Conformational ensemble of the NSP1 CTD in SARS-CoV-2: Perspectives from the free energy landscape.

The nonstructural protein-1 (NSP1) of the severe acute respiratory syndrome-associated coronavirus 2 plays a crucial role in the translational shutdown and immune evasion inside host cells. Despite its known intrinsic disorder, the C-terminal domain (CTD) of NSP1 has been reported to form a double α-helical structure and block the 40S-ribosomal channel for mRNA translation. Experimental studies indicate that NSP1 CTD functions independently from the globular N-terminal region separated with a long linker domain, underscoring the necessity of exploring the standalone conformational ensemble. In this contribution, we utilize exascale computing resources to yield unbiased molecular dynamics simulation of NSP1 CTD in all-atom resolution starting from multiple initial seed structures. A data-driven approach elicits collective variables (CVs) that are significantly superior to conventional descriptors in capturing the conformational heterogeneity. The free energy landscape as a function of the CV space is estimated using the modified expectation maximized molecular dynamics. Originally developed by us for small peptides, here, we establish the efficacy of expectation maximized molecular dynamics in conjunction with data-driven CV space for a more complex and relevant biomolecular system. The results reveal the existence of two disordered metastable populations in the free energy landscape that are separated from the conformation resembling ribosomal subunit bound state by high kinetic barriers. Chemical shift correlation and secondary structure analysis capture significant differences among key structures of the ensemble. Altogether, these insights can underpin drug development studies and mutational experiments that help induce population shifts to alter translational blocking and understand its molecular basis in further detail.

Efficient Interrogation of the Kinetic Barriers Demarcating Catalytic States of a Tyrosine Kinase with Optimal Physical Descriptors and Mixture Models.

Computer simulations are increasingly used to access thermo-kinetic information underlying structural transformation of protein kinases. Such information are necessary to probe their roles in disease progression and interactions with drug targets. However, the investigations are frequently challenged by forbiddingly high computational expense, and by the lack of standard protocols for the design of low dimensional physical descriptors that encode system features important for transitions. Here, we consider the demarcating characteristics of the different states of Abelson tyrosine kinase associated with distinct catalytic activity to construct a set of physically meaningful, orthogonal collective variables that preserve the slow modes of the system. Independent sampling of each metastable state is followed by the estimation of global partition function along the appropriate physical descriptors using the modified Expectation Maximized Molecular Dynamics method. The resultant free energy barriers are in excellent agreement with experimentally known rate-limiting dynamics and activation energy computed with conventional enhanced sampling methods. We discuss possible directions for further development and applications.

Efficacy of clinically used anthelmintics against toxocariasis of buffalo calves in Bangladesh.

Toxocariasis is a paramount parasitic disease having > 50% prevalence among newborn buffalo calves in Bangladesh. The objective of this study was to compare the efficacy of clinically used anthelmintics and their subsequent effect on the haematological parameters and body weight in buffalo calves in commercial buffalo farms in coastal region. Thirty-two buffalo calves below 3 months of age with clinical Toxocara infection had been selected and treated with albendazole (ABZ), levamisole (LVM) and ivermectin (IVM). The EPG counts, hematological parameters and initial body weight of buffalo calves were recorded on the day of anthelmintic treatment (day 0). Fecal samples were collected on day 14 and 28 including hematological parameters and body weight were recorded on day 28 post-treatment. The efficacy (%) of anthelmintics were estimated by fecal egg count reduction test (FECRT). The parameters like Hb, PCV, ESR, TEC, TLC were analyzed from the blood samples. The FECRT revealed 96.83% efficacy for IVM followed by 94.23% and 85.84% for LVM and ABZ, respectively. Anthelmintic treated calves showed significant (p < 0.01) increase in Hb, PCV, TEC and body weight, and decrease in ESR and TLC as a result of worm expulsion from buffalo calves after 28 days of post-treatment. Among the tested anthelmintics, IVM was found to be more effective against toxocariasis in buffalo calves. This is a novel information on anthelmintics efficacy in buffalo calves in Bangladesh. Details study is recommended on the efficacy of anthelmintics in different buffalo management systems by in vitro egg hatch assay (EHA) test.

Effects of External Perturbations on Protein Systems: A Microscopic View.

Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.

Prevalence and risk factors of Toxocara vitulorum infection in buffalo calves in coastal, northeastern and northwestern regions of Bangladesh.

Buffalo (Bubalus bubalis) is popularly known as the black gold of South Asia, consisting of 97% of the world buffalo population. Among the parasitic infections, Toxocara vitulorum is one of the most common and harmful parasites of buffalo calves in Bangladesh. A cross-sectional study was conducted to explore the prevalence and associated risk factors of T. vitulorum infection of buffalo calves in four regions of Bangladesh. A total of 1751 fecal samples were collected and examined using flotation followed by the McMaster technique for counting the eggs per gram of feces (EPG) of T. vitulorum. The overall prevalence of T. vitulorum infection in buffalo calves was 22.9%. Significantly (p < 0.001) higher prevalence was found in the Barishal coastal area (35.7%) followed by Chattogram coastal area (29.2%), northeastern region (15.5%) and northwestern region (8.3%). Buffalo calves aged 1-3 months were heavily infected with T. vitulorum (51.7%) which was statistically different (p < 0.001) compared to those >3-6 months (27.6%) and > 6-12 months (6.5%). According to univariate analysis, coastal regions, rainy season, young age, gender, indigenous river type, buffalo calves with poor body condition and soft feces were found significantly associated with T. vitulorum infections. Coastal regions, rainy season and young age were identified as the risk factors of T. vitulorum infection in buffalo calves by final logistic regression model. This study reveals that T. vitulorum infection is endemic in Bangladesh and widely distributed in the coastal regions. Therefore, attention to buffalo calves regarding in-depth clinical effects and current therapeutic approaches against this nematode should be evaluated along with the economic impact of infection. Exploring the genetic diversity of T. vitulorum may help to reveal the host-parasite relationship in the future.

Knowledge, attitude and practices (KAP) towards Anthrax among livestock farmers in selected rural areas of Bangladesh.

BACKGROUND: Bacillus anthracis is a zoonotic bacterium that affects wide numbers of vertebrate animals and man and has life threating potential both in animal s as well as humans. METHODS: A cross sectional study was conducted to assess the knowledge about, attitudes towards, and practices addressing (KAPs) anthrax among community members in selected upazillas' of Meherpur and Sirajgonj districts for the prevention and control of anthrax using a structured questionnaire. RESULTS: A total of 424 community members were considered in this study irrespective of their age and sex. Most of the respondents were female (57.54%) and about half were illiterate (47.40%). Most of the respondents (86.32%) were self-employed with crop and livestock farming. Among the self-employed farmers, cattle (63.73%) were the highest reared animals. Among the respondents, 37.26% had no knowledge about anthrax. On the other hand, among the existing knowledge level, 46.69% received information of anthrax from neighbour, 74.05% and 56.82% were concerned about the mode of transmission of anthrax from animal to human through eating, handling and soil. Respondents usually collected vaccine from quack (58.25%) and vaccination status was highest in Kamarkhand (52.03%) and lowest in Gangni upazilla (10.82%). Overall 62.74% community members considered that anthrax is a fatal disease for livestock and 82.54% people disposed carcass in buried method. CONCLUSION: The study findings indicated that the community members had average knowledge on cause, symptoms, transmission and prevention of anthrax. The supplied vaccine was found negligible with the number of livestock in the studied upazilas. Veterinary and Medical health planners should design and implement interventions for awareness building on anthrax under One Health (OH) approach for educating the community people on anthrax control and prevention.

Expectation maximized molecular dynamics: Toward efficient learning of rarely sampled features in free energy surfaces from unbiased simulations.

Biophysical processes often encounter high energy transition states that lie in regions of the free energy landscape (FEL) inaccesible to conventional molecular dynamics simulations. Various enhanced sampling methods have been developed to handle the inherent quasi-nonergodicity, either by adding a biasing potential to the underlying Hamiltonian or by forcing the transitions with parallel tempering. However, when attempting to probe systems of increasing complexity with limited computational resources, there arises an imminent need for fast and efficient FEL exploration with sufficient accuracy. Herein, we present a computationally efficient algorithm based on statistical inference for fast estimation of key features in the two-dimensional FEL. Unlike conventional enhanced sampling methods, this newly developed method avoids direct sampling of high free energy states. Rather, the transition states connecting metastable regions of comparable free energies are estimated using Bayesian likelihood maximization. Furthermore, the method incorporates a tunable self-feedback mechanism with classical molecular dynamics for preventing unnecessary sampling that no more effectively contributes to the underlying distributions of metastable states. We have applied this novel protocol in three independent case studies and compared the results against a conventional method. We conclude with the scope of further developments for improved accuracy of the new method and its generalization toward estimation of features in more complex FELs.

Comparison of multivariate preprocessing techniques as applied to electronic tongue based pattern classification for black tea.

In an electronic tongue, preprocessing on raw data precedes pattern analysis and choice of the appropriate preprocessing technique is crucial for the performance of the pattern classifier. While attempting to classify different grades of black tea using a voltammetric electronic tongue, different preprocessing techniques have been explored and a comparison of their performances is presented in this paper. The preprocessing techniques are compared first by a quantitative measurement of separability followed by principle component analysis; and then two different supervised pattern recognition models based on neural networks are used to evaluate the performance of the preprocessing techniques.