A review of the genus Muusoctopus (Cephalopoda: Octopoda) from Arctic waters.

We report two Arctic species of incirrate octopods new to science. One is formally described here as Muusoctopus aegir Golikov, Gudmundsson & Sabirov sp. nov. while the other, Muusoctopus sp. 1, is not formally described due to a limited number of samples (all are immature individuals). These two species differ from each other, and from other Muusoctopus, especially in: 1) absence of stylets (in M. aegir sp. nov.); 2) proportions of mantle and head; 3) funnel organ morphology (W-shaped with medial and marginal limbs of equal length in M. aegir sp. nov., or medial are slightly longer; V V-shaped with medial limbs slightly longer and broader than marginal in Muusoctopus sp. 1); 4) sucker and gill lamellae counts; 5) relative arm length and sucker diameter; and 6) male reproductive system relative size and morphology. Species of Muusoctopus now comprise four of 12 known Arctic cephalopods. Additionally, this study provides: a) new data on the morphology and reproductive biology of M. johnsonianus and M. sibiricus, and a diagnosis of M. sibiricus; b) the equations to estimate mantle length and body mass from beak measurements of M. aegir sp. nov. and M. johnsonianus; c) a cytochrome c oxidase subunit I gene barcode for M. sibiricus; d) new data on the ecology and distribution of all studied species; and e) a data table for the identification of northern North Atlantic and Arctic species of Muusoctopus.

Lynch Syndrome Germline Mutations in Breast Cancer: Next Generation Sequencing Case-Control Study of 1,263 Participants.

Genome instability-the increased tendency of acquiring mutations in the genome and ability of a cell to tolerate high mutation burden-is one of the drivers of cancer. Genome instability results from many causes including defects in DNA repair systems. Previously, it has been shown that germline pathogenic mutations in DNA Mismatch Repair (MMR) pathway cause cancer-predisposing Lynch Syndrome. We proposed that Lynch Syndrome-related germline mutations (LS-mutations) are associated with breast cancer (BC). In this study, we performed Targeted Next-Generation Sequencing of MMR pathway genes MLH1, MSH2, MSH6, EPCAM, and PMS2 in a cohort of 711 patients with hereditary BC, 60 patients with sporadic BC, and 492 healthy donors. Sixty-nine patients (9.7%) with hereditary BC harbored at least one germline mutation in the MMR pathway genes, of them 32 patients (4.5%) harbored mutations in MMR pathway genes which we define as pathogenic or likely pathogenic, and of them 26 patients (3.6%) did not have any pathogenic mutations in DDR pathway genes, compared to two mutations in MMR pathway genes (0.4%) detected in a group of 492 healthy donors [p = 0.00013, OR = 8.9 (CI 95% 2.2-78.4)]. Our study demonstrates that LS-mutations are present in patients with hereditary BC more frequently than in healthy donors, and that there is an association of hereditary BC and mutations c.1321G>A in MLH1, c.260C>G and c.2178G>C in MSH2, c.3217C>T in MSH6, c.1268C>G and c.86G>C in PMS2 genes. This finding provides a rationale for including pathogenic LS-mutations into genetic counseling tests for patients with hereditary BC.

Comparative Genome Analysis of Uropathogenic Morganella morganii Strains.

Morganella morganii is an opportunistic bacterial pathogen shown to cause a wide range of clinical and community-acquired infections. This study was aimed at sequencing and comparing the genomes of three M. morganii strains isolated from the urine samples of patients with community-acquired urinary tract infections. Draft genome sequencing was conducted using the Illumina HiSeq platform. The genomes of MM 1, MM 4, and MM 190 strains have a size of 3.82-3.97 Mb and a GC content of 50.9-51%. Protein-coding sequences (CDS) represent 96.1% of the genomes, RNAs are encoded by 2.7% of genes and pseudogenes account for 1.2% of the genomes. The pan-genome containes 4,038 CDS, of which 3,279 represent core genes. Six to ten prophages and 21-33 genomic islands were identified in the genomes of MM 1, MM 4, and MM 190. More than 30 genes encode capsular biosynthesis proteins, an average of 60 genes encode motility and chemotaxis proteins, and about 70 genes are associated with fimbrial biogenesis and adhesion. We determined that all strains contained urease gene cluster ureABCEFGD and had a urease activity. Both MM 4 and MM 190 strains are capable of hemolysis and their activity correlates well with a cytotoxicity level on T-24 bladder carcinoma cells. These activities were associated with expression of RTX toxin gene hlyA, which was introduced into the genomes by a phage similar to Salmonella phage 118970_sal4.

Draft genome sequence and analysis of Klebsiella oxytoca strain NK-1 isolated from ureteral stent.

Klebsiella oxytoca is a facultative aerobic, gram-negative, rod-shaped bacterium capable of causing nosocomial infections, in particular catheter-associated urinary tract infections (CAUTIs). Data on the possible roles of uncommon pathogens such as K. oxytoca in the pathogenesis of biofilm-associated infections such as CAUTIs have been already reported. Herein, we describe the draft genome sequence of K. oxytoca strain NK-1 isolated from the surface of ureteral stent retrieved from a Russian female. The genome comprises 6,232,464 bp, with a G + C content of 55.60% and an L 50 of 7. A total of 6246 putative protein-encoding genes were predicted, including considerable number of genes responsible for adhesion, invasion, drug resistance, iron acquisition and other genes relevant for virulence. The NK-1 strain was ascribed a sequence type (ST) as ST 216 (4, 6, 19, 10, 46, 24, 31). Data comparison of the recA gene sequences confirmed that the strain belongs to the species K. oxytoca. Minimal inhibitory concentration of different antibiotics have been determined. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number QPKC00000000.1.

