bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eukaryotic aspects of translation initiation brought into focus
Authors: Aylett Christopher H. S. , Ban Nenad 
Published: January 2017

In all organisms, mRNA-directed protein synthesis is catalysed by ribosomes. Although the basic aspects of translation are preserved in all kingdoms of life, important differences are found in the process of translation initiation, which is rate-limiting and the most important step for translation regulation. While great strides had been taken towards a complete structural understanding of the initiation of translation in eubacteria, our understanding of the eukaryotic process, which includes numerous eukaryotic-specific initiation factors, was until recently limited owing to a lack of structural information. In this review, we discuss recent results in the field that provide an increasingly complete molecular description of the eukaryotic initiation process. The structural snapshots obtained using a range of methods now provide insights into the architecture of the initiation complex, start-codon recognition by the initiator tRNA and the process of subunit joining. Future advances will require both higher-resolution insights into previously characterized complexes and mapping of initiation factors that control translation on an additional level by interacting only peripherally or transiently with ribosomal subunits.
This article is part of the themed issue ‘Perspectives on the ribosome’.
Systematic review and meta‐analysis of the diagnostic accuracy of low‐dose computed tomography of the kidneys, ureters and bladder for urolithiasis
Authors: Xiang Hao , Chan Michael , Brown Victoria , Huo Ya Ruth , Chan Lewis , Ridley Lloyd 
Published: January 2017

SummaryRenal colic is a common clinical condition which is often investigated with a CT of the kidneys, ureters and bladder (CTKUB). Recent technological improvements have allowed a reduction in dose with the emergence of low‐dose CTKUB (LD‐CTKUB) techniques. The present meta‐analysis aims to determine the diagnostic accuracy of LD‐CTKUB in the diagnosis of clinically significant uroliths. A systematic review was performed using nine electronic databases from their dates of inception to May 2016. Inclusion criteria included studies reporting comparative outcomes using LD‐CTKUB with a dose less than 3 millisieverts compared to an imaging gold standard or clinical and surgical evaluation. The primary endpoint was detection of a urolith ≥3 mm where specified and any urolith when size was unspecified. Twelve studies were identified according to selection criteria, involving 1250 patients. LD‐CTKUB demonstrated a pooled sensitivity of 93.1% (95%CI 91.5–94.4), specificity of 96.6% (95%CI 95.1–97.7%), positive likelihood ratio of 19.9 (95%CI 12.7–31.2), negative likelihood ratio of 0.05 (95%CI 0.02–0.10) and AUC of 0.9877 in the detection of clinically significant uroliths. Although 86 alternative diagnoses were noted across seven studies, none assessed the accuracy of LD‐CTKUB in their detection. The majority of newer studies report an average radiation dose from 1 to 1.5 millisieverts. This study demonstrates a high sensitivity, specificity and positive predictive value in the detection of uroliths, however, its accuracy in the detection of alternative diagnoses is unknown. Therefore, we recommend using LD‐CTKUB when the pre‐test probability of stone disease is significantly higher than the pre‐test probability of alternative diagnoses, such as follow‐up of known calculi. We suggest caution when the pre‐test probability of alternative diagnoses is high, such as the initial presentation of renal colic.
Google Trends terms reporting rhinitis and related topics differ in European countries
Authors: Bousquet J. , Agache I. , Anto J. M. , Bergmann K. C. , Bachert C. , Annesi‐Maesano I. , Bousquet P. J. , D'Amato G. , Demoly P. , De Vries G. , Eller E. , Fokkens W.J. , Fonseca J. , Haahtela T. , Hellings P. W. , Just J. , Keil T. , Klimek L. , Kuna P. , Lodrup Carlsen K. C. , Mösges R. , Murray R. , Nekam K. , Onorato G. , Papadopoulos N. G. , Samolinski B. , Schmid‐Grendelmeier P. , Thibaudon M. , Tomazic P. , Triggiani M. , Valiulis A. , Valovirta E. , Van Eerd M. , Wickman M. , Zuberbier T. , Sheikh A. 
Published: January 2017

