Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode

The work described herein demonstrates the utility of structure-based drug design (SBDD) in shifting the binding mode of an HTS hit from a DFG-in to a DFG-out binding mode resulting in a class of novel potent CSF-1R kinase inhibitors suitable for lead development.     

A self-consistent cell flux expression for simultaneous chemotaxis and contact guidance in tissues

During wound healing, both chemotaxis and contact guidance can contribute to the migration of blood and tissue cells to the wound. In order to understand the wound healing process, we must thus understand how cells respond to both these simultaneous directional cues, which are not necessarily coaligned. Although chemotaxis and contact guidance have been studied individually, the interaction between them has not been addressed. We extend a stochastic cell movement model, developed by Dickinson and Tranquillo (1995) [6] for individual cues, for simultaneous chemotaxis and contact guidance by a two-parameter perturbation analysis in terms of the two associated cues, a chemotactic factor gradient and aligned tissue fibers. We present results from analysis of the first-order perturbation, which includes the cell flux expression heuristically proposed by others, but reveals paradoxical results for other indices of cell movement, such as the mean-squared displacement. We then present second-order perturbation results that resolve these paradoxical results. Finally, we relate these results to a continuum mechanical model developed by Barocas and Tranquillo (1997) [3] that predicts fiber alignment due to cell traction induced tissue contraction. Received: 30 April 1999 / Revised version: 30 October 1999 / Published online: 14 September 2000     

Genetic Diversity and Population Structure in Western Hoolock (Hoolock hoolock) Gibbons in India

International Journal of Primatology - Geographic and anthropogenic barriers can result in creating population structure in primates. We hypothesized that such features in the Northeast India could...     

Major improvements in biolistic transformation of suspension-cultured tobacco cells

Summary Suspension cultures of the NT1 line ofNicotiana tabacum L. were used as a model system to study plant biolistic transformation, because of their uniformity, rapid growth, and ease of handling. The β-glucuronidase gene and the neomycin phosphotransferase genes were used to assay transient and stable transformation. Numerous factors were studied and optimized, such that the frequency of transformation was increased roughly 60-fold for transient transformants and 20-fold for stable transformants. Both biological parameters (the promoter used to drive gene expression, osmotic preconditioning and posbombardment handling of the cells) and physical parameters of the bombardment process (particle acceleration device and accelerator parameters) were tested. The factors that increased transformation rates the most were promoter strength, use of a helium-driven particle accelerator, and osmotic preconditioning of the cells.     

Multilocus sequence typing for phylogenetic view and <Emphasis Type="Italic">vip</Emphasis> gene diversity of <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> strains of the Assam soil of North East India

An agriculturally important insecticidal bacterium, Bacillus thuringiensis have been isolated from the soil samples of various part of Assam including the Kaziranga National Park. Previously, the isolates were characterized based on morphology, 16S rDNA sequencing, and the presence of the various classes’ crystal protein gene(s). In the present study, the phylogenetic analysis of a few selected isolates was performed by an unambiguous and quick method called the multiple locus sequence typing (MLST). A known B. thuringiensis strain kurstaki 4D4 have been used as a reference strain for MLST. A total of four the MLST locus of housekeeping genes, recF, sucC, gdpD and yhfL were selected. A total of 14 unique sequence types (STs) was identified. A total number of alleles identified for the locus gdpD and sucC was 12, followed by locus yhfL was 11, however, only 6 alleles were detected for the locus recF. The phylogenetic analysis using MEGA 7.0.26 showed three major lineages. Approximately, 87% of the isolates belonged to the STs corresponding to B. thuringiensis, whereas two isolates, BA07 and BA39, were clustered to B. cereus. The isolates were also screened for the diversity of vegetative insecticidal protein (vip) genes. In all, 8 isolates showed the presence of vip1, followed by 7 isolates having vip2 and 6 isolates for vip3 genes. The expression of Vip3A proteins was analyzed by western blot analyses and expression of the Vip3A protein was observed in the isolate BA20. Thus, the phylogenetic relationship and diversity of Bt isolates from Assam soil was established based on MLST, in addition, found isolates having vip genes, which could be used for crop improvement.     

Explaining global variation in the latitudinal diversity gradient: Meta‐analysis confirms known patterns and uncovers new ones

Aim

The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for > 200 years. Empirical studies have documented this pattern across many different organisms and locations. Our goal was to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors. We performed a meta‐analysis on a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground‐breaking meta‐analysis of the LDG, using meta‐analysis and meta‐regression approaches largely new to the fields of ecology and biogeography.

