A Novel Approach to Revealing Positive and Negative Co-Regulated Genes

As explored by biologists, there is a real and emerging need to identify co-regulated gene clusters, which include both positive and negative regulated gene clusters. However, the existing pattern-based and tendency-based clustering approaches are only designed for finding positive regulated gene clusters. In this paper, a new subspace clustering model called g-Cluster is proposed for gene expression data. The proposed model has the following advantages： 1） find both positive and negative co-regulated genes in a shot, 2） get away from the restriction of magnitude transformation relationship among co-regulated genes, and 3） guarantee quality of clusters and significance of regulations using a novel similarity measurement gCode and a user-specified regulation threshold δ, respectively. No previous work measures up to the task which has been set. Moreover, MDL technique is introduced to avoid insignificant g-Clusters generated. A tree structure, namely GS-tree, is also designed, and two algorithms combined with efficient pruning and optimization strategies to identify all qualified g-Clusters. Extensive experiments are conducted on real and synthetic datasets. The experimental results show that 1） the algorithm is able to find an amount of co-regulated gene clusters missed by previous models, which are potentially of high biological significance, and 2） the algorithms are effective and efficient, and outperform the existing approaches.

Co-regulated gene module detection for time series gene expression data

It is important to detect interaction effect of multiple genes during certain biological process. In this paper, we proposed, from systems biology perspective, the concept of co-regulated gene module, which consists of genes that are regulated by the same regulator（s）. Given a time series gene expression data, a hidden Markov model-based Bayesian model was developed to calculate the likelihood of the observed data, assuming the co-regulated gene modules are known. We further developed a Gibbs sampling strategy that is integrated with reversible jump Markov chain Monte Carlo to obtain the posterior probabilities of the co-regulated gene modules. Simulation study validated the proposed method. When compared with two existing methods, the proposed approach significantly outperformed the conventional methods.

Dual-Ion Co-Regulation System Enabling High-Performance Electrochemical Artificial Yarn Muscles with Energy-Free Catch States

Artificial yarn muscles show great potential in applications requiring low-energy consumption while maintaining high performance. However, conventional designs have been limited by weak ion-yarn muscle interactions and inefficient “rocking-chair” ion migration. To address these limitations, we present an electrochemical artificial yarn muscle design driven by a dual-ion co-regulation system. By utilizing two reaction channels, this system shortens ion migration pathways, leading to faster and more efficient actuation. During the charging/discharging process, PF_6~- ions react with carbon nanotube yarn, while Li~+ ions react with an Al foil. The intercalation reaction between PF_6~- and collapsed carbon nanotubes allows the yarn muscle to achieve an energy-free high-tension catch state. The dual-ion coordinated yarn muscles exhibit superior contractile stroke, maximum contractile rate, and maximum power densities, exceeding those of “rocking-chair” type ion migration yarn muscles. The dual-ion co-regulation system enhances the ion migration rate during actuation, resulting in improved performance. Moreover, the yarn muscles can withstand high levels of isometric stress, displaying a stress of 61 times that of skeletal muscles and 8 times that of “rocking-chair” type yarn muscles at higher frequencies. This technology holds significant potential for various applications, including prosthetics and robotics.

Food safety regulatory systems in Europe and China:A study of how co-regulation can improve regulatory effectiveness

Food safety has received a great deal of attention in both developed and developing countries in recent years. In China, the numerous food scandals and scares that have struck over the past decade have spurred significant food safety regulatory reform, which has been increasingly oriented towards the public-private partnership model adopted by the Europe Union＇s （EU） food safety regulatory system. This paper analyzes the development of both the EU＇s and China＇s food safety regu- latory systems, identifies the current challenges for China and additionally considers the role of public-private partnership. The success of co-regulation in the food regulatory system would bring significant benefits and opportunities for China. Finally, this paper recommends additional measures like training and grants to improve the private＇s sector effectiveness in co-regulating China＇s food safety issues.

Co-regulator NCOA5 and cancer

NCOA5 encodes a co-regulator for estrogen receptors(ERαand ERβ),orphan nuclear receptors(REV-ERBαand REV-ERBβ)and liver X receptor.It can influence many cellular processes by either promoting or inhibiting gene expression through its two important functional motifs:LxxLL(co-activator)andΦxxΦΦ(co-repressor).Many reports have revealed the important roles of NCOA5 in diseases,such as diabetes,reproductive defects and autoimmune disease.In this review,we focus on its function in cancers and summary the current research progresses regarding its different roles in various cancers.

