Spatial mismatch in morphological,ecological and phylogenetic diversity,in historical and contemporary European freshwater fish faunas

Biodiversity encompasses multiple facets, among which taxonomic, functional and phylogenetic aspects are the most often considered. Understanding how those diversity facets are distributed and what are their determinants has become a central concern in the current context of biodiversity crisis, but such multi‐faceted measures over large geographical areas are still pending. Here, we measured the congruence between the biogeographical patterns of freshwater fish morphological, ecological and phylogenetic diversity across Europe and identified the natural and anthropogenic drivers shaping those patterns. Based on freshwater fish occurrence records in 290 European river catchments, we computed richness and evenness for morphological, ecological and phylogenetic diversity using standardized effect sizes for each diversity index. We then used linear models including climatic, geo‐morphological, biotic and human‐related factors to determine the key drivers shaping freshwater fish biodiversity patterns across Europe. We found a weak spatial congruence between facets of diversity. Patterns of diversity were mainly driven by elevation range, climatic seasonality and species richness while other factors played a minor role. Finally, we found that non‐native species introductions significantly affected diversity patterns and influenced the effects of some environmental drivers. Morphological, ecological and phylogenetic diversity constitute complementary facets of fish diversity rather than surrogates, testifying that they deserve to be considered altogether to properly assess biodiversity. Although the same environmental and anthropogenic factors overall explained those diversity facets, their relative influence varied. In the current context of global change, non‐native species introductions may also lead to important reshuffling of assemblages resulting in profound changes of diversity patterns.     

Identification of a Lifespan Extending Mutation in the Schizosaccharomyces pombe Cyclin Gene clg1 + by Direct Selection of Long-Lived Mutants

Model organisms such as budding yeast, worms and flies have proven instrumental in the discovery of genetic determinants of aging, and the fission yeast Schizosaccharomyces pombe is a promising new system for these studies. We devised an approach to directly select for long-lived S. pombe mutants from a random DNA insertion library. Each insertion mutation bears a unique sequence tag called a bar code that allows one to determine the proportion of an individual mutant in a culture containing thousands of different mutants. Aging these mutants in culture allowed identification of a long-lived mutant bearing an insertion mutation in the cyclin gene clg1 ⁺. Clg1p, like Pas1p, physically associates with the cyclin-dependent kinase Pef1p. We identified a third Pef1p cyclin, Psl1p, and found that only loss of Clg1p or Pef1p extended lifespan. Genetic and co-immunoprecipitation results indicate that Pef1p controls lifespan through the downstream protein kinase Cek1p. While Pef1p is conserved as Pho85p in Saccharomyces cerevisiae, and as cdk5 in humans, genome-wide searches for lifespan regulators in S. cerevisiae have never identified Pho85p. Thus, the S. pombe system can be used to identify novel, evolutionarily conserved lifespan extending mutations, and our results suggest a potential role for mammalian cdk5 as a lifespan regulator.     

利用回交导入系剖析水稻苗期和分蘖期耐盐性的遗传重叠

以籼稻品种IR64为受体,来自伊朗的粳稻农家品种Binam为供体培育的99个BC2F8回交导入系为材料,定位了水稻在2叶1心期和分蘖期控制耐盐相关性状的数量性状基因座（QTL）．共检测到影响苗期叶片盐害级别、幼苗存活天数和地上部钾、钠离子浓度的QTL 13个,影响分蘖期株高、分蘖数和地上部鲜重的QTL 22个．多数分蘖期QTL对盐胁迫表现出明显的表达差异,根据表达情况将这些QTL分成3组,第1组为在对照条件下表达的11个QTL;第2组为在对照和盐胁迫条件下共同表达的5个QTL,其中有3个（QPh5,QPh8,QTn9）在两种环境下的基因效应大小和方向一致,其表达受盐胁迫影响较小;第3组为受盐胁迫诱导表达的6个QTL．检测到13个影响胁迫与对照差值即性状稳定性的QTL,除QPh4,QTn2和QFw2a外,其余10个基因座增加性状稳定性或提高耐盐性的等位基因均来自Binam．上述受盐胁迫影响较小的3个QTL和影响性状稳定性的13个QTL对耐盐性有贡献,属耐盐QTL．比较苗期和分蘖期耐盐QTL的分布,发现多数（69％）影响苗期和分蘖期的耐盐QTL在遗传上相互独立,仅在第1,2,8和11染色体的4个相同或相邻区域定位到影响两个时期的耐盐QTL,表明苗期和分蘖期的耐盐性存在部分的遗传重叠．通过标记辅助选择将苗期和分蘖期的重要耐盐QTL进行累加,或针对苗期和分蘖期的重叠耐盐QTL进行选择,有可能培育出苗期和分蘖期均耐盐的水稻品种．     

Identification of a linear B-cell epitope on the Schistosoma japonicum saposin protein,SjSAP4: Potential as a component of a multi-epitope diagnostic assay

BackgroundSchistosoma japonicum is one of three major species of blood flukes causing schistosomiasis, a disease, which continues to be a major public health issue in the Philippines. SjSAP4, a member of a multigene family of saposin-like proteins, is a recognized immunodiagnostic biomarker for schistosomiasis japonica. This study aimed to identify linear B-cell epitopes on SjSAP4 and to validate their potential as components of a multi-epitope assay for the serological diagnosis of schistosomiasis japonica.MethodologySjSAP4-derived peptides were expressed as GST-peptide-fused proteins and these were Western blot probed with human serum samples from S. japonicum Kato-Katz (KK)-positive individuals and uninfected controls. A core epitope was further identified by Western blotting through probing a series of truncated peptides with the schistosomiasis patient sera. The diagnostic performance of the core epitope-containing peptides and the full-length SjSAP4 was evaluated by enzyme-linked immunosorbent assay (ELISA) using a panel of sera collected from subjects resident in a schistosomiasis-endemic area of the Philippines.Main findingsAs a result of the peptide mapping, one peptide (P15) was found to be highly immunogenic in the KK-positive individuals. We subsequently showed that -S¹⁶³QCSLVGDIFVDKYLD¹⁷⁸- is a core B-cell epitope of P15. Subsequent ELISAs incorporating SjSAP4, SjSAP4-Peptide and SjSP-13V2-Peptide showed a sensitivity of 94.0%, 46.0% and 74.0%, respectively, and a specificity of 97.1%, 100% and 100%, respectively. Notably, complementary recognition of the B-cell epitopes (SjSAP4-Peptide and SjSP-13V2-Peptide) was observed in a subset of the KK-positive individuals. A dual epitope-ELISA (SjSAP4-Peptide + SjSP-13V2-Peptide-ELISA) showed a diagnostic sensitivity of 84.0% and a specificity of 100%.Conclusions/SignificanceIn this study, -S¹⁶³QCSLVGDIFVDKYLD¹⁷⁸- was identified as a dominant linear B-cell epitope on SjSAP4. This peptide and the complementary recognition of other B-cell epitopes using sera from different KK-positive individuals can provide the basis of developing a multi-epitope assay for the serological diagnosis of schistosomiasis.     

A locus conferring tolerance to Theileria infection in African cattle

East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T. parva (h² = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa’s most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.     

Pseudomonas aeruginosa polysaccharide Psl supports airway microbial community development

Pseudomonas aeruginosa dominates the complex polymicrobial cystic fibrosis (CF) airway and is a leading cause of death in persons with CF. Oral streptococcal colonization has been associated with stable CF lung function. However, no studies have demonstrated how Streptococcus salivarius, the most abundant streptococcal species found in individuals with stable CF lung disease, potentially improves lung function or becomes incorporated into the CF airway biofilm. By utilizing a two-species biofilm model to probe interactions between S. salivarius and P. aeruginosa, we discovered that the P. aeruginosa exopolysaccharide Psl promoted S. salivarius biofilm formation. Further, we identified a S. salivarius maltose-binding protein (MalE) that is required for promotion of biofilm formation both in vitro and in a Drosophila melanogaster co-infection model. Finally, we demonstrate that promotion of dual biofilm formation with S. salivarius is common among environmental and clinical P. aeruginosa isolates. Overall, our data supports a model in which S. salivarius uses a sugar-binding protein to interact with P. aeruginosa exopolysaccharide, which may be a strategy by which S. salivarius establishes itself within the CF airway microbial community.Subject terms: Bacteriology, Biofilms, Microbiome, Clinical microbiology     

The Relationship Between Lesion Size and Load to Failure After Stabilization of Simulated Metastatic Lesions of the Proximal Femur

