CHD proteins: a diverse family with strong tiesThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2007 ◽  
Vol 85 (4) ◽  
pp. 463-476 ◽  
Author(s):  
J. Adam Hall ◽  
Philippe T. Georgel
Keyword(s):  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Multiple Roles ◽  
Main Role ◽  
Helicase Domain ◽  
Structural Domains ◽  
Potential Activity ◽  
Or Gene ◽  
Selection Of

Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.

MeCP2: structure and functionThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2011 ◽  
Vol 89 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Nicholas L. Adkins ◽  
Philippe T. Georgel
Keyword(s):  
Current Knowledge ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Dependent Manner ◽  
Structural Domains ◽  
Architectural Proteins ◽  
Protein Mecp2 ◽  
Selection Of

Despite a vast body of literature linking chromatin structure to regulation of gene expression, the role of architectural proteins in higher order chromatin transitions required for transcription activation and repression has remained an under-studied field. To demonstrate the current knowledge of the role of such proteins, we have focused our attention on the methylated DNA binding and chromatin-associated protein MeCP2. Structural studies using chromatin assembled in vitro have revealed that MeCP2 can associate with nucleosomes in an N-terminus dependent manner and efficiently condense nucleosome arrays. The present review attempts to match MeCP2 structural domains, or lack thereof, and specific chromatin features needed for the proper recruitment of MeCP2 to its multiple functions as either activator or repressor. We specifically focused on MeCP2’s role in Rett syndrome, a neurological disorder associated with specific MeCP2 mutations.

scholarly journals The Main Role of Srs2 in DNA Repair Depends on Its Helicase Activity, Rather than on Its Interactions with PCNA or Rad51

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Alex Bronstein ◽  
Lihi Gershon ◽  
Gilad Grinberg ◽  
Elisa Alonso-Perez ◽  
Martin Kupiec
Keyword(s):  
Dna Damage ◽  
Dna Replication ◽  
Genome Stability ◽  
Dna Helicase ◽  
Main Role ◽  
Helicase Domain ◽  
Helicase Activity ◽  
C Terminus ◽  
Srs2 Helicase

ABSTRACTHomologous recombination (HR) is a mechanism that repairs a variety of DNA lesions. Under certain circumstances, however, HR can generate intermediates that can interfere with other cellular processes such as DNA transcription or replication. Cells have therefore developed pathways that abolish undesirable HR intermediates. TheSaccharomyces cerevisiaeyeast Srs2 helicase has a major role in one of these pathways. Srs2 also works during DNA replication and interacts with the clamp PCNA. The relative importance of Srs2’s helicase activity, Rad51 removal function, and PCNA interaction in genome stability remains unclear. We created a newSRS2allele [srs2(1-850)] that lacks the whole C terminus, containing the interaction site for Rad51 and PCNA and interactions with many other proteins. Thus, the new allele encodes an Srs2 protein bearing only the activity of the DNA helicase. We find that the interactions of Srs2 with Rad51 and PCNA are dispensable for the main role of Srs2 in the repair of DNA damage in vegetative cells and for proper completion of meiosis. On the other hand, it has been shown that in cells impaired for the DNA damage tolerance (DDT) pathways, Srs2 generates toxic intermediates that lead to DNA damage sensitivity; we show that this negative Srs2 activity requires the C terminus of Srs2. Dissection of the genetic interactions of thesrs2(1-850) allele suggest a role for Srs2’s helicase activity in sister chromatid cohesion. Our results also indicate that Srs2’s function becomes more central in diploid cells.IMPORTANCEHomologous recombination (HR) is a key mechanism that repairs damaged DNA. However, this process has to be tightly regulated; failure to regulate it can lead to genome instability. The Srs2 helicase is considered a regulator of HR; it was shown to be able to evict the recombinase Rad51 from DNA. Cells lacking Srs2 exhibit sensitivity to DNA-damaging agents, and in some cases, they display defects in DNA replication. The relative roles of the helicase and Rad51 removal activities of Srs2 in genome stability remain unclear. To address this question, we created a new Srs2 mutant which has only the DNA helicase domain. Our study shows that only the DNA helicase domain is needed to deal with DNA damage and assist in DNA replication during vegetative growth and in meiosis. Thus, our findings shift the view on the role of Srs2 in the maintenance of genome integrity.

