, maintenance and progression. We first provide an overview of the basic molecular and electrophysiological mechanisms that lead and characterize AF. Next, we discuss the upstream regulatory factors conducting the underlying mechanisms which drive electrical and structural AF-associated remodeling, including genetic factors (risk variants associated to AF as transcriptional regulators and genetic changes associated to AF), neurohormonal regulation (i.e., cAMP) and oxidative stress imbalance (cGMP and mitochondrial dysfunction). Finally, we discuss the potential therapeutic implications of those findings, the knowledge gaps and consider future approaches to improve clinical management.

Analyzing Molecular Basis of Heat-Induced Loss-of-Wheat Resistance to Hessian Fly (Diptera: Cecidomyiidae) Infestation Using RNA-Sequencing

2020 ◽  
Vol 113 (3) ◽  
pp. 1504-1512
Author(s):  
Lieceng Zhu ◽  
Jiazheng (John) Yuan ◽  
Jordan O’Neal ◽  
Daria Brown ◽  
Ming-Shun Chen
Keyword(s):  
Heat Stress ◽  
Rna Sequencing ◽  
Molecular Basis ◽  
Hessian Fly ◽  
Auxin Signaling ◽  
Primary Metabolism ◽  
Rna Seq ◽  
Tissue Samples ◽  
Expression Of Genes ◽  
The Impact

Abstract Heat stress compromises wheat resistance to Hessian fly (HF, Mayetiola destructor (Say)) (Diptera: Cecidomyiidae) infestation. The objective of this research is to analyze the molecular basis of heat-induced loss of wheat resistance to HF infestation using RNA Sequencing (RNA-seq). To this end, two resistant wheat cultivars ‘Molly’ and ‘Caldwell’ containing the resistance genes H13 and H6, respectively, were infested with an avirulent HF biotype GP and treated with different temperatures to examine the impact of heat stress on their resistance phenotypes. Tissue samples collected from HF feeding sites in Molly plants were subjected to RNA-seq analysis to determine the effect of heat stress on transcript expression of genes in wheat plants. Our results indicate that resistance to HF infestation in Caldwell is more sensitive to heat stress than that in Molly, and that heat stress down-regulates most genes involved in primary metabolism and biosynthesis of lignin and cuticular wax, but up-regulate most or all genes involved in auxin and 12-oxo-phytodienoic acid (OPDA) signaling pathways. Our results and previous reports suggest that heat stress may impair the processes in wheat plants that produce and mobilize chemical resources needed for synthesizing defensive compounds, weaken cell wall and cuticle defense, decrease OPDA signaling, but increase auxin signaling, leading to the suppressed resistance and activation of susceptibility.

In situ microprobe quantitation of inorganic particle burden in paraffin sections of lung tissue

1988 ◽  
Vol 46 ◽  
pp. 990-991
Author(s):  
Jerrold L. Abraham
Keyword(s):  
Lung Tissue ◽  
Quantitative Information ◽  
Particulate Material ◽  
Paraffin Sections ◽  
Tissue Samples ◽  
Qualitative And Quantitative ◽  
The Past ◽  
Quantitative Analyses ◽  
Data Result

Inorganic particulate material of diverse types is present in the ambient and occupational environment, and exposure to such materials is a well recognized cause of some lung disease. To investigate the interaction of inhaled inorganic particulates with the lung it is necessary to obtain quantitative information on the particulate burden of lung tissue in a wide variety of situations. The vast majority of diagnostic and experimental tissue samples (biopsies and autopsies) are fixed with formaldehyde solutions, dehydrated with organic solvents and embedded in paraffin wax. Over the past 16 years, I have attempted to obtain maximal analytical use of such tissue with minimal preparative steps. Unique diagnostic and research data result from both qualitative and quantitative analyses of sections. Most of the data has been related to inhaled inorganic particulates in lungs, but the basic methods are applicable to any tissues. The preparations are primarily designed for SEM use, but they are stable for storage and transport to other laboratories and several other instruments (e.g., for SIMS techniques).

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.

