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Aeromonads resides in aquatic environments and infect humans and fish among other animals. This opportunistic pathogen is predicted to have several pili and fimbriae genes which may promote biofilm formation and attachment affecting the infection process. The present study compares biofilm formation and subsequent infection on MDCK cell lines using wildtype Aeromonas hydrophila and putative type IV pilin biosynthesis gene mutant generated by standard protocol. The results indicate the involvement of putative pilus biosynthesis operon AHA0686-AHA0696 in biofilm formation of Aeromonas hydrophila and infection of MDCK cells. In silico analysis of the operon predicts to contain putative type IV pili and pilin biosynthetic genes. Detailed analysis of these genes is required to evaluate the applicability of these mutant strains as potential vaccine candidates.

The high altitude of the Himalayan cold desert represents a valuable habitat of natural resources. The extreme climatic condition manifested by intense mutagenic UV-radiation, physiological drought, desiccation and strong winds, makes the survival of plants really difficult. As a consequence of this atmospheric stressor, the plants produce unique metabolites which play a preventive role in intrinsic mechanism of sustenance. Many plant species of this region have been investigated in search of novel antioxidants and antimicrobials. Plants synthesize several antioxidants that aid in antioxidant defense system, thereby protecting plants against damage caused by active ROS. These compounds include chlorophyll derivatives, alkaloids, essential oils, phytosterols, phenolics and polyphenolics. Some of the antioxidants that have been isolated from plants include curcumin, quercetin, ascorbic acid, resveratrol amongst many other compounds. Additionally, the emergence of resistance to multiple antimicrobial agents has become a major threat to public health. Hence, fresh efforts towards new drug identification and development are greatly needed. Plants have long been used in traditional Indian medicine for numerous therapeutic benefits and low toxicity. Considering the growing interest in quest for search of plant based antimicrobials and antioxidants; an effort has been carried to systematically record the antioxidants and antimicrobial potential of plants of Himalayan region.

Plants have a complex system of stress response that deals with different types of stresses. Maize (Zea mays L.), one of the most important crops grown throughout the world, across a range of agro-ecological environments, employs complex mechanisms of gene regulation in response to drought stress. HKI 335 is a tropical maize inbred line showing remarkable adaptation to drought stress. Abiotic stresses, like drought, trigger the production of reactive oxygen species (ROS) due to the incomplete reduction or excitation of molecular oxygen, eventually leading to cell damage. Superoxide dismutase (SOD, EC 1.15.1.1) is a metalloenzyme that acts as the first line of defense against ROS. We cloned the Sod2 gene from HKI 335 inbred line and analyzed its protein through detailed in silico characterization. Our comparative modeling revealed that at the level of tertiary structure, the HKI 335 SOD2 protein is highly similar to Potentilla atrosanguinea SOD2, which had been previously identified as highly thermostable SOD that can tolerate autoclaving as well as sub-zero temperatures. We performed phylogenetic analysis, estimated physicochemical properties, post-translational modifications, protein-protein interactions, and domain composition of this SOD2. The phylogenetic analysis showed that orthologous sequences of SOD from different species were clustered into two clusters. Secondary structure prediction indicates that SOD2 is a soluble protein and no transmembrane domains have been found. Most of the beta sheets have RSA value greater than 2. The Ramachandran plot from PDBsum revealed that most of the residues fall in the highly favored region. It was estimated that the value of the instability index was less than 40, the value of the aliphatic index was extremely high and the GRAVY value lies between −2 and +2. We could identify only one phosphorylation site, located at position 20 with a score of 0.692. Overall, the unique stress-tolerant properties of the HKI 335 SOD2, may be one of the reasons contributing to the high drought tolerance trait exhibited by HKI 335 maize inbred line. Further research may reveal more insights into the drought adaptation mechanism in maize and the eventual deployment of the trait in maize hybrids.

Let"s play lego game of blocks on life biomolecules, can we? Yes we can, that"s what is the era of translational world of science, where synthetic biology envisions to build novel patterns of cellular function from the available blocks by engineering designs on the biological blocks - DNA and protein. The blocks here are the sequence components that are characterized in their most simple forms and then anchored together as a string of co-regulated genetic parts with desired functions. Synthetic biology dwells on high-throughput biological engineering and rational redesigning of biological substrates that have intricate but partially characterized details posing their unique set of challenges. The conceptual biological engineering includes design patterns, genetic or DNA components as libraries, computational tools for design, circuit design scaffolds, with the final aim of application specific designs. These synthetic genetic circuits possess the capacity to manipulate and probe biological interfaces. The comprehensive review aims to shed light on the progress, challenges and applications of key areas where synthetic biology is impacting biological sciences.

