LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells.

Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.

A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability.

The human genome encodes thousands of long noncoding RNA (lncRNA) genes; the function of majority of them is poorly understood. Aberrant expression of a significant number of lncRNAs is observed in various diseases, including cancer. To gain insights into the role of lncRNAs in breast cancer progression, we performed genome-wide transcriptome analyses in an isogenic, triple negative breast cancer (TNBC/basal-like) progression cell lines using a 3D cell culture model. We identified significantly altered expression of 1853 lncRNAs, including ~500 natural antisense transcript (NATs) lncRNAs. A significant number of breast cancer-deregulated NATs displayed co-regulated expression with oncogenic and tumor suppressor protein-coding genes in cis. Further studies on one such NAT, PDCD4-AS1 lncRNA reveal that it positively regulates the expression and activity of the tumor suppressor PDCD4 in mammary epithelial cells. Both PDCD4-AS1 and PDCD4 show reduced expression in TNBC cell lines and in patients, and depletion of PDCD4-AS1 compromised the cellular levels and activity of PDCD4. Further, tumorigenic properties of PDCD4-AS1-depleted TNBC cells were rescued by exogenous expression of PDCD4, implying that PDCD4-AS1 acts upstream of PDCD4. Mechanistically, PDCD4-AS1 stabilizes PDCD4 RNA by forming RNA duplex and controls the interaction between PDCD4 RNA and RNA decay promoting factors such as HuR. Our studies demonstrate crucial roles played by NAT lncRNAs in regulating post-transcriptional gene expression of key oncogenic or tumor suppressor genes, thereby contributing to TNBC progression.

CARLo-7-A plausible biomarker for bladder cancer.

Cancer is defined as undifferentiated and unchecked growth of cells damaging the surrounding tissue. Cancers manifest altered gene expression. Gene expression is regulated by a diverse array of non-protein-coding RNA. Aberrant expression of long non-coding RNAs (lncRNAs) has been recently found to have functional consequences in cancers. In the current study, we report CARLo-7 as the only bladder cancer-specific lncRNA from the CARLos cluster. The expression of this lncRNA correlates with bladder cancer grade. We propose that CARLo-7 has an oncogenic potential and might be regulator of cell proliferation. Furthermore, by comparison the expression of proto-oncogene MYC, which is the only well-annotated gene close to the cancer - associated linkage disequilibrium blocks of this region, does not show a pronounced change in expression between the low- and high-grade tumours. Our results indicate that CARlo-7 can act as a prognostic marker for bladder cancer.

Increased expression levels of Syntaxin 1A and Synaptobrevin 2/Vesicle-Associated Membrane Protein-2 are associated with the progression of bladder cancer.

Gene expression is tightly regulated in time and space through a multitude of factors consisting of signaling molecules. Soluble N-ethylmaleimide-sensitive-factor attachment protein receptors (SNARE) are membrane proteins responsible for the intercellular trafficking of signals through endocytosis and exocytosis of vesicles. Altered expression of SNARE proteins in cellular communication is the major hallmark of cancer phenotypes as indicated in recent studies. SNAREs play an important role in maintaining cell growth and epithelial membrane permeability of the bladder and are not only involved in cancer progression but also metastatic cell invasion through SNARE-mediated trafficking. Synaptobrevin2/Vesicle associated membrane protein-2 (v-SNARE) and Syntaxin (t-SNARE) form a vesicular docking complex during endocytosis. Some earlier studies have shown a critical role of SNARE in colon, lungs, and breast cancer progression and metastasis. In this study, we analyzed the relative expression of the STX1A and VAMP2 (SYB2) for their possible association in the progression and metastasis of bladder cancer. The profiling of the genes showed a significant increase in STX1A and VAMP2 expression (p < 0.001) in high-grade tumor cells compared to normal and low-grade tumors. These findings suggest that elevated expression of STX1A and VAMP2 might have caused the abnormal progression and invasion of cancer cells leading to the transformation of cells into high-grade tumor in bladder cancer.

RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation.

