Optimizing speed breeding and seed/pod chip based genotyping techniques in pigeonpea: A way forward for high throughput line development.

BACKGROUND: The challenge of pigeonpea breeding lies in its photosensitivity and seasonal specificity. This poses a problem to the breeder, as it restricts to single generation advancement in a year. Currently, the cross to cultivar gap is twelve to thirteen years resulting in a limited number of varietal releases over the past six decades. Shortening the breeding cycle was need of the hour, unlikely achieved by conventional breeding. To overcome these hindrances speed breeding was a necessary leap. An experiment was planned to optimize the speed breeding coupled with single seed descent and seed or pod chip-based genotyping to shorten the breeding cycle in pigeonpea at ICRISAT, Hyderabad. Monitored photoperiod, light wavelength, temperature and crop management regime were the indicators attributing to the success of speed breeding. RESULT: A photoperiod of 13 h: 8 h: 13 h at vegetative: flowering and pod filling stages is ideal for shortening the breeding cycle. Broad spectrum light (5700 K LED) hastened early vegetative growth and pod formation. Whereas far-red (735 nm) light favoured early flowering. A significant difference between the photoperiods, genotypes as well as photoperiod x genotype interaction for both days to flowering and plant height was noted. CONCLUSION: The optimized protocol serves as a road map for rapid generation advancement in pigeonpea. Deploying this protocol, it is possible to advance 2-4 generations per year. The breeding cycle can be reduced to 2-4 years which otherwise takes 7 years under conventional breeding. Single Seed Descent and seed or pod chip-based genotyping for early generation marker assisted selection, strengthened the precision of this technique aiding in high throughput line development.

Characterization of plastic debris from surface waters of the eastern Arabian Sea-Indian Ocean.

The quantity of floating plastic debris (FPD) is continuously being increased in the oceans. To assess their size, structure, and composition along the eastern Arabian Sea (EAS), FPD samples were collected by using a surface plankton net. The microplastic size fraction (0.5-5 mm) was the most prevalent accounting for >50% of the total, followed by mesoplastics (5-25 mm; ~40%) and macroplastics (>25 mm; ~10%). The collected FPDs were categorized into five different types and eight colours. Attenuated Total Reflectance-Fourier Transform Infrared Spectrometry (ATR-FTIR) analysis of the plastics revealed that polypropylene, polyethylene, and nylon were the most dominant polymers, and these comprised mostly of fibre/fishing line. The abundance of FPD in the EAS (0.013 ± 0.012 no.s/m3) was found to be very low compared to elsewhere. The prevalent microplastics presence in the oceans might have occurred mainly by the degradation of larger items. It increases bioavailability, and hence, is a risk to marine ecosystems.

Premature chromosome condensation assay to study influence of high-level natural radiation on the initial DNA double strand break repair in human G0 lymphocytes.

The inherent capacity of individuals to efficiently repair ionizing radiation induced DNA double strand breaks (DSBs) may be inherited, however, it is influenced by several epigenetic and environmental factors. A pilot study tested whether chronic low dose natural radiation exposure influences the rejoining of initial DNA DSBs induced by a 2 Gy γ-irradiation in 22 individuals from high (>1.5 mGy/year) and normal (≤1.5 mGy/year) level natural radiation areas (H&NLNRA) of Kerala. Rejoining of DSBs (during 1 h at 37 °C, immediately after irradiation) was evaluated at the chromosome level in the presence and absence of wortmannin (a potent inhibitor of DSB repair in normal human cells) using a cell fusion-induced premature chromosome condensation (PCC) assay. The PCC assay quantitates DSBs in the form of excess chromosome fragments in human G0 lymphocytes without the requirement for cell division. A quantitative difference was observed in the early rejoining of DNA DSBs between individuals from HLNRA and NLNRA, with HLNRA individuals showing a higher (P = 0.05) mean initial repair ratio. The results indicate an influence of chronic low dose natural radiation on initial DNA DSB repair in inhabitants of HLNRA of the Kerala coast.