Inflammatory bowel disease (IBD) is an idiopathic prolonged ailment accountable for inflammatory conditions of the intestine. Moreover, arthritis is responsible for joints' stiffness and painful inflammation. IBD shows certain articular extra-intestinal manifestations associating IBD with arthritis. IBD associated arthritis is found to be linked with ankylosing spondylitis (AS). The present study insights for the potential and putative drug targets and biomarkers of IBD associated with arthritis using in silico approaches. Microarray data analysis of datasets involving IBD affected and AS affected vs controls were done to explore the differentially expressed genes (DEGs). In majority of the datasets, the common DEGs found were sterile alpha motif domain containing 9 like (SAMD9L), inhibin beta A subunit (INHBA), transmembrane protein 45A (TMEM45A) and transmembrane and tetratricopeptide repeat containing 1 (TMTC1). The common functions and pathways found between the DEGs were control of macromolecule metabolism process, control of metabolic process, control of primary metabolic process, and control of protein metabolic process, cell differentiation, organ development, single-organism development process, multicellular organism development process, development of system, single-multicellular organism development process, developmental process, development of anatomical structure, multicellular organismal development process, control of biological process, cell proliferation, hematopoietic progenitor cell differentiation and immune system process. TMTC1 and INBHA were found to be more biologically significant genes according to the topological properties of the network. This study also suggests that TMTC1, INBHA, TMEM45A and SAMD9L DEGs and their accompanying pathways might have the potential to be exploited as drug targets and biomarkers in the diagnosis and/or treatment of IBD linked arthritis and warrants for further experimental validation.

Background Obstructive sleep apnoea (OSA) is a prevalent form of sleep disordered breathing which results in sleep fragmentation and deprivation. Obesity and cardiovascular disorders are the major risk factors associated with OSA. Molecular analysis of the factors associated with OSA could demarcate the clinical analysis pattern in a population. Objective This study pertains to in-silico analyses of miRNA and their gene targets with validation for their potential role in OSA as putative biomarker candidates. Methods miRDB, TargetScan and miRanda databases were used to identify targets of miR-27 and let-7 that have documented role in OSA and co-related obesity and cardiovascular disorders. Quantitative PCR was used to analyze expression pattern of miR-27 and let-7 in obese and non-obese OSA patient cohorts with respective controls. In-silico analysis was done using PatchDoc to obtain atomic contact energy (ACE) scores that indicated the docked gene targets to the predicted miRNA structures. The docked structures were analysed using Maestro Suite 11 for the hydrogen and aromatic interactions. Results Downregulation of miR-27 and let-7 in OSA compared to controls was observed. In-silico data analysis was performed for gene targets (TGFBR1, TGFBR2, SMAD2, SMAD4, CRY2 and CNR1) of the selected miRNAs (miR-27 and let-7). Among all, CNR1 and CRY2 were found to be better targets for miR-27 and let-7 respectively as per ACE scores, ROC scores and expression fold change in OSA. Conclusion Our study gives insights to the expression profiling of miR-27 and let-7 and explore a set of potential target genes (CNR1 and CRY2) of these two miRNAs for a promising clinical relevance in OSA.