RNA editing by adenosine deaminases that act on RNA (ADARs) diversifies the transcriptome by changing adenosines to inosines. In mammals, editing levels vary in different tissues, during development, and also in pathogenic conditions. From a screen for repressors of editing we have isolated three proteins that repress ADAR2-mediated RNA editing. The three proteins RPS14, SFRS9 and DDX15 interact with RNA. Overexpression or depletion of these proteins can decrease or increase editing levels by 15%, thus allowing a modulation of RNA editing up to 30%. Interestingly, the three proteins alter RNA editing in a substrate-specific manner that correlates with their RNA binding preferences. In mammalian cells, SFRS9 significantly affects editing of the two substrates CFLAR and cyFIP2, while the ribosomal protein RPS14 mostly inhibits editing of cyFIP2 messenger RNA. The helicase DDX15, in turn, has a strong effect on editing in Caenorhabditis elegans. Expression of the three factors decreases during mouse brain development. Moreover, expression levels of SFRS9 and DDX15 respond strongly to neuronal stimulation or repression, showing an inverse correlation with editing levels. Colocalization and immunoprecipitation studies demonstrate a direct interaction of SFRS9 and RPS14 with ADAR2, while DDX15 associates with other helicases and splicing factors. Our data show that different editing sites can be specifically altered in their editing pattern by changing the local RNP landscape.

A high-throughput screen to identify enhancers of ADAR-mediated RNA-editing.

Adenosine to inosine deamination of RNA is widespread in metazoa. Inosines are recognized as guanosines and, therefore, this RNA-editing can influence the coding potential, localization and stability of RNAs. Therefore, RNA editing contributes to the diversification of the transcriptome in a flexible manner. The editing reaction is performed by adenosine deaminases that act on RNA (ADARs), which are essential for normal life and development in many organisms. Changes in editing levels are observed during development but also in neurological pathologies like schizophrenia, depression or tumors. Frequently, changes in editing levels are not reflected by changes in ADAR levels suggesting a regulation of enzyme activity. Until now, only a few factors are known that influence the activity of ADARs. Here we present a two-stage in vivo editing screen aimed to isolate enhancers of editing. A primary, high-throughput yeast-screen is combined with a more accurate secondary screen in mammalian cells that uses a fluorescent read-out to detect minor differences in RNA-editing. The screen was successfully employed to identify DSS1/SHFM1, the RNA binding protein hnRNP A2/B1 and a 3' UTR as enhancers of editing. By varying intracellular DSS1/SHFM1 levels, we can modulate A to I editing by up to 30%. Proteomic analysis indicates an interaction of DSS1/SHFM1 and hnRNP A2/B1 suggesting that both factors may act by altering the cellular RNP landscape. An extension of this screen to cDNAs from different tissues or developmental stages may prove useful for the identification of additional enhancers of RNA-editing.

Preparation and in Vitro Evaluation of Tamoxifen-Conjugated, Eco-Friendly, Agar-Based Hybrid Magnetic Nanoparticles for Their Potential Use in Breast Cancer Treatment.

Tamoxifen is the drug of choice as hormonal therapy for hormone receptor-positive breast cancers and can reduce the risk of breast cancer recurrence. However, oral tamoxifen has a low bioavailability due to liver and intestinal metabolic passes. To overcome this problem and utilize the potential of this drug to its maximum, inorganic nanoparticle carriers have been exploited and tested to increase its bioavailability. Biocompatibility and unique magnetic properties make iron oxide nanoparticles an excellent choice as a drug delivery system. In this study, we developed and tested a "green synthesis" approach to synthesize iron nanoparticles from green tea extract and coated them with agar for longer stability (AG-INPs). Later, these hybrid nanoparticles were conjugated with tamoxifen (TMX). By using this approach, we synthesized stable agar-coated tamoxifen-conjugated iron nanoparticles (TMX-AG-INPs) and characterized them with Fourier-transform infrared (FTIR) spectroscopy. The average particle size of AG-INPs was 26.8 nm, while the average particle size of tamoxifen-loaded iron nanoparticles, TMX-AG-INPs, was 32.1 nm, as measured by transmission and scanning electron microscopy. The entrapment efficiency of TMX-AG-INPs obtained by the drug release profile was 88%, with a drug loading capacity of 43.5%. TMX-AG-INPs were significantly (p < 0.001) efficient in killing breast cancer cells when tested in vitro on the established breast cancer cell line MCF-7 by cell viability assay, indicating their potential to control cell proliferation.

