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FtsZ is a promising target for developing new antibacterials. A cell-based screen was developed and used to understand the mechanism of resistance to PC190723. It is reported for the first time that salt bridge interactions within the FtsZ structure prevent PC190723 binding and PC190723 targets FtsZ from a Gram-negative bacterium such as Helictobacter pylori.

Elastic Full wave-field (eFWI) inversion is aimed at inferring physical properties of the subsurface directly from seismic data. Goal is use highest level of physics to produce reliable properties to impact upstream business decisions. We focus on elastic parameters particularly the ratio between pressure (P) and shear (S) wave velocity, Vp/Vs that can be indicative of the type of fluid present in subsurface reservoir and P-wave impedance, Ip to impact porosity estimation.Our eFWI methodology derives the wavelet directly from seismic shots rather than using well information. Using field examples we explain the eFWI workflow, outline key steps and provide analysis of the results. The first field example is from a structurally simple clastic setting. The second field example is from a complex sub-salt environment and is focused on differentiating net versus non-net in pre-salt carbonate reservoirs - a challenging problem when using narrow azimuth streamer data. The third field example is from a clastic setting and uses well information to scale the wavelet and is applicable in development and production settings.Our experiments with the two exploration style field examples show that it is possible to directly invert shot data to obtain geologically meaningful elastic properties useful in exploration and early development phases. However, challenges remain. The inverted Ip has higher fidelity compared to the Vp/Vs ratio. In fact, Ip is sufficiently accurate to be reliably used for porosity prediction. The eFWI Vp/Vs inversion results are only in qualitative agreement with well information (as a blind test) for the clastic example, but sufficient to discriminate the net versus non-net for the pre-salt example. A qualitative match may be insufficient to determine fluid type via rock property inversion without any well control. In an environment without well control, further research is needed to investigate the sensitivity of Vp/Vs and determine if data quality is a key factor, in addition to stabilizing the extraction of elastic parameters in a multi-parameter inverse problem.The novel aspect for our approach is in developing a practical eFWI methodology in 3D and working with raw seismic shots with very minimal processing. Examples from different geological settings and use of well versus no-well provide valuable insights into current application space and potential research direction on improvements to eFWI algorithm.

Bacterial cell division proteins, especially the tubulin homolog FtsZ, have emerged as strong targets for developing new antibiotics. Here, we have utilized the fission yeast heterologous expression system to develop a cell-based assay to screen for small molecules that directly and specifically target the bacterial cell division protein FtsZ. The strategy also allows for simultaneous assessment of the toxicity of the drugs to eukaryotic yeast cells. As a proof-of-concept of the utility of this assay, we demonstrate the effect of the inhibitors sanguinarine, berberine and PC190723 on FtsZ. Though sanguinarine and berberine affect FtsZ polymerization, they exert a toxic effect on the cells. Further, using this assay system, we show that PC190723 affectsHelicobacter pyloriFtsZ function and gain new insights into the molecular determinants of resistance to PC190723. Based on sequence and structural analysis and site-specific mutations, we demonstrate that the presence of salt-bridge interactions between the central H7 helix and beta-strands S9 and S10 mediate resistance to PC190723 in FtsZ. The single-stepin vivocell-based assay using fission yeast enabled us to dissect the contribution of sequence-specific features of FtsZ and cell permeability effects associated with bacterial cell envelopes. Thus, our assay serves as a potent tool to rapidly identify novel compounds targeting polymeric bacterial cytoskeletal proteins like FtsZ to understand how they alter polymerization dynamics and address resistance determinants in targets.

Sequence alignments are models that capture the structural, functional and evolutionary relationships between proteins. Structure-guided sequence alignments are helpful in the case of distantly related proteins with poor sequence identity, thus rendering routine sequence alignment methods ineffective. Protein Alignment organized as Structural Superfamilies or PASS2 database provides such sequence alignments of protein domains within a superfamily as per the Structural Classification of Proteins extended (SCOPe) database. The current update of PASS2 (i.e. PASS2.7) is following the latest release of SCOPe (2.07) and we provide data for 14 323 protein domains that are Database URL The updated version of the PASS2 database is available at http://caps.ncbs.res.in/pass2/.

