The multiscale architecture of tessellated cartilage and its relation to function

When describing the architecture and ultrastructure of animal skeletons, introductory biology, anatomy and histology textbooks typically focus on the few bone and cartilage types prevalent in humans. In reality, cartilage and bone are far more diverse in the animal kingdom, particularly within fishes (Chondrichthyes and Actinopterygii), where cartilage and bone types are characterized by features that are anomalous or even pathological in human skeletons. This review discusses the curious and complex architectures of shark and ray tessellated cartilage, highlighting similarities and differences with their mammalian skeletal tissue counterparts. By synthesizing older anatomical literature with recent high-resolution structural and materials characterization work, this review frames emerging pictures of form–function relationships in this tissue and of the evolution and true diversity of cartilage and bone.     

miR-145-5p targets paxillin to attenuate angiotensin II-induced pathological cardiac hypertrophy via downregulation of Rac 1, pJNK,p-c-Jun,NFATc3, ANP and by Sirt-1 upregulation

Pathological cardiac hypertrophy is associated with many diseases including hypertension. Recent studies have identified important roles for microRNAs (miRNAs) in many cardiac pathophysiological processes, including the regulation of cardiomyocyte hypertrophy. However, the role of miR-145-5p in the cardiac setting is still unclear. In this study, H9C2 cells were overexpressed with microRNA-145-5p, and then treated with Ang-II for 24 h, to study the effect of miR-145-5p on Ang-II-induced myocardial hypertrophy in vitro. Results showed that Ang-II treatment down-regulated miR-145-5p expression were revered after miR-145-5p overexpression. Based on results of bioinformatics algorithms, paxillin was predicted as a candidate target gene of miR-145-5p, luciferase activity assay revealed that the luciferase activity of cells was substantial downregulated the following co-transfection with wild paxillin 3′UTR and miR-145-5p compared to that in scramble control, while the inhibitory effect of miR-145-5p was abolished after transfection of mutant paxillin 3′UTR. Additionally, overexpression of miR-145-5p markedly inhibited activation of Rac-1/ JNK /c-jun/ NFATc3 and ANP expression and induced SIRT1 expression in Ang-II treated H9c2 cells. Jointly, our study suggested that miR-145-5p inhibited cardiac hypertrophy by targeting paxillin and through modulating Rac-1/ JNK /c-jun/ NFATc3/ ANP / Sirt1 signaling, therefore proving novel downstream molecular pathway of miR-145-5p in cardiac hypertrophy

     

Morphological and molecular characterization of new plant type core set for yield and culm strength traits in rice (Oryza sativa L.)

New plant type core set comprising indica and tropical japonica accessions along with checks were evaluated for yield and culm strength related traits and characterized with gene specific markers viz., Gn1a, DEP1, Ghd7, SPL14, GS5, TGW6 and SCM2. Analysis of variance revealed significant differences as well as presence of variability among the genotypes for all the traits. Seven genotypes (IRGC25510, IRGC1742, Haorei machang, Azhoghi, Thangmoi, BPT5204 and Swarnadhan) do not possess similar allele as that of the assessed genes based on combined analysis for all the traits and genes. Of them, four genotypes IRGC1742, Azhoghi, BPT5204 and Swarnadhan possess ideal trait combination (90–100 days to 50% flowering, 100–120 cm plant height, grain number of > 200, 11–15 productive tillers) but with weak culm can be ideal sources for identification of new genes for yield attributing traits and direct introgression of SCM2. Based on single trait-gene analysis, nine trait wise donors with high value for the trait (also with desirable plant type) but without similar allele of the corresponding gene were identified. One genotype IRGC7486 with high grain number (300), four genotypes (IRGC50448, IRGC43741, IRGC15147 and IRGC39111) with strong culm (1195–2655 g.f), three genotypes viz., IRGC15147, IRGC39111 and IRGC10658 with high panicle weight and one genotype Solumpiket with high 1000-grain weight and high panicle weight can be considered for identification of novel gene(s) for respective traits.

     

Finding gene regulatory network candidates using the gene expression knowledge base

Background

Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ‘omics’ data can be interpreted. The background information required for the construction of such networks is often dispersed across a multitude of knowledge bases in a variety of formats. The seamless integration of this information is one of the main challenges in bioinformatics. The Semantic Web offers powerful technologies for the assembly of integrated knowledge bases that are computationally comprehensible, thereby providing a potentially powerful resource for constructing biological networks and network-based analysis.

