Computational Analysis of the Spatiotemporal Coordination of Polarized PI3K and Rac1 Activities in Micro-Patterned Live Cells

Polarized molecular activities play important roles in guiding the cell toward persistent and directional migration. In this study, the polarized distributions of the activities of phosphatidylinositol 3-kinase (PI3K) and the Rac1 small GTPase were monitored using chimeric fluorescent proteins (FPs) in cells constrained on micro-patterned strips, with one end connecting to a neighboring cell (junction end) and the other end free of cell-cell contact (free end). The recorded spatiotemporal dynamics of the fluorescent intensity from different cells was scaled into a uniform coordinate system and applied to compute the molecular activity landscapes in space and time. The results revealed different polarization patterns of PI3K and Rac1 activity induced by the growth factor stimulation. The maximal intensity of different FPs, and the edge position and velocity at the free end were further quantified to analyze their correlation and decipher the underlying signaling sequence. The results suggest that the initiation of the edge extension occurred before the activation of PI3K, which led to a stable extension of the free end followed by the Rac1 activation. Therefore, the results support a concerted coordination of sequential signaling events and edge dynamics, underscoring the important roles played by PI3K activity at the free end in regulating the stable lamellipodia extension and cell migration. Meanwhile, the quantification methods and accompanying software developed can provide a convenient and powerful computational analysis platform for the study of spatiotemporal molecular distribution and hierarchy in live cells based on fluorescence images

The tale of TILs in breast cancer: A report from The International Immuno-Oncology Biomarker Working Group

The advent of immune-checkpoint inhibitors (ICI) in modern oncology has significantly improved survival in several cancer settings. A subgroup of women with breast cancer (BC) has immunogenic infiltration of lymphocytes with expression of programmed death-ligand 1 (PD-L1). These patients may potentially benefit from ICI targeting the programmed death 1 (PD-1)/PD-L1 signaling axis. The use of tumor-infiltrating lymphocytes (TILs) as predictive and prognostic biomarkers has been under intense examination. Emerging data suggest that TILs are associated with response to both cytotoxic treatments and immunotherapy, particularly for patients with triple-negative BC. In this review from The International Immuno-Oncology Biomarker Working Group, we discuss (a) the biological understanding of TILs, (b) their analytical and clinical validity and efforts toward the clinical utility in BC, and (c) the current status of PD-L1 and TIL testing across different continents, including experiences from low-to-middle-income countries, incorporating also the view of a patient advocate. This information will help set the stage for future approaches to optimize the understanding and clinical utilization of TIL analysis in patients with BC

Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Contains fulltext : 95738.pdf (publisher's version ) (Open Access)BACKGROUND: Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. RESULTS: We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. CONCLUSION: Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm

Benthic community patterns and the composition of feeding types and reproductive modes in freshwater nematodes

Michiels IC, Traunspurger W. Benthic community patterns and the composition of feeding types and reproductive modes in freshwater nematodes. NEMATOLOGY. 2005;7(1):21-36.We characterised benthic invertebrate community composition in 11 oligotrophic, alpine lakes. Nematodes were the most abundant benthic taxa in most lakes but community composition differed markedly. Several relationships between the invertebrate taxa were found but there was no strong evidence that competition or predation shaped the benthic community structure. Most lakes were dominated by a few nematode species with cosmopolitan distribution. Obligate and/or facultative parthenogenetic species were most abundant. With increasing species richness, the overall sex-ratio increased and the relative abundance of parthenogenetic species decreased

Seasonal variation of biodiversity and assemblage structure in freshwater nematodes