Molecular investigation of possible relationships concerning bovine leukemia virus and breast cancer.

Worldwide, breast cancer has an eminent morbidity and mortality rate, as it is a neoplastic disease among females. The query of the prospective danger of bovine leukemia virus (BLV) to humans is an old but exceedingly topical focus of scientific debate. The objective of the current study was to determine the possible relationship between BLV and breast cancer. A total of 2710 formalin-fixed paraffin-embedded (FFPE) breast cancer samples were selected regardless of the age, ethnicity, or municipality origin of the subjects. The presence of BLV in human breast cancer was determined through nested PCR by amplifying tax and gag genes followed by partial sequencing. Homology was confirmed by using the online BLAST Tool. BLV genes were found to be positive in 26.8% (728/2710) of the samples from breast cancer patients and 10% (10/80) of the samples without cancer (negative control). The results indicated a correlation between the presence of the BLV gene and breast cancer (odds ratio = 0.3889; confidence interval = 1,18; p = 0.0029). The current findings suggest a possible link between BLV and human breast carcinoma. Therefore, screening cattle herds and milk products is suggested to reduce the viral transmission risk to humans.

Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan.

Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains.

Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae.

Salmonella Typhimurium, a foodborne pathogen, is a major concern for food safety. Its MDR serovars of animal origin pose a serious threat to the human population. Phage therapy can be an alternative for the treatment of such MDR Salmonella serovars. In this study, we report on detailed genome analyses of a novel Salmonella phage (Salmonella-Phage-SSBI34) and evaluate its therapeutic potential. The phage was evaluated for latent time, burst size, host range, and bacterial growth reduction in liquid cultures. The phage stability was examined at various pH levels and temperatures. The genome analysis (141.095 Kb) indicated that its nucleotide sequence is novel, as it exhibited only 1-7% DNA coverage. The phage genome features 44% GC content, and 234 putative open reading frames were predicted. The genome was predicted to encode for 28 structural proteins and 40 enzymes related to nucleotide metabolism, DNA modification, and protein synthesis. Further, the genome features 11 tRNA genes for 10 different amino acids, indicating alternate codon usage, and hosts a unique hydrolase for bacterial lysis. This study provides new insights into the subfamily Vequintavirinae, of which SSBI34 may represent a new genus.

Capillary-Driven Flow Microfluidics Combined with Smartphone Detection: An Emerging Tool for Point-of-Care Diagnostics.

Point-of-care (POC) or near-patient testing allows clinicians to accurately achieve real-time diagnostic results performed at or near to the patient site. The outlook of POC devices is to provide quicker analyses that can lead to well-informed clinical decisions and hence improve the health of patients at the point-of-need. Microfluidics plays an important role in the development of POC devices. However, requirements of handling expertise, pumping systems and complex fluidic controls make the technology unaffordable to the current healthcare systems in the world. In recent years, capillary-driven flow microfluidics has emerged as an attractive microfluidic-based technology to overcome these limitations by offering robust, cost-effective and simple-to-operate devices. The internal wall of the microchannels can be pre-coated with reagents, and by merely dipping the device into the patient sample, the sample can be loaded into the microchannel driven by capillary forces and can be detected via handheld or smartphone-based detectors. The capabilities of capillary-driven flow devices have not been fully exploited in developing POC diagnostics, especially for antimicrobial resistance studies in clinical settings. The purpose of this review is to open up this field of microfluidics to the ever-expanding microfluidic-based scientific community.

HriGFP Novel Flourescent Protein: Expression and Applications.