Preparation, characterization and efficacy of lysostaphin-chitosan gel against Staphylococcus aureus.

Lysostaphin (LST) is a bacteriocin that cleaves within the pentaglycine cross bridge of Staphylococcus aureus peptidoglycan. Previous studies have reported the high efficiency of LST even against multi drug resistant S. aureus including methicillin resistant S. aureus (MRSA). In this study, we have developed a new chitosan based hydrogel formulation of LST to exploit its anti-staphylococcal activity. The atomic interactions of LST with chitosan were studied by molecular docking studies. The rheology and the antibacterial properties of the developed LSTC gel were evaluated. The developed LST containing chitosan hydrogel (LSTC gel) was flexible, flows smoothly and remains stable at physiological temperature. The in vitro studies by agar well diffusion and ex vivo studies in porcine skin model exhibited a reduction in S. aureus survival by ∼3 Log10CFU/mL in the presence of LSTC gel. The cytocompatibility of the gel was tested in vitro using macrophage RAW 264.7 cell line and in vivo in Drosophila melanogaster. A gradual disruption of S. aureus biofilms with the increase of LST concentrations in the LSTC gel was observed which was confirmed by SEM analysis. We conclude that LSTC gel could be highly effectual and advantageous over antibiotics in treating staphylococcal-topical and biofilm infections.

Current Status and Future Prospects of Next-Generation Data Management and Analytical Decision Support Tools for Enhancing Genetic Gains in Crops.

Agricultural disciplines are becoming data intensive and the agricultural research data generation technologies are becoming sophisticated and high throughput. On the one hand, high-throughput genotyping is generating petabytes of data; on the other hand, high-throughput phenotyping platforms are also generating data of similar magnitude. Under modern integrated crop breeding, scientists are working together by integrating genomic and phenomic data sets of huge data volumes on a routine basis. To manage such huge research data sets and use them appropriately in decision making, Data Management Analysis & Decision Support Tools (DMASTs) are a prerequisite. DMASTs are required for a range of operations including generating the correct breeding experiments, maintaining pedigrees, managing phenotypic data, storing and retrieving high-throughput genotypic data, performing analytics, including trial analysis, spatial adjustments, identifications of MTAs, predicting Genomic Breeding Values (GEBVs), and various selection indices. DMASTs are also a prerequisite for understanding trait dynamics, gene action, interactions, biology, GxE, and various other factors contributing to crop improvement programs by integrating data generated from various science streams. These tools have simplified scientists' lives and empowered them in terms of data storage, data retrieval, data analytics, data visualization, and sharing with other researchers and collaborators. This chapter focuses on availability, uses, and gaps in present-day DMASTs. Graphical Abstract.

Comparative analysis of endodontic smear layer removal efficacy of 17% ethylenediaminetetraacetic acid, 7% maleic acid, and 2% chlorhexidine using scanning electron microscope: An in vitro study.

AIM: The aim of the present study was to evaluate the efficiency of different endodontic irrigants in the removal of smear layer through scanning electron microscopic image analysis. MATERIALS AND METHODS: The present in vitro study was carried out on 45 single-rooted extracted human mandibular premolar teeth with single canal and complete root formation. Teeth were randomly assigned to three groups with 15 teeth in each group. Group I samples were irrigated with 17% ethylenediaminetetraacetic (EDTA) irrigation, Group II with 7% maleic acid irrigation, and Group III with 2% chlorhexidine irrigation. Scanning electron microscope evaluation was done for the assessment of smear layer removal in the coronal, middle, and apical thirds. Comparison of the smear layer removal between the three different groups was done by Kruskal-Wallis test, followed by Mann-Whitney U test for comparing individual groups. A P value less than 0.05 was considered to be statistically significant. RESULTS: Statistically significant difference was seen between the two test groups (17% EDTA vs. 7% maleic acid and 17% EDTA vs. 2% chlorhexidine) in smear layer removal at coronal, middle, and apical thirds of the root canal. The most efficient smear layer removal was seen in Group I with 17% EDTA irrigation compared with other groups (P < 0.05) and the least by 2% chlorhexidine. CONCLUSION: The present study shows that 17% EDTA efficiently removes the smear layer from root canal walls.

