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Jisun Kim, Woojun Park
Polycyclic aromatic hydrocarbons (PAHs), including naphthalene, are widely distributed in nature. Naphthalene has been regarded as a model PAH compound for investigating the mechanisms of bacterial PAH biodegradation. Pseudomonas sp. AS1 isolated from an arsenic-contaminated site is capable of growing on various aromatic compounds such as naphthalene, salicylate, and catechol, but not on gentisate. The genome of strain AS1 consists of a 6,126,864 bp circular chromosome and the 81,841 bp circular plasmid pAS1...
November 25, 2017: Journal of Microbiology and Biotechnology
Nicholas A Willis, Richard L Frock, Francesca Menghi, Erin E Duffey, Arvind Panday, Virginia Camacho, E Paul Hasty, Edison T Liu, Frederick W Alt, Ralph Scully
Small, approximately 10-kilobase microhomology-mediated tandem duplications are abundant in the genomes of BRCA1-linked but not BRCA2-linked breast cancer. Here we define the mechanism underlying this rearrangement signature. We show that, in primary mammalian cells, BRCA1, but not BRCA2, suppresses the formation of tandem duplications at a site-specific chromosomal replication fork barrier imposed by the binding of Tus proteins to an array of Ter sites. BRCA1 has no equivalent role at chromosomal double-stranded DNA breaks, indicating that tandem duplications form specifically at stalled forks...
November 22, 2017: Nature
Andrés Castillo, Mario Tello, Kenneth Ringwald, Lillian G Acuña, Raquel Quatrini, Omar Orellana
Horizontal gene transfer is crucial for the adaptation of microorganisms to environmental cues. The acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans encodes an integrative-conjugative genetic element (ICEAfe1) inserted in the gene encoding a tRNA(Ala). This genetic element is actively excised from the chromosome upon induction of DNA damage. A similar genetic element (ICEAcaTY.2) is also found in an equivalent position in the genome of Acidithiobacillus caldus. The local genomic context of both mobile genetic elements is highly syntenous and the cognate integrases are well conserved...
November 23, 2017: RNA Biology
Kristen L Fessele, Fay Wright
The epigenome is a collection of chemical compounds that attach to and overlay the DNA sequence to direct gene expression. Epigenetic marks do not alter DNA sequence but instead allow or silence gene activity and the subsequent production of proteins that guide the growth and development of an organism, direct and maintain cell identity, and allow for the production of primordial germ cells (PGCs; ova and spermatozoa). The three main epigenetic marks are (1) histone modification, (2) DNA methylation, and (3) noncoding RNA, and each works in a different way to regulate gene expression...
January 1, 2017: Biological Research for Nursing
Tiia Maria Luukkonen, Mana M Mehrjouy, Minna Pöyhönen, Anna-Kaisa Anttonen, Päivi Lahermo, Pekka Ellonen, Lars Paulin, Niels Tommerup, Aarno Palotie, Teppo Varilo
BACKGROUND: The risk of serious congenital anomaly for de novo balanced translocations is estimated to be at least 6%. We identified two apparently independent families with a balanced t(1;12)(q43;q21.1) as an outcome of a "Systematic Survey of Balanced Chromosomal Rearrangements in Finns." In the first family, carriers (n = 6) manifest with learning problems in childhood, and later with unexplained neurological symptoms (chronic headache, balance problems, tremor, fatigue) and cerebral infarctions in their 50s...
November 23, 2017: Molecular Genetics & Genomic Medicine
Toshiki Takenouchi, Mie Inaba, Tomoko Uehara, Takao Takahashi, Kenjiro Kosaki, Seiji Mizuno
Loss-of function mutations in NALCN on chromosome 13q, a sodium leak channel that maintains baseline neuronal excitability, cause infantile hypotonia with psychomotor retardation and characteristic faces 1 (IHPRF1, OMIM #615419). Here, we document two individuals with early onset hypotonia with poor feeding and intellectual disability who were compatible with a diagnosis of IHPRF1. The two patients had bi-allelic mutations in NALCN through two different genetic mechanisms: Patient 1 had bi-allelic splice site mutations, that is c...