BackgroundAs overall cancer survival continues to improve, the incidence of metastatic lesions to the bone continues to increase. The subsequent skeletal related events that can occur with osseous metastasis can be debilitating. Complete and impending pathologic femur fractures are common with patients often requiring operative fixation. However, the efficacy of an intramedullary nail construct, on providing stability, continue to be debated. Therefore, the purpose of this study was to utilize a synthetic femur model to determine 1) how proximal femur defect size and cortical breach impact femur load to failure (strength) and stiffness, and 2) and how the utilization of an IMN, in a prophylactic fashion, subsequently alters the overall strength and stiffness of the proximal femur.MethodsA total of 21 synthetic femur models were divided into four groups: 1) intact (no defect), 2) 2 cm defect, 3) 2.5 cm defect, and 4) 4 cm defect. An IMN was inserted in half of the femur specimens that had a defect present. This procedure was performed using standard antegrade technique. Specimens were mechanically tested in offset torsion. Force-displacement curves were utilized to determine each constructs load to failure and overall torsional stiffness. The ultimate load to failure and construct stiffness of the synthetic femurs with defects were compared to the intact synthetic femur, while the femurs with the placement of the IMN were directly compared to the synthetic femurs with matching defect size.ResultsThe size of the defect invertedly correlated with the load the failure and overall stiffness. There was no difference in load to failure or overall stiffness when comparing intact models with no defect and the 2 cm defect group (p=0.98, p=0.43). The 2.5 cm, and 4.5 cm defect groups demonstrated significant difference in both load to failure and overall stiffness when compared to intact models with results demonstrating 1313 N (95% CI: 874-1752 N; p<0.001) and 104 N/mm (95% CI: 98-110 N/mm; p=0.03) in the 2.5 cm defect models, and 512 N (95% CI: 390-634 N, p<0.001) and 21 N/mm (95% CI: 9-33 N/mm, p<0.001) in the models with a 4 cm defect. Compared to the groups with defects, the placement an IMN increased overall stiffness in the 2.5 cm defect group (125 N/mm; 95% CI:114-136 N/mm; p=0.003), but not load to failure (p=0.91). In the 4 cm defect group, there was a significant increase in load to failure (1067 N; 95% CI: 835-1300 N; p=0.002) and overall stiffness (57 N/mm; 95% CI:46-69 N/mm; p=0.001).ConclusionProphylactic IMN fixation significantly improved failure load and overall stiffness in the group with the largest cortical defects, but still demonstrated a failure loads less than 50% of the intact model. This investigation suggests that a cortical breach causes a loss of strength that is not completely restored by intramedullary fixation. Level of Evidence: II     

Hypothetical Outcome Plots Outperform Error Bars and Violin Plots for Inferences about Reliability of Variable Ordering

Many visual depictions of probability distributions, such as error bars, are difficult for users to accurately interpret. We present and study an alternative representation, Hypothetical Outcome Plots (HOPs), that animates a finite set of individual draws. In contrast to the statistical background required to interpret many static representations of distributions, HOPs require relatively little background knowledge to interpret. Instead, HOPs enables viewers to infer properties of the distribution using mental processes like counting and integration. We conducted an experiment comparing HOPs to error bars and violin plots. With HOPs, people made much more accurate judgments about plots of two and three quantities. Accuracy was similar with all three representations for most questions about distributions of a single quantity.     

The Heat-Resistant Agglutinin Family Includes a Novel Adhesin from Enteroaggregative Escherichia coli Strain 60A

Heat-resistant agglutinin 1 (Hra1) is an accessory colonization factor of enteroaggregative Escherichia coli (EAEC) strain 042. Tia, a close homolog of Hra1, is an invasin and adhesin that has been described in enterotoxigenic E. coli. We devised a PCR-restriction fragment length polymorphism screen for the associated genes and found that they occur among 55 (36.7%) of the enteroaggregative E. coli isolates screened, as well as lower proportions of enterotoxigenic, enteropathogenic, enterohemorrhagic, and commensal E. coli isolates. Overall, 25%, 8%, and 3% of 150 EAEC strains harbored hra1 alone, tia alone, or both genes, respectively. One EAEC isolate, 60A, produced an amplicon with a unique restriction profile, distinct from those of hra1 and tia. We cloned and sequenced the full-length agglutinin gene from strain 60A and have designated it hra2. The hra2 gene was not detected in any of 257 diarrheagenic E. coli isolates in our collection but is present in the genome of Salmonella enterica serovar Heidelberg strain SL476. The cloned hra2 gene from strain 60A, which encodes a predicted amino acid sequence that is 64% identical to that of Hra1 and 68% identical to that of Tia, was sufficient to confer adherence on E. coli K-12. We constructed an hra2 deletion mutant of EAEC strain 60A. The mutant was deficient in adherence but not autoaggregation or invasion, pointing to a functional distinction from the autoagglutinin Hra1 and the Tia invasin. Hra1, Tia, and the novel accessory adhesin Hra2 are members of a family of integral outer membrane proteins that confer different colonization-associated phenotypes.