Reactive Arthritis (ReA), a rare seronegative inflammatory arthritis, lacks exquisite classification under rheumatic autoimmunity. ReA is solely established using differential clinical diagnosis of the patient cohorts, where pathogenic triggers linked to enteric and urogenital microorganisms e.g. Salmonella, Shigella, Yersinia, Campylobacter, Chlamydia have been reported. Inflammatory Bowel Disease (IBD), an idiopathic enteric disorder co-evolved and attuned to present gut microbiome dysbiosis, can be correlated to the genesis of enteropathic arthropathies like ReA. Gut microbes symbolically modulate immune system homeostasis and are elementary for varied disease patterns in autoimmune disorders. The gut-microbiota axis structured on the core host-microbe interactions execute an imperative role in discerning the etiopathogenesis of ReA and IBD. This study predicts the molecular signatures for ReA with co-evolved IBD through the enveloped host-microbe interactions and microbe-microbe ‘interspecies communication’, using synonymous gene expression data for selective microbes. We have utilized a combinatorial approach that have concomitant in-silico work-pipeline and experimental validation to corroborate the findings. In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. Cross validation of the target/s or biomarker/s was done by targeted gene expression analysis following a non-probabilistic convenience sampling. Studies were performed to substantiate the host-microbe disease network consisting of protein-marker-symptom/disease-pathway-drug associations resulting in possible identification of vital drug targets, biomarkers, pathways and inhibitors for IBD and ReA.Our study identified Na(+)/H(+) anti-porter (NHAA) and Kynureninase (KYNU) to be robust early and essential host-microbe interacting targets for IBD co-evolved ReA. Other vital host-microbe interacting genes, proteins, pathways and drugs include Adenosine Deaminase (ADA), Superoxide Dismutase 2 (SOD2), Catalase (CAT), Angiotensin I Converting Enzyme (ACE), carbon metabolism (folate biosynthesis) and methotrexate. These can serve as potential prognostic/theranostic biomarkers and signatures that can be extrapolated to stratify ReA and related autoimmunity patient cohorts for further pilot studies.

Inflammatory bowel disease (IBD) is a persistent idiopathic disorder responsible for intestinal inflammatory conditions. IBD exhibits several extraintestinal manifestations, the most common being arthropathy, that are important triggers and risk factors for adverse progression of the disease. Due to a lack of definite diagnostic criteria and treatment regime, a need arises for early diagnosis and management of IBD associated arthropathy to reduce its morbidity. The present study utilizes a machine learning approach for development and validation of a risk prediction and early diagnostic disease model for IBD associated arthropathy. A publically available IBD cases vs control dataset from University of Massachusetts Medical School’s institutional repository was taken and the data was filtered into 54 IBD individuals along with their demographic and clinical characteristics. The arthropathy characteristics were incorporated from literature in the IBD dataset. Data was randomly split into training (50%; n=27) and testing (50%; n=27) for development and validation of model using logistic regression. Out of 54 IBD cases, 21 had a higher risk of developing arthropathy. The area under the receiver operator curve for the validated model was 0.90 (95% CI 0.80–0.99; accuracy 96%). This disease model can aid in identification of high-risk individuals and for early diagnosis of arthropathy in IBD cases before reaching the imaging and invasive diagnostic stage. This model warrants for prospective case-control trials validation.

Obstructive sleep apnoea (OSA) is a sleep respiration disorder with multiple pathophysiological risks. The study of OSA is important from a public health perspective due to increased risk of cardiovascular morbidity and metabolic disorders.The review content contributes to amalgamate the clinico-molecular analysis of microRNAs, single-nucleotide polymorphisms (SNPs), transcriptome profiles and epigenetics in the prognosis of OSA. The conceptual focus here is to demarcate the involvement of regulatory players like miRNAs that have most probable contributions towards other changes in patients leading to clinical outcomes.Literature survey was done by retrieving data from databases such as Google Scholar, PubMed and Science Direct.Abundant reports have suggested the involvement and role of biomarkers such as CRP, TNF-α, IL-6, IL-8 and CAMs but there are interspersed speculations about the involvement of epigenetics in OSA.miRNA and transcriptome profiling, DNA methylation and SNPs are some of the less researched aspects that aim to bridge the gap in the molecular mechanisms underlying the pathophysiology of OSA. The quest for biomarkers in OSA is now distinctly achieving new heights. In the context of diagnosis, the above mentioned epigenetic regulators are likely to emerge as viable contenders.

The photoreactions of recombinant phytochrome CphA from cyanobacterium Calothrix sp. PCC7601 reconstituted with phycocyanobilin were investigated using UV-Vis and Fourier transform infrared (FTIR) difference spectroscopy, stabilizing intermediates at low temperature. The yield of the forward reaction strongly depends on temperature, unlike the backward reaction. Because of the very fast thermal relaxation processes in the Pr to Pfr pathway, no pure difference spectra of the Pr photoconversion products could be directly measured. Thus, the contribution of the Pfr:Pr pathway was taken into account by applying an appropriate correction procedure both in the UV-Vis and FTIR experiments. Three intermediates have been trapped at -25, -45 and -120 degrees C, which show the characteristic vibrational band pattern of the plant phytochrome phyA intermediates meta-Rc, meta-Ra and lumi-R, respectively. In the backward reaction, two intermediates corresponding to meta-F and lumi-F were trapped at -70 and -140 degrees C, respectively. FTIR spectra of all intermediates, as well as of the Pfr state, show remarkable similarities with the corresponding spectra of Cph1 phytochrome from cyanobacterium Synechocystis and the 59 kDa N-terminal fragment of Cph1, and, albeit not so pronounced, also with plant phyA. The spectral similarities and differences between the various phytochromes are discussed in terms of structural changes of the chromophore and the chromophore-protein interactions.

