Structure, mechanism and cooperation of bacterial multidrug transporters.

Cells from all domains of life encode energy-dependent trans-membrane transporters that can expel harmful substances including clinically applied therapeutic agents. As a collective body, these transporters perform as a super-system that confers tolerance to an enormous range of harmful compounds and consequently aid survival in hazardous environments. In the Gram-negative bacteria, some of these transporters serve as energy-transducing components of tripartite assemblies that actively efflux drugs and other harmful compounds, as well as deliver virulence agents across the entire cell envelope. We draw together recent structural and functional data to present the current models for the transport mechanisms for the main classes of multi-drug transporters and their higher-order assemblies.BL and DD are supported by the Medical Research Council (MRC), Human Frontiers Science Program (HFSP), and the Wellcome Trust. Work in the Van Veen lab is supported by the Biotechnology and Biological Sciences Research Council (BBSRC), MRC, HFSP, Royal Society, Society for Antimicrobial Chemotherapy (BSAC), Herchel Smith Foundation, and Commonwealth Trust. Work in the Pos lab is supported by the German Research Foundation (SFB 807, Transport and Communication across Biological Membranes and FOR2251, Adaptation and persistence of the emerging pathogen Acinetobacter baumannii), the DFG-EXC115 (Cluster of Excellence Macromolecular Complexes at the Goethe-University Frankfurt), Innovative Medicines Initiative Joint Undertaking Project Translocation (IMI-Translocation), EU Marie Curie Actions ITN, HFSP and the German-Israeli Foundation (GIF). The SM laboratory is supported by ERATO Murata Lipid Active Structure Project, Japan Science and Technology Agency, the Advanced Research for Medical Products Mining Program of the National Institute of Biomedical Innovation (NIBIO) and HFSP.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.sbi.2015.07.01

OC-0052: Late toxicity in the randomized phase III Dutch Hypofractionation Trial for prostate cancer patients (HYPRO)

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GM-CSF/IL-3/IL-5 receptor common β chain (CD131) expression as a biomarker of antigen-stimulated CD8+ T cells

<p>Abstract</p> <p>Background</p> <p>Upon Ag-activation cytotoxic T cells (CTLs) produce IFN-γ GM-CSF and TNF-α, which deliver simultaneously pro-apoptotic and pro-inflammatory signals to the surrounding microenvironment. Whether this secretion affects in an autocrine loop the CTLs themselves is unknown.</p> <p>Methods</p> <p>Here, we compared the transcriptional profile of Ag-activated, Flu-specific CTL stimulated with the FLU M1:58-66 peptide to that of convivial CTLs expanded <it>in vitro </it>in the same culture. PBMCs from 6 HLA-A*0201 expressing donors were expanded for 7 days in culture following Flu M1:58-66 stimulation in the presence of 300 IU/ml of interleukin-2 and than sorted by high speed sorting to high purity CD8+ expressing T cells gated according to FluM1:58-66 tetrameric human leukocyte antigen complexes expression.</p> <p>Results</p> <p>Ag-activated CTLs displayed higher levels of IFN-γ, GM-CSF (CSF2) and GM-CSF/IL-3/IL-5 receptor common β- chain (CD131) but lacked completely expression of IFN-γ receptor-II and IFN-stimulated genes (ISGs). This observation suggested that Ag-activated CTLs in preparation for the release of IFN-γ and GM-CSF shield themselves from the potentially apoptotic effects of the former entrusting their survival to GM-SCF. <it>In vitro </it>phenotyping confirmed the selective surface expression of CD131 by Ag-activated CTLs and their increased proliferation upon exogenous administration of GM-CSF.</p> <p>Conclusion</p> <p>The selective responsiveness of Ag-activated CTLs to GM-CSF may provide an alternative explanation to the usefulness of this chemokine as an adjuvant for T cell aimed vaccines. Moreover, the selective expression of CD131 by Ag-activated CTLs proposes CD131 as a novel biomarker of Ag-dependent CTL activation.</p