Role of the histone methyltransferases Ezh2 and Suv4-20h1/Suv4-20h2 in neurogenesis

Mechanisms regulating neurogenesis involve broad and complex processes that represent intriguing therapeutic targets in the field of regenerative medicine.One influential factor guiding neural stem cell proliferation and cellular differentiation during neurogenesis are epigenetic mechanisms.We present an overview of epigenetic mechanisms including chromatin structure and histone modifications;and discuss novel roles of two histone modifiers,Ezh2 and Suv4-20h1/Suv4-20h2(collectively referred to as Suv4-20h),in neurodevelopment and neurogenesis.This review will focus on broadly reviewing epigenetic regulatory components,the roles of epigenetic components during neurogenesis,and potential applications in regenerative medicine.

Co-regulation of mitochondrial and chloroplast function: Molecular components and mechanisms

The metabolic interdependence,interactions,and coordination of functions between chloroplasts and mitochondria are established and intensively studied.However,less is known about the regulatory components that control these interactions and their responses to external stimuli.Here,we outline how chloroplastic and mitochondrial activities are coordinated via common components involved in signal transduction pathways,gene regulatory events,and post-transcriptional processes.The endoplasmic reticulum emerges as a point of convergence for both transcriptional and post-transcriptional pathways that coordinate chloroplast and mitochondrial functions.Although the identification of molecular components and mechanisms of chloroplast and mitochondrial signaling increasingly suggests common players,this raises the question of how these allow for distinct organelle-specific downstream pathways.Outstanding questions with respect to the regulation of post-transcriptional pathways and the cell and/or tissue specificity of organelle signaling are crucial for understanding how these pathways are integrated at a wholeplant level to optimize plant growth and its response to changing environmental conditions.

Preparation of N-B doped composite electrode for iron-chromium redox flow battery

Iron-chromium redox flow battery(ICRFB)is an electrochemical energy storage technology that plays a vital role in dealing with the problems of discontinuity and instability of massive new energy generation and improving the acceptance capacity of the power grid.Carbon cloth electrode(CC)is the main site where the electrochemical reaction occurs,which always suffers from the disadvantages of poor electrochemical reactivity.A new N-B codoped co-regulation Ti composite CC electrode(T-B-CC)is firstly generated and applied to ICRFB,where the REDOX reaction can be promoted significantly owing to the plentiful active sites generated on the modified electrode.As contrasted with ICRFB with normal CC electrode,after 50 battery charge/discharge cycles,the discharge capacity(1,990.3 mAh vs 1,155.8 mAh)and electrolyte utilization(61.88%vs 35.94%)of ICRFB with CC electrode(T-B-CC)are significantly improved.Furthermore,the energy efficiency(EE)is maintained at about 82.7%under 50 cycles,which is 9.3%higher than that of the pristine electrically assembled cells.The comodulation of heteroatom doping and the introduction of Ti catalysts is a simple and easy method to improve the dynamics of the Cr^(3+)/Cr^(2+)and Fe^(3+)/Fe^(2+)reactions,enhancing the performance of ICRFBs.

Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens

miRNAs are non-coding small RNAs that involve diverse biological processes. Until now, little is known about their roles in plant drought resistance. Physcomitrella patens is highly tolerant to drought; however, it is not clear about the basic biology of the traits that contribute P. patens this important character. In this work, we discovered 16 drought stress-associated miRNA （DsAmR） families in P. patens through computational analysis. Due to the possible discrepancy of expression periods and tissue distributions between potential DsAmRs and their targeting genes, and the existence of false positive results in computational identification, the prediction results should be examined with further experimental validation. We also constructed an miRNA co-regulation network, and identi- fied two network hubs, miR902a-Sp and miR414, which may play important roles in regulating drought-resistance traits. We distributed our results through an online database named ppt-miRBase, which can be accessed at http：/Poioinfor.cnu.edu.cn/ppt_miRBase/index.php. Our methods in finding DsAmR and miRNA co-regulation network showed a new direction for identifying miRNA functions.

From chemical mixtures to antibiotic resistance

In real environment, it is unlikely that contaminants exist singly; environmental contamination with chemical mixtures is a norm. However, the impacts of chemical mixtures on environmental quality and ecosystem health have been overlooked in the past.Among the complex interactions between different contaminants, their relationship with the rise of antibiotic resistance（AR） is an emerging environmental concern. In this paper,we review recent progresses on how chemicals or chemical mixtures promote AR. We propose that, through co-selection, agents causing stress to bacteria may induce AR. The mechanisms for chemical mixtures to promote AR are also discussed. We also propose that,mechanistic understanding of co-selection of chemical mixtures for AR should be a future research priority in environmental health research.