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Frontiers in Molecular Biosciences

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https://www.readbyqxmd.com/read/28083537/comparative-normal-mode-analysis-of-the-dynamics-of-denv-and-zikv-capsids
#1
Yin-Chen Hsieh, Frédéric Poitevin, Marc Delarue, Patrice Koehl
Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell and its maturation process, relate to an intricate interplay between the structure and the dynamics of its constituent proteins, especially those that define its capsid, much akin to an envelope that protects its genomic material. We present a comprehensive, comparative analysis of such interplay for the capsids of two viruses from the flaviviridae family, Dengue (DENV) and Zika (ZIKV). We use for that purpose our own software suite, DD-NMA, which is based on normal mode analysis...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28083536/conformational-rigidity-within-plasticity-promotes-differential-target-recognition-of-nerve-growth-factor
#2
Francesca Paoletti, Cesira de Chiara, Geoff Kelly, Sonia Covaceuszach, Francesca Malerba, Robert Yan, Doriano Lamba, Antonino Cattaneo, Annalisa Pastore
Nerve Growth Factor (NGF), the prototype of the neurotrophin family, is essential for maintenance and growth of different neuronal populations. The X-ray crystal structure of NGF has been known since the early '90s and shows a β-sandwich fold with extensive loops that are involved in the interaction with its binding partners. Understanding the dynamical properties of these loops is thus important for molecular recognition. We present here a combined solution NMR/molecular dynamics study which addresses the question of whether and how much the long loops of NGF are flexible and describes the N-terminal intrinsic conformational tendency of the unbound NGF molecule...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28066774/pipe-chipsad-a-pipeline-for-the-analysis-of-high-density-arrays-of-bacterial-transcriptomes
#3
Silvia Bottini, Elena Del Tordello, Luca Fagnocchi, Claudio Donati, Alessandro Muzzi
PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28018906/chaperonopathies-spotlight-on-hereditary-motor-neuropathies
#4
REVIEW
Vincenzo Lupo, Carmen Aguado, Erwin Knecht, Carmen Espinós
Distal hereditary motor neuropathies (dHMN) are a group of rare hereditary neuromuscular disorders characterized by an atrophy that affects peroneal muscles in the absence of sensory symptoms. To date, 23 genes are thought to be responsible for dHMN, four of which encode chaperones: DNAJB2, which encodes a member of the HSP40/DNAJ co-chaperone family; and HSPB1, HSPB3, and HSPB8, encoding three members of the small heat shock protein family. While around 30 different mutations in HSPB1 have been identified, the remaining three genes are altered in many fewer cases...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28018905/the-mutational-landscape-of-the-oncogenic-mzf1-scan-domain-in-cancer
#5
Mads Nygaard, Thilde Terkelsen, André Vidas Olsen, Valentina Sora, Juan Salamanca Viloria, Fabio Rizza, Sanne Bergstrand-Poulsen, Miriam Di Marco, Mette Vistesen, Matteo Tiberti, Matteo Lambrughi, Marja Jäättelä, Tuula Kallunki, Elena Papaleo
SCAN domains in zinc-finger transcription factors are crucial mediators of protein-protein interactions. Up to 240 SCAN-domain encoding genes have been identified throughout the human genome. These include cancer-related genes, such as the myeloid zinc finger 1 (MZF1), an oncogenic transcription factor involved in the progression of many solid cancers. The mechanisms by which SCAN homo- and heterodimers assemble and how they alter the transcriptional activity of zinc-finger transcription factors in cancer and other diseases remain to be investigated...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28008398/dynamic-complexes-in-the-chaperonin-mediated-protein-folding-cycle
#6
REVIEW
Celeste Weiss, Fady Jebara, Shahar Nisemblat, Abdussalam Azem
The GroEL-GroES chaperonin system is probably one of the most studied chaperone systems at the level of the molecular mechanism. Since the first reports of a bacterial gene involved in phage morphogenesis in 1972, these proteins have stimulated intensive research for over 40 years. During this time, detailed structural and functional studies have yielded constantly evolving concepts of the chaperonin mechanism of action. Despite of almost three decades of research on this oligomeric protein, certain aspects of its function remain controversial...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27990419/mutations-in-the-human-aaa-chaperone-p97-and-related-diseases
#7
REVIEW
Wai Kwan Tang, Di Xia