Biosensors based on microbial cells have been developed to monitor environmental pollutants. These biosensors serve as inexpensive and convenient alternatives to the conventional lab based instrumental analysis of environmental pollutants. Small monomeric naturally occurring fluorescent proteins (fp) can be exploited by converting them as small biosensing devices for biomedical and environmental applications. Moreover, they can withstand exposure to denaturants, high temperature, and a wide pH range variation. The current study employs newly identified novel fluorescent protein HriGFP from Hydnophora rigida to detect environmental contaminants like heavy metals and organo-phosphorous (pesticide) compounds such as methyl parathion. The HriGFP was initially tested or its expression in bacterial systems (Gram positive and Gram negative) and later on for its biosensing capability in E coli (BL21DE3) for detection of heavy metals and methyl parathion was evaluated. Our results indicated the discrete and stable expression of HriGFP and a profound fluorescent quenching were observed in the presence of heavy metals (Hg, Cu, As) and methyl parathion. Structural analysis revealed heavy metal ions binding to HriGFP via amino acid residues. In-silico-analysis further revealed strong interaction via hydrogen bonds between methyl parathion phosphate oxygen atoms and the amino group of Arg119 of HriGFP. This study implies that HriGFP can act as a biosensor for detecting harmful carcinogenic pesticide like methyl parathion in water resources in the vicinity of heavily pesticide impregnated agricultural lands and heavy metal contaminated water bodies around industrial areas.

Biosorption of arsenic through bacteria isolated from Pakistan.

The aim of this study was to isolate arsenic-resistant bacteria and to further exploit it for remediation purposes. In the present study, we have isolated arsenic-resistant strain from ground water of Pakistan AT-01. The strain was cultivated at 37 °C in Luria Bertani broth supplemented with different concentrations of arsenate and arsenite. The minimum inhibitory concentration of arsenic against the bacterial isolate was 7 g/L (7000 mg/L) for arsenate and 1.4 g/L (1400 mg/L) for arsenite salt. The bacterial isolate was also characterized both on molecular and biochemical basis. The isolated strain belonged to the Pseudomonas aeruginosa. The high resistance against arsenic offered by the bacteria was exploited further for bioremediation purposes. The bacterial biomass generated from AT-01 strain was able to efficiently remove arsenic with 98% efficiency. Arsenic contamination of ground water is a widespread worldwide problem. The present study shows the potential of high arsenic-resistant bacteria for efficient arsenic removal.

Comparative analysis of the Magnesium Ferrite (MgFe2O4) nanoparticles synthesised by three different routes.

The toxicity of arsenic in drinking water is hazardous for human health. Different strategies are used for arsenic removal from drinking water. Nanoparticles with higher adsorption capacities are useful for arsenic remediation. In the current study, magnesium ferrite nanoparticles were synthesised by three different methods followed by their characterisation XRD, SEM, and EDX. The SEM morphology and the porosity of magnesium ferrite nanoparticles were best in case of auto-combustion method. These particles had an average particle size of about 20-50 nm with spherical shape. These particles showed efficient remediation of arsenic up to 96% within 0.5 h. However, the co-precipitation and sol-gel-based nanoparticles showed arsenic remediation upto85 and 87% at 0.5-h time point. Moreover, the minimum inhibitory concentration of nanoparticles against two strains E.coli and Pseudomonas aeruginosa was found to be4.0 mg/L of these nanoparticles. However, the sol-gel-based nanoparticles showed efficient anti-microbial activity against E.coli at 4.0 and 8.0 mg/L against Pseudomonas aeruginosa. The co-precipitation-based nanoparticles were least efficient both for arsenic remediation and anti-microbial purposes. Thus, the synthesised auto-combustion-based nanoparticles are multifunctional in nature.

Modulation of ADAR mRNA expression in patients with congenital heart defects.

