Policies, Socioeconomic, Institutional and Biophysical Factors Influencing the Change from Rice to Sugarcane in Nong Bua Lamphu Province, Thailand.

For the past decade, Thailand pursued a strategy of promoting biofuel crop production, including sugarcane, to meet the ever increasing energy demand and to increase the income of farmers. This study analyzed the influence of policy instruments implemented to promote the sugarcane cultivation, farm household socioeconomic levels, biophysical, and institutional factors driving the conversion of rice fields into sugarcane farms. Primary information was collected from 230 farm households through a structured questionnaire. Relevant policy documents published by the responsible government agencies were the main sources of secondary information collected for policy analysis. The analyses revealed that farmers in the study area converted 25-75% of their rice fields into sugarcane farms as a result of implementation of policy instruments that made sugarcane financially far more attractive than rice. The results of the regression analysis showed that eight variables were found significant and positively influenced the conversion of rice fields into sugarcane farms. These were access to extension services, information, sugarcane loading stations, and ground water for irrigation, and duration of experience in sugarcane farming as well as household head's age and education. Irrespective of landholding size, the majority of farmers were not concerned about food security. In view of the finding, if feasible, in the form of additional price supports and commercial cane sugar index-based pricing strategies to promote sugarcane production should benefit all concerned farmers. Likewise, attention should be paid to deliver essential extension and marketing services in an effective way, particularly to those farmers who are not receiving such services.

Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA σ-anti-σ complex.

The host-pathogen interactions in Mycobacterium tuberculosis infection are significantly influenced by redox stimuli and alterations in the levels of secreted antigens. The extracytoplasmic function (ECF) σ factor σ(K) governs the transcription of the serodominant antigens MPT70 and MPT83. The cellular levels of σ(K) are regulated by the membrane-associated anti-σ(K) (RskA) that localizes σ(K) in an inactive complex. The crystal structure of M. tuberculosis σ(K) in complex with the cytosolic domain of RskA (RskAcyto) revealed a disulfide bridge in the -35 promoter-interaction region of σ(K). Biochemical experiments reveal that the redox potential of the disulfide-forming cysteines in σ(K) is consistent with its role as a sensor. The disulfide bond in σ(K) influences the stability of the σ(K)-RskAcyto complex but does not interfere with σ(K)-promoter DNA interactions. It is noted that these disulfide-forming cysteines are conserved across homologues, suggesting that this could be a general mechanism for redox-sensitive transcription regulation.

Eight-and-a-half syndrome: a rare presentation of pontine infarction.

"Eight-and-a-half" syndrome is "one-and-a-half" syndrome (conjugated horizontal gaze palsy and internuclear ophthalmoplegia) plus ipsilateral fascicular cranial nerve seventh palsy. This rare condition, particularly when isolated, is caused by circumscribed lesions of the pontine tegmentum involving the abducens nucleus, the ipsilateral medial longitudinal fasciculus, and the adjacent facial colliculus. Its recognition is therefore of considerable diagnostic value. We report a case of a 65-year-old man who presented with eight-and-a-half syndrome in which brain magnetic resonance imaging scan revealed a lacunar pontine infarction.

Alterations in minute ventilation, maximum voluntary ventilation and dyspneic index in different trimesters of pregnancy.

Respiratory function in pregnancy is of special importance since the life of fetus depends primarily upon its oxygen supply. Thus this study was designed to evaluate the Minute ventilation (MV), Maximum Voluntary Ventilation (MVV) & Dyspneic Index (DI) in different trimesters of pregnancy & compare the results with non- pregnant control group. A cross-sectional study was carried out in 200 healthy women in the age range of 19-35 years with 50 subjects each in 1st, 2nd, 3rd trimesters of pregnancy and non-pregnant control group. We recorded respiratory parameters in study and control groups. Statistical analysis was done by ANOVA and Tukey Krammer post Hoc tests. It was observed that there was a significant decrease in MVV and dyspneic index in all trimesters of pregnancy and an insignificant variation in MV when compared to the control group. The changes in pulmonary function are influenced by the mechanical pressure of enlarging gravid uterus, elevating the diaphragm and restricting the movements of lungs thus hampering forceful expiration. The decrease seen in MVV in 1st trimester might be due to bronchoconstriction effect of decreased alveolar Pco2 on the bronchial smooth muscles.