We propose a model-based Amplitude Variation with Offset (AVO) approach to address the assumption of weak elastic contrast in the linearized approximations of Aki-Richard equation. Existing approximations, especially for the Class 1 AVO response, which indicates the positive elastic contrast, deviate significantly from the Zoeppritz equation in presence of large elastic contrast. Results of the proposed approach show that it can minimize the deviation from the Zoeppritz equation, improve AVO attributes, and is capable of providing the desired attribute for characterizing a reservoir. The method starts with two matrices. One matrix is of the simulated rock properties termed as the rock-property-matrix and the other of the Zoeppritz AVO responses for those rock properties termed as the response-matrix. A model-based AVO equation or the basis-function-matrix is computed utilizing the rock-property-matrix and the response-matrix. The inverse of the basis-function-matrix is applied to the real data to get the AVO attributes from this approach. The conventional AVO (Aki-Richards) and model-based AVO attributes are compared in a class 1 AVO environment from the offshore east coast of India. The curvature attribute based on model-based AVO shows significant improvement. The synthetic-seismic correlation of the curvature attribute improves from −0.03 to 0.9 while synthetic-seismic correlation of the gradient attribute improves from 0.5 to 0.77. The improved AVO attribute volumes add significant values in the reservoir characterization.

Background:WFDC1/Prostate stromal 20 (ps20) is a small secreted protein highly expressed within the prostate stroma. WFDC1/ps20 expression is frequently downregulated or lost in prostate cancer (PCa) and ps20 has demonstrated growth-suppressive functions in numerous tumour model systems, although the mechanisms of this phenomenon are not understood.Methods:Ps20 was cloned and overexpressed in DU145, PC3, LNCaP and WPMY-1 cells. Cellular growth, cell cycle and apoptosis were characterised. WPMY-1 stromal cells expressing ps20 were characterised by transcriptome microarray and the function of WPMY-1 conditioned media on growth of PCa cell lines was assessed.Results:Prostrate stromal 20 expression enhanced the proliferation of LNCaP cells, whereas stromal WPMY-1 cells were inhibited and underwent increased apoptosis. Prostrate stromal 20-expressing WPMY-1 cells secrete a potently proapoptotic conditioned media. Prostrate stromal 20 overexpression upregulates expression of cyclooxygenase-2 (COX-2) in LNCaP and WPMY-1 cells, and induces expression of a growth-suppressive phenotype, which inhibits proliferation of PCa cells by ps20-expressing WPMY-1 conditioned media. This growth suppression was subsequently shown to be dependent on COX-2 function.Conclusions:This work posits that expression of ps20 in the prostate stroma can regulate growth of epithelial and other tissues through the prostaglandin synthase pathway, and thereby restricts development and progression of neoplasms. This provides a rational for selective pressure against ps20 expression in tumour- associated stroma.

Vaccines that confer protection through induction of adaptive T-cell immunity rely on understanding T-cell epitope (TCE) evolution induced by immune escape. This is poorly understood in tuberculosis (TB), an ancient, chronic disease, where CD4 T-cell immunity is of recognized importance. We probed 905 functionally validated, curated human CD4 T cell epitopes in 79 Mycobacterium tuberculosis (Mtb) whole genomes from India. This screen resulted in identifying 64 mutated epitopes in these strains initially using a computational pipeline and subsequently verified by single nucleotide polymorphism (SNP) analysis. SNP based phylogeny revealed the 79 Mtb strains to cluster to East African Indian (EAI), Central Asian Strain (CAS), and Beijing (BEI) lineages. Eighty-nine percent of the mutated T-cell epitopes (mTCEs) identified in the 79 Mtb strains from India has not previously been reported. These mTCEs were encoded by genes with high nucleotide diversity scores including seven mTCEs encoded by six antigens in the top 10% of rapidly divergent Mtb genes encoded by these strains. Using a T cell functional assay readout, we demonstrate 62% of mTCEs tested to significantly alter CD4 T-cell IFN gamma and/or IL2 secretion with associated changes in predicted HLA-DR binding affinity: the gain of function mutations displayed higher predicted HLA-DR binding affinity and conversely mutations resulting in loss of function displayed lower predicted HLA-DR binding affinity. Most mutated antigens belonged to the cell wall/cell processes, and, intermediary metabolism and respiration families though all known Mtb proteins encoded mutations. Analysis of the mTCEs in an SNP database of 5,310 global Mtb strains identified 82% mTCEs to be significantly more prevalent in Mtb strains isolated from India, including 36 mTCEs identified exclusively in strains from India. These epitopes had a significantly higher predicted binding affinity to HLA-DR alleles that were highly prevalent in India compared to HLA-DR alleles rare in India, highlighting HLA-DR maybe an important driver of these mutations. This first evidence of region-specific TCE mutations potentially employed by Mtb to escape host immunity has important implications for TB vaccine design.