A number of neurodegenerative diseases have been linked to mutations in the human protein p97, an abundant cytosolic AAA(+) (ATPase associated with various cellular activities) ATPase, that functions in a large number of cellular pathways. With the assistance of a variety of cofactors and adaptor proteins, p97 couples the energy of ATP hydrolysis to conformational changes that are necessary for its function. Disease-linked mutations, which are found at the interface between two main domains of p97, have been shown to alter the function of the protein, although the pathogenic mutations do not appear to alter the structure of individual subunit of p97 or the formation of the hexameric biological unit...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27933298/non-targeted-plasma-metabolome-of-early-and-late-lactation-gilts
#8
Lea A Rempel, Jeremy R Miles, William T Oliver, Corey D Broeckling
Female pigs nursing their first litter (first-parity gilts) have increased energy requirements not only to support their piglets, but they themselves are still maturing. Non-targeted plasma metabolomics were used to investigate the differences between (1) post-farrowing and weaning (early or late lactation), (2) degree of body condition loss after lactation (extreme or minimal), and (3) interactions; to potentially identify compounds or pathways that could aide in alleviating energetic demands of lactation in gilts...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#9
Evan A Clayton, Lu Wang, Lavanya Rishishwar, Jianrong Wang, John F McDonald, I King Jordan
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27900321/genome-wide-transcriptional-regulation-and-chromosome-structural-arrangement-by-galr-in-e-coli
#10
Zhong Qian, Andrei Trostel, Dale E A Lewis, Sang Jun Lee, Ximiao He, Anne M Stringer, Joseph T Wade, Thomas D Schneider, Tim Durfee, Sankar Adhya
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27891505/comparative-genomics-of-the-conjugation-region-of-f-like-plasmids-five-shades-of-f
#11
Raul Fernandez-Lopez, Maria de Toro, Gabriel Moncalian, M Pilar Garcillan-Barcia, Fernando de la Cruz
The F plasmid is the foremost representative of a large group of conjugative plasmids, prevalent in Escherichia coli, and widely distributed among the Enterobacteriaceae. These plasmids are of clinical relevance, given their frequent association with virulence determinants, colicins, and antibiotic resistance genes. Originally defined by their sensitivity to certain male-specific phages, IncF plasmids share a conserved conjugative system and regulatory circuits. In order to determine whether the genetic architecture and regulation circuits are preserved among these plasmids, we analyzed the natural diversity of F-like plasmids...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27882317/bacterial-rna-polymerase-dna-interaction-the-driving-force-of-gene-expression-and-the-target-for-drug-action
#12
REVIEW
Jookyung Lee, Sergei Borukhov
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27878121/corrigendum-designer-leptin-receptor-antagonist-allo-aca-inhibits-vegf-effects-in-ophthalmic-neoangiogenesis-models
#13
Roberta Coroniti, Rafal Farjo, Didier J Nuno, Laszlo Otvos, Laura Scolaro, Eva Surmacz
[This corrects the article on p. 67 in vol. 3, PMID: 27790618.].
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27878120/advances-in-stem-cell-research-a-ray-of-hope-in-better-diagnosis-and-prognosis-in-neurodegenerative-diseases
#14
REVIEW
Shripriya Singh, Akriti Srivastava, Pranay Srivastava, Yogesh K Dhuriya, Ankita Pandey, Dipak Kumar, Chetan S Rajpurohit
Neurodegeneration and neurodegenerative disorders have been a global health issue affecting the aging population worldwide. Recent advances in stem cell biology have changed the current face of neurodegenerative disease modeling, diagnosis, and transplantation therapeutics. Stem cells also serve the purpose of a simple in-vitro tool for screening therapeutic drugs and chemicals. We present the application of stem cells and induced pluripotent stem cells (iPSCs) in the field of neurodegeneration and address the issues of diagnosis, modeling, and therapeutic transplantation strategies for the most prevalent neurodegenerative disorders...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27833912/sacb-sacr-gene-cassette-as-the-negative-selection-marker-to-suppress-agrobacterium-overgrowth-in-agrobacterium-mediated-plant-transformation
#15
Yiming Liu, Jiamin Miao, Sy Traore, Danyu Kong, Yi Liu, Xunzhong Zhang, Zachary L Nimchuk, Zongrang Liu, Bingyu Zhao