Significant Alloy Elements in Welded Steel Structures of Car Body

2012 ◽  
Vol 57 (1) ◽  
pp. 45-52 ◽  
Author(s):  
T. Węgrzyn ◽  
R. Wieszała
Keyword(s):  
Steel Structure ◽  
Steel Structures ◽  
Filler Materials ◽  
Main Role ◽  
Welded Steel ◽  
Car Body ◽  
Welding Method ◽  
Welding Steel ◽  
Selection Of

Significant Alloy Elements in Welded Steel Structures of Car Body Structure, safety and exploitation conditions of welding steel in car body depend on many factors. The main role of that conditions is connected with car body material, welding technology, state of stress and temperature. Because of that, a good selection of steel and welding method is very important for proper steel structure. Low alloy steel is used for car body structure, very often with small amount of carbon and the amount of alloy elements such as Ni, Mn, Mo, Cr and V in car body and welded joints. Depending on the kind of steel which is used, a proper welding method and adequate filler materials should be applied. The present paper describes the influence of Mn, Ni, Mo, Cr, V in WMD (Weld Metal Deposit) on the behaviour of steel structure especially for low temperature service.

scholarly journals Thirty-five years of research into ribozymes and nucleic acid catalysis: where do we stand today?

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1511 ◽  
Author(s):  
Sabine Müller ◽  
Bettina Appel ◽  
Darko Balke ◽  
Robert Hieronymus ◽  
Claudia Nübel
Keyword(s):  
Nucleic Acid ◽  
Rna World ◽  
Regulation Of Gene Expression ◽  
Catalytic Rna ◽  
Rna Motifs ◽  
Bioinformatic Approaches ◽  
Catalytic Mechanisms ◽  
Genomic Locations ◽  
Selection Of

Since the discovery of the first catalytic RNA in 1981, the field of ribozyme research has developed from the discovery of catalytic RNA motifs in nature and the elucidation of their structures and catalytic mechanisms, into a field of engineering and design towards application in diagnostics, molecular biology and medicine. Owing to the development of powerful protocols for selection of nucleic acid catalysts with a desired functionality from random libraries, the spectrum of nucleic acid supported reactions has greatly enlarged, and importantly, ribozymes have been accompanied by DNAzymes. Current areas of research are the engineering of allosteric ribozymes for artificial regulation of gene expression, the design of ribozymes and DNAzymes for medicinal and environmental diagnostics, and the demonstration of RNA world relevant ribozyme activities. In addition, new catalytic motifs or novel genomic locations of known motifs continue to be discovered in all branches of life by the help of high-throughput bioinformatic approaches. Understanding the biological role of the catalytic RNA motifs widely distributed in diverse genetic contexts belongs to the big challenges of future RNA research.

scholarly journals Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
A. Prieto ◽  
M. Bernabeu ◽  
L. Falgenhauer ◽  
T. Chakraborty ◽  
M. Hüttener ◽  
...  
Keyword(s):  
Regulation Of Gene Expression ◽  
Coli Strain ◽  
Regulatory Activity ◽  
Chromosome Architecture ◽  
The Third ◽  
Eaec Strain ◽  
Relevant Role ◽  
Regulatory Properties ◽  
Selection Of

Abstract Members of the H-NS protein family play a role both in the chromosome architecture and in the regulation of gene expression in bacteria. The genomes of the enterobacteria encode an H-NS paralogue, the StpA protein. StpA displays specific regulatory properties and provides a molecular backup for H-NS. Some enterobacteria also encode third H-NS paralogues. This is the case of the enteroaggregative E. coli (EAEC) strain 042, which encodes the hns, stpA and hns2 genes. We provide in this paper novel information about the role of the H-NS2 protein in strain 042. A C > T transition in the hns2 promoter leading to increased H-NS2 expression is readily selected in hns mutants. Increased H-NS2 expression partially compensates for H-NS loss. H-NS2 levels are critical for the strain 042 fitness. Under some circumstances, high H-NS2 expression levels dictated by the mutant hns2 promoter can be deleterious. The selection of T > C revertants or of clones harboring insertional inactivations of the hns2 gene can then occur. Temperature also plays a relevant role in the H-NS2 regulatory activity. At 37 °C, H-NS2 targets a subset of the H-NS repressed genes contributing to their silencing. When temperature drops to 25 °C, the repressory ability of H-NS2 is significantly reduced. At low temperature, H-NS plays the main repressory role.

Adjunct Cultures in Cheese Technology

2018 ◽  
pp. 234-256 ◽  
Author(s):  
Ayşe Gürsoy ◽  
Nazlı Türkmen
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
The Other ◽  
Main Role ◽  
Positive Effects ◽  
Cheese Ripening ◽  
Adjunct Cultures ◽  
Ripening Time ◽  
Selection Of

Cheese ripening involves highly complex biochemical events. Coagulant enzymes as well as the utilized starters play an important role in these events. Two types of starters are used: primary and secondary. The main role of the primary culture, which consists of lactic acid bacteria, is to carry out lactic production during fermentation. They contribute to proteolysis and limited flavor formation with the enzymes they possess. Secondary or adjunct cultures are used to develop the texture and to accelerate the ripening. During the selection of this type of culture, enzyme profiles (i.e., proteolytic and lipolytic activities and their autolyse levels) in cheese are the primary factors to be taken into consideration. Apart from these, the other factors are their positive effects on health, availability, and economy. Adjunct cultures include yeast, molds, and bacteria. Some of the heterofermentative lactobacilli species, in particular weakened strains, are used as adjunct cultures in order to accelerate the ripening and shorten the ripening time in fat-reduced and low-fat cheeses. This chapter explores adjunct cultures in cheese technology.