AbstractGoogle Trends (GT) searches trends of specific queries in Google and reflects the real‐life epidemiology of allergic rhinitis. We compared Google Trends terms related to allergy and rhinitis in all European Union countries, Norway and Switzerland from 1 January 2011 to 20 December 2016. The aim was to assess whether the same terms could be used to report the seasonal variations of allergic diseases. Using the Google Trend 5‐year graph, an annual and clear seasonality of queries was found in all countries apart from Cyprus, Estonia, Latvia, Lithuania and Malta. Different terms were found to demonstrate seasonality depending on the country ‐ namely ‘hay fever’, ‘allergy’ and ‘pollen’ – showing cultural differences. A single set of terms cannot be used across all European countries, but allergy seasonality can be compared across Europe providing the above three terms are used. Using longitudinal data in different countries and multiple terms, we identified an awareness‐related spike of searches (December 2016).
Fcγ receptor expression on splenic macrophages in adult immune thrombocytopenia
Authors: Audia S , Santegoets K , Laarhoven A G , Vidarsson G , Facy O , Ortega-Deballon P , Samson M , Janikashvili N , Saas P , Bonnotte B , Radstake T R 
Published: January 2017

Summary
Splenic macrophages play a key role in immune thrombocytopenia (ITP) pathogenesis by clearing opsonized platelets. Fcγ receptors (FcγR) participate in this phenomenon, but their expression on splenic macrophages and their modulation by treatment have scarcely been studied in human ITP. We aimed to compare the phenotype and function of splenic macrophages between six controls and 24 ITP patients and between ITP patients according to the treatments they received prior to splenectomy. CD86, human leucocyte antigen D-related (HLA-DR) and FcγR expression were measured by flow cytometry on splenic macrophages. The major FcγR polymorphisms were determined and splenic macrophage function was assessed by a phagocytosis assay. The expression of the activation markers CD86 and HLA-DR was higher on splenic macrophages during ITP compared to controls. While the expression of FcγR was not different between ITP and controls, the phagocytic function of splenic macrophages was reduced in ITP patients treated with intravenous immunoglobulin (IVIg) within the 2 weeks prior to splenectomy. The FCGR3A (158V/F) polymorphism, known to increase the affinity of FcγRIII to IgG, was over-represented in ITP patients. Thus, these are the first results arguing for the fact that the therapeutic use of IVIg during human chronic ITP does not modulate FcγR expression on splenic macrophages but decreases their phagocytic capabilities.
Multiple founder effects are followed by range expansion and admixture during the invasion process of the raccoon (Procyon lotor) in Europe
Authors: Fischer Marietta L. , Salgado Iván , Beninde Joscha , Klein Roland , Frantz Alain C. , Heddergott Mike , Cullingham Catherine I. , Kyle Christopher J. , Hochkirch Axel 
Published: January 2017

AbstractAimUnderstanding colonization dynamics is crucial for management of invasive species. We compare the genetic structure of historical (Central Europe) and recent (Spain) invasive populations with native and captive populations of the North American raccoon (Procyon lotor). Our aim was to analyse the effects of colonization age on genetic population structure, understand the role of captive individuals as potential founders and test the role of rivers for the dispersal of the species.LocationNorth America, Spain, Central Europe.MethodsWe genotyped wild‐caught raccoons from Spain and Central Europe (N = 596), zoos (N = 57) and the native range (N = 153) at 16 microsatellite loci and sequenced a mitochondrial DNA fragment (Control Region). We analysed population genetic structuring with Bayesian assignment methods and a FCA. In a landscape genetic analysis, we tested the effect of waterways in the dispersal of the species.ResultsWe detected 16 genetic clusters (in baps), supporting the hypothesis of multiple introductions and ongoing releases in the invasive range. The native population showed nearly no genetic structure, the Central European clusters showed signals of admixture, whereas the Spanish clusters were clearly separated. Admixture of the Central European clusters was probably caused by recent contact of populations with different origin. The landscape genetic analysis showed that rivers represent neither barriers nor corridors in Central Europe.Main conclusionsAs the Spanish populations are genetically more diverse than the Central European, we expect increased within‐population diversity when the still isolated populations merge after range expansion. As our results provide evidence for gene flow between zoos and free‐ranging populations, better control of pet trade is essential in the management efforts concerning this invasive species. Our study shows that genetic analyses can help to reconstruct invasion processes, which is important for better understanding and effective management of invasive species.
Effects of fine root characteristics of beech on carbon turnover in the topsoil and subsoil of a sandy Cambisol
Authors: Vormstein S. , Kaiser M. , Piepho H.‐P. , Joergensen R. G. , Ludwig B. 
Published: January 2017

