Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach.

Rice is an important staple food grain consumed by most of the population around the world. With climate and environmental changes, rice has undergone a tremendous stress state which has impacted crop production and productivity. Plant growth hormones are essential component that controls the overall outcome of the growth and development of the plant. Cytokinin is a hormone that plays an important role in plant immunity and defense systems. Trans-zeatin is an active form of cytokinin that can affect plant growth which is mediated by a multi-step two-component phosphorelay system that has different roles in various developmental stages. Systems biology is an approach for pathway analysis to trans-zeatin treated rice that could provide a deep understanding of different molecules associated with them. In this study, we have used a weighted gene co-expression network analysis method to identify the functional modules and hub genes involved in the cytokinin pathway. We have identified nine functional modules comprising of different hub genes which contribute to the cytokinin signaling route. The biological significance of these identified hub genes has been tested by applying well-proven statistical techniques to establish the association with the experimentally validated QTLs and annotated by the DAVID server. The establishment of key genes in different pathways has been confirmed. These results will be useful to design new stress-resistant cultivars which can provide sustainable yield in stress-specific conditions.

Malachite green-conjugated multi-walled carbon nanotubes potentiate antimicrobial photodynamic inactivation of planktonic cells and biofilms of Pseudomonas aeruginosa and Staphylococcus aureus.

Purpose: Infections associated with medical devices that are caused by biofilms remain a considerable challenge for health care systems owing to their multidrug resistance patterns. Biofilms of Pseudomonas aeruginosa and Staphylococcus aureus can result in life-threatening situations which are tough to eliminate by traditional methods. Antimicrobial photodynamic inactivation (aPDT) constitutes an alternative method of killing deadly pathogens and their biofilms using reactive oxygen species (ROS). This study investigated the efficacy of enhanced in vitro aPDT of P. aeruginosa and S. aureus using malachite green conjugated to carboxyl-functionalized multi-walled carbon nanotubes (MGCNT). Both the planktonic cells and biofilms of test bacteria were demonstrated to be susceptible to the MGCNT conjugate. These MGCNT conjugates may thus be employed as a facile strategy for designing antibacterial and anti-biofilm coatings to prevent the infections associated with medical devices. Methods: Conjugation of the cationic dye malachite green to carbon nanotube was studied by UV-visible spectroscopy, high-resolution transmission electron microscopy, and Fourier transform infrared spectrometry. P. aeruginosa and S. aureus photodestruction were studied using MGCNT conjugate irradiated for 3 mins with a red laser of wavelength 660 nm and radiant exposure of 58.49 J cm-2. Results: Upon MGCNT treatment, S. aureus and P. aeruginosa were reduced by 5.16 and 5.55 log10 , respectively. Compared to free dye, treatment with MGCNT afforded improved phototoxicity against test bacteria, concomitant with greater ROS production. The results revealed improved biofilm inhibition, exopolysaccharide inhibition, and reduced cell viability in test bacteria treated with MGCNT conjugate. P. aeruginosa and S. aureus biofilms were considerably reduced to 60.20±2.48% and 67.59±3.53%, respectively. Enhanced relative MGCNT phototoxicity in test bacteria was confirmed using confocal laser scanning microscopy. Conclusion: The findings indicated that MGCNT conjugate could be useful to eliminate the biofilms formed on medical devices by S. aureus and P. aeruginosa.

A Comparative Study of Single-Trait and Multi-Trait Genomic Selection.