The stable traits of melanoma genetics: an alternate approach to target discovery

<p>Abstract</p> <p>Background</p> <p>The weight that gene copy number plays in transcription remains controversial; although in specific cases gene expression correlates with copy number, the relationship cannot be inferred at the global level. We hypothesized that genes steadily expressed by 15 melanoma cell lines (CMs) and their parental tissues (TMs) should be critical for oncogenesis and their expression most frequently influenced by their respective copy number.</p> <p>Results</p> <p>Functional interpretation of 3,030 transcripts concordantly expressed (Pearson's correlation coefficient p-value < 0.05) by CMs and TMs confirmed an enrichment of functions crucial to oncogenesis. Among them, 968 were expressed according to the transcriptional efficiency predicted by copy number analysis (Pearson's correlation coefficient p-value < 0.05). We named these genes, "genomic delegates" as they represent at the transcriptional level the genetic footprint of individual cancers. We then tested whether the genes could categorize 112 melanoma metastases. Two divergent phenotypes were observed: one with prevalent expression of cancer testis antigens, enhanced cyclin activity, WNT signaling, and a Th17 immune phenotype (Class A). This phenotype expressed, therefore, transcripts previously associated to more aggressive cancer. The second class (B) prevalently expressed genes associated with melanoma signaling including <it>MITF</it>, melanoma differentiation antigens, and displayed a Th1 immune phenotype associated with better prognosis and likelihood to respond to immunotherapy. An intermediate third class (C) was further identified. The three phenotypes were confirmed by unsupervised principal component analysis.</p> <p>Conclusions</p> <p>This study suggests that clinically relevant phenotypes of melanoma can be retraced to stable oncogenic properties of cancer cells linked to their genetic back bone, and offers a roadmap for uncovering novel targets for tailored anti-cancer therapy.</p

Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle.

Chaperones TAPBPR and tapasin associate with class I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, wherein the lifetime and structural features of transiently bound peptides control the regulation of a conformational switch located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex

Patterns of Recurrence and Survival After Pelvic Treatment for Locally Advanced Penile Cancer

BACKGROUND: Penile cancer (PeCa) is rare, and the survival of patients with advanced disease remains poor. A better understanding of where treatment fails could aid the development of new treatment strategies. OBJECTIVE: To describe the disease course after pelvic lymph node (LN) treatment for PeCa. DESIGN, SETTING, AND PARTICIPANTS: We retrospectively analysed 228 patients who underwent pelvic LN treatment with curative intent from 1969 to 2016. The main treatment modalities were neoadjuvant chemotherapy, chemoradiation, and pelvic LN dissection. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: In the case of multiple recurrence locations, the most distant location was taken and recorded as follows: local (penis), regional (inguinal and pelvic LN), and distant (any other location). A competing risk analysis was used to calculate the time to recurrence per location, and a Kaplan-Meier analysis was used for overall survival (OS). RESULTS AND LIMITATIONS: The median follow-up of the surviving patients was 79 mo. The reason for pelvic treatment was pelvic involvement on imaging (29%), two or more tumour-positive inguinal LNs (61%), or inguinal extranodal extension (52%). More than half of the patients (61%) developed a recurrence. The median recurrence-free survival was 11 mo. The distribution was local in 9%, regional in 27%, and distant in 64% of patients. The infield control rate of nonsystemically treated patients was 61% (113/184). From the start of pelvic treatment, the median OS was 17 mo (95% confidence interval 12–22). After regional or distant recurrence, all but one patient died of PeCa with median OS after a recurrence of 4.4 (regional) and 3.1 (distant) mo. This study is limited by its retrospective nature. CONCLUSIONS: The prognosis of PeCa patients treated on their pelvis who recur despite locoregional treatment is poor. The tendency for systemic spread emphasises the need for more effective systemic treatment strategies. PATIENT SUMMARY: In this report, we looked at the outcomes of penile cancer patients in an expert centre undergoing various treatments on their pelvis. We found that survival is poor after recurrence despite locoregional treatment. Therefore, better systemic treatments are necessary