Results

We have developed the Gene eXpression Knowledge Base (GeXKB), a semantic web technology based resource that contains integrated knowledge about gene expression regulation. To affirm the utility of GeXKB we demonstrate how this resource can be exploited for the identification of candidate regulatory network proteins. We present four use cases that were designed from a biological perspective in order to find candidate members relevant for the gastrin hormone signaling network model. We show how a combination of specific query definitions and additional selection criteria derived from gene expression data and prior knowledge concerning candidate proteins can be used to retrieve a set of proteins that constitute valid candidates for regulatory network extensions.

Conclusions

Semantic web technologies provide the means for processing and integrating various heterogeneous information sources. The GeXKB offers biologists such an integrated knowledge resource, allowing them to address complex biological questions pertaining to gene expression. This work illustrates how GeXKB can be used in combination with gene expression results and literature information to identify new potential candidates that may be considered for extending a gene regulatory network.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0386-y) contains supplementary material, which is available to authorized users.     

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.

Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.     

Start codon targeted (SCoT) polymorphism-based genetic relationships and diversity among populations of <Emphasis Type="Italic">Tecomella undulata</Emphasis> (Sm.) Seem—an endangered timber tree of hot arid regions

Tecomella undulata (Sm.) Seem commonly called Rohida or Desert teak (family bignoniaceae) is an important agroforestry tree having an important pharmacological and therapeutic uses. Its distribution is restricted to hot arid regions of India and Pakistan having <150 to 500 mm annual rainfall. Genetic diversity status of this important endangered timber tree species designated state flower of Rajasthan remains unrevealed. Genetic diversity of 21 populations (108 accessions) encompassing yellow, red and orange coloured flower bearing morphotypes collected from all 12 districts of western Rajasthan, India, has been examined using start codon targeted (SCoT) polymorphism for the first time. Fingerprinting with 22 SCoT primers (out of 36 screened) generated 294 amplicons of 100 to 3000 bp size, of which 212 (71.6%) were polymorphic. Amplicon number varied from 4 (SCoT-9) to 24 (SCoT-15) with an average of 13.4 amplicons per primer. Average polymorphism information content (PIC), Nei’s diversity index (H) and Shannon index (I) were 0.54, 0.22 and 0.36, respectively. Dendrogram generated using unweighted pair-group method with arithmetic mean (UPGMA) delineated the 108 accessions into 5 clusters while 2 accessions out grouped. Principal coordinate analysis (PCoA) also revealed similar clustering. High level of genetic differentiation among accessions/populations was attributed to cross pollination and continuous evolution under harsh agro-climatic conditions.     

Bare fiber Bragg grating immunosensor for real‐time detection of Escherichia coli bacteria

Escherichia coli (E. coli) bacteria have been identified to be the cause of variety of health outbreaks resulting from contamination of food and water. Timely and rapid detection of the bacteria is thus crucial to maintain desired quality of food products and water resources. A novel methodology proposed in this paper demonstrates for the first time, the feasibility of employing a bare fiber Bragg grating (bFBG) sensor for detection of E. coli bacteria. The sensor was fabricated in a photo‐sensitive optical fiber (4.2 µm/80 µm). Anti‐E. coli antibody was immobilized on the sensor surface to enable the capture of target cells/bacteria present in the sample solution. Strain induced on the sensor surface as a result of antibody immobilization and subsequent binding of E. coli bacteria resulted in unique wavelength shifts in the respective recording of the reflected Bragg wavelength, which can be exploited for the application of biosensing. Functionalization and antibody binding on to the fiber surface was cross validated by the color development resulting from the reaction of an appropriate substrate solution with the enzyme label conjugated to the anti‐E. coli antibody. Scanning electron microscope image of the fiber, further verified the E. coli cells bound to the antibody immobilized sensor surface.

     

Fiber bragg grating sensor based device for simultaneous measurement of respiratory and cardiac activities

This paper reports a novel optical ballistocardiography technique, which is non‐invasive, for the simultaneous measurement of cardiac and respiratory activities using a Fiber Bragg Grating Heart Beat Device (FBGHBD). The unique design of FBGHBD offers additional capabilities such as monitoring nascent morphology of cardiac and breathing activity, heart rate variability, heart beat rhythm, etc., which can assist in early clinical diagnosis of many conditions associated with heart and lung malfunctioning. The results obtained from the FBGHBD positioned around the pulmonic area on the chest have been evaluated against an electronic stethoscope which detects and records sound pulses originated from the cardiac activity. In order to evaluate the performance of the FBGHBD, quantitative and qualitative studies have been carried out and the results are found to be reliable and accurate, validating its potential as a standalone medical diagnostic device. The developed FBGHBD is simple in design, robust, portable, EMI proof, shock proof and non‐electric in its operation which are desired features for any clinical diagnostic tool used in hospital environment.