A summary of beach nourishment in China: The past decade of practices

Shore & Beach ◽  
2020 ◽  
pp. 65-73
Author(s):  
Gen Liu ◽  
Feng Cai ◽  
Hongshuai Qi ◽  
Jianhui Liu ◽  
Gang Lei ◽  
...  
Keyword(s):  
Beach Nourishment ◽  
Developed Countries ◽  
Ecological Design ◽  
Optimized Design ◽  
Limited Information ◽  
Personal Communications ◽  
Design Considerations ◽  
The Past ◽  
Technological Advances ◽  
Urban Beaches

Beach nourishment has been widely used for beach protection around the world. However, there is limited information about beach nourishment in China. This study offers an overview of beach nourishment practices, status and technological advances in China, based on the literature, reports, and personal communications. The results demonstrate that beach nourishment has been recognized as an effective and environmentally friendly measure to combat coastal erosion and has been increasingly adopted in China, especially in the past decade. The unique characteristics of coastal China resulted in a difference in beach nourishment between China and Western developed countries in terms of the types, objectives, and shapes of beach nourishment. For the types of nourishments in China, there were approximately the same number of restored beaches and newly constructed beaches. For fill sediment, homogeneous fill and heterogeneous fill comprised 51.1% and 48.9% of projects, respectively. The objective of beach nourishment was mainly to promote coastal tourism, and the shape of nourished beaches was dominated by headland bays. This study also indicated that China has achieved a number of technological advances in beach nourishment, including methods of beach nourishment on severely eroded coasts and muddy coasts, an optimized design of drain pipes involved in urban beaches, and ecological design considerations. From the past decade of practices, four aspects were proposed as considerations for future nourishment: sand sources, technique advances, ecological effects, and management of beach nourishments.

Novel Findings of Anti-cancer Property of Propofol

2018 ◽  
Vol 18 (2) ◽  
pp. 156-165 ◽  
Author(s):  
Jiaqiang Wang ◽  
Chien-shan Cheng ◽  
Yan Lu ◽  
Xiaowei Ding ◽  
Minmin Zhu ◽  
...  
Keyword(s):  
General Anesthesia ◽  
Cancer Progression ◽  
Molecular Mechanisms ◽  
Intravenous Anesthetic ◽  
The Past ◽  
Anti Cancer ◽  
Underlying Mechanisms ◽  
Recent Attention

Background: Propofol, a widely used intravenous anesthetic agent, is traditionally applied for sedation and general anesthesia. Explanation: Recent attention has been drawn to explore the effect and mechanisms of propofol against cancer progression in vitro and in vivo. Specifically, the proliferation-inhibiting and apoptosis-inducing properties of propofol in cancer have been studied. However, the underlying mechanisms remain unclear. Conclusion: This review focused on the findings within the past ten years and aimed to provide a general overview of propofol's malignance-modulating properties and the potential molecular mechanisms.

scholarly journals Structural and Functional Remodeling of Mitochondria in Cardiac Diseases

2021 ◽  
Vol 22 (8) ◽  
pp. 4167
Author(s):  
Xiaonan Sun ◽  
Jalen Alford ◽  
Hongyu Qiu
Keyword(s):  
Regulatory Network ◽  
Molecular Basis ◽  
Therapeutic Potential ◽  
Research Direction ◽  
Future Research ◽  
Cardiac Diseases ◽  
Functional Remodeling ◽  
Underlying Mechanisms ◽  
Mitochondrial Remodeling ◽  
Normal Cellular Function

Mitochondria undergo structural and functional remodeling to meet the cell demand in response to the intracellular and extracellular stimulations, playing an essential role in maintaining normal cellular function. Merging evidence demonstrated that dysregulation of mitochondrial remodeling is a fundamental driving force of complex human diseases, highlighting its crucial pathophysiological roles and therapeutic potential. In this review, we outlined the progress of the molecular basis of mitochondrial structural and functional remodeling and their regulatory network. In particular, we summarized the latest evidence of the fundamental association of impaired mitochondrial remodeling in developing diverse cardiac diseases and the underlying mechanisms. We also explored the therapeutic potential related to mitochondrial remodeling and future research direction. This updated information would improve our knowledge of mitochondrial biology and cardiac diseases’ pathogenesis, which would inspire new potential strategies for treating these diseases by targeting mitochondria remodeling.

scholarly journals SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells

2021 ◽  
Vol 7 (8) ◽  
pp. eabe3610
Author(s):  
Conor J. Kearney ◽  
Stephin J. Vervoort ◽  
Kelly M. Ramsbottom ◽  
Izabela Todorovski ◽  
Emily J. Lelliott ◽  
...  
Keyword(s):  
Single Cell ◽  
Posttranslational Modification ◽  
Cellular Differentiation ◽  
Single Cells ◽  
Simultaneous Detection ◽  
Surface Protein ◽  
Rna Seq ◽  
Cell Level ◽  
Simultaneous Integration ◽  
Unique Surface

Multimodal single-cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states but does not allow for simultaneous integration of critical posttranslational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq), a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes, and the transcriptome at the single-cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor-infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.

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