Adenosine (A) to inosine (I) RNA editing is a hydrolytic deamination reaction catalyzed by the adenosine deaminase (ADAR) enzyme acting on double-stranded RNA. This posttranscriptional process diversifies a plethora of transcripts, including coding and noncoding RNAs. Interestingly, few studies have been carried out to determine the role of RNA editing in vascular disease. The aim of this study was to determine the potential role of ADARs in congenital heart disease. Strong downregulation of ADAR2 and increase in ADAR1 expression was observed in blood samples from congenital heart disease (CHD) patients. The decrease in expression of ADAR2 was in line with its downregulation in ventricular tissues of dilated cardiomyopathy patients. To further decipher the plausible regulatory pathway of ADAR2 with respect to heart physiology, miRNA profiling of ADAR2 was performed on tissues from ADAR2-/- mouse hearts. Downregulation of miRNAs (miR-29b, miR-405, and miR-19) associated with cardiomyopathy and cardiac fibrosis was observed. Moreover, the upregulation of miR-29b targets COL1A2 and IGF1, indicated that ADAR2 might be involved in cardiac myopathy. The ADAR2 target vascular development associated protein-coding gene filamin B (FLNB) was selected. The editing levels of FLNB were dramatically reduced in ADAR2-/- mice; however, no observable changes in FLNB expression were noted in ADAR2-/- mice compared to wild-type mice. This study proposes that sufficient ADAR2 enzyme activity might play a vital role in preventing cardiovascular defects.

Caveolin-1 and dynamin-2 overexpression is associated with the progression of bladder cancer.

Caveolae-mediated endocytosis regulates cell adhesion and growth in an anchorage-dependent manner. Studies of the endocytic function of caveolae have suggested a wide-ranging list of cargoes, including a number of receptors and extracellular proteins, ligands and nutrients from the extracellular matrix. Disruption of the processes of caveolae-mediated endocytosis mediated by signaling proteins is critical to cellular integrity. Caveolin-1 and dynamin-2 are the 2 major proteins associated with endocytotic function. Mechanistically, dynamin-2 has a co-equal role with caveolin-1 in terms of caveolae-derived endosome formation. Recent studies have revealed the pathological outcomes associated with the dysregulation of caveolin-1 and dynamin-2 expression. Increased expression levels of the gene for caveolin, Cav-1, resulting in augmented cellular metastasis and invasion, have been demonstrated in various types of cancer, and overexpression of the gene for dynamin-2, DNM2, has been associated with tumorigenesis in cervical, pancreatic and lung cancer. An increased expression of Cav-1 and DNM2 is known to be associated with the invasive behavior of cancer cells, and with cancer progression. Furthermore, it has been previously demonstrated that, in caveolar assembly and caveolae mediated endocytosis, Cav-1 interacts directly with DNM2 during the processes. Altered expression of the 2 genes is critical for the normal function of the cell. The expression patterns of Cav-1 and DNM2 have been previously examined in bladder cancer cell lines, and were each demonstrated to be overexpressed. In the present study, the expression levels of these 2 genes in bladder cancer samples were quantified. The gene expression levels of Cav-1 and DNM2 were identified to be increased 8.88- and 8.62-fold, respectively, in tumors compared with the normal controls. Furthermore, high-grade tumors exhibited significantly increased expression levels of Cav-1 and DNM2 (both P<0.0001) compared with the low-grade tumors. In addition, compared with normal control samples, the expression of the 2 genes in tumor samples was observed to be highly significant (P<0.0001), with a marked positive correlation identified for the tumors (Pearson's correlation coefficient, r=0.80 for the tumor samples vs. r=0.32 in the normal control samples). Taken together, the results of the present study demonstrated that the overexpression of Cav-1 and DNM2 genes, and a determination of their correlation coefficients, may be a potential risk factor for bladder cancer, in addition to other clinical factors.

Localization of a novel autosomal recessive nonsyndromic hearing impairment locus DFNB65 to chromosome 20q13.2-q13.32.

Autosomal recessive nonsyndromic hearing impairment (ARNSHI) is the most frequent form of prelingual hereditary hearing loss in humans. Between 75 and 80% of all nonsyndromic deafness is inherited in an autosomal recessive pattern. Using linkage analysis, we have mapped a novel gene responsible for this form of nonsyndromic hearing impairment, DFNB65, in a consanguineous family from the Azad Jammu and Kashmir regions, which border Pakistan and India. A maximum multipoint LOD score of 3.3 was obtained at marker D20S840. The three-unit support interval is contained between markers D20S902 and D20S430, while the region of homozygosity is flanked by markers D20S480 and D20S430. The novel locus maps to a 10.5-cM region on chromosome 20q13.2-q13.32 and corresponds to a physical map distance of 4.3 Mb. DFNB65 represents the first ARNSHI locus to map to chromosome 20.

In-silico analysis of Pasteurella multocida to identify common epitopes between fowl, goat and buffalo.

Pasteurella multocida represents a highly diverse group of bacteria infecting various hosts like the fowl, goat and buffalo leading to huge economic loss to the poultry and cattle industry. Previous reports indicated that the outer membrane proteins contribute significantly to the pathogenesis of Pasteurella multocida. The comparative in-silico genome wide analysis of four pathogenic Pasteurella multocida strains (Anand1-poultry, Anand1-goat, PMTB and VTCCBAA264) with their respective hosts was performed. A pipeline was developed to identify the list of non-homologous proteins of Pasteurella multocida strains and their hosts. The list was further analyzed for the identification of the essential outer membrane proteins responsible for the pathogenicity. Outer membrane proteins were further selected from these antigenic proteins on the basis of their pathogenic potential. A common B-cell epitope (TDYRNRDRS, ARRSVTSKEN, and KINDQWRW) determined via sequential and structural approach from the lipopolysaccharide (LPS) assembly outer membrane complex protein was predicted from fowl, goat and buffalo. Furthermore, we identified T-cell epitopes based on the lipopolysaccharide (LPS) assembly outer membrane complex protein via docking studies which were either similar to the B-cell epitopes or were occurring in the same patch except for MHC class II M fowl. We propose that this difference in epitope sequence is due to different interacting MHC class II protein predicted from the fowl. Hence, in the current study we found that a unique epitope based on the common antigenic lipopolysaccharide (LPS) outer membrane complex protein present in fowl, goat and buffalo can be a suitable target for vaccine development against the two economic devastating diseases; fowl cholera (FC) and hemorrhagic septicemia (HS).

Is atomic rearrangement of type IV PHA synthases responsible for increased PHA production?

BACKGROUND: Type IV PHA synthase is a key enzyme responsible for catalyzing the formation of non-toxic, biocompatible, and biodegradable short-chain-length polyhydroxyalkanoates (scl-PHA) under the growth-limiting conditions in the members of the genus Bacillus. RESULTS: The comparative in vitro and in silico analysis of the phaC subunit of type IV PHA synthases among Bacillus cereus FA11, B. cereus FC11, and B. cereus FS1 was done in our study to determine its structural and functional properties. Conserved domain analysis demonstrated that phaC subunit belongs to the alpha/beta (α/ß) hydrolase fold. The catalytic triad comprising of cysteine (Cys), histidine (His), and aspartate (Asp) was found to be present at the active site. A shorter inter-atomic distance was found between the carboxyl (-COO) group of Asp and amino (NH2) group of His. Furthermore, slightly long inter-atomic distances between sulfhydryl (SH) group of Cys and NH2 group of His may be pointing toward the broader substrate specificity of type IV PHA synthases. However, a shorter distance between the SH group of Cys and NH2 group of His in case of B. cereus FC11 leads to a higher enzymatic activity and maximum PHA yield (49.26%). CONCLUSION: The in silico study verifies that the close proximity between SH group of Cys and NH2 group of His in phaC subunit of type IV PHA synthases can be crucial for synthesis of scl-PHA. However, the catalytic activity of type IV PHA synthases declines as the distance between the sulfur (S) atom of the SH group of Cys and the nitrogen (N) atom of NH2 group of His increases.

Transcript diversification in the nervous system: a to I RNA editing in CNS function and disease development.

RNA editing by adenosine deaminases that act on RNA converts adenosines to inosines in coding and non-coding regions of mRNAs. Inosines are interpreted as guanosines and hence, this type of editing can change codons, alter splice patterns, or influence the fate of an RNA. A to I editing is most abundant in the central nervous system (CNS). Here, targets for this type of nucleotide modification frequently encode receptors and channels. In many cases, the editing-induced amino acid exchanges alter the properties of the receptors and channels. Consistently, changes in editing patterns are frequently found associated with diseases of the CNS. In this review we describe the mechanisms of RNA editing and focus on target mRNAs of editing that are functionally relevant to normal and aberrant CNS activity.