Antibiotic resistance in Pseudomonas aeruginosa and alternative therapeutic options.

Pseudomonas aeruginosa is a leading cause of nosocomial infections and is responsible for ∼10% of all hospital-acquired infections worldwide. It continues to pose a therapeutic challenge because of the high rate of morbidity and mortality associated with it and the possibility of development of drug resistance during therapy. Standard antibiotic regimes against P. aeruginosa are increasingly becoming ineffective due to the rise in drug resistance. With the scope for developing new antibiotics being limited, alternative treatment options are gaining more and more attention. A number of recent studies reported complementary and alternative treatment options to combat P. aeruginosa infections. Quorum sensing inhibitors, phages, probiotics, anti-microbial peptides, vaccine antigens and antimicrobial nanoparticles have the potential to act against drug resistant strains. Unfortunately, most studies considering alternative treatment options are still confined in the pre-clinical stages, although some of these findings have tremendous potential to be turned into valuable therapeutics. This review is intended to raise awareness of several novel approaches that can be considered further for combating drug resistant P. aeruginosa infections.

Inhibiting diffusion of complex contagions in social networks: theoretical and experimental results.

We consider the problem of inhibiting undesirable contagions (e.g. rumors, spread of mob behavior) in social networks. Much of the work in this context has been carried out under the 1-threshold model, where diffusion occurs when a node has just one neighbor with the contagion. We study the problem of inhibiting more complex contagions in social networks where nodes may have thresholds larger than 1. The goal is to minimize the propagation of the contagion by removing a small number of nodes (called critical nodes) from the network. We study several versions of this problem and prove that, in general, they cannot even be efficiently approximated to within any factor ρ ≥ 1, unless P = NP. We develop efficient and practical heuristics for these problems and carry out an experimental study of their performance on three well known social networks, namely epinions, wikipedia and slashdot. Our results show that these heuristics perform significantly better than five other known methods. We also establish an efficiently computable upper bound on the number of nodes to which a contagion can spread and evaluate this bound on many real and synthetic networks.

Tricuspid valve mycetoma in an infant successfully treated by excision and complex tricuspid valve repair followed by fluconazole therapy.

BACKGROUND: Fungal valve endocarditis in children is an uncommon and lethal disease. The risk increases with use of central venous catheters (CVC), total parenteral nutrition (TPN), and use of broad-spectrum antibiotics during the neonatal period. Due to high mortality, a combination of surgery and antifungal therapy is usually recommended for treatment. METHODS: Case report and review of the literature. RESULTS: We present a case of an asymptomatic infant with multiple Candida tricuspid valve mycetomas. Complete cure was achieved by combined tricuspid valve repair and fluconazole therapy. We also review 26 cases of tricuspid valve Candida endocarditis in children published in the literature. CONCLUSION: From being uniformly fatal five decades ago to a current survival rate of 64% to 100%, the prognosis of Candida endocarditis has changed dramatically with the use of antifungal therapy alone or in combination with surgery. Our case re-emphasizes the role of valve-sparing debridement with repair of the native valve using autologous pericardium in combination with long-term antifungal therapy as a feasible option in managing tricuspid valve Candida endocarditis.

Establishment of cell suspension culture in Marchantia linearis Lehm & Lindenb. for the optimum production of flavonoids.

