Foraging strategies in the ants Myrmicaria brunnea and Diacamma ceylonense- some preliminary observations

Myrmicaria brunnea forager communicates by means of chemical and/or acoustic signals so that other foragers present nearby can move towards it and find the bait sooner than they would on their own. However, this sort of communication seem to have not been present in Diacamma sp. foragers

Evidence for avian mafia

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Contributions to the biology of the queenless ponerine ant Diacamma ceylonense Emery (Formicillae)

All ants are generally classified as highly eusocial, However, there are some 100 species of ants belonging to the morphologically primitive subfamily Ponerinae, which lack a morphologically differentiated queen. One or a small number of mated workers (gamergates) function as queens, i.e. they produce male as well as female offspring. Such ant species are of great interest as they provide unique opportunities to understand the causes and consequences of queenlessness. This is the first report ofa long-term field study we have initiated on a large population of the queenless ponerine ant, Diacamma ceylonense Emery, on the campus of the Indian Institute of Science, Bangalore. Data are provided on the numbers of colonies present during a 213-week period, from which the probable time of colonisation of the site by D. ceylonense is suggested. Twenty-six entire colonies were excavated to study the adult and brood composition. While some colonies did not appear to have a gamergate at the time of excavation, others had only one gamergate per colony. Only the gamergate was mated and had well developed ovaries, while all the workers were unmated and had undeveloped ovaries. Excavated colonies had an average of 230 adult females, 2 males and 80 items of brood. The gamergates were indistinguishable from their workers in body size but there was significant variation in the size of workers between colonies. On an average, colonies employed 24% of their workers outside the nest for foraging and other duties. The relative constancy of this proportion permits estimation of total colony size by merely estimating the number of extranidal workers and thus without having to excavate the nests. In the five colonies studied, foragers spent an average of 9 to 23 days of their lives in performing foraging duties. Most foragers remained faithful to one or a narrow range of compass directions, although such directional preferences of all of them put together permitted colonies to exploit resources in all directions

Crystallization and preliminary X‐ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109357/1/S2053230X14017415.pd

Anterior Hippocampus and Goal-Directed Spatial Decision Making

Contains fulltext : 115487.pdf (publisher's version ) (Open Access

Investigation of the effect of PD-L1 blockade on triple negative breast cancer cells using fourier transform infrared spectroscopy

Interactions between programmed death-1 (PD-1) with its ligand PD-L1 on tumor cells can antagonize T cell responses. Inhibiting these interactions using immune checkpoint inhibitors has shown promise in cancer immunotherapy. MDA-MB-231 is a triple negative breast cancer cell line that expresses PD-L1. In this study, we investigated the biochemical changes in MDA-MB-231 cells following treatment with atezolizumab, a specific PD-L1 blocker. Our readouts were Fourier Transform Infrared (FTIR) spectroscopy and flow cytometric analyses. Chemometrical analysis, such as principal component analysis (PCA), was applied to delineate the spectral differences. We were able to identify the chemical alterations in both protein and lipid structure of the treated cells. We found that there was a shift from random coil and ?-helical structure to ?-sheet conformation of PD-L1 on tumor cells due to atezolizumab treatment, which could hinder binding with its receptors on immune cells, ensuring sustained T cell activation for potent immune responses. This work provides novel information about the effects of atezolizumab at molecular and cellular levels. FTIR bio-spectroscopy, in combination with chemometric analyses, may expedite research and offer new approaches for cancer immunology. - 2019 by the authors. Licensee MDPI, Basel, Switzerland.Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O. Box 34110 Doha, Qatar Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O. Box 34110 Doha, Qatar Department of Chemistry and Earth Sciences, Qatar University (QU), P.O. Box 2713 Doha, Qatar Qatar Computing Research Institute, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O. Box 34110 Doha, Qatar Qatar Environment & Energy Research Institute (QEERI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O. Box 34110 Doha, Qatar Correspondence: [email protected] (M.H.M.A.); [email protected] (E.E.

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors

© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox- Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers.Link_to_subscribed_fulltex

Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content analysis of single circulating tumor cells

Timely characterization of a cancer's evolution is required to predict treatment efficacy and to detect resistance early. High content analysis of single Circulating Tumor Cells (CTCs) enables sequential characterization of genotypic, morphometric and protein expression alterations in real time over the course of cancer treatment. This concept was investigated in a patient with castrate-resistant prostate cancer progressing through both chemotherapy and targeted therapy. In this case study, we integrate across four timepoints 41 genome-wide copy number variation (CNV) profiles plus morphometric parameters and androgen receptor (AR) protein levels. Remarkably, little change was observed in response to standard chemotherapy, evidenced by the fact that a unique clone (A), exhibiting highly rearranged CNV profiles and AR+ phenotype was found circulating before and after treatment. However, clinical response and subsequent progression after targeted therapy was associated with the drastic depletion of clone A, followed by the sequential emergence of two distinct CTC sub-populations that differed in both AR genotype and expression phenotype. While AR- cells with flat or pseudo-diploid CNV profiles (clone B) were identified at the time of response, a new tumor lineage of AR+ cells (clone C) with CNV altered profiles was detected during relapse. We showed that clone C, despite phylogenetically related to clone A, possessed a unique set of somatic CNV alterations, including MYC amplification, an event linked to hormone escape. Interesting, we showed that both clones acquired AR gene amplification by deploying different evolutionary paths. Overall, these data demonstrate the timeframe of tumor evolution in response to therapy and provide a framework for the multi-scale analysis of fluid biopsies to quantify and monitor disease evolution in individual patients

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles

Accurately characterizing transcription factor (TF)-DNA affinity is a central goal of regulatory genomics. Although thermodynamics provides the most natural language for describing the continuous range of TF-DNA affinity, traditional motif discovery algorithms focus instead on classification paradigms that aim to discriminate 'bound' and 'unbound' sequences. Moreover, these algorithms do not directly model the distribution of tags in ChIP-seq data. Here, we present a new algorithm named Thermodynamic Modeling of ChIP-seq (TherMos), which directly estimates a positionspecific binding energy matrix (PSEM) from ChIPseq/exo tag profiles. In cross-validation tests on seven genome-wide TF-DNA binding profiles, one of which we generated via ChIP-seq on a complex developing tissue, TherMos predicted quantitative TF-DNA binding with greater accuracy than five well-known algorithms. We experimentally validated TherMos binding energy models for Klf4 and Esrrb, using a novel protocol to measure PSEMs in vitro. Strikingly, our measurements revealed strong nonadditivity at multiple positions within the two PSEMs. Among the algorithms tested, only TherMos was able to model the entire binding energy landscape of Klf4 and Esrrb. Our study reveals new insights into the energetics of TF-DNA binding in vivo and provides an accurate first-principles approach to binding energy inference from ChIP-seq and ChIP-exo data. © 2013 The Author(s).Link_to_subscribed_fulltex