Fine roots that enter mineral soil at different depths are a major source of organic carbon stored in forest soil. Little is known about the key factors that govern the mineralization kinetics of fine roots in topsoil compared with subsoil. Therefore, we analysed the effects of concentration, spatial distribution and size of fine beech roots on their rates of decomposition in the topsoil and subsoil of a sandy Cambisol. Undisturbed (intact soil columns) and disturbed (soil sieved < 2 mm) samples from the topsoil (2–10 cm) and subsoil (145–153 cm) were incubated for 365 days to determine the carbon dioxide emissions. The treatments included applications of fine roots that varied in size (length: <2 mm and 1–2 cm), different rates of application (2 and 8 g kg‐1) and spatial distribution (homogeneous and locally concentrated, i.e. localized). The mineralization was affected significantly at both depths by the rate of application (large rate > small rate) and in the topsoil by distribution (localized > homogeneous). The spatial distribution of large roots, but not smaller ones, affected rates of emission in subsoil but not in topsoil. Correlation analyses suggest an effect of the calcium and potassium supply on the microbial biomass and on the turnover of roots if these are locally concentrated. The data of this study suggest that in sandy soil the availability of macronutrients has to be considered complementary to root characteristics such as concentration, size and distribution to elucidate their decomposition kinetics throughout the soil profile.HighlightsAnalysis of effects of characteristics of fine beech roots on organic matter decomposition in top‐ and subsoil.
The rate of decomposition in the topsoil was larger if the fine roots were locally concentrated.
The rate of mineralization of fine beech roots in the subsoil increased with increasing root size.
Soil microbial biomass carbon is affected by the supply of calcium and potassium if the fine beech roots are locally concentrated.
Probing whole‐stream metabolism: influence of spatial heterogeneity on rate estimates
Authors: Siders Adam C. , Larson Danelle M. , Rüegg Janine , Dodds Walter K. 
Published: January 2017

Summary

Whole‐stream metabolism has been estimated by measuring in‐stream oxygen (O2) concentrations since the method was introduced over 50 years ago. However, the influence of measurement location and estimation method on metabolism rates is understudied. We examined how the placement of O2 probes (i.e. depth, separation from the thalweg), differences in methodology (1‐station, 2‐station, area‐weighted) and reach lengths influenced estimated rates of whole‐stream metabolism in a tallgrass prairie watershed.

Metabolism estimates made in the thalweg differed from estimates made in backwaters due to disconnection in flow, and estimates made in deep pools differed from surface estimates due to thermal stratification (temporary flow disconnection). The 1‐station respiration estimates differed from short 2‐station reach‐scale estimates (c. 20 m) but were more similar to larger 2‐station reach‐scale estimates (c. 100 m). In contrast, the 1‐station gross primary production was most similar to the short 2‐station reaches occurring immediately upstream and became less similar at longer 2‐station reach lengths. The different estimation methodologies (1‐station, 2‐station, area‐weighted) accounting for the longest reach scale did not result in different metabolism rates.

The temporary phenomena of thermal stratification of stream pools during a warm day, which disconnected pool bottoms from the surface waters, likely affected not only the pool estimates but also estimates made in the downstream thalweg (i.e. an O2 deficit accrued from respiration during the day in the bottom of the pool abruptly moved downstream during mixing).