Bryophytes are the second largest group in the plant kingdom, but studies conducted to better understand their chemical composition are limited and scattered. Axenically grown bryophytes expressed potential in biotechnological processes. The present study was designed to investigate the in vitro cell growth, culture parameters and their effect on flavonoid synthesis. Chlorophyll-containing callus cells of Marchantia linearis Lehm & Lindenb. is able to grow under low light in the presence of organic carbon source and retain the ability to produce flavonoids. Highest flavonoid production was achieved using 2,4-dichlorophenoxyacetic acid as growth hormone. Inoculum size, light intensity, organic carbon source and cations are the culture parameters affecting flavonoid productivity. Maximum flavonoid productivity is observed under low light intensity, with a photon flux density ca. 20 µmol/m2/s. Optimal inoculum size and glucose concentration for flavonoid production are 10-14 and 2-3 %, respectively. Cations like ferrous trigger flavonoid synthesis by increasing its intracellular concentrations. Flavonoid production in the cell culture is shown to be significantly growth related. Osmotic stress is ineffective in triggering flavonoid synthesis. Methyl jasmonate and 2-(2-fluoro-6-nitrobenzylsulfanyl) pyridine-4-carbothioamide elicitors showed positive effect on intracellular flavonoid content in cultured cells. Using the standard plot of quercetin (y = 0.0148x, R2 = 0.975), the flavonoid contents of in vitro samples were found ranging from 4.0 to 17.7 mg quercetin equivalent/g tissue. Flavonoids are fractionated by HPLC-PAD revealed the presence of quercetin (182.5 µg/g), luteolin (464.5 µg/g) and apigenin (297.5 µg/g). Further studies are warranted to analyze the therapeutic potentiality of the flavonoids in the liverwort.

Multidrug-resistant endemic clonal strain of Candida auris in India.

Candida auris is a recently described rare agent of fungemia. It is notable for its antifungal resistance. A total of 15 C. auris isolates, originating from seven cases of fungemia, three cases of diabetic gangrenous foot, and one case of bronchopneumonia from a tertiary care hospital in south India, were investigated. All of the 15 isolates were identified by sequencing and 14 of these along with 12 C. auris isolates previously reported from two hospitals in Delhi, north India, two each from Japan and Korea were genotyped by amplified fragment length polymorphism (AFLP). In vitro antifungal susceptibility testing (AFST) was done by the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method. Candida auris isolates were misidentified as Candida haemulonii by VITEK. All were resistant to fluconazole [geometric mean minimum inhibitory concentration (MIC) 64 µg/ml] and 11 isolates were resistant to voriconazole (MIC ≥1 µg/ml). Forty-seven percent of the C. auris isolates were resistant to flucytosine (MIC ≥64 µg/ml) and 40% had high MIC (≥1 µg/ml) of caspofungin. Breakthrough fungemia developed in 28.6% of patients and therapeutic failure in 4 (66.7%) patients. Interestingly, the 26 Indian C. auris isolates from north and south India were clonal and phenotypically and genotypically distinct from Korean and Japanese isolates. The present study demonstrates that C. auris is a potential emerging pathogen that can cause a wide spectrum of human mycotic infections. The prevalence of a C. auris endemic clonal strain resistant to azoles and other antifungals in Indian hospitals with high rates of therapeutic failure in cases of fungemia is worrisome.

Innate immune recognition of microbial cell wall components and microbial strategies to evade such recognitions.

The innate immune system constitutes the first line of defence against invading microbes. The basis of this defence resides in the recognition of defined structural motifs of the microbes called "Microbial associated molecular patterns" that are absent in the host. Cell wall, the outer layer of both bacterial and fungal cells, a unique structure that is absent in the host and is recognized by the germ line encoded host receptors. Nucleotide oligomerization domain proteins, peptidoglycan recognition proteins and C-type lectins are host receptors that are involved in the recognition of bacterial cell wall (usually called peptidoglycan), whereas fungal cell wall components (N- and O-linked mannans, ß-glucans etc.) are recognized by host receptors like C-type lectins (Dectin-1, Dectin-2, mannose receptor, DC-SIGN), Toll like receptors-2 and -4 (TLR-2 and TLR-4). These recognitions lead to activation of a variety of host signaling cascades and ultimate production of anti-microbial compounds including phospholipase A2, antimicrobial peptides, lysozyme, reactive oxygen and nitrogen species. These molecules act in cohort against the invading microbes to eradicate infections. Additionally pathogen recognition leads to the production of cytokines, which further activate the adaptive immune system. Both pathogenic and commensal bacteria and fungus use numerous strategies to subvert the host defence. These strategies include bacterial peptidoglycan glycan backbone modifications by O-acetylation, N-deacetylation, N-glycolylation and stem peptide modifications by amidation of meso-Diaminopimelic acid; fungal cell wall modifications by shielding the ß-glucan layer with mannoproteins and α-1,3 glucan. This review focuses on the recent advances in understanding the role of bacterial and fungal cell wall in their innate immune recognition and evasion strategies.