The functional heterogeneity of T cell responses to diverse antigens expressed at different stages of Mycobacterium tuberculosis (Mtb) infection, in particular early secreted versus dormancy related latency antigens expressed later, that distinguish subjects with latent (LTBI), pulmonary (PTB) or extrapulmonary (EPTB) tuberculosis remains unclear. Here we show blood central memory CD4 T-cell responses specific to Mtb dormancy related (DosR) latency, but not classical immunodominant secretory antigens, to clearly differentiate LTBI from EPTB and PTB. The polyfunctionality score integrating up to 31 DosR-specific CD4 T-cell functional profiles was significantly higher in LTBI than EPTB or PTB subjects. Further analysis of 256 DosR-specific T-cell functional profiles identified regulatory IL10 + Th17 cells (IL10+IL17A+IL17F+IL22+) to be significantly enriched in LTBI; in contrast to pro-inflammatory Th17 cells (IFNγ+IL17A+/IL10−) in the blood and lung of EPTB and PTB subjects respectively. A blood polyfunctional, Mtb DosR latency antigen specific, regulatory, central memory response is therefore a novel functional component of T-cell immunity in latent TB and potential correlate of protection.

Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n = 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. The genome of A. hypochondriacus, codes for at least 24,829 proteins, shares the paleohexaploidy event with species under the superorders Rosids and Asterids, harbours 1 SNP in 1,000 bases, and contains 13.76% of repeat elements. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. As the first grain species under Caryophyllales and the first C4 dicot genome reported, the work presented here will be beneficial in improving crops and in expanding our understanding of angiosperm evolution.

Healthcare costs continue to increase dramatically, while quality remains a significant problem. Reform measures initiated by the government will drive expansion of these costs, further stressing taxpayers and employers, and forcing hospitals to adopt fundamental changes as they try to adjust to increased demands for services and to lessening reimbursements from all payers. This struggle is best seen at the point of entry for many at a hospital: the emergency department (ED). It is at the emergency department that patients’ expectations regarding staff communication with patients, wait times, the triage process, capacity and payment will determine a significant part of a hospital’s revenue. Using Dr. Eliyahu M. Goldratt’s Thinking Process, we will determine what core problem(s) are causing a 362-bed regional West Texas hospital emergency department to lose revenue. Evaluation of the current emergency department will determine the Undesirable Effects (UDE). Using that information will lead to the construction of the Current Reality Tree (CRT), which will bring focus to the core problem(s). To break the constraints, which are the core problem(s), an Evaporative Cloud (EC) is generated. And, the end result will be to construct a Future Reality Tree (FRT), which will validate the idea(s) generated in the EC. It was determined that there are ten major UDE’s that affected this hospital’s emergency department. They were focused around staff communication, wait times, triage process, information management, service provided and bill collections. A conclusion was made that the core problem dealt with triaging patients and utilization of the services provided by the hospital. Since the reimbursement rate is affected by the patient’s satisfaction, the areas to focus on would be: triage, education, communication and retention. Although it may be neither feasible nor desirable to meet all the patient’s expectations, increased focus on those areas may increase the emergency department’s efficiency and the hospital’s bottom line.

Phosphogypsum (PG) is produced as a solid waste from phosphatic fertilizer plants. The waste slurry is disposed off in settling ponds or in heaps. This solid waste is now increasingly being used as a calcium supplement in agriculture. This study reports the effectof PG amendmenton soil physico chemical properties, bacterial and fungal count and activities of soil enzymes such as invertase, cellulase and amylase over an incubation period of 28 days. The highest mean percent carbon loss (55.98%) was recorded in 15% PG amended soil followed by (55.28%) in 10% PG amended soil and the minimum (1.68%) in control soil. The highest number of bacterial colonies (47.4 CFU g(-1) soil), fungal count (17.8 CFU g(-1) soil), highest amylase activity (38.4 microg g(-1) soil hr(-1)) and cellulase activity (38.37 microg g(-1) soil hr(-1)) were recorded in 10% amended soil. Statistically significant difference (p0.05) has been recorded in the activities of amylase and cellulase over the period of incubation irrespective of amendments. Considering the bacterial and fungal growth and the activities of the three soil enzymes in the control and amended sets, it appears that 10% PG amendment is optimal for microbial growth and soil enzyme activities.