Self-driving autonomous machines to engineer novel enzymes.

Can one design and automate a computational and experimental platform such that each platform iteratively guides and drives the other to achieve a pre-determined goal? Rapp and colleagues (2024) describe just this possibility in a paper that details a prototype of a self-driven laboratory that can navigate autonomously to yield an engineered enzyme with a desired attribute. This laboratory, rather, the automated protocol, is referred to by an acronym - SAMPLE. This refers to Self-driving Autonomous Machines for Protein Landscape Exploration. The paper describes a prototype involving the engineering of a glycoside hydrolase for enhanced thermostability. The 'brain', the computational component behind this automated system, was designed to learn protein sequence- function relationships from a curated dataset. These designer proteins were then evaluated by a fully automated robotic system that could synthesize and experimentally characterize the designed protein and provide feedback to the agent, i.e., the computational component, to fine-tune its understanding of the system. The SAMPLE agents were thus designed to continually refine their understanding of the protein landscape by actively acquiring information in the search process. As this intelligent agent learns protein sequence-function relationships from a curated, diverse dataset, this feedback is crucial to refine landscape exploration and the design of new proteins based on the updated hypothesis. In this prototype, four SAMPLE agents were tasked with this goal. The goal of each of these agents was to navigate the glycoside hydrolase landscape and identify enzymes with enhanced thermal tolerance. Differences in the search behavior of individual agents primarily arise from experimental measurement noise. However, despite differences in their search behavior, all four agents could converge on a thermostable glycoside hydrolase - a remarkable feat as it apparently did not need any human intervention.

Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A.

The two protein tyrosine phosphatase (PTP) domains in bi-domain PTPs share high sequence and structural similarity. However, only one of the two PTP domains is catalytically active. Here we describe biochemical studies on the two tandem PTP domains of the bi-domain PTP, PTP99A. Phosphatase activity, monitored using small molecule as well as peptide substrates, revealed that the inactive (D2) domain activates the catalytic (D1) domain. Thermodynamic measurements suggest that the inactive D2 domain stabilizes the bi-domain (D1-D2) protein. The mechanism by which the D2 domain activates and stabilizes the bi-domain protein is governed by few interactions at the inter-domain interface. In particular, mutating Lys990 at the interface attenuates inter-domain communication. This residue is located at a structurally equivalent location to the so-called allosteric site of the canonical single domain PTP, PTP1B. These observations suggest functional optimization in bi-domain PTPs whereby the inactive PTP domain modulates the catalytic activity of the bi-domain enzyme.

Structural insights into the role of Bacillus subtilis YwfH (BacG) in tetrahydrotyrosine synthesis.

The synthesis of the dipeptide antibiotic bacilysin involves the sequential action of multiple enzymes in the bac operon. YwfH (also referred to as BacG) catalyzes the stereoselective reduction of dihydro-hydroxyphenylpyruvate (H2HPP) to tetrahydro-hydroxyphenylpyruvate (H4HPP) in this biosynthetic pathway. YwfH is an NADPH-dependent reductase that facilitates the conjugate addition of a hydride at the C4 olefin terminus of H2HPP. Here, the structure of YwfH is described at three conformational steps: the apo form, an apo-like conformation and the NADPH complex. YwfH is structurally similar to other characterized short-chain dehydrogenase/reductases despite having marginal sequence similarity. The structures of YwfH in different conformational states provide a rationale for the ping-pong reaction mechanism. The identification and role of the residues in the catalytic tetrad (Lys113-Tyr117-Ser155-Asn158) in proton transfer were examined by mutational analysis. Together, the structures and biochemical features revealed synchronized conformational changes that facilitate cofactor specificity and catalysis of H4HPP formation en route to tetrahydrotyrosine synthesis.

