Determination and analysis of the complete mitochondrial genome of <i>Barilius barila</i> (Cypriniformes: Danionidae: Chedrinae)

Cyprinid fish Barilius barila found in the Irrawaddy water system is a valuable fishery resource and has been listed as Least Concern by the IUCN. This study determined the complete mitochondrial genome of B. barila from Yunnan, China, for the first time. Circular molecule of B. barila mitogenome was sequenced to be 16,560 bp in length, with the typical gene structure of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two noncoding areas (control region and the origin of L-strand replication). Overall nucleotides composition appeared to be 27.5% A, 24.8% T, 19.2% G, and 28.6% C, with a slight AT (52.3%) bias. The topology of the phylogenetic tree showed that B. barila was well grouped with Opsarius caudiocellatus, and clustered together with the genus Opsarius instead of Barilius, revealing that it was more reasonable for Barilius barila to belong to Opsarius rather than Barilius.</p

Additional file 4: Figure S3. of Nascent osteoblast matrix inhibits osteogenesis of human mesenchymal stem cells in vitro

Effects of OBC co-culture on MSC osteogenic gene expression is variable. mRNA levels of osteogenic genes (OC, Runx2, ALP, and Col I) in MSC control cultures and MSC/OBC co-cultures were measured via real-time RT-PCR, and normalized to GAPDH. Each value was then expressed as a percentage of the maximum level reached for that gene in cells from a given donor within a given experiment. Values shown are the mean ± SEM from two experiments. No statistically significant differences were observed. (JPEG 238 kb

Additional file 6: Figure S5 of Nascent osteoblast matrix inhibits osteogenesis of human mesenchymal stem cells in vitro

Microarray analysis confirms the suppression of osteogenesis by OBC matrices. MSCs from three donors were cultured in OM on OBC matrices prepared by water or DOC lysis, and gene expression analyzed by real-time RT-PCR using the SuperArray System. Gene-of –interest CT values were normalized to the average of five housekeeping genes. Shown are those genes that showed mean fold changes > 3-fold when comparing MSCs on matrix to MSCs on plastic in OM at days 6 and 12. Genes were assigned to graph (A) or (B) based on alphabetical order. Asterisks indicate significance between an experimental condition and the OM plastic control. There was no statistical significance in any differences >3-fold between matrix treatments. *, p < 0.05; **, p < 0.01. (JPEG 427 kb

Additional file 2: Figure S1. of Nascent osteoblast matrix inhibits osteogenesis of human mesenchymal stem cells in vitro

DiI labeling does not affect MSC osteogenic gene expression. MSCs were labeled with DiI and cultured in EM or OM for 21 days. Osteocalcin (OC) mRNA expression was measured by real-time RT-PCR and normalized to GAPDH. Unlabeled MSCs were used as controls. Values shown are mean ± SD from cells isolated from a 61-year-old male donor, plated at 3,000/cm2. (JPEG 305 kb

Additional file 8: Table S2. of Nascent osteoblast matrix inhibits osteogenesis of human mesenchymal stem cells in vitro

Protein symbols used for proteomic analysis. (DOCX 122 kb

Additional file 3: Figure S2. of Nascent osteoblast matrix inhibits osteogenesis of human mesenchymal stem cells in vitro

Morphology of DiI-labeled MSCs in co-culture with unlabeled OBCs. Images of MSCs on culture days 6 and 12 show no obvious morphological differences due to co-culture with OBCs. Shown are unlabeled MSCs in EM; DiI-labeled MSCs mixed with unlabeled MSCs in OM as a control (MSC/MSC*); and DiI-labeled MSCs mixed with unlabeled OBCs in OM (OBC/MSC*). MSCs were derived from a 73-year-old male donor, plated at 9,000 cells/cm2 and cultured in a 1:4 ratio with OBCs induced from the same MSCs for 15 days prior to co-culture. MSC* indicates MSCs labeled with DiI (red). 10× magnification. (JPEG 1025 kb

Complete mitochondrial genome sequence and annotation of <i>Rhinogobius lentiginis</i> (Gobiiformes: Gobiidae: Gobionellinae)

We report the complete mitochondrial genome of Rhinogobius lentiginis, which was found to be a circular molecule of 16,633 bp in length and included 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding control region. The overall base composition was 28.44% A, 26.21% T, 16.33% G, and 29.02% C. Phylogenetic analyses using maximum-likelihood and Bayesian inference methods revealed a close genome relationship among R. lentiginis, R. niger, R. shennongensis and R. maculagenys. The complete mitogenome of R. lentiginis will provide a valuable resource for species classification and conservation.</p

Genome-Wide Identification of Hsp40 Genes in Channel Catfish and Their Regulated Expression after Bacterial Infection

<div><p>Heat shock proteins (HSPs) consist of a large group of chaperones whose expression is induced by high temperature, hypoxia, infection and a number of other stresses. Among all the HSPs, Hsp40 is the largest HSP family, which bind to Hsp70 ATPase domain in assisting protein folding. In this study, we identified 57 hsp40s in channel catfish (<i>Ictalurus punctatus</i>) through <i>in silico</i> analysis using RNA-Seq and genome databases. These genes can be classified into three different types, Type I, II and III, based on their structural similarities. Phylogenetic and syntenic analyses provided strong evidence in supporting the orthologies of these HSPs. Meta-analyses of RNA-Seq datasets were conducted to analyze expression profile of Hsp40s following bacterial infection. Twenty seven hsp40s were found to be significantly up- or down-regulated in the liver after infection with <i>E. ictaluri</i>; 19 hsp40s were found to be significantly regulated in the intestine after infection with <i>E. ictaluri</i>; and 19 hsp40s were found to be significantly regulated in the gill following infection with <i>F. columnare</i>. Altogether, a total of 42 Hsp40 genes were regulated under disease situations involving three tissues and two bacterial infections. The significant regulated expression of Hsp40 genes after bacterial infection suggested their involvement in disease defenses in catfish.</p></div