Transcriptional and epigenetic functions of histone variant H2A.ZThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Ryan Draker ◽  
Peter Cheung
Keyword(s):  
Gene Expression ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Histone Variants ◽  
Histone Variant ◽  
Post Translational Modifications ◽  
Chromatin Dynamics ◽  
Transcription Process ◽  
A Genome ◽  
Selection Of

The chromatin organization of a genome ultimately dictates the gene expression profile of the cell. It is now well recognized that key mechanisms that regulate chromatin structure include post-translational modifications of histones and the incorporation of histone variants at strategic sites within the genome. H2A.Z is a variant of H2A that is localized to the 5′ end of many genes and is required for proper regulation of gene expression. However, its precise function in the transcription process is not yet well defined. In this review, we discuss some of the recent findings related to this histone variant, how it associates with other histone epigenetic marks, and how post-translational modifications of H2A.Z further define its function.

Regulatory noncoding RNAs at Hox lociThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Hugh W. Brock ◽  
Jacob W. Hodgson ◽  
Svetlana Petruk ◽  
Alexander Mazo
Keyword(s):  
Gene Expression ◽  
Hox Genes ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Chromatin Dynamics ◽  
Spatial Regulation ◽  
Positional Identity ◽  
In Trans ◽  
In Cis

There is growing awareness of the importance of noncoding (nc)RNAs in the regulation of gene expression during pattern formation in development. Spatial regulation of Hox gene expression in development controls positional identity along the antero–posterior axis. In this review, we will focus on the role of short ncRNAs that repress Hox genes in Drosophila and mammals by RNA interference (RNAi), on long ncRNAs that may repress a Hox in cis in Drosophila by transcriptional interference, and on a novel long ncRNA that functions in trans to regulate Hox genes mammals.

Chromatin and chromatin-modifying proteins in adipogenesisThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosomes Conference, and has undergone the Journal's usual peer review process.

2007 ◽  
Vol 85 (4) ◽  
pp. 397-410 ◽  
Author(s):  
Melina M. Musri ◽  
Ramon Gomis ◽  
Marcelina Párrizas
Keyword(s):  
Adipose Tissue ◽  
Peer Review Process ◽  
Gene Expression Pattern ◽  
Detailed Knowledge ◽  
Medical Problems ◽  
Endocrine Organ ◽  
Bona Fide ◽  
And Function ◽  
Selection Of

Long considered scarcely more than an uninteresting energy depot, adipose tissue has recently achieved star status. Far from being mere fat droplets, the adipocytes secrete a number of hormones and bioactive peptides, collectively known as adipokines, which participate in the regulation of a variety of functions, from haemostasis to angiogenesis to energy balance. Adipose tissue constitutes a bona-fide endocrine organ whose main dysfunctions, obesity and lipodystrophy, are related to the development of diabetes, hypertension, or dyslipidemia. The renewed interest in this tissue has prompted an escalation in the number of studies focusing on every aspect of the biology of the adipose cell, in the belief that a detailed knowledge of the mechanisms involved in the differentiation and function of adipocytes may contribute new therapeutical approaches to the treatment of such alarming medical problems. Adipogenesis is the result of an intertwined network of transcription factors and coregulators with chromatin-modifying activities that together, are responsible for the establishment of the gene expression pattern of mature adipocytes. Although the exquisitely regulated transcription factor cascade controlling adipogenesis has been extensively studied, the role of chromatin and chromatin-modifying proteins has become apparent only in recent times.

scholarly journals The Basal Ganglia and Motor Control

2003 ◽  
Vol 10 (1-2) ◽  
pp. 107-120 ◽  
Author(s):  
Henk J. Groenewegen
Keyword(s):  
Motor Control ◽  
Basal Ganglia ◽  
Functional Organization ◽  
Functional Anatomy ◽  
Main Role ◽  
Brain Functions ◽  
Wide Range ◽  
Selection Mechanisms ◽  
Selection Of

This paper briefly reviews the functional anatomy of the basal ganglia and their relationships with the thalamocortical system. The basal ganglia, including the striatum, pallidum, subthalamic nucleus, and substantia nigra, are involved in a number of parallel, functionally segregated cortical-subcortical circuits. These circuits support a wide range of sensorimotor, cognitive and emotional-motivational brain functions. A main role of the basal ganglia is the learning and selection of the most appropriate motor or behavioral programs. The internal functional organization of the basal ganglia is very well suited for such selection mechanisms, both in development and in adulthood. The question of whether clumsiness may be, at least in part, attributed to dysfunction of the basal ganglia is discussed in the context of the differential, complementary, or interactive roles of the basal ganglia and the cerebellum in the development of motor control.

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