Structure of an amidohydrolase, SACOL0085, from methicillin-resistant Staphylococcus aureus COL.

Staphylococcus aureus is an opportunistic pathogen that rapidly acquires resistance to frontline antibiotics. The characterization of novel protein targets from this bacterium is thus an important step towards future therapeutic strategies. Here, the crystal structure of an amidohydrolase, SACOL0085, from S. aureus COL is described. SACOL0085 is a member of the M20D family of peptidases. Unlike other M20D peptidases, which are either monomers or dimers, SACOL0085 adopts a butterfly-shaped homotetrameric arrangement with extensive intersubunit interactions. Each subunit of SACOL0085 contains two Mn(2+) ions at the active site. A conserved cysteine residue at the active site distinguishes M20D peptidases from other M20 family members. This cysteine, Cys103, serves as bidentate ligand coordinating both Mn(2+) ions in SACOL0085.

Effect of yoga on short-term heart rate variability measure as a stress index in subjunior cyclists: a pilot study.

Subjunior athletes experience mental stress due to pressure from the coach, teachers and parents for better performance. Stress, if remains for longer period and not managed appropriately can leads to negative physical, mental and cognitive impact on children. The present study was aimed to evaluate the effect of integrated yoga module on heart rate variability (HRV) measure as a stress index in subjunior cyclists. Fast furrier transform technique of frequency domain method was used for the analysis of HRV. We have found a significant increase in high frequency (HF) component by 14.64% (P < 0.05) and decrease in the low frequency component (LF) of HRV spectrum by 5.52% (P < 0.05) and a decrease in LF/HF ratio by 19.63% (P < 0.01) in yoga group. In the control group, there was decrease in the HF component and, no significant difference in the LF component of HRV spectrum and LF/HF ratio. The results show that yoga practice decreases sympathetic activity and causes a shift in the autonomic balance towards parasympathetic dominance indicating a reduction in stress. In conclusion, yoga practice helps to reduce stress by optimizing the autonomic functions. So, it is suggested to incorporate yoga module as a regular feature to keep subjunior athletes both mentally and physically fit.

Underlying factors determining grain morphologies in high-strength titanium alloys processed by additive manufacturing.

In recent research, additions of solute to Ti and some Ti-based alloys have been employed to produce equiaxed microstructures when processing these materials using additive manufacturing. The present study develops a computational scheme for guiding the selection of such alloying additions, and the minimum amounts required, to effect the columnar to equiaxed microstructural transition. We put forward two physical mechanisms that may produce this transition; the first and more commonly discussed is based on growth restriction factors, and the second on the increased freezing range effected by the alloying addition coupled with the imposed rapid cooling rates associated with AM techniques. We show in the research described here, involving a number of model binary as well as complex multi-component Ti alloys, and the use of two different AM approaches, that the latter mechanism is more reliable regarding prediction of the grain morphology resulting from given solute additions.

Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase.

Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug-an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme.

Biodiversity monitoring at the Tonle Sap Lake of Cambodia: a comparative assessment of local methods.

This paper assesses local biodiversity monitoring methods practiced in the Tonle Sap Lake of Cambodia. For the assessment we used the following criteria: methodological rigor, perceived cost, ease of use (user friendliness), compatibility with existing activities, and effectiveness of intervention. Constraints and opportunities for execution of the methods were also considered. Information was collected by use of: (1) key informant interview, (2) focus group discussion, and (3) researcher's observation. The monitoring methods for fish, birds, reptiles, mammals and vegetation practiced in the research area have their unique characteristics of generating data on biodiversity and biological resources. Most of the methods, however, serve the purpose of monitoring biological resources rather than biodiversity. There is potential that the information gained through local monitoring methods can provide input for long-term management and strategic planning. In order to realize this potential, the local monitoring methods should be better integrated with each other, adjusted to existing norms and regulations, and institutionalized within community-based organization structures.