November 23, 2017: American Journal of Medical Genetics. Part A
Indrani Manna, Maumita Bandyopadhyay
Concentration of engineered nickel oxide nanoparticle (NiO-NP) in nature is on the rise, owing to large scale industrial uses, which have accreted the scope of its exposure to plants, the primary producers of the ecosystem. Though an essential micronutrient for the animal system, supported by numerous studies confirming its toxicity at higher dosages, nickel oxide is graded as a human carcinogen by WHO. A few studies do depict toxicity and bioaccumulation of nickel in plants; however, interaction of NiO-NP with plants is not well-elucidated...
2017: Frontiers in Chemistry
Aman Imran, Hafiza Yasara Qamar, Qurban Ali, Hafsa Naeem, Mariam Riaz, Saima Amin, Naila Kanwal, Fawad Ali, Muhammad Farooq Sabar, Idrees Ahmad Nasir
Background: Cancer is a genetic disease and mainly arises due to a number of reasons include activation of onco-genes, malfunction of tumor suppressor genes or mutagenesis due to external factors. Methods: This article was written from the data collected from PubMed, Nature, Science Direct, Springer and Elsevier groups of journals. Results: Oncogenes are deregulated form of normal proto-oncogenes required for cell division, differentiation and regulation...
November 2017: Iranian Journal of Public Health
Priyanka G Bhosale, Manishkumar Pandey, Simona Cristea, Mickey Shah, Asawari Patil, Niko Beerenwinkel, Alejandro A Schäffer, Manoj B Mahimkar
A key feature in the pathogenesis of OSCC is genetic instability, which results in altered expression of genes located in amplified/deleted chromosomal regions. In a previous study we have shown that the amplification of the 11q22.1-q22.2 region, encoding cIAP1 and cIAP2, is associated with lymph node metastasis and poor clinical outcome in OSCC. Here, we validate the aCGH results by nuc ish and detect a weak amplification at the 11q22.1-q22.2 locus in 37% of the 182 samples tested. We find positive correlation of 11q22...
November 22, 2017: Scientific Reports
Saskia van de Poel, Marcel Dreer, Ana Velic, Boris Macek, Praveen Baskaran, Thomas Iftner, Frank Stubenrauch
The papillomavirus E2 protein regulates transcription, replication and nuclear retention of viral genomes. Phosphorylation of E2 in the hinge region has been suggested to modulate protein stability, DNA-binding activity and chromosomal attachment. The papillomavirus E8^E2 protein shares the hinge domain with E2 and acts as a repressor of viral replication. Mass spectrometry analyses of HPV31 E8^E2 and E2 proteins identify phosphorylated S78, S81 and S100 in E8^E2 and S266 and S269 in E2 in their hinge regions...
November 22, 2017: Journal of Virology
Simon Jenni, Yoana N Dimitrova, Roberto Valverde, Stephen M Hinshaw, Stephen C Harrison
Kinetochore molecular architecture exemplifies "form follows function." The simplifications that generated the one-chromosome:one-microtubule linkage in point-centromere yeast have enabled strategies for systematic structural analysis and high-resolution visualization of many kinetochore components, leading to specific proposals for molecular mechanisms. We describe here some structural features that allow a kinetochore to remain attached to the end of a depolymerizing microtubule (MT) and some characteristics of the connections between substructures that permit very sensitive regulation by differential kinase activities...
November 22, 2017: Cold Spring Harbor Symposia on Quantitative Biology
Josh Lawrimore, Brandon Friedman, Ayush Doshi, Kerry Bloom
ChromoShake is a three-dimensional simulator designed to explore the range of configurational states a chromosome can adopt based on thermodynamic fluctuations of the polymer chain. Here, we refine ChromoShake to generate dynamic simulations of a DNA-based motor protein such as condensin walking along the chromatin substrate. We model walking as a rotation of DNA-binding heat-repeat proteins around one another. The simulation is applied to several configurations of DNA to reveal the consequences of mechanical stepping on taut chromatin under tension versus loop extrusion on single-tethered, floppy chromatin substrates...