Michiels IC, Traunspurger W. Seasonal variation of biodiversity and assemblage structure in freshwater nematodes. Archiv für Hydrobiologie. 2005;163(2):183-194.In a three-year field study we determined the seasonal and annual variation of abundance, biomass, species richness, and community structure of freshwater nematodes at a single station in the eutrophic Lake Obersee. The seasonal patterns observed were consistent and varied little between sampling years. Nematode abundance and biomass were highest in summer. Species richness and diversity peaked in winter. With 152 identified species, Obersee is the most species-rich lake ever described. Species number was not constant over years but the main assemblage structure hardly changed. The community was dominated by the same 4 species throughout the study. Colonization was very strong in winter while extinction rates were high in summer. This study shows that the community structure of free-living nematodes depends strongly on the season investigated

Impact of resource availability on species composition and diversity in freshwater nematodes

Michiels IC, Traunspurger W. Impact of resource availability on species composition and diversity in freshwater nematodes. OECOLOGIA. 2005;142(1):98-103.This study investigates the long-term effects of resource availability in a freshwater nematode community. We carried out a mesocosm experiment where natural nematode communities were exposed to nutrient addition/ depletion over 2 years. Compared to the nutrient-addition treatment, species richness and diversity were strongly reduced upon nutrient depletion. The functional group of bacterial feeders particularly suffered severely from nutrient depletion. The decrease in diversity of bacterial feeders was linked to reduced species richness and diversity of large omnivorous species, as predicted by trophic-dynamic models. Tilman's ( 1976) statement, that under low nutrient levels the best competitor dominates the system, was applicable in our system. Upon nutrient depletion, resource depletion led to a monoculture of 1 small bacterial feeder, but even after 2 years of resource depletion, up to 16 species still coexisted. Our results provide strong evidence that freshwater nematode systems can be regulated by nutrient competition

A three year study of seasonal dynamics of a zoobenthos community in a eutrophic lake

Michiels IC, Traunspurger W. A three year study of seasonal dynamics of a zoobenthos community in a eutrophic lake. NEMATOLOGY. 2004;6(5):655-669.The meiofauna community in the eutrophic Lake Obersee was investigated, with special emphasis on nematodes, from March 2001 to December 2003. Meiobenthos showed a stable annual and seasonal pattern with oligochaetes contributing most to benthic biomass and nematodes to benthic abundance. With 152 nematode species, Lake Obersee is the most nematode species-rich lentic habitat described so far. The nematode community was dominated by the family Monhysteridae. Bacterial feeders were the most abundant feeding type; omnivorous nematodes contributed most to total nematode biomass. Reproduction occurred throughout the year, with most species reproducing parthenogenetically. No seasonal pattern in reproductive strategies was found

Relation between nematode communities and trophic state in southern Swedish lakes

Ristau K, Traunspurger W. Relation between nematode communities and trophic state in southern Swedish lakes. Hydrobiologia. 2011;663(1):121-133

Combined influence of river discharge and wind on littoral nematode communities of a river mouth area of Lake Constance

Witthoeft-Muehlmann A, Traunspurger W, Rothhaupt KO. Combined influence of river discharge and wind on littoral nematode communities of a river mouth area of Lake Constance. AQUATIC ECOLOGY. 2007;41(2):231-242.The littoral nematode community adjacent to a river mouth (River Schussen) on Lake Constance (Germany) was studied from February 1999 to January 2000 in order to determine the influence of stress resulting from fluctuations in river discharge on local nematode assemblages. Additionally, the influence of wind as a second important stress factor was considered. Six sample sites were chosen, reflecting a gradient of river influence within the broader river mouth area. Nematode communities, varying in a mean range from 121 to 165 ind/10 cm(2), were found to differ significantly in terms of abundance, feeding type composition and species diversity. Deposit feeders were most abundant at all sites followed by chewers. Deposit feeders were affected mainly by wind events, while species diversity and the occurrence of chewers were influenced mainly by river discharge. The impact of both these stress factors was modified by a third variable, water level. Moderate and high levels of combined habitat stress led to significant changes in community structure. Under conditions of calm weather and low discharge, reduced species diversity and an increased predominance of deposit feeders were observed. In most cases, species diversity was found to be higher under moderate stress conditions, an observation that offers support for Connel's Intermediate Disturbance Hypothesis