Inferring population-level contact heterogeneity from common epidemic data.

Models of infectious disease spread that incorporate contact heterogeneity through contact networks are an important tool for epidemiologists studying disease dynamics and assessing intervention strategies. One of the challenges of contact network epidemiology has been the difficulty of collecting individual and population-level data needed to develop an accurate representation of the underlying host population's contact structure. In this study, we evaluate the utility of common epidemiological measures (R0, epidemic peak size, duration and final size) for inferring the degree of heterogeneity in a population's unobserved contact structure through a Bayesian approach. We test the method using ground truth data and find that some of these epidemiological metrics are effective at classifying contact heterogeneity. The classification is also consistent across pathogen transmission probabilities, and so can be applied even when this characteristic is unknown. In particular, the reproductive number, R0, turns out to be a poor classifier of the degree heterogeneity, while, unexpectedly, final epidemic size is a powerful predictor of network structure across the range of heterogeneity. We also evaluate our framework on empirical epidemiological data from past and recent outbreaks to demonstrate its application in practice and to gather insights about the relevance of particular contact structures for both specific systems and general classes of infectious disease. We thus introduce a simple approach that can shed light on the unobserved connectivity of a host population given epidemic data. Our study has the potential to inform future data-collection efforts and study design by driving our understanding of germane epidemic measures, and highlights a general inferential approach to learning about host contact structure in contemporary or historic populations of humans and animals.

From biological and social network metaphors to coupled bio-social wireless networks.

Biological and social analogies have been long applied to complex systems. Inspiration has been drawn from biological solutions to solve problems in engineering products and systems, ranging from Velcro to camouflage to robotics to adaptive and learning computing methods. In this paper, we present an overview of recent advances in understanding biological systems as networks and use this understanding to design and analyse wireless communication networks. We expand on two applications, namely cognitive sensing and control and wireless epidemiology. We discuss how our work in these two applications is motivated by biological metaphors. We believe that recent advances in computing and communications coupled with advances in health and social sciences raise the possibility of studying coupled bio-social communication networks. We argue that we can better utilise the advances in our understanding of one class of networks to better our understanding of the other.

CYP1A1m2 polymorphisms regulate estrogen and interleukin-6 in lung cancer.

Lung cancer, the most common cause of cancer-related death in men and women, is responsible for 1.3 million deaths worldwide annually. Women are diagnosed to a greater extent than men with adenocarcinoma and small cell carcinoma, both of which are secretory-type tumors. Never smokers diagnosed with lung cancer are also predominantly female, demonstrating the association of genetic factors with lung carcinogenesis. Several epidemiologic studies have associates certain CYP1A1 genotypes, alone or in combination, with an increased risk of estrogen-related cancer. The aim of this study was to investigate the impact of the CYP and GST polymorphisms along with estrogen and interleukin-6 (IL-6) levels on the risk of lung cancer. Eighty-six lung cancer patients and 60 controls were included in the study. A significantly higher frequency of polymorphisms in the genes was observed in lung cancer patients compared to controls. Mean estradiol concentration was reduced and IL-6 levels were elevated in patients compared to controls. In conclusion, increased polymorphisms in metabolic genes may be the reason for the reduced estradiol and, thereby, the increased expression of IL-6 in the serum of lung cancer patients.