Role of exercise and nutrition on cardiopulmonary fitness and pulmonary functions on residential and non-residential school children.

Physical fitness is the prime criterion for survival and to lead a healthy life. Our aim is to find out effect of exercise and nutrition on physical fitness on growing children with scientific records. The present study was designed on healthy school children of a Residential-Sainik (100) and Non-Residential (100) school children (12-16 yrs) of Bijapur. To evaluate cardiopulmonary fitness parameters included are VO2Max (ml/kg/min) and Physical Fitness Index (PFI %). Harvard Step Test determined VO2 Max and PFI. Also recorded pulmonary function parameters like Forced Expiratory Volume in 1 sec (FEV1 in %) by recording spirometry. Peak Expiratory Flow Rate (PEFR in L/Min) by Peak flow meter and Maximal Expiratory Pressure (MEP in mmHg) by modified Black's apparatus. We found statistically significant higher values (p = 0.000) of VO2Max, PFI, FEV1, PEFR and MEP in residential school children compared to nonresidential school children higher. So, our study shows that regular exercise and nutritious food increase the cardiopulmonary fitness values and pulmonary functions in Residential school children.

Conformational basis for substrate recruitment in protein tyrosine phosphatase 10D.

The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activity suggests that other, less conserved sequence and structural features could contribute to this process. Here we describe the crystal structures of Drosophila melanogaster PTP10D in the apo form as well as in a complex with a substrate peptide and an inhibitor. These studies reveal the role of aromatic ring stacking interactions at the boundary of the active site of PTPs in mediating substrate recruitment. We note that phenylalanine 76, of the so-called KNRY loop, is crucial for orienting the phosphotyrosine residue toward the nucleophilic cysteine. Mutation of phenylalanine 76 to leucine results in a 60-fold decrease in the catalytic efficiency of the enzyme. Fluorescence measurements with a competitive inhibitor, p-nitrocatechol sulfate, suggest that Phe76 also influences the formation of the enzyme-substrate intermediate. The structural and biochemical data for PTP10D thus highlight the role of relatively less conserved residues in PTP domains in both substrate recruitment and modulation of reaction kinetics.

Optimizing image contrast of second phases in metal alloys.

Novel imaging strategies in the scanning electron microscope aimed at significantly improved image contrast of second phases in metal alloys are described. These include the use of low accelerating voltages, small working distances, and a novel detection system. Contrast is assessed as a function of voltage and optimized imaging conditions which result in much improved image quality are presented. These strategies are applied to two precipitation hardened Ni-base alloys, a cast single crystal and a hot isostatically pressed sample.

Molecular basis for the role of Staphylococcus aureus penicillin binding protein 4 in antimicrobial resistance.

Penicillin binding proteins (PBPs) are membrane-associated proteins that catalyze the final step of murein biosynthesis. These proteins function as either transpeptidases or carboxypeptidases and in a few cases demonstrate transglycosylase activity. Both transpeptidase and carboxypeptidase activities of PBPs occur at the D-Ala-D-Ala terminus of a murein precursor containing a disaccharide pentapeptide comprising N-acetylglucosamine and N-acetyl-muramic acid-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala. Beta-lactam antibiotics inhibit these enzymes by competing with the pentapeptide precursor for binding to the active site of the enzyme. Here we describe the crystal structure, biochemical characteristics, and expression profile of PBP4, a low-molecular-mass PBP from Staphylococcus aureus strain COL. The crystal structures of PBP4-antibiotic complexes reported here were determined by molecular replacement, using the atomic coordinates deposited by the New York Structural Genomics Consortium. While the pbp4 gene is not essential for the viability of S. aureus, the knockout phenotype of this gene is characterized by a marked reduction in cross-linked muropeptide and increased vancomycin resistance. Unlike other PBPs, we note that expression of PBP4 was not substantially altered under different experimental conditions, nor did it change across representative hospital- or community-associated strains of S. aureus that were examined. In vitro data on purified recombinant S. aureus PBP4 suggest that it is a beta-lactamase and is not trapped as an acyl intermediate with beta-lactam antibiotics. Put together, the expression analysis and biochemical features of PBP4 provide a framework for understanding the function of this protein in S. aureus and its role in antimicrobial resistance.