Draft genome sequence of Staphylococcus sp. EZ-P03 isolated from a mesophilic anaerobic digester.

OBJECTIVES: Staphylococcus species of the family Staphylococcaceae are facultatively anaerobic Gram-positive cocci growing in clusters, pairs and occasionally in short chains. Staphylococci can be detected in different environments. They are common commensals, but some can also cause infections in humans. Hence, their investigation is required to understand ecology and genetics and to create an opportunity for comparative studies. DATA DESCRIPTION: In this study, we report the determination of a draft genome sequence of Staphylococcus sp. strain EZ-P03 which was isolated from anaerobically digested chicken waste materials. The draft genome of Staphylococcus sp. EZ-P03 constituted a total of 62 contigs (> 500 bp) amounting to 2,689,358 bp with a G+C content of 37.3% and a N50 contig size of 126,562 bp. The whole genome shotgun project of Staphylococcus sp. strain EZ-P03 has been deposited at DDBJ/ENA/GenBank under the accession number QPMO00000000.

Draft genome sequence of Bacillus pumilus strain EZ-C07 isolated from digested agricultural wastes.

OBJECTIVES: Bacillus species, belonging to the family Bacillaceae, are rod-shaped aerobic or facultative anaerobic Gram-positive bacteria that can be isolated from various environmental niches. Bacillus pumilus strains are resistant to unfavorable conditions such as UV, H2O2 and chemical disinfection. Furthermore, B. pumilus strains synthesize multifarious important enzymes and can be used in the production of some fermented foods, bioremediation of wastewater systems and biodegradation of environmental contaminants. Hence, investigation at the genomic level is required to understand their ecology, genetics and potential applications. DATA DESCRIPTION: In this research, we provide the genomic insights into one Bacillus species (EZ-C07) isolated from digested agricultural waste materials. The draft genome of the strain EZ-C07 consists of 3,724,869 bp with 3890 coding sequences and 41.5% G + C content. Based on 16S rRNA gene sequence analysis followed by in silico DNA-DNA hybridization studies, the strain EZ-C07 was identified as Bacillus pumilus belonging to the family Bacillaceae within the phylum Firmicutes. The whole genome shotgun project of B. pumilus strain EZ-C07 can be accessed at DDBJ/ENA/GenBank under the Accession QLVI00000000.

Draft genome sequence data of Lysinibacillus fusiformis strain GM, isolated from potato phyllosphere as a potential probiotic.

Here we present the morphological and physiological properties of isolated Lysinibacillus fusiformis strain GM, its draft genome sequence as well as annotation and analysis of its genome. Initial analysis of MALDI-TOF mass spectrometry, 16S rRNA gene analysis and in silico DNA-DNA hybridization revealed that the strain belongs to the species Lysinibacillus fusiformis. The 4,678,122 bp draft genome consist of 17 scaffolds encoding 4588 proteins and 137 RNAs. Annotation of the genome sequence revealed cellulase and protease encoding genes, genes of adhesion proteins and putative genes responsible for the biosynthesis of antimicrobial metabolites. The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number NTMQ00000000.1 (https://www.ncbi.nlm.nih.gov/nuccore/NZ_NTMQ00000000.1).

Cerebellar Atrophy and Changes in Cytokines Associated with the CACNA1A R583Q Mutation in a Russian Familial Hemiplegic Migraine Type 1 Family.

Background: Immune mechanisms recently emerged as important contributors to migraine pathology with cytokines affecting neuronal excitation. Therefore, elucidating the profile of cytokines activated in various forms of migraine, including those with a known genetic cause, can help in diagnostic and therapeutic approaches. Methods: Here we (i) performed exome sequencing to identify the causal gene mutation and (ii) measured, using Bio-Plex technology, 22 cytokines in serum of patients with familial migraine (two with hemiplegic migraine and two with migraine with aura) from a Russian family that ethnically belongs to the Tatar population. MRI scanning was used to assess cerebellar atrophy associated with migraine in mutation carriers. Results: Whole-exome sequencing revealed the R583Q missense mutation in the CACNA1A gene in the two patients with hemiplegic migraine and cerebellar ataxia with atrophy, confirming a FHM1 disorder. Two further patients did not have the mutation and suffered from migraine with aura. Elevated serum levels of pro-inflammatory and pro-nociceptive IL-6 and IL-18 were found in all four patients (compared to a reference panel), whereas pro-apoptotic SCGF-ß and TRAIL were higher only in the patients with the FHM1 mutation. Also, cytokines CXCL1, HGF, LIF, and MIF were found particularly high in the two mutation carriers, suggesting a possible role of vascular impairment and neuroinflammation in disease pathogenesis. Notably, some "algesic" cytokines, such as ß-NGF and TNFß, remained unchanged or even were down-regulated. Conclusion: We present a detailed genetic, neurological, and biochemical characterization of a small Russian FHM1 family and revealed evidence for higher levels of specific cytokines in migraine patients that support migraine-associated neuroinflammation in the pathology of migraine.