Location

Global.

Time period

January 2003–September 2015.

Major taxa studied

Bacteria, protists, plants, fungi and animals.

Methods

We synthesized the outcomes of 389 individual cases of LDGs from 199 papers published since 2003, using hierarchical mixed‐effects meta‐analysis and multiple meta‐regression. Additionally, we re‐analysed Hillebrand's original dataset using modern methods.

Results

We confirmed the generality of the LDG, but found the pattern to be weaker than was found in Hillebrand's study. We identified previously unreported variation in LDG strength and slope across longitude, with evidence that the LDG is strongest in the Western Hemisphere. Locational characteristics, such as habitat and latitude range, contributed significantly to LDG strength, whereas organismal characteristics, including taxonomic group and trophic level, did not. Modern meta‐analytical models that incorporate hierarchical structure led to more conservative and sometimes contrasting effect size estimates relative to Hillebrand's initial analysis, whereas meta‐regression revealed underlying patterns in Hillebrand's dataset that were not apparent with a traditional analysis.

Main conclusions

We present evidence of global latitudinal, longitudinal and habitat‐based patterns in the LDG, which are apparent across both marine and terrestrial realms and over a broad taxonomic range of organisms, from bacteria to plants and vertebrates.     

Living with dolphins: Local ecological knowledge and perceptions of small cetaceans along the Sindhudurg coastline of Maharashtra,India

Two near shore small cetaceans occur commonly along the Maharashtra coast, the Indian Ocean humpback dolphin and Indo Pacific finless porpoise. These cetaceans frequently interact with fisheries in this region due to overlap in space and resource use. Besides stranding records, little ecological information is available about these species from Maharashtra. We conducted 143 semistructured interviews to document local ecological knowledge and community perceptions of small cetaceans in 30 coastal fishing villages in Sindhudurg. Perceptions of finless porpoises were largely neutral, whereas humpback dolphins were negative. A classification regression tree (CART) analysis (root node error: 60%) showed that the annual cost of gear damage was an important predictor variable of humpback dolphin perceptions, followed by occupation (gear type) and age. Entanglements were reported for both species in large and small gill nets, and shore seines. Perceived net damage and catch loss due to humpback dolphins was six times greater than that of finless porpoises. However, finless porpoises were reportedly more frequently entangled in gear than humpback dolphins. We provide an insight into the perceptions of cetaceans in the local community and the fisheries‐cetacean interactions that shape them.     

Controlled micelle conjugation via charged peptide amphiphiles

Abstract We report the first demonstration of nonionic detergent micelle conjugation and phase separation using purpose‐synthesized, peptide amphiphiles, C₁₀‐(Asp)₅ and C₁₀‐(Lys)₅. Clustering is achieved in two different ways. Micelles containing the negatively charged peptide amphiphile C₁₀‐(Asp)₅ are conjugated (a) via a water‐soluble, penta‐Lys mediator or (b) to micelles containing the C₁₀‐(Lys)₅ peptide amphiphile. Both routes lead to phase separation in the form of oil‐rich globules visible in the light microscope. The hydrophobic nature of these regions leads to spontaneous partitioning of hydrophobic dyes into globules that were found to be stable for weeks to months. Extension of the conjugation mechanism to micelles containing a recently discovered, light‐driven proton pump King Sejong 1‐2 (KS1‐2) demonstrates that a membrane protein may be concentrated using peptide amphiphiles while preserving its native conformation as determined by characteristic UV absorption. The potential utility of these peptide amphiphiles for biophysical and biomedical applications is discussed.     

Open science and meta‐analysis allow for rapid advances in ecology: A response to Menegotto et al. (2019)

Menegotto and colleagues’ (2019) commentary on our paper (Kinlock et al., 2018) does not negate our findings, but by recategorizing and reanalysing a portion of our data set, advances our knowledge of the latitudinal diversity gradients (LDGs) in marine ecosystems, particularly emphasizing different findings for benthic LDGs as a result of the recategorization of the data. Furthermore, we see the contribution by Menegotto et al. (2019) as highlighting the importance of scientific transparency; we believe that this insight into the nature of LDGs in marine systems would have been delayed, if not unobtainable, had we not provided fully transparent methods and complete data in our paper.