November 22, 2017: Cold Spring Harbor Symposia on Quantitative Biology
Allan C Spradling
Polytene chromosomes have for 80 years provided the highest resolution view of interphase genome structure in an animal cell nucleus. These chromosomes represent the normal genomic state of nearly all Drosophila larval and many adult cells, and a better understanding of their striking banded structure has been sought for decades. A more recently appreciated characteristic of Drosophila polytene cells is somatic genome instability caused by unfinished replication (UR). Repair of stalled forks generates enough deletions in polytene salivary gland cells to alter 10%-90% of the DNA strands within more than 100 UR regions comprising 20% of the euchromatic genome...
November 22, 2017: Cold Spring Harbor Symposia on Quantitative Biology
Kata Sarlós, Andreas Biebricher, Erwin J G Petermann, Gijs J L Wuite, Ian D Hickson
To survive and proliferate, cells have to faithfully segregate their newly replicated genomic DNA to the two daughter cells. However, the sister chromatids of mitotic chromosomes are frequently interlinked by so-called ultrafine DNA bridges (UFBs) that are visible in the anaphase of mitosis. UFBs can only be detected by the proteins bound to them and not by staining with conventional DNA dyes. These DNA bridges are presumed to represent entangled sister chromatids and hence pose a threat to faithful segregation...
November 22, 2017: Cold Spring Harbor Symposia on Quantitative Biology
Daya Marasini, Mohamed K Fakhr
We report the complete genome sequences of multidrug-resistant Campylobacter jejuni and Campylobacter coli isolated from retail turkey and pork, respectively. The chromosomes of these two isolates contained type VI secretion system genes. The two isolates also harbored large plasmids with antimicrobial resistance genes possibly contributing to their multidrug resistance.
November 22, 2017: Genome Announcements
Daya Marasini, Mohamed K Fakhr
Genome sequences of Campylobacter jejuni FJ3124 and ZP3204 isolated from retail chicken gizzards and Campylobacter jejuni TS1218 isolated from retail chicken showed the presence of 1,694,324-, 1,763,161-, and 1,762,596-bp circular chromosomes, respectively. Campylobacter jejuni ZP3204 and TS1218 harbored large tetracycline resistance plasmids with type IV secretion systems.
November 22, 2017: Genome Announcements
Laura E Williams, David A Baltrus, Sean D O'Donnell, Tara J Skelly, Mark O Martin
We report here the complete genome sequence of the facultative predatory bacterium Ensifer adhaerens strain Casida A. The genome was assembled into three circular contigs, with a main chromosome as well as two large secondary replicons, that totaled 7,267,502 bp with 6,641 predicted open reading frames.
November 22, 2017: Genome Announcements
Daya Marasini, Carolyn R Cornell, Opeoluwa Oyewole, Robert J Sheaff, Mohamed K Fakhr
The whole-genome sequence of Bacillus velezensis strain SB1216, isolated from the Great Salt Plains of Oklahoma, showed the presence of a 3,814,720-bp circular chromosome and no plasmids. The presence of a novel 870-bp extracellular RNase gene is predicted to be responsible for this strain's antitumor activity.
November 22, 2017: Genome Announcements
Mitsunori Yoshida, Shinji Izumiyama, Hanako Fukano, Kanji Sugiyama, Masato Suzuki, Keigo Shibayama, Yoshihiko Hoshino
Mycobacterium sp. strain shizuoka-1 is a rapidly growing scotochromogenic mycobacterium and was isolated from well water for a bathing facility in Shizuoka Prefecture in Japan. Here, we report the draft sequence of its genome, comprising a 6.5-Mb chromosome. This mycobacterium has 83.1% identity with Mycobacterium rhodesiae, a human pathogen.
November 22, 2017: Genome Announcements
Hani Boshra, Wioleta M Zelek, Timothy R Hughes, Santiago Rodriguez de Cordoba, B Paul Morgan
CD59 is a membrane-bound regulatory protein that inhibits the assembly of the terminal membrane attack complex (C5b-9) of complement. From its original discovery in humans almost 30 years ago, CD59 has been characterized in a variety of species, from primates to early vertebrates, such as teleost fish. CD59 is ubiquitous in mammals; however, we have described circumstantial evidence suggesting that guinea pigs (Cavia porcellus) lack CD59, at least on erythrocytes. In this study, we have used a combination of phylogenetic analyses with syntenic alignment of mammalian CD59 genes to identify the only span of genomic DNA in C...
November 22, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
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