Oxygen probe placement mattered and affected rate estimates according to habitat type and reach length (i.e. scale) due to the influence of small‐scale heterogeneity on community respiration. Selection of reach length can be critical for studies depending on whether local heterogeneity is of interest or should be averaged.

We conclude that the intuitive use of thalwegs and reaches that are at least 10 times the stream width are likely appropriate for whole‐stream metabolism estimates, although the exact reach length necessary and potential stream‐specific characteristics, such as stratified pools, need to be carefully considered in probe placement. We encourage other studies to report the placement characteristics of O2 probes in streams as well as consider the potential confounding factor of local habitat heterogeneity.
Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments
Authors: Xiao Xiao , Chen Weimin , Zong Le , Yang Jun , Jiao Shuo , Lin Yanbing , Wang Entao , Wei Gehong 
Published: January 2017

AbstractThe microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high‐throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments – the nodule endosphere, root endosphere, rhizosphere and root zone – as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged toEnsiferfor alfalfa andEnsifer–Bradyrhizobiumfor soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.
MtDNA metagenomics reveals large‐scale invasion of belowground arthropod communities by introduced species
Authors: Cicconardi Francesco , Borges Paulo A. V. , Strasberg Dominique , Oromí Pedro , López Heriberto , Pérez‐Delgado Antonio J. , Casquet Juliane , Caujapé‐Castells Juli , Fernández‐Palacios José María , Thébaud Christophe , Emerson Brent C. 
Published: January 2017

AbstractUsing a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large‐scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil‐dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNArelatedness among Collembola implicate human‐mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen
Authors: Robin Cécile , Andanson Audrey , Saint‐Jean Gilles , Fabreguettes Olivier , Dutech Cyril 
Published: January 2017

AbstractRange‐expanding species are expected to gain an increasing importance in the context of global change. They provide a great opportunity to study contemporary evolutionary changes and to unravel the mechanisms of evolution. Cryphonectria parasitica, the causal agent of chestnut blight, originating from Asia, has been spread since the beginning of the 20th century into different continents. We took advantage of the C. parasitica recent emergence in northern France to study the changes in population genetic structure and in phenotypic traits along this colonization and climatic gradient. Four hundred twenty‐seven C. parasitica isolates were sampled in 47 chestnut sites in northern France. The C. parasitica outbreak in the north was found to be due to the expansion of five dominant clonal groups from southern France and to the emergence of a few rare recombined genotypes. The evolutionary changes during C. parasitica range expansion were studied by analysing phenotypic changes in isolates from the same clonal lineage, with or without a geographic shift. Growth rates were assessed in vitro, at four temperatures. The northern isolates grew faster at 12 and 15 °C and more slowly at 28 and 32 °C than the southern isolates. These results strongly suggest local adaptation to low temperatures in C. parasitica, with a trade‐off of slower growth at high temperatures. They also reflect the high evolutionary potential of C. parasitica along a colonization gradient and show that clonal evolution is not a limitation for the rapid thermal adaptation of this invasive fungal species.
Spatial regulation of the KH domain RNA‐binding protein Rnc1 mediated by a Crm1‐independent nuclear export system in Schizosaccharomyces pombe
Authors: Satoh Ryosuke , Matsumura Yasuhiro , Tanaka Akitomo , Takada Makoto , Ito Yuna , Hagihara Kanako , Inari Masahiro , Kita Ayako , Fukao Akira , Fujiwara Toshinobu , Hirai Shinya , Tani Tokio , Sugiura Reiko 
Published: January 2017