Two phytochromes, CphA and CphB, from the cyanobacterium Calothrix PCC7601, with similar size (768 and 766 amino acids) and domain structure, were investigated for the essential length of their protein moiety required to maintain the spectral integrity. Both proteins fold into PAS-, GAF-, PHY-, and Histidine-kinase (HK) domains. CphA binds a phycocyanobilin (PCB) chromophore at a "canonical" cysteine within the GAF domain, identically as in plant phytochromes. CphB binds biliverdin IXalpha at cysteine24, positioned in the N-terminal PAS domain. The C-terminally located HK and PHY domains, present in both proteins, were removed subsequently by introducing stop-codons at the corresponding DNA positions. The spectral properties of the resulting proteins were investigated. The full-length proteins absorb at (CphA) 663 and 707 nm (red-, far red-absorbing P (r) and P (fr) forms of phytochromes) and at (CphB) 704 and 750 nm. Removal of the HK domains had no effect on the absorbance maxima of the resulting PAS-GAF-PHY constructs (CphA: 663/707 nm, CphB: 704/750 nm, P (r)/P (fr), respectively). Further deletion of the "PHY" domains caused a blue-shift of the P (r) and P (fr) absorption of CphA (lambda (max): 658/698 nm) and increased the amount of unproperly folded apoprotein, seen by a reduced capability to bind the chromophore in photoconvertible manner. In CphB, however, it practically impaired the formation of P (fr), i.e., showing a very low oscillator strength absorption band, whereas the P (r) form remains unchanged (702 nm). This finding clearly indicates a different interaction between domains in the "typical", PCB binding and in the biliverdin-binding phytochromes, and demonstrates a loss of oscillator strength for the latter, most probably due to a strong conformational distortion of the chromophore in the CphB P (fr) form.

The resonance Raman spectra of the Pr state of the N-terminal 65-kDa fragment of plant phytochrome phyA have been measured and analyzed in terms of the configuration and conformation of the tetrapyrroles methine bridges. Spectra were obtained from phyA adducts reconstituted with the natural chromophore phytochromobilin as well as phycocyanobilin and its isotopomers labeled at the terminal methine bridges through C-13/C-12 and D/H substitution. Upon comparing the resonance Raman spectra of the various phyA adducts, it was possible to identify the bands that originate from normal modes dominated by the stretching coordinates of the terminal methine bridges A-B and C-D. Quantum chemical calculations of the isolated tetrapyrroles reveal that these modes are sensitive indicators for the methine bridge configuration and conformation. For all phyA adducts, the experimental spectra of Pr including this marker band region are well reproduced by the calculated spectra obtained for the ZZZasa configuration. In contrast, there are substantial discrepancies between the experimental spectra and the spectra calculated for the ZZZssa configuration, which has been previously shown to be the chromophore geometry in the Pr state of the bacterial, biliverdin-binding phytochrome from Deinococcus radiodurans (Wagner, J. R., J. S. Brunzelle, K. T. Forest, R. D. Vierstra. 2005. Nature. 438: 325-331). The results of this work, therefore, suggest that plant and bacterial (biliverdin-binding) phytochromes exhibit different structures in the parent state although the mechanism of the photoinduced reaction cycle may be quite similar. Fil: Murgida, Daniel Horacio. Technische Universitat Berlin; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina Fil: von Stetten, David. Technische Universitat Berlin; Alemania Fil: Hildebrandt, Peter. Technische Universitat Berlin; Alemania Fil: Schwinté, Pascale. Universidad de Friburgo; Alemania Fil: Siebert, Friedrich. Universidad de Friburgo; Alemania Fil: Sharda, Shivani. Max-Planck-Institut fur Bioanorganische Chemie; Alemania Fil: Gärtner, Wolfgang. Technische Universitat Berlin; Alemania. Max-Planck-Institut fur Bioanorganische Chemie; Alemania Fil: Mroginski, Maria Andrea. Max-Planck-Institut fur Bioanorganische Chemie; Alemania