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https://www.readbyqxmd.com/read/28106859/burkholderia-cepacia-complex-regulation-of-virulence-gene-expression-a-review
#1
REVIEW
Sílvia A Sousa, Joana R Feliciano, Tiago Pita, Soraia I Guerreiro, Jorge H Leitão
Burkholderia cepacia complex (Bcc) bacteria emerged as opportunistic pathogens in cystic fibrosis and immunocompromised patients. Their eradication is very difficult due to the high level of intrinsic resistance to clinically relevant antibiotics. Bcc bacteria have large and complex genomes, composed of two to four replicons, with variable numbers of insertion sequences. The complexity of Bcc genomes confers a high genomic plasticity to these bacteria, allowing their adaptation and survival to diverse habitats, including the human host...
January 19, 2017: Genes
https://www.readbyqxmd.com/read/28106858/regulation-of-dna-replication-in-early-embryonic-cleavages
#2
REVIEW
Chames Kermi, Elena Lo Furno, Domenico Maiorano
Early embryonic cleavages are characterized by short and highly synchronous cell cycles made of alternating S- and M-phases with virtually absent gap phases. In this contracted cell cycle, the duration of DNA synthesis can be extraordinarily short. Depending on the organism, the whole genome of an embryo is replicated at a speed that is between 20 to 60 times faster than that of a somatic cell. Because transcription in the early embryo is repressed, DNA synthesis relies on a large stockpile of maternally supplied proteins stored in the egg representing most, if not all, cellular genes...
January 19, 2017: Genes
https://www.readbyqxmd.com/read/28106814/genome-analysis-of-a-novel-broad-host-range-proteobacteria-phage-isolated-from-a-bioreactor-treating-industrial-wastewater
#3
Marina de Leeuw, Maayan Baron, Asher Brenner, Ariel Kushmaro
Bacteriophages are viruses that infect bacteria, and consequently they have a major impact on the development of a microbial population. In this study, the genome of a novel broad host range bacteriophage, Aquamicrobium phage P14, isolated from a wastewater treatment plant, was analyzed. The Aquamicrobium phage P14 was found to infect members of different Proteobacteria classes (Alphaproteobacteria and Betaproteobacteria). This phage contains a 40,551 bp long genome and 60% of its genes had blastx hits. Furthermore, the bacteriophage was found to share more than 50% of its genes with several podoviruses and has the same gene order as other polyvalent bacteriophages...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28106799/rna-editing-adar1-and-the-innate-immune-response
#4
REVIEW
Qingde Wang, Xiaoni Li, Ruofan Qi, Timothy Billiar
RNA editing, particularly A-to-I RNA editing, has been shown to play an essential role in mammalian embryonic development and tissue homeostasis, and is implicated in the pathogenesis of many diseases including skin pigmentation disorder, autoimmune and inflammatory tissue injury, neuron degeneration, and various malignancies. A-to-I RNA editing is carried out by a small group of enzymes, the adenosine deaminase acting on RNAs (ADARs). Only three members of this protein family, ADAR1-3, exist in mammalian cells...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28106797/the-complex-relationship-between-virulence-and-antibiotic-resistance
#5
REVIEW
Meredith Schroeder, Benjamin D Brooks, Amanda E Brooks
Antibiotic resistance, prompted by the overuse of antimicrobial agents, may arise from a variety of mechanisms, particularly horizontal gene transfer of virulence and antibiotic resistance genes, which is often facilitated by biofilm formation. The importance of phenotypic changes seen in a biofilm, which lead to genotypic alterations, cannot be overstated. Irrespective of if the biofilm is single microbe or polymicrobial, bacteria, protected within a biofilm from the external environment, communicate through signal transduction pathways (e...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28106789/centromere-stability-the-replication-connection
#6
REVIEW
Susan L Forsburg, Kuo-Fang Shen
The fission yeast centromere, which is similar to metazoan centromeres, contains highly repetitive pericentromere sequences that are assembled into heterochromatin. This is required for the recruitment of cohesin and proper chromosome segregation. Surprisingly, the pericentromere replicates early in the S phase. Loss of heterochromatin causes this domain to become very sensitive to replication fork defects, leading to gross chromosome rearrangements. This review examines the interplay between components of DNA replication, heterochromatin assembly, and cohesin dynamics that ensures maintenance of genome stability and proper chromosome segregation...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28106786/sulfolobus-acidocaldarius-udg-can-remove-du-from-the-rna-backbone-insight-into-the-specific-recognition-of-uracil-linked-with-deoxyribose
#7
Gang-Shun Yi, Wei-Wei Wang, Wei-Guo Cao, Feng-Ping Wang, Xi-Peng Liu
Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28106732/familial-lung-cancer-a-brief-history-from-the-earliest-work-to-the-most-recent-studies
#8
REVIEW
Anthony M Musolf, Claire L Simpson, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li, Ming You, Elena Y Kupert, Marshall W Anderson, Ann G Schwartz, Susan M Pinney, Christopher I Amos, Joan E Bailey-Wilson
Lung cancer is the deadliest cancer in the United States, killing roughly one of four cancer patients in 2016. While it is well-established that lung cancer is caused primarily by environmental effects (particularly tobacco smoking), there is evidence for genetic susceptibility. Lung cancer has been shown to aggregate in families, and segregation analyses have hypothesized a major susceptibility locus for the disease. Genetic association studies have provided strong evidence for common risk variants of small-to-moderate effect...
