Soil Metagenomics: Concepts and Applications

Soil is a living entity of the Earth, and considered as one of the main reservoir of microbial diversity. Studying the soil microbial diversity is very much necessary, as they play an important role in maintaining the health of soil by recycling the nutrients, creating soil structure and humus. However, the culture dependent approaches fail to provide clear estimates of the diversity and untapped resources. Hence, study of the microbial diversity using culture independent approaches become necessary. The field of metagenomics helps in studying the genomes of the diverse soil organisms collectively in their natural habitat which holds the promising for accessing novel genetic resources. Application of the metagenomics to the soil environment is very challenging due to several difficulties; one of which is co-extraction of humic acid with nucleic acids which hinder downstream high throughout processes. However, applying sequencing methods to soil microbial communities will help in uncovering the hidden resources like novel genes, biomolecules and other valuable products which are yet to be discovered or still unknown. Different culture independent techniques and applications of the metagenomics to study the abundant microflora of the complex and changing environment of soil discussed herein

G × E interactions in QTL introgression lines of Spanish-type groundnut (Arachis hypogaea L.)

Multi-environment testing at five locations for rust and late leaf spot (LLS) resistance with 41 introgressed lines (ILs) bred using marker-assisted backcross breeding in the genetic background Spanish- type groundnut varieties identified significant genotype, and genotype 9 environment interactions (GEI) for LLS disease resistance and yield parameters. Significant GEI effects suggest the need to identify location specific breeding lines to achieve gains in pod yield and LLS resistance. The observed variable LLS disease reaction among the ILs in part suggests influence of background genotype on the level of resistance. A breeding scheme with early generation selection using molecular markers followed by phenotyping for LLS, and multi-location testing of fixed breeding lines was optimized to enhance selection intensity and accuracy in groundnut breeding. The ILs, ICGVs 14431, 14436 and 14438 with pooled LLS score at 90 DAS of 3.5–3.7 were superior to respective recurrent parent for pod yield, with early maturing similar to recurrent parents. The pod yield advantage in ILs is attributed by more number of pods, besides resistance to LLS that contributes to better filling

Elimination of human rabies in Goa, India through an integrated One Health approach

Dog-mediated rabies kills tens of thousands of people each year in India, representing one third of the estimated global rabies burden. Whilst the World Health Organization (WHO), World Organization for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO) have set a target for global dog-mediated human rabies elimination by 2030, examples of large-scale dog vaccination programs demonstrating elimination remain limited in Africa and Asia. We describe the development of a data-driven rabies elimination program from 2013 to 2019 in Goa State, India, culminating in human rabies elimination and a 92% reduction in monthly canine rabies cases. Smartphone technology enabled systematic spatial direction of remote teams to vaccinate over 95,000 dogs at 70% vaccination coverage, and rabies education teams to reach 150,000 children annually. An estimated 2249 disability-adjusted life years (DALYs) were averted over the program period at 526 USD per DALY, making the intervention ‘very cost-effective’ by WHO definitions. This One Health program demonstrates that human rabies elimination is achievable at the state level in India

Forced Solid-State Interactions for the Selective “Turn-On” Fluorescence Sensing of Aluminum Ions in Water Using a Sensory Polymer Substrate

Selective and sensitive solid sensory substrates for detecting Al(III) in pure water are reported. The material is a flexible polymer film that can be handled and exhibits gel behavior and membrane performance. The film features a chemically anchored salicylaldehyde benzoylhydrazone derivative as an aluminum ion fluorescence sensor. A novel procedure for measuring Al(III) at the ppb level using a single solution drop in 20 min was developed. In this procedure, a drop was allowed to enter the hydrophilic material for 15 min before a 5 min drying period. The process forced the Al(III) to interact with the sensory motifs within the membrane before measuring the fluorescence of the system. The limit of detection of Al(III) was 22 ppm. Furthermore, a water-soluble sensory polymer containing the same sensory motifs was developed with a limit of detection of Al(III) of 1.5 ppb, which was significantly lower than the Environmental Protection Agency recommendations for drinking water.Spanish Ministerio de Economía y Competitividad-Feder (MAT2011-22544) and by the Consejería de Educación - Junta de Castilla y León (BU232U13)

Molecular breeding tools improved drought tolerant groundnut variety for resistance to foliar fungal diseases

A largely rainfed crop in India, drought tolerance, particularly mid- and end-season tolerance, is a key trait in groundnut varieties. A combination of both empirical and trait-based approaches was used in breeding programs of ICAR and ICRISAT, resulting in release of few tolerant varieties that have superior pod yield under drought stress and/or have enhanced water-use-efficiency. There is a need to breed varieties with drought tolerance, disease resistance and quality traits that suit different production ecologies as well as meet the needs of the farmers, consumers and industries. ICRISAT has released an early-maturing (90-95 d) and drought- tolerant variety ICGV 91114 for the drought-prone Ananthapur district of Andhra Pradesh, India, where about 0.7 m ha area is under groundnut cultivation and has low (300 mm) and erratic (30-40 rainy days) rainfall. On-farm studies conducted with ICGV 91114 during 2008-10 showed 30% reduction in yield variability over the years. Following screening in hot-spots of both rust and LLS disease during 2014 rainy season, a total of 27 introgression lines derived from ICGV 91114 were selected and advanced for evaluation in multi-location trials at six locations in 2015 under rainfed conditions. Based on the pod yield under rainfed conditions and disease resistance, three superior introgression lines (ICGV 14410, ICGV 13189, ICGV 14421) were proposed for the first-ever NILs trial (near-isogenic lines trial) along with eight others conducted under All India Coordinated Research Project on Groundnut (AICRP-G) at national level

