Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing

The high-throughput next-generation sequencing technologies provide an excellent opportunity for the detection of less-abundance transcripts that may not be identifiable by previously available techniques. Here, we report a discovery of thousands of novel transcripts (mostly non-coding RNAs) that are expressed in mouse cerebrum, testis, and embryonic stem (ES) cells, through an in-depth analysis of rmRNA-seq data. These transcripts show significant associations with transcriptional start and elongation signals. At the upstream of these transcripts we observed significant enrichment of histone marks (histone H3 lysine 4 trimethylation, H3K4me3), RNAPII binding sites, and cap analysis of gene expression tags that mark transcriptional start sites. Along the length of these transcripts, we also observed enrichment of histone H3 lysine 36 trimethylation (H3K36me3). Moreover, these transcripts show strong purifying selection in their genomic loci, exonic sequences, and promoter regions, implying functional constraints on the evolution of these transcripts. These results define a collection of novel transcripts in the mouse genome and indicate their potential functions in the mouse tissues and cells

Managing iron supply during the infection cycle of a flea borne pathogen, Bartonella henselae.

Bartonella are hemotropic bacteria responsible for emerging zoonoses. Most Bartonella species appear to share a natural cycle that involves an arthropod transmission, followed by exploitation of a mammalian host in which they cause long-lasting intra-erythrocytic bacteremia. Persistence in erythrocytes is considered an adaptation to transmission by bloodsucking arthropod vectors and a strategy to obtain heme required for Bartonella growth. Bartonella genomes do not encode for siderophore biosynthesis or a complete iron Fe3+ transport system. Only genes, sharing strong homology with all compounds of a Fe2+ transport system, are present in Bartonella genomes. Also, Bartonella genomes encode for a complete heme transport system. Bartonella must face various environments in their hosts and vectors. In mammals, free heme and iron are rare and oxygen concentration is low. In arthropod vectors, toxic heme level is found in the gut where oxygen concentration is high. Bartonella genomes encode for three to five heme binding proteins. In Bartonella henselae heme binding proteins were shown to be involved in heme uptake process, oxidative stress response and survival inside endothelial cells and in the flea. In this report, we discuss the use of the heme uptake and storage system of B. henselae during its infection cycle. Also, we establish a comparison with the use of the iron and heme uptake systems by Yersinia pestis during its infection cycle

The effects of various land reclamation scenarios on the succession of soil Bacteria, Archaea, and fungi over the short and long term

Ecological restoration of mining areas has mainly focused on the succession dynamics of vegetation and the fate of microbial communities remains poorly understood. We examined changes in soil characteristics and plant and microbial communities with increasing reclamation period in an open coal mine. Bacterial, archaeal and fungal communities were assessed by tag-encoded 454 pyrosequencing. At the phylum level, Proteobacteria, Crenarchaeota, and Ascomycota had the highest detected relative abundance within bacteria, archaea, and fungi, respectively. Partial regressions and canonical correspondence analysis demonstrated that vegetation played a major role in bacterial and archaeal diversity and assemblies, and soil characteristics, especially nitrogen, were important for fungal diversity and assemblies. Spearman rank correlation indicated that bacterial and archaeal communities showed synergistic succession with plants; whereas, fungal communities showed no such pattern. Overall, our data suggest that there are different drivers of bacterial, archaeal and fungal succession during secondary succession in a reclaimed open mine

Effect of diatom silica content on copepod grazing, growth and reproduction

Diatoms are often a major food source for zooplankton and contribute significantly to vertical POC flux through sinking of dead cells, aggregates and zooplankton fecal pellets. The silica content of diatoms varies among different species and within a species growing under different environmental conditions and physiological status. However, to-date there has been no investigation of the effect of diatom silica content on zooplankton grazing, growth and reproduction. We conducted a series of experiments using the diatom Thalassiosira weissflogii with different silica content achieved by growth under high and low light and these cells were fed to a copepod, Parvocalanus crassirostris. Our results show that this copepod strongly preferred cells with low silica content over high silica-containing cells, with the ingestion rate on low silica diatoms being 2-3 times higher than that on high silica diatoms. Fecal pellet production rate was significantly higher for copepods feeding on highly silicified cells. Furthermore, copepod growth rate (measured as an increase in wet weight), egg production rate and hatching success were all severely compromised under a high silica diatom diet. Females of P. crassirostris feeding on a low silica diatom diet produced an average 90 eggs during a one day incubation, while those fed with high silica diatoms produced only 11 eggs per day. Similarly, the hatching success during a 3-day period was 82 ± 17% and 23 ± 36% for the low and high silica diatom treatments, respectively, with zero success observed in ~65% of the females feeding on high Si diatoms. Our findings have important ecological implications for the biological pump and may alter our previous view of the role of diatoms in planktonic food webs and the role of the degree of silicification in controlling amount of POC flux to deeper waters

Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice

Maternal alcohol consumption inflicts a multitude of phenotypic consequences that range from undetectable changes to severe dysmorphology. Using tightly controlled murine studies that deliver precise amounts of alcohol at discrete developmental stages, our group and other labs demonstrated in prior studies that the C57BL/6 and DBA/2 inbred mouse strains display differential susceptibility to the teratogenic effects of alcohol. Since the phenotypic diversity extends beyond the amount, dosage and timing of alcohol exposure, it is likely that an individual’s genetic background contributes to the phenotypic spectrum. To identify the genomic signatures associated with these observed differences in alcohol-induced dysmorphology, we conducted a microarray-based transcriptome study that also interrogated the genomic signatures between these two lines based on genetic background and alcohol exposure. This approach is called a gene x environment (GxE) analysis; one example of a GxE interaction would be a gene whose expression level increases in C57BL/6 animals, but decreases in DBA/2 embryos, following alcohol exposure. We identified 35 candidate genes exhibiting GxE interactions. To identify cis-acting factors that mediated these interactions, we interrogated the proximal promoters of these 35 candidates and found 241 single nucleotide variants (SNVs) in 16 promoters. Further investigation indicated that 186 SNVs (15 promoters) are predicted to alter transcription factor binding. In addition, 62 SNVs created, removed or altered the placement of a CpG dinucleotide in 13 of the proximal promoters; 53 of which overlapped putative transcription factor binding sites. These 53 SNVs are our top candidates for future studies aimed at examining the effects of alcohol on epigenetic gene regulation

Stimulation of airway and intestinal mucosal secretion by natural coumarin CFTR activators

Mutations of cystic fibrosis transmembrane conductance regulator (CFTR) cause lethal hereditary disease cystic fibrosis (CF) that involves extensive destruction and dysfunction of serous epithelium. Possible pharmacological therapy includes correction of defective intracellular processing and abnormal channel gating. In a previous study, we identified five natural coumarin potentiators of Δ508-CFTR including osthole, imperatorin, isopsoralen, praeruptorin A and scoparone. The present study was designed to determine the activity of these coumarine compounds on CFTR activity in animal tissues as a primary evaluation of their therapeutic potential. In the present study, we analyzed the affinity of these coumarin potentiators in activating wild-type CFTR and found that they are all potent activators. Osthole showed the highest affinity with Kd values <50 nmol/L as determined by Ussing chamber short-circuit current assay. Stimulation of rat colonic mucosal secretion by osthole was tested by the Ussing chamber short-circuit current assay. Osthole reached maximal activation of colonic Cl- secretion at 5 mol/L. Stimulation of mouse tracheal mucosal secretion was analyzed by optical measurement of single gland secretion. Fluid secretion rate of tracheal single submucosal gland stimulated by osthole at 10mol/L was 3-fold more rapid than that in negative control. In both cases the stimulated secretions were fully abolished by CFTRinh-172. In conclusion, the effective stimulation of Cl– and fluid secretion in colonic and tracheal mucosa by osthole suggested the therapeutic potential of natural coumarine compounds for the treatment of cystic fibrosis and other CFTR-related diseases

Alterations of Functional and Structural Networks in Schizophrenia Patients with Auditory Verbal Hallucinations

Background: There have been many attempts at explaining the underlying neuropathological mechanisms of auditory verbal hallucinations (AVH) in schizophrenia on the basis of regional brain changes, with the most consistent findings being that AVH are associated with functional and structural impairments in auditory and speech-related regions. However, the human brain is a complex network and the global topological alterations specific to AVH in schizophrenia remain unclear. Methods: 35 schizophrenia patients with AVH, 41 patients without AVH and 50 healthy controls underwent resting-state functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI). The whole-brain functional and structural networks were constructed and analyzed using graph theoretical approaches. Inter-group differences in global network metrics (including small-world properties and network efficiency) were investigated. Results: We found that three groups had a typical small-world topology in both functional and structural networks. More importantly, schizophrenia patients with and without AVH exhibited common disruptions of functional networks, characterized by decreased clustering coefficient, global efficiency and local efficiency, and increased characteristic path length; structural networks of only schizophrenia patients with AVH showed increased characteristic path length compared with those of healthy controls. Conclusions: Our findings suggest that less small-worldization and lower network efficiency of functional networks may be an independent trait characteristic of schizophrenia, and regularization of structural networks may be the underlying pathological process engaged in schizophrenic AVH symptom expression

An updated role of MicroRNA-124 in central nervous system disorders: a review

MicroRNA-124 (miR-124) is the most abundant miRNA in the brain. Biogenesis of miR-124 displays specific temporal and spatial profiles in various cell and tissue types and affects a broad spectrum of biological functions in the central nervous system (CNS). Recently, the link between dysregulation of miR-124 and CNS disorders, such as neurodegeneration, CNS stress, neuroimmune disorders, stroke, and brain tumors, has become evident. Here, we provide an overview of the specific molecular function of miR-124 in the CNS and a revealing insight for the therapeutic potential of miR-124 in the treatment of human CNS diseases

NLRP3 inflammasome and its inhibitors: a review

Inflammasomes are newly recognized, vital players in innate immunity. The best characterized is the NLRP3 inflammasome, so-called because the NLRP3 protein in the complex belongs to the family of nucleotide-binding and oligomerization domain-like receptors (NLRs) and is also known as pyrin domain-containing protein 3. The NLRP3 inflammasome is associated with onset and progression of various diseases, including metabolic disorders, multiple sclerosis, inflammatory bowel disease, cryopyrin-associated periodic fever syndrome (CAPS), as well as other auto-immune and auto-inflammatory diseases. Several NLRP3 inflammasome inhibitors have been described, some of which show promise in the clinic. The present review will describe the structure and mechanisms of activation of the NLRP3 inflammasome, its association with various auto-immune and auto-inflammatory diseases, and the state of research into NLRP3 inflammasome inhibitors

Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb) and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome