Recrafting the neighbor-joining method

Background  

The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n ³) algorithm upon which all existing implementations are based.     

Microbial transformation of tannin-rich substrate to gallic acid through co-culture method

Modified solid-state fermentation (MSSF) of tannin-rich substrate yielding tannase and gallic acid was carried out using a co-culture of the filamentous fungi, Rhizopus oryzae (RO IIT RB-13, NRRL 21498) and Aspergillus foetidus (GMRB013 MTCC 3557). Powdered fruits of Terminalia chebula and powdered pod cover of Caesalpinia digyna was used in the process and the different process parameters for maximum production of tannase and gallic acid by co-culture method were optimized through media engineering. MSSF was carried out at the optimum conditions of 30 degrees C and 80% relative humidity. The optimal pH and incubation period was 5.0 and 48 h respectively. Through the co-culture technique the maximum yield of tannase and gallic acid was found to be 41.3 U/ml and 94.8% respectively.     

Sanitation,Stress, and Life Stage: A Systematic Data Collection Study among Women in Odisha,India

Emerging evidence demonstrates how inadequate access to water and sanitation is linked to psychosocial stress, especially among women, forcing them to navigate social and physical barriers during their daily sanitation routines. We examine sanitation-related psychosocial stress (SRPS) across women’s reproductive lives in three distinct geographic sites (urban slums, rural villages, and rural tribal villages) in Odisha, India. We explored daily sanitation practices of adolescent, newly married, pregnant, and established adult women (n = 60) and identified stressors encountered during sanitation. Responding to structured data collection methods, women ranked seven sanitation activities (defecation, urination, menstruation, bathing, post-defecation cleaning, carrying water, and changing clothes) based on stress (high to low) and level of freedom (associated with greatest freedom to having the most restrictions). Women then identified common stressors they encountered when practicing sanitation and sorted stressors in constrained piles based on frequency and severity of each issue. The constellation of factors influencing SRPS varies by life stage and location. Overall, sanitation behaviors that were most restricted (i.e., menstruation) were the most stressful. Women in different sites encountered different stressors, and the level of perceived severity varied based on site and life stage. Understanding the influence of place and life stage on SRPS provides a nuanced understanding of sanitation, and may help identify areas for intervention.     

Influence of switchgrass generated producer gas pre-adaptation on growth and product distribution of Clostridium ragsdalei

Gasification-fermentation is a thermo chemical-biological process for the production of fuels and chemicals. Producer gas cleanup is a major issue that must be addressed for integration of these platforms. Pre-adaptation of producer gas fermenting microbes to gas impurities has improved tolerances to impurities and production of alcohols in certain bacteria. In this research, the effect of switchgrass generated producer gas was studied with adapted and unadapted cultures of C. ragsdalei and compared to fermentations with a control of clean custom producer gas. Results indicated no inhibition to microbial growth with unadapted cells and final cell mass concentrations were 22% higher when cells were exposed to switchgrass-based producer gas compared to control. The ethanol productivity with adapted cells was 1.9 and 2.8 times higher than unadapted and control treatments, respectively. Similarly, the ethanol yield (Y_ETOH/X) of C. ragsdalei adapted to producer gas was 119% more than the control and 35% greater than the unadapted cells used in this study. The presence of switchgrass-based producer gas also induced metabolic shifts resulting in reduction of acetic acid to ethanol that increased ethanol to acetate ratios from 0.7 g/g in control to 4.9 g/g with unadapted cells and 13.7 g/g with adapted cells. Isopropanol was also observed as a product when switchgrass generated producer gas was used. We conclude that cultural adaptation of C. ragsdalei to biomass generated producer gas during preculture stages could be used as an important strategy to enhance ethanol yields for integrating gasification and fermentation platforms using C. ragsdalei.     

Unclonable fluorescence of MgO-ZrO2:Tb3+ nanocomposite for versatile applications in data security,dermatoglyphics

Latent fingerprints (LFPs) are one among the most important types of evidences at crime scenes because of the distinctiveness and tenacity of the friction ridges in fingerprints (FPs). Therefore, it is essential in forensic science to develop a reliable method to detect LFPs. Traditional detection methods still face a number of difficulties, such as limited sensitivity, low contrast, strong background, and complex processing stages. In this study, MgO-ZrO₂:Tb³⁺ (1–5 mol%) (MZ:Tb) nanocomposites (NCs) were prepared via a simple solution combustion (SC) method at low temperature. The photoluminescence (PL) investigation demonstrates that when excited at 379 nm, the produced NCs emits distinctive emission peaks of terbium ions (Tb³⁺). According to the photometric results, the NCs can be employed as warm light NCs and emit light in the green portion of the colour spectrum. The estimated optical band gap from diffuse reflectance spectra is found to be in the range 4.84–4.97 eV. Regardless of the type of surface being used, the optimized MgO-ZrO₂:Tb³⁺ (4 mol%) (MZ:4Tb) NCs has a strong ability to minimize background fluorescence interference. With high contrast LFP and I–V type of cheiloscopy, these NCs present a flexible fluorescent mark for the identification of levels 1–3 details in forensic investigation.     

CoaSim: A flexible environment for simulating genetic data under coalescent models

Background  

Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these.     

Trends in Malaria in Odisha,India—An Analysis of the 2003–2013 Time-Series Data from the National Vector Borne Disease Control Program

Background

Although Odisha is the largest contributor to the malaria burden in India, no systematic study has examined its malaria trends. Hence, the spatio-temporal trends in malaria in Odisha were assessed against the backdrop of the various anti-malaria strategies implemented in the state.

Methods

Using the district-wise malaria incidence and blood examination data (2003–2013) from the National Vector Borne Disease Control Program, blood examination-adjusted time-trends in malaria incidence were estimated and predicted for 2003–2013 and 2014–2016, respectively. An interrupted time series analysis using segmented regression was conducted to compare the disease trends between the pre (2003–2007) and post-intensification (2009–2013) periods. Key-informant interviews of state stakeholders were used to collect the information on the various anti-malaria strategies adopted in the state.

Results

The state annual malaria incidence declined from 10.82/1000 to 5.28/1000 during 2003–2013 (adjusted annual decline: -0.54/1000, 95% CI: -0.78 to -0.30). However, the annual blood examination rate remained almost unchanged from 11.25% to 11.77%. The keyinformants revealed that intensification of anti-malaria activities in 2008 led to a more rapid decline in malaria incidence during 2009–2013 as compared to that in 2003–2007 [adjusted decline: -0.83 (-1.30 to -0.37) and -0.27 (-0.41 to -0.13), respectively]. There was a significant difference in the two temporal slopes, i.e., -0.054 (-0.10 to -0.002, p = 0.04) per 1000 population per month, between these two periods, indicating almost a 200% greater decline in the post-intensification period. Although, the seven southern high-burden districts registered the highest decline, they continued to remain in that zone, thereby, making the achievement of malaria elimination (incidence <1/1000) unlikely by 2017.

Conclusion

The anti-malaria strategies in Odisha, especially their intensification since 2008, have helped improve its malaria situation in recent years. These successful measures need to be sustained and perhaps intensified further for eliminating malaria from Odisha.     

Biomass downdraft gasifier with internal cyclonic combustion chamber: design, construction, and experimental results

An exploratory downdraft gasifier design with unique biomass pyrolysis and tar cracking mechanism is evolved at Oklahoma State University. This design has an internal separate combustion section where turbulent, swirling high-temperature combustion flows are generated. A series of research trials were conducted using wood shavings as the gasifier feedstock. Maximum tar cracking temperatures were above 1100°C. Average volumetric concentration levels of major combustible components in the product gas were 22% CO and 11% H(2). Hot and cold gas efficiencies were 72% and 66%, respectively.     

Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations

Background

Extinction and re-colonisation of local populations is common in ephemeral habitats such as temporary streams. In most cases, such population turnover leads to reduced genetic diversity within populations and increased genetic differentiation among populations due to stochastic founder events, genetic drift, and bottlenecks associated with re-colonisation. Here, we examined the spatio-temporal genetic structure of 8 alpine caddisfly populations inhabiting permanent and temporary streams from four valleys in two regions of the Swiss Alps in years before and after a major stream drying event, the European heat wave in summer 2003.

Results

We found that population turnover after 2003 led to a loss of allelic richness and gene diversity but not to significant changes in observed heterozygosity. Within all valleys, permanent and temporary streams in any given year were not differentiated, suggesting considerable gene flow and admixture between streams with differing hydroperiods. Large changes in allele frequencies after 2003 resulted in a substantial increase in genetic differentiation among valleys within one to two years (1-2 generations) driven primarily by drift and immigration. Signatures of genetic bottlenecks were detected in all 8 populations after 2003 using the M-ratio method, but in no populations when using a heterozygosity excess method, indicating differential sensitivity of bottleneck detection methods.

Conclusions

We conclude that genetic differentiation among A. uncatus populations changed markedly both temporally and spatially in response to the extreme climate event in 2003. Our results highlight the magnitude of temporal population genetic changes in response to extreme events. More specifically, our results show that extreme events can cause rapid genetic divergence in metapopulations. Further studies are needed to determine if recovery from this perturbation through gradual mixing of diverged populations by migration and gene flow leads to the pre-climate event state, or whether the observed changes represent a new genetic equilibrium.