Darwin wasps: a new name heralds renewed efforts to unravel the evolutionary history of Ichneumonidae

The parasitoid wasp family Ichneumonidae is arguably one of the groups for which current knowledge lags most strongly behind their enormous diversity. In a five-day meeting in Basel (Switzerland) in June 2019, 22 researchers from 14 countries met to discuss the most important issues in ichneumonid research, including increasing the speed of species discovery, resolving higher-level relationships, and studying the radiation of these parasitoids onto various host groups through time. All agreed that it is time to advertise ichneumonid research more broadly and thereby attract young talents to this group for which specialists are sorely lacking, as well as increase public awareness about their exciting biology and ecological impact. In order to popularize the group, we here suggest a new vernacular name for the family, “Darwin wasps”, to reflect the pivotal role they played in convincing Charles Darwin that not all of creation could have been created by a benevolent god. We hope that the name catches on, and that Darwin wasps start buzzing more loudly across all disciplines of biology

The Amazon Epiphyte Network: A First Glimpse Into Continental-Scale Patterns of Amazonian Vascular Epiphyte Assemblages

Epiphytes are still an understudied plant group in Amazonia. The aim of this study was to identify distributional patterns and conservation priorities for vascular epiphyte assemblages (VEA) across Amazonia. We compiled the largest Amazonian epiphyte plot database to date, through a multinational collaborative effort of 22 researchers and 32 field sites located across four Amazonian countries – the Amazonian Epiphyte Network (AEN). We addressed the following continental-scale questions by utilizing the AEN database comprising 96,448 epiphyte individuals, belonging to 518 vascular taxa, and growing on 10,907 tree individuals (phorophytes). Our objectives here are, first, to present a qualitative evaluation of the geographic distribution of the study sites and highlight regional lacunae as priorities for future quantitative inventories. Second, to present the floristic patterns for Amazonia-wide VEA and third, to combine multivariate analyses and rank abundance curves, controlled by major Amazonian habitat types, to determine how VEA vary geographically and ecologically based on major Amazonian habitat types. Three of the most striking patterns found are that: (1) VEA are spatially structured as floristic similarity decays with geographic distance; (2) a core group of 22 oligarchic taxa account for more than a half of all individuals; and (3) extensive floristic sampling gaps still exist, mainly across the highly threatened southern Amazonian deforestation belt. This work represents a first step toward unveiling distributional pattern of Amazonian VEA, which is important to guide future questions on ecology and species distribution ranges of VEA once the collaborative database grows allowing a clearer view of patterns

Longitudinal Study of Recurrent Metastatic Melanoma Cell Lines Underscores the Individuality of Cancer Biology.

Recurrent metastatic melanoma provides a unique opportunity to analyze disease evolution in metastatic cancer. Here, we followed up eight patients with an unusually prolonged history of metastatic melanoma, who developed a total of 26 recurrences over several years. Cell lines derived from each metastasis were analyzed by comparative genomic hybridization and global transcript analysis. We observed that conserved, patient-specific characteristics remain stable in recurrent metastatic melanoma even after years and several recurrences. Differences among individual patients exceeded within-patient lesion variability, both at the DNA copy number (P<0.001) and RNA gene expression level (P<0.001). Conserved patient-specific traits included expression of several cancer/testis antigens and the c-kit proto-oncogene throughout multiple recurrences. Interestingly, subsequent recurrences of different patients did not display consistent or convergent changes toward a more aggressive disease phenotype. Finally, sequential recurrences of the same patient did not descend progressively from each other, as irreversible mutations such as homozygous deletions were frequently not inherited from previous metastases. This study suggests that the late evolution of metastatic melanoma, which markedly turns an indolent disease into a lethal phase, is prone to preserve case-specific traits over multiple recurrences and occurs through a series of random events that do not follow a consistent stepwise process.Journal of Investigative Dermatology advance online publication, 2 January 2014; doi:10.1038/jid.2013.495