In recent years of animal and plant breeding research, genomic selection (GS) became a choice for selection of appropriate candidate for breeding as it significantly contributes to enhance the genetic gain. Various studies related to GS have been carried out in the recent past. These studies were mostly confined to single trait. Although GS methods based on single trait have not performed very well in cases like pleiotropy, missing data and when the trait under study has low heritability. Gradually, some studies were carried out to explore the possibility of methods for GS based on multiple traits in the view of overcoming the above-mentioned problems in the method of single-trait GS (STGS). Currently, multi-trait-based GS methods are getting importance as it exploits the information of correlated structure among response. In this study, we have compared various methods related to STGS, such as stepwise regression, ridge regression, least absolute shrinkage and selection operator (LASSO), Bayesian, best linear unbiased prediction, and support vector machine, and multi-trait-based GS methods, such as multivariate regression with covariance estimation, conditional Gaussian graphical models, mixed model, and LASSO. In almost all cases, multi-trait-based methods are found to be more accurate. Based on the results of this study, it may be concluded that multi-trait-based methods have great potential to increase genetic gain as they utilize the correlation among the response variable as extra information, which contributes to estimate breeding value more precisely. This study is a comprehensive review of the methods of GS right from single trait to multiple traits and comparisons among these two classes.

Correction: Synthesis and antimicrobial photodynamic effect of methylene blue conjugated carbon nanotubes on E. coli and S. aureus.

Correction for 'Synthesis and antimicrobial photodynamic effect of methylene blue conjugated carbon nanotubes on E. coli and S. aureus' by Paramanantham Parasuraman et al., Photochem. Photobiol. Sci., 2019, DOI: 10.1039/c8pp00369f.

Deciphering foot-and-mouth disease (FMD) virus-host tropism.

The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of Bos taurus, Gallus and Canis. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp 143RGD145 and at domain 676SIPLQ680 in alpha-integrin of B. taurus. Notably, in-silico site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and B. taurus integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, in-vitro analysis demonstrates the persistence of the putative tropism site 'SIPLQ' in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma.

Synthesis and antimicrobial photodynamic effect of methylene blue conjugated carbon nanotubes on E. coli and S. aureus.

Catheter-related bloodstream infections (CRBSIs) are one of the leading causes of high morbidity and mortality in hospitalized patients. The proper management, prevention and treatment of CRBSIs rely on the understanding of these highly resistant bacterial infections. The emergence of such a challenge to public health has resulted in the development of an alternative antimicrobial strategy called antimicrobial photodynamic therapy (aPDT). In the presence of a photosensitizer (PS), light of the appropriate wavelength, and molecular oxygen, aPDT generates reactive oxygen species (ROS) which lead to microbial cell death and cell damage. We investigated the enhanced antibacterial and antibiofilm activities of methylene blue conjugated carbon nanotubes (MBCNTs) on biofilms of E. coli and S. aureus using a laser light source at 670 nm with radiant exposure of 58.49 J cm-2. Photodynamic inactivation in test cultures showed 4.86 and 5.55 log10 reductions in E. coli and S. aureus, respectively. Biofilm inhibition assays, cell viability assays and EPS reduction assays showed higher inhibition in S. aureus than in E. coli, suggesting that pronounced ROS generation occurred due to photodynamic therapy in S. aureus. Results from a study into the mechanism of action proved that the cell membrane is the main target for photodynamic inactivation. Comparatively higher photodynamic inactivation was observed in Gram positive bacteria due to the increased production of free radicals inside these cells. From this study, we conclude that MBCNT can be used as a promising nanocomposite for the eradication of dangerous pathogens on medical devices.

An efficient algorithm for protein structure comparison using elastic shape analysis.

BACKGROUND: Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have been proposed in literature for comparing protein structures but they have their own limitations in terms of accuracy and complexity with respect to computational time and space. There is a need to improve the computational complexity in comparison/alignment of proteins through incorporation of important biological and structural properties in the existing techniques. RESULTS: An efficient algorithm has been developed for comparing protein structures using elastic shape analysis in which the sequence of 3D coordinates atoms of protein structures supplemented by additional auxiliary information from side-chain properties are incorporated. The protein structure is represented by a special function called square-root velocity function. Furthermore, singular value decomposition and dynamic programming have been employed for optimal rotation and optimal matching of the proteins, respectively. Also, geodesic distance has been calculated and used as the dissimilarity score between two protein structures. The performance of the developed algorithm is tested and found to be more efficient, i.e., running time reduced by 80-90 % without compromising accuracy of comparison when compared with the existing methods. Source codes for different functions have been developed in R. Also, user friendly web-based application called ProtSComp has been developed using above algorithm for comparing protein 3D structures and is accessible free. CONCLUSIONS: The methodology and algorithm developed in this study is taking considerably less computational time without loss of accuracy (Table 2). The proposed algorithm is considering different criteria of representing protein structures using 3D coordinates of atoms and inclusion of residue wise molecular properties as auxiliary information.

Effects of caloric restriction on skeletal muscle mitochondrial proton leak in aging rats.

Long-term caloric restriction (CR) retards aging processes and increases maximum life span. We investigated the influence of CR on mitochondrial proton leaks in rat skeletal muscle. Because CR lowers oxidative damage to mitochondrial membrane lipids and proteins, we hypothesized that leak would be lower in mitochondria from old CR rats than in age-matched controls. Three groups (n = 12) were studied: 4-month-old "young" control rats (body weight: 404 g +/- 7 SEM), 33-month-old CR rats (body weight: 262 g +/- 3), and 33-month-old control rats (body weight: 446 g +/- 5). CR rats received 67% of the energy intake of old control rats, with adequate intakes of all essential nutrients. Maximum leak-dependent O2 consumption (State 4) was 23% lower in CR rats than in age-matched controls, whereas protonmotive force values were similar, supporting our hypothesis. The overall kinetics of leak were similar between the two groups of old rats; in the young, kinetics indicated higher protonmotive force values. The latter indication is consistent with aging-induced alterations in proton leak kinetics that are independent of dietary intervention. There was no influence of age or diet on serum T4 level, whereas T3 was lower in young than in old control rats. These results support and extend the oxidative stress hypothesis of aging.

Physicochemical alterations in blood, cerebrospinal fluid and urine in experimental lactic acidosis in sheep.

Ruminal acidosis was induced in six adult sheep by oral feeding of wheat grain at 90 g kg-1 body-weight. Ruminal fluid, blood, cerebrospinal fluid (CSF) and urine samples were collected before grain feeding (0 h) and thereafter at 12, 24, 48, 72, 96 and 120 hour intervals. Decrease in the rumen pH was associated with decreased pH in blood, CSF and urine and increased total lactic acid concentrations in rumen liquor, blood, CSF and urine. Significantly (P < 0.05) increased levels of sodium, inorganic phosphorus and decreased levels of potassium and calcium were observed in the serum of acidotic sheep. CSF analysis revealed decreased potassium and chloride levels and increased glucose concentration and total leucocyte count within 12 hours of the grain feeding. Pandy's test was positive in half of the surviving sheep at 12 hours and in all the sheep at 96 and 120 hours of observation. In urine, sodium and chloride levels decreased while potassium and inorganic phosphorus increased. The changes in the biochemical parameters started within 12 hours and lasted up to 48 to 120 hours of the observation period.

Biochemical alterations in serum and cerebrospinal fluid in experimental acidosis in goats.

Experimental acidosis was induced in six goats aged between one and two years by administration of whole wheat grain at 100 g kg-1 bodyweight given intraruminally. Blood and cerebrospinal fluid (CSF) samples were collected from these goats before administration of wheat grain (0 hour) and thereafter at 12, 24, 48, 72, 96 and 120 hour intervals. These were analysed for serum enzyme activities and physicochemical characters of CSF. Significantly (P less than 0.05) higher activities of amylase (at 12 hours), lactate dehydrogenase (12 to 48 hours), creatine phosphokinase (12 to 48 hours), aspartate aminotransferase (12 to 24 hours), and gamma-glutamyl transferase (12 to 96 hours) were found in serum samples of acidotic goats. Changes in CSF included decrease of pH and chloride content and higher glucose values. No difference was seen in the physical character of CSF collected at different time intervals from acidotic goats.