Analysis of multiple crystal forms of Bacillus subtilis BacB suggests a role for a metal ion as a nucleant for crystallization.

Bacillus subtilis BacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded beta-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalized B-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.

Role of a PAS sensor domain in the Mycobacterium tuberculosis transcription regulator Rv1364c.

The Mycobacterium tuberculosis transcriptional regulator Rv1364c regulates the activity of the stress response sigma factor sigma(F). This multi-domain protein has several components: a signaling PAS domain and an effector segment comprising of a phosphatase, a kinase and an anti-anti-sigma factor domain. Based on Small Angle X-ray Scattering (SAXS) data, Rv1364c was recently shown to be a homo-dimer and adopt an elongated conformation in solution. The PAS domain could not be modeled into the structural envelope due to poor sequence similarity with known PAS proteins. The crystal structure of the PAS domain described here provides a structural basis for the dimerization of Rv1364c. It thus appears likely that the PAS domain regulates the anti-sigma activity of Rv1364c by oligomerization. A structural comparison with other characterized PAS domains reveal several sequence and conformational features that could facilitate ligand binding - a feature which suggests that the function of Rv1364c could potentially be governed by specific cellular signals or metabolic cues.

Over-expression and purification strategies for recombinant multi-protein oligomers: a case study of Mycobacterium tuberculosis σ/anti-σ factor protein complexes.

The function of a protein in a cell often involves coordinated interactions with one or several regulatory partners. It is thus imperative to characterize a protein both in isolation as well as in the context of its complex with an interacting partner. High resolution structural information determined by X-ray crystallography and Nuclear Magnetic Resonance offer the best route to characterize protein complexes. These techniques, however, require highly purified and homogenous protein samples at high concentration. This requirement often presents a major hurdle for structural studies. Here we present a strategy based on co-expression and co-purification to obtain recombinant multi-protein complexes in the quantity and concentration range that can enable hitherto intractable structural projects. The feasibility of this strategy was examined using the σ factor/anti-σ factor protein complexes from Mycobacterium tuberculosis. The approach was successful across a wide range of σ factors and their cognate interacting partners. It thus appears likely that the analysis of these complexes based on variations in expression constructs and procedures for the purification and characterization of these recombinant protein samples would be widely applicable for other multi-protein systems.

Role of alpha-tocopherol in cardiopulmonary fitness in endurance athletes, cyclists.

Exercise increases oxygen consumption and causes a disturbance of intracellular pro-oxidant-antioxidant homeostasis. Athletes are exposed to acute and chronic stress that may lead to increased generation of oxidative species. Hence oxidative stress increases in athletes. Administration of antioxidant like alpha-tocopherol as supplementation may reduce the cell damage caused due to oxidative stress. In the present study, our aim was to study the effects of alpha-tocopherol supplementation on the cardiopulmonary fitness in endurance athletes (cyclists) and non-athletes. Our study included 40 cyclists who were trained under District Youth Service & Sports Office. 40 controls were randomly selected from student group of B.L.D.E.A's Medical College. Alpha-tocopherol (Vitamin E) 200 mg/day for 21 days wasgiven to study group and placebo was given to placebo group. Various physiological parameters like heart rate, blood pressure, respiratory rate were recorded, for assessing cardiopulmonary fitness: Physical Fitness Index (PFI) and VO2 max ml/min/kg were recorded before and after supplementation of vitamin E in athletes, and were compared with placebo group before and after supplementation of placebo and also with non-athletes. The results obtained from present study indicate that antioxidant like alpha-tocopherol supplementation did not contribute significantly to improve the cardiopulmonary fitness of endurance athletes.