January 17, 2017: Genes
https://www.readbyqxmd.com/read/28098823/integrative-mirna-gene-expression-analysis-enables-refinement-of-associated-biology-and-prediction-of-response-to-cetuximab-in-head-and-neck-squamous-cell-cancer
#9
Loris De Cecco, Marco Giannoccaro, Edoardo Marchesi, Paolo Bossi, Federica Favales, Laura D Locati, Lisa Licitra, Silvana Pilotti, Silvana Canevari
This paper documents the process by which we, through gene and miRNA expression profiling of the same samples of head and neck squamous cell carcinomas (HNSCC) and an integrative miRNA-mRNA expression analysis, were able to identify candidate biomarkers of progression-free survival (PFS) in patients treated with cetuximab-based approaches. Through sparse partial least square-discriminant analysis (sPLS-DA) and supervised analysis, 36 miRNAs were identified in two components that clearly separated long- and short-PFS patients...
January 14, 2017: Genes
https://www.readbyqxmd.com/read/28098820/applying-human-adar1p110-and-adar1p150-for-site-directed-rna-editing-g-c-substitution-stabilizes-guidernas-against-editing
#10
Madeleine Heep, Pia Mach, Philipp Reautschnig, Jacqueline Wettengel, Thorsten Stafforst
Site-directed RNA editing is an approach to reprogram genetic information at the RNA level. We recently introduced a novel guideRNA that allows for the recruitment of human ADAR2 to manipulate genetic information. Here, we show that the current guideRNA design is already able to recruit another human deaminase, ADAR1, in both isoforms, p110 and p150. However, further optimization seems necessary as the current design is less efficient for ADAR1 isoforms. Furthermore, we describe hotspots at which the guideRNA itself is edited and show a way to circumvent this auto-editing without losing editing efficiency at the target...
January 14, 2017: Genes
https://www.readbyqxmd.com/read/28098815/replication-fork-protection-factors-controlling-r-loop-bypass-and-suppression
#11
REVIEW
Emily Yun-Chia Chang, Peter C Stirling
Replication-transcription conflicts have been a well-studied source of genome instability for many years and have frequently been linked to defects in RNA processing. However, recent characterization of replication fork-associated proteins has revealed that defects in fork protection can directly or indirectly stabilize R-loop structures in the genome and promote transcription-replication conflicts that lead to genome instability. Defects in essential DNA replication-associated activities like topoisomerase, or the minichromosome maintenance (MCM) helicase complex, as well as fork-associated protection factors like the Fanconi anemia pathway, both appear to mitigate transcription-replication conflicts...
January 14, 2017: Genes
https://www.readbyqxmd.com/read/28098800/characterization-of-the-transcriptome-and-gene-expression-of-brain-tissue-in-sevenband-grouper-hyporthodus-septemfasciatus-in-response-to-nnv-infection
#12
Jong-Oh Kim, Jae-Ok Kim, Wi-Sik Kim, Myung-Joo Oh
Grouper is one of the favorite sea food resources in Southeast Asia. However, the outbreaks of the viral nervous necrosis (VNN) disease due to nervous necrosis virus (NNV) infection have caused mass mortality of grouper larvae. Many aqua-farms have suffered substantial financial loss due to the occurrence of VNN. To better understand the infection mechanism of NNV, we performed the transcriptome analysis of sevenband grouper brain tissue, the main target of NNV infection. After artificial NNV challenge, transcriptome of brain tissues of sevenband grouper was subjected to next generation sequencing (NGS) using an Illumina Hi-seq 2500 system...
January 13, 2017: Genes
https://www.readbyqxmd.com/read/28098792/acknowledgement-to-reviewers-of-genes-in-2016
#13
EDITORIAL
Genes Editorial Office
The editors of Genes would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2016. We greatly appreciate the contribution of expert reviewers, which is crucial to the journal's editorial process. We aim to recognize reviewer contributions through several mechanisms, of which the annual publication of reviewer names is one. Reviewers receive a voucher entitling them to a discount on their next MDPI publication and can download a certificate of recognition directly from our submission system...