Agrobacterium overgrowth is a common problem in Agrobacterium-mediated plant transformation. To suppress the Agrobacterium overgrowth, various antibiotics have been used during plant tissue culture steps. The antibiotics are expensive and may adversely affect plant cell differentiation and reduce plant transformation efficiency. The SacB-SacR proteins are toxic to most Agrobacterium tumefaciens strains when they are grown on culture medium supplemented with sucrose. Therefore, SacB-SacR genes can be used as negative selection markers to suppress the overgrowth of A...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27826551/noncoding-rna-regulation-of-dopamine-signaling-in-diseases-of-the-central-nervous-system
#16
REVIEW
William T Carrick, Brandi Burks, Murray J Cairns, Jannet Kocerha
Dopaminergic neurotransmission mediates a majority of the vital central nervous system functions. Disruption of these synaptic events provokes a multitude of neurological pathologies, including Parkinson's, schizophrenia, depression, and addiction. Growing evidence supports a key role for noncoding RNA (ncRNA) regulation in the synapse. This review will discuss the role of both short and long ncRNAs in dopamine signaling, including bioinformatic examination of the pathways they target. Specifically, we focus on the contribution of ncRNAs to dopaminergic dysfunction in neurodegenerative as well as psychiatric disease...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27826550/lysosomal-cathepsin-a-plays-a-significant-role-in-the-processing-of-endogenous-bioactive-peptides
#17
Zehra Kevser Timur, Secil Akyildiz Demir, Volkan Seyrantepe
Lysosomal serine carboxypeptidase Cathepsin A (CTSA) is a multifunctional enzyme with distinct protective and catalytic function. CTSA present in the lysosomal multienzyme complex to facilitate the correct lysosomal routing, stability and activation of with beta-galactosidase and alpha-neuraminidase. Beside CTSA has role in inactivation of bioactive peptides including bradykinin, substances P, oxytocin, angiotensin I and endothelin-I by cleavage of 1 or 2 amino acid(s) from C-terminal ends. In this study, we aimed to elucidate the regulatory role of CTSA on bioactive peptides in knock-in mice model of CTSA(S190A) ...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27800482/stabilization-of-the-virulence-plasmid-pslt-of-salmonella-typhimurium-by-three-maintenance-systems-and-its-evaluation-by-using-a-new-stability-test
#18
Damián Lobato-Márquez, Laura Molina-García, Inma Moreno-Córdoba, Francisco García-Del Portillo, Ramón Díaz-Orejas
Certain Salmonella enterica serovars belonging to subspecies I carry low-copy-number virulence plasmids of variable size (50-90 kb). All of these plasmids share the spv operon, which is important for systemic infection. Virulence plasmids are present at low copy numbers. Few copies reduce metabolic burden but suppose a risk of plasmid loss during bacterial division. This drawback is counterbalanced by maintenance modules that ensure plasmid stability, including partition systems and toxin-antitoxin (TA) loci...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27790618/designer-leptin-receptor-antagonist-allo-aca-inhibits-vegf-effects-in-ophthalmic-neoangiogenesis-models
#19
Roberta Coroniti, Rafal Fario, Didier J Nuno, Laszlo Otvos, Laura Scolaro, Eva Surmacz
Experimental and clinical data suggest that pro-angiogenic, pro-inflammatory and mitogenic cytokine leptin can be implicated in ocular neovascularization and other eye pathologies. At least in part, leptin action appears to be mediated through functional interplay with vascular endothelial growth factor (VEGF). VEGF is a potent regulator of neoangiogenesis and vascular leakage with a proven role in conditions such as proliferative diabetic retinopathy, age-related macular degeneration and diabetic macular edema...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27774450/effects-of-a-mutation-in-the-hspe1-gene-encoding-the-mitochondrial-co-chaperonin-hsp10-and-its-potential-association-with-a-neurological-and-developmental-disorder
#20
Anne S Bie, Paula Fernandez-Guerra, Rune I D Birkler, Shahar Nisemblat, Dita Pelnena, Xinping Lu, Joshua L Deignan, Hane Lee, Naghmeh Dorrani, Thomas J Corydon, Johan Palmfeldt, Liga Bivina, Abdussalam Azem, Kristin Herman, Peter Bross
We here report molecular investigations of a missense mutation in the HSPE1 gene encoding the HSP10 subunit of the HSP60/ HSP10 chaperonin complex that assists protein folding in the mitochondrial matrix. The mutation was identified in an infant who came to clinical attention due to infantile spasms at 3 months of age. Clinical exome sequencing revealed heterozygosity for a HSPE1 NM_002157.2:c.217C>T de novo mutation causing replacement of leucine with phenylalanine at position 73 of the HSP10 protein. This variation has never been observed in public exome sequencing databases or the literature...
2016: Frontiers in Molecular Biosciences
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