journal
MENU ▼
Read by QxMD icon Read
search

Frontiers in Molecular Biosciences

journal
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27766255/fapr-from-control-of-membrane-lipid-homeostasis-to-a-biotechnological-tool
#13
Daniela Albanesi, Diego de Mendoza
Phospholipids and fatty acids are not only one of the major components of cell membranes but also important metabolic intermediates in bacteria. Since the fatty acid biosynthetic pathway is essential and energetically expensive, organisms have developed a diversity of homeostatic mechanisms to fine-tune the concentration of lipids at particular levels. FapR is the first global regulator of lipid synthesis discovered in bacteria and is largely conserved in Gram-positive organisms including important human pathogens, such as Staphylococcus aureus, Bacillus anthracis, and Listeria monocytogenes...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27747217/dnajb6-myopathies-focused-review-on-an-emerging-and-expanding-group-of-myopathies
#14
Alessandra Ruggieri, Simona Saredi, Simona Zanotti, Maria Barbara Pasanisi, Lorenzo Maggi, Marina Mora
Mutations in the DNAJB6 gene have been associated with the autosomal dominant limb girdle muscular dystrophy type 1D (LGMD1D), a disorder characterized by abnormal protein aggregates and rimmed vacuoles in muscle fibers. DNAJB6 is a ubiquitously expressed Hsp40 co-chaperone characterized by a J domain that specifies Hsp70 functions in the cellular environment. DNAJB6 is also a potent inhibitor of expanded polyglutamine (polyQ) aggregation preventing aggregate toxicity in cells. In DNAJB6-mutated patients this anti-aggregation property is significantly reduced, albeit not completely lost...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27747216/opening-the-strands-of-replication-origins-still-an-open-question
#15
Jyoti K Jha, Revathy Ramachandran, Dhruba K Chattoraj
The local separation of duplex DNA strands (strand opening) is necessary for initiating basic transactions on DNA such as transcription, replication, and homologous recombination. Strand opening is commonly a stage at which these processes are regulated. Many different mechanisms are used to open the DNA duplex, the details of which are of great current interest. In this review, we focus on a few well-studied cases of DNA replication origin opening in bacteria. In particular, we discuss the opening of origins that support the theta (θ) mode of replication, which is used by all chromosomal origins and many extra-chromosomal elements such as plasmids and phages...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27747215/the-multifaceted-activity-of-the-virf-regulatory-protein-in-the-shigella-lifestyle
#16
Maria Letizia Di Martino, Maurizio Falconi, Gioacchino Micheli, Bianca Colonna, Gianni Prosseda
Shigella is a highly adapted human pathogen, mainly found in the developing world and causing a severe enteric syndrome. The highly sophisticated infectious strategy of Shigella banks on the capacity to invade the intestinal epithelial barrier and cause its inflammatory destruction. The cellular pathogenesis and clinical presentation of shigellosis are the sum of the complex action of a large number of bacterial virulence factors mainly located on a large virulence plasmid (pINV). The expression of pINV genes is controlled by multiple environmental stimuli through a regulatory cascade involving proteins and sRNAs encoded by both the pINV and the chromosome...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27747214/mgaspn-and-h-ns-two-unrelated-global-regulators-with-similar-dna-binding-properties
#17
Virtu Solano-Collado, Mário Hüttener, Manuel Espinosa, Antonio Juárez, Alicia Bravo
Global regulators play an essential role in the adaptation of bacterial cells to specific niches. Bacterial pathogens thriving in the tissues and organs of their eukaryotic hosts are a well-studied example. Some of the proteins that recognize local DNA structures rather than specific nucleotide sequences act as global modulators in many bacteria, both Gram-negative and -positive. To this class of regulators belong the H-NS-like proteins, mainly identified in γ-Proteobacteria, and the MgaSpn-like proteins identified in Firmicutes...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27747213/dereplication-of-natural-products-using-gc-tof-mass-spectrometry-improved-metabolite-identification-by-spectral-deconvolution-ratio-analysis
#18
Fausto Carnevale Neto, Alan C Pilon, Denise M Selegato, Rafael T Freire, Haiwei Gu, Daniel Raftery, Norberto P Lopes, Ian Castro-Gamboa
Dereplication based on hyphenated techniques has been extensively applied in plant metabolomics, thereby avoiding re-isolation of known natural products. However, due to the complex nature of biological samples and their large concentration range, dereplication requires the use of chemometric tools to comprehensively extract information from the acquired data. In this work we developed a reliable GC-MS-based method for the identification of non-targeted plant metabolites by combining the Ratio Analysis of Mass Spectrometry deconvolution tool (RAMSY) with Automated Mass Spectral Deconvolution and Identification System software (AMDIS)...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27734017/dna-damage-in-healthy-individuals-and-respiratory-patients-after-treating-whole-blood-in-vitro-with-the-bulk-and-nano-forms-of-nsaids
#19
Mojgan Najafzadeh, Charmaine Normington, Badie K Jacob, Mohammad Isreb, Rajendran C Gopalan, Diana Anderson
Non-steroidal anti-inflammatory drugs (NSAIDs) inhibit COX enzyme activity which affects the inflammatory response. Inflammation is associated with increasing cancer incidence. Pre-clinical and clinical studies have shown that NSAID treatment could cause an anti-tumor effect in cancers. In the present study, blood was taken from healthy individuals (n = 17) and patients with respiratory diseases or lung cancer (n = 36). White blood cells (WBC) were treated with either a micro-suspension, i.e., bulk (B) or nano-suspension (N) of aspirin (ASP) or ibuprofen (IBU) up to 500 μg/ml in the comet assay and up to 125 μg/ml in the micronucleus assay...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27730127/functionality-of-in-vitro-reconstituted-group-ii-intron-rmint1-derived-ribonucleoprotein-particles
#20
Maria D Molina-Sánchez, Fernando M García-Rodríguez, Nicolás Toro
The functional unit of mobile group II introns is a ribonucleoprotein particle (RNP) consisting of the intron-encoded protein (IEP) and the excised intron RNA. The IEP has reverse transcriptase activity but also promotes RNA splicing, and the RNA-protein complex triggers site-specific DNA insertion by reverse splicing, in a process called retrohoming. In vitro reconstituted ribonucleoprotein complexes from the Lactococcus lactis group II intron Ll.LtrB, which produce a double strand break, have recently been studied as a means of developing group II intron-based gene targeting methods for higher organisms...
2016: Frontiers in Molecular Biosciences
journal
journal
50073
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"