January 13, 2017: Genes
https://www.readbyqxmd.com/read/28085119/transgenic-tobacco-expressing-the-tat-helicokinin-i-cpti-fusion-protein-show-increased-resistance-and-toxicity-to-helicoverpa-armigera-lepidoptera-noctuidae
#14
Zhou Zhou, Yongli Li, Chunyan Yuan, Yongan Zhang, Liangjian Qu
Insect kinins were shown to have diuretic activity, inhibit weight gain, and have antifeedant activity in insects. In order to study the potential of the TAT-fusion approach to deliver diuretic peptides per os to pest insects, the HezK I peptide from Helicoverpa zea, as a representative of the kinin family, was selected. The fusion gene TAT-HezK I was designed and was used to transform tobacco plants. As a means to further improve the stability of TAT-HezK I, a fusion protein incorporating HezK I, transactivator of transcription (TAT), and the cowpea trypsin inhibitor (CpTI) was also designed...
January 12, 2017: Genes
https://www.readbyqxmd.com/read/28085095/erratum-pan-y-et-al-cucumber-metallothionein-like-2-csmtl2-exhibits-metal-binding-properties-genes-2016-7-106
#15
https://www.readbyqxmd.com/read/28085061/origin-dna-melting-an-essential-process-with-divergent-mechanisms
#16
REVIEW
Matthew P Martinez, John M Jones, Irina Bruck, Daniel L Kaplan
Origin DNA melting is an essential process in the various domains of life. The replication fork helicase unwinds DNA ahead of the replication fork, providing single-stranded DNA templates for the replicative polymerases. The replication fork helicase is a ring shaped-assembly that unwinds DNA by a steric exclusion mechanism in most DNA replication systems. While one strand of DNA passes through the central channel of the helicase ring, the second DNA strand is excluded from the central channel. Thus, the origin, or initiation site for DNA replication, must melt during the initiation of DNA replication to allow for the helicase to surround a single-DNA strand...
January 11, 2017: Genes
https://www.readbyqxmd.com/read/28085060/identification-of-the-ovine-keratin-associated-protein-22-1-kap22-1-gene-and-its-effect-on-wool-traits
#17
Shaobin Li, Huitong Zhou, Hua Gong, Fangfang Zhao, Jiqing Wang, Xiu Liu, Yuzhu Luo, Jon G H Hickford
Keratin-associated proteins (KAPs) are structural components of wool and hair fibers. To date, eight high glycine/tyrosine KAP (HGT-KAP) families have been identified in humans, but only three have been identified in sheep. In this study, the putative ovine homolog of the human KAP22-1 gene (KRTAP22-1) was amplified using primers designed based on a human KRTAP22-1 sequence. Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) was used to screen for variation in KRTAP22-1 in 390 Merino × Southdown-cross lambs and 75 New Zealand (NZ) Romney sheep...
January 11, 2017: Genes
https://www.readbyqxmd.com/read/28075396/translesion-synthesis-insights-into-the-selection-and-switching-of-dna-polymerases
#18
REVIEW
Linlin Zhao, M Todd Washington
DNA replication is constantly challenged by DNA lesions, noncanonical DNA structures and difficult-to-replicate DNA sequences. Two major strategies to rescue a stalled replication fork and to ensure continuous DNA synthesis are: (1) template switching and recombination-dependent DNA synthesis; and (2) translesion synthesis (TLS) using specialized DNA polymerases to perform nucleotide incorporation opposite DNA lesions. The former pathway is mainly error-free, and the latter is error-prone and a major source of mutagenesis...
January 10, 2017: Genes
https://www.readbyqxmd.com/read/28075391/aac-as-a-potential-target-gene-to-control-verticillium-dahliae
#19
Xiaofeng Su, Latifur Rehman, Huiming Guo, Xiaokang Li, Rui Zhang, Hongmei Cheng
Verticillium dahliae invades the roots of host plants and causes vascular wilt, which seriously diminishes the yield of cotton and other important crops. The protein AAC (ADP, ATP carrier) is responsible for transferring ATP from the mitochondria into the cytoplasm. When V. dahliae protoplasts were transformed with short interfering RNAs (siRNAs) targeting the VdAAC gene, fungal growth and sporulation were significantly inhibited. To further confirm a role for VdAAC in fungal development, we generated knockout mutants (ΔVdACC)...
January 10, 2017: Genes
https://www.readbyqxmd.com/read/28075389/control-of-initiation-of-dna-replication-in-bacillus-subtilis-and-escherichia-coli
#20
REVIEW
Katie H Jameson, Anthony J Wilkinson
Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication...
January 10, 2017: Genes
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