OTUs and assignments for bacteria associated to the shell of Cancer pagurus according to ENA PRJEB27139.
Contributors: Philipp Kraemer
... Bacterial OTUs found associated to the shell of Cancer pagurus. OTUs were calculated based on samples from the accession PRJEB27139 in ENA. Provided is the OTUs.fasta for sequence information and the associated assignments in Assignments.txt.
Effects of enzyme additives and Lactobacillus plantarum on the bacterial community as determined of Medicago sativa silageby Illumina sequencing
Contributors: Zong Fu HU
... more and more research are used new technique to investigate bacterial community of silage, such as next generation sequencing. This study aimed to evaluate the effects of enzymes (cellulase combined with alpha-galactosidase), Lactobacillus plantarum (LP), and combinations of these enzymes with LP on the bacterial diversity and fermentation quality of alfalfa silage. Three repetitions for each treated were evaluated by ensiling for 56 days: (1) control with no additives; (2) treated with enzyme (a mix of cellulase and alpha-galactosidase) (EN), 2.5g/kg forgae of each enzyme; (3) 1 ×1 ×107 CFU/g LP; (4) 2.5g/kg forgae of EN combined with 1 ×107 CFU/g LP (CENLP). Illumina sequencing was used to reveal the bacterial community of these silage. As revealed by data, treatment of the silage significantly changed the bacterial community, as determined by the PCoA test. At the class level, Bacilli and Clostridia were predominant in the untreated silage, with abundances of 51.21% and 37.08%, respectively, while only Bacilli dominated the bacterial communities of all the treated silages, with an abundance of 94.98% in the EN silage, 98.61% in the LP silage, 98.57% in the ENLP silage. Gammaproteobacteria were present in all the silages. At the genus level, Garciella, Enterococcus, Lactobacillus and Pediococcus were predominant in the control silage, while Lactobacillus and Pediococcus were predominant in the EN silage, and Lactobacillus was predominant in the LP, ENLP silages. As showed below, 1_1 to 1_3 represent three samples of each treated silage. 1_1 to 1_3 represent control silage, 2_1 to 2_3 represent EN silage, 3_1 to 3_3 represent LP silage, 4_1 to 4_3 represent ENLP silage.
Contributors: Qinglin Kang
... MCDS is an autosomal dominant disorder caused by COL10A1 mutations, which is characterized by short stature, waddling gait, coxa vara and bowing of the long bones. However, descriptions of the expressivity of MCDS are rare. Two probands and available family members affected with MCDS were subjected to clinical and radiological examination. Genomic DNA was subjected to whole-exome sequencing and Sanger sequencing in all available family members. A spatial model of the type X collagen (α1) C-terminal noncollagenous (NC1) domain was further constructed. Based on these, we found that the phenotype of affected family members exhibited incomplete dominance. Mutation analysis indicated that there were two novel heterozygous missense mutations, [c.1765T>A (p.Phe589Ile)] and [c.1846A>G (p.Lys616Glu)] in the COL10A1 gene in family 1 and 2, respectively. The two novel substitution sites were highly conserved and the mutations were predicted to be deleterious by in silico analysis. Furthermore, protein modeling revealed that the two substitutions were located in the NC1 domain of collagen X (α1), which potentially impacted the trimerization of collagen X (α1) and combination with molecules in the pericellular matrix. We draw the conclusion that two novel mutations were identified in the present work, which will further expand the spectrum of the COL10A1 mutations associated with MCDS patients. In addition, our research revealed the phenomenon of incomplete dominance in MCDS.
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Contributors: Zong Fu HU
... The bacterial community dynamics of cellulase, Lactobacillus casei, and air treated alfalfa silage were studied using Illumina Miseq sequencing. Medicago sativa was ensiled without (CON) or with L. casei (LC) or cellulose (CE) for 56 days, then exposed to air for 3 days (PO). The bacterial communities were obviously different among groups and sample times; and Lactobacillus developed to a dominant status in all silages. Lactobacillus became dominant in bacterial communities of LC and CE silages from days 7 to 56, and their relative abundances reached 94.17% and 83.93% at 56 d, respectively. For CON silage, Lactobacillus were not the dominant genus on day 7; samples were mainly composed of several genera, including Lactobacillus, and Lactococcus, Enterococcus, and Enterobacter. Lactobacillus (75.10%) were the dominant genera in silage on day 56. After 3 days of oxygen exposure, Lactobacillus and Enterococcus were predominant in CON, and Lactobacillus remained dominant in LC and CE silages. The results indicate that, compared to untreated treated silages, L. casei could be a priority inoculant for alfalfa silage to boost Lactobacillus abundance and improve fermentation quality.
Constraining Interseismic Deformation of the Cascadia Subduction Zone: New Insights from Estimates of Vertical Land Motion over Different Timescales
Contributors: Maryam Yousefi, Glenn Milne, Shaoyang Li, Kelin Wang, Alan Bartholet
... urate_glacier.grd: The present-day vertical land motion rates (mm/yr) due to the 20th-century glacier mass loss on a 10-arc minute resolution grid along the Pacific coast of North America urate_gwd.grd: The present-day vertical land motion rates (mm/yr) due to the ground water extraction on a 10-arc minute resolution grid along the Pacific coast of North America
Contributors: Trina Tallei
... Data on Community Structure and Diversity of the Intestinal Bacteria in Wild Elver and Fingerling Stages of Indonesian Shortfin Eel (Anguilla bicolor bicolor)
Contributors: Ahmad Zidan, Eman Saad, Nasser Ibrahim, Amal Mahmoud, medhat hashem, Alaa Hemeida
... 1-Files that resulted from application of PHARMIP insilico method to explore adverse drug reactions on 2 examples of domperidone related cardio-toxicity and ranitidine related thrombocytopenia . 2-Files that are used to apply the step of molecular docking on the previous examples.
Contributors: Tetsuji Okada
... DSA files of human (N to Z, by gene name) : UniProt ID is used for a protein to which no gene name is assigned.
Contributors: Tetsuji Okada
... DSA files of E. coli (N to Z, by gene name) : UniProt ID is used for a protein to which no gene name is assigned.