SummaryRNA‐binding proteins (RBPs) play important roles in the posttranscriptional regulation of gene expression, including mRNA stability, transport and translation. Fission yeast rnc1+ encodes a K Homology (KH)‐type RBP, which binds and stabilizes the Pmp1 MAPK phosphatase mRNA thereby suppressing the Cl− hypersensitivity of calcineurin deletion and MAPK signaling mutants. Here, we analyzed the spatial regulation of Rnc1 and discovered a putative nuclear export signal (NES)Rnc1, which dictates the cytoplasmic localization of Rnc1 in a Crm1‐independent manner. Notably, mutations in the NESRnc1 altered nucleocytoplasmic distribution of Rnc1 and abolished its function to suppress calcineurin deletion, although the Rnc1 NES mutant maintains the ability to bind Pmp1 mRNA. Intriguingly, the Rnc1 NES mutant destabilized Pmp1 mRNA, suggesting the functional importance of the Rnc1 cytoplasmic localization. Mutation in Rae1, but not Mex67 deletion or overproduction, induced Rnc1 accumulation in the nucleus, suggesting that Rnc1 is exported from the nucleus to the cytoplasm via the mRNA export pathway involving Rae1. Importantly, mutations in the Rnc1 KH‐domains abolished the mRNA‐binding ability and induced nuclear localization, suggesting that Rnc1 may be exported from the nucleus together with its target mRNAs. Collectively, the functional Rae1‐dependent mRNA export system may influence the cytoplasmic localization and function of Rnc1.
Phosphatidylserine synthase 2 and phosphatidylserine decarboxylase are essential for aminophospholipid synthesis in Trypanosoma brucei
Authors: Farine Luce , Jelk Jennifer , Choi Jae‐Yeon , Voelker Dennis R. , Nunes Jon , Smith Terry K. , Bütikofer Peter 
Published: January 2017

SummaryPhosphatidylethanolamine (PE) and phosphatidylserine (PS) are ubiquitously expressed and metabolically interconnected glycerophospholipids in eukaryotes and prokaryotes. In Trypanosoma brucei, PE synthesis has been shown to occur mainly via the Kennedy pathway, one of the three routes leading to PE synthesis in eukaryotes, while PS synthesis has not been studied experimentally. We now reveal the importance of T. brucei PS synthase 2 (TbPSS2) and T. brucei PS decarboxylase (TbPSD), two key enzymes involved in aminophospholipid synthesis, for trypanosome viability. By using tetracycline‐inducible down‐regulation of gene expression and in vivo and in vitro metabolic labeling, we found that TbPSS2 (i) is necessary for normal growth of procyclic trypanosomes, (ii) localizes to the endoplasmic reticulum and (iii) represents the unique route for PS formation in T. brucei. In addition, we identified TbPSD as type I PS decarboxylase in the mitochondrion and found that it is processed proteolytically at a WGSS cleavage site into a heterodimer. Down‐regulation of TbPSD expression affected mitochondrial integrity in both procyclic and bloodstream form trypanosomes, decreased ATP production via oxidative phosphorylation in procyclic form and affected parasite growth.
Aspergillus sensitisation in bidi smokers with and without chronic obstructive lung disease
Authors: Agarwal Ritesh , Bhogal Sumita , Choudhary Hansraj , Aggarwal Ashutosh N. , Sehgal Inderpaul S. , Dhooria Sahajal , Behera Digambar , Chakrabarti Arunaloke 
Published: January 2017

SummaryRecent studies have described fungal sensitisation in patients with chronic obstructive pulmonary disease (COPD). However, no study has evaluated fungal sensitisation specifically in bidi smokers. Herein, we evaluate the prevalence of Aspergillus sensitisation in bidi smokers. Bidi smokers with and without COPD underwent chest radiography, spirometry, Aspergillus skin test, A. fumigatus precipitins, A. fumigatus‐specific IgE and total IgE. Aspergillus sensitisation was defined as the presence of either immediate cutaneous hyperreactivity to Aspergillus antigen or raised A. fumigatus‐specific IgE level >0.35 kUA/L. Bidis were obtained from a subset of cases and controls and cultured for the growth of any fungus. Two hundred subjects with COPD and 72 chronic bidi smokers without COPD were included in the study (258 men; mean age, 56.8 years). Aspergillus sensitisation was found to be significantly higher in bidi smokers without COPD (27.8%) compared to the COPD cases (16%). Age, COPD, lung function, severity of smoking and current smoking were not associated with Aspergillus sensitisation, on a multivariate logistic regression analysis. We found a high prevalence of Aspergillus sensitisation in bidi‐smoking subjects. More studies are required to confirm the findings of our study.