Novel Crystalline SiO2 Nanoparticles via Annelids Bioprocessing of Agro-Industrial Wastes

The synthesis of nanoparticles silica oxide from rice husk, sugar cane bagasse and coffee husk, by employing vermicompost with annelids (Eisenia foetida) is reported. The product (humus) is calcinated and extracted to recover the crystalline nanoparticles. X-ray diffraction (XRD), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM) and dynamic light scattering (DLS) show that the biotransformation allows creating specific crystalline phases, since equivalent particles synthesized without biotransformation are bigger and with different crystalline structure

Diversity among clients of female sex workers in India: comparing risk profiles and intervention impact by site of solicitation. implications for the vulnerability of less visible female sex workers.

BACKGROUND: It seems generally accepted that targeted interventions in India have been successful in raising condom use between female sex workers (FSWs) and their clients. Data from clients of FSWs have been under-utilised to analyse the risk environments and vulnerability of both partners. METHODS: The 2009 Integrated Biological and Behavioural Assessment survey sampled clients of FSWs at hotspots in Andhra Pradesh, Maharashtra and Tamil Nadu (n=5040). The risk profile of clients in terms of sexual networking and condom use are compared across usual pick-up place. We used propensity score matching (PSM) to estimate the average treatment effect on treated (ATT) of intervention messages on clients' consistent condom use with FSW. RESULTS: Clients of the more hidden sex workers who solicit from home or via phone or agents had more extensive sexual networks, reporting casual female partners as well as anal intercourse with male partners and FSW. Clients of brothel-based sex workers, who were the least educated, reported the fewest number/categories of partners, least anal sex, and lowest condom use (41%). Consistent condom use varied widely by state: 65% in Andhra Pradesh, 36% in Maharashtra and 29% in Tamil Nadu. Exposure to intervention messages on sexually transmitted infections was lowest among men frequenting brothels (58%), and highest among men soliciting less visible sex workers (70%). Exposure had significant impact on consistent condom use, including among clients of home-based sex workers (ATT 21%; p=0.001) and among men soliciting other more hidden FSW (ATT 17%; p=0.001). In Tamil Nadu no impact could be demonstrated. CONCLUSION: Commercial sex happens between two partners and both need to be, and can be, reached by intervention messages. Commercial sex is still largely unprotected and as the sex industry gets more diffuse a greater focus on reaching clients of sex workers seems important given their extensive sexual networks

Effect of sitagliptin on cardiovascular outcomes in type 2 diabetes

BACKGROUND: Data are lacking on the long-term effect on cardiovascular events of adding sitagliptin, a dipeptidyl peptidase 4 inhibitor, to usual care in patients with type 2 diabetes and cardiovascular disease. METHODS: In this randomized, double-blind study, we assigned 14,671 patients to add either sitagliptin or placebo to their existing therapy. Open-label use of antihyperglycemic therapy was encouraged as required, aimed at reaching individually appropriate glycemic targets in all patients. To determine whether sitagliptin was noninferior to placebo, we used a relative risk of 1.3 as the marginal upper boundary. The primary cardiovascular outcome was a composite of cardiovascular death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for unstable angina. RESULTS: During a median follow-up of 3.0 years, there was a small difference in glycated hemoglobin levels (least-squares mean difference for sitagliptin vs. placebo, -0.29 percentage points; 95% confidence interval [CI], -0.32 to -0.27). Overall, the primary outcome occurred in 839 patients in the sitagliptin group (11.4%; 4.06 per 100 person-years) and 851 patients in the placebo group (11.6%; 4.17 per 100 person-years). Sitagliptin was noninferior to placebo for the primary composite cardiovascular outcome (hazard ratio, 0.98; 95% CI, 0.88 to 1.09; P<0.001). Rates of hospitalization for heart failure did not differ between the two groups (hazard ratio, 1.00; 95% CI, 0.83 to 1.20; P = 0.98). There were no significant between-group differences in rates of acute pancreatitis (P = 0.07) or pancreatic cancer (P = 0.32). CONCLUSIONS: Among patients with type 2 diabetes and established cardiovascular disease, adding sitagliptin to usual care did not appear to increase the risk of major adverse cardiovascular events, hospitalization for heart failure, or other adverse events

Governance and Conservation Effectiveness in Protected Areas and Indigenous and Locally Managed Areas

Increased conservation action to protect more habitat and species is fueling a vigorous debate about the relative effectiveness of different sorts of protected areas. Here we review the literature that compares the effectiveness of protected areas managed by states and areas managed by Indigenous peoples and/or local communities. We argue that these can be hard comparisons to make. Robust comparative case studies are rare, and the epistemic communities producing them are fractured by language, discipline, and geography. Furthermore the distinction between these different forms of protection on the ground can be blurred. We also have to be careful about the value of this sort of comparison as the consequences of different forms of conservation for people and nonhuman nature are messy and diverse. Measures of effectiveness, moreover, focus on specific dimensions of conservation performance, which can omit other important dimensions. With these caveats, we report on findings observed by multiple study groups focusing on different regions and issues whose reports have been compiled into this article. There is a tendency in the data for community-based or co-managed governance arrangements to produce beneficial outcomes for people and nature. These arrangements are often accompanied by struggles between rural groups and powerful states. Findings are highly context specific and global generalizations have limited value

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival