Mass extinctions do not explain skew in interspecific body size distributions

In several higher animal taxa, such as mammals and birds, the distribution of species body sizes is heavily skewed towards small size. Previous studies have suggested that small‐bodied organisms are less prone to extinction than large‐bodied species. If small body size is favourable during mass extinction events, a post mass extinction excess of small‐bodied species may proliferate and maintain skewed body size distributions sometime after. Here, we modelled mass extinctions and found that even unrealistically strong body mass selection has little effect on the skew of interspecific body size distributions. Moreover, selection against large body size may, counter intuitively, skew size distributions towards large body size. In any case, subsequent evolutionary diversification rapidly erases these rather small effects mass extinctions may have on size distributions. Next, we used body masses of extant species and phylogenetic methods to investigate possible changes in body size distributions across the Cretaceous–Paleogene (K‐Pg) mass extinction. Body size distributions of extant clades that originated during the Cretaceous are on average more skewed than their subclades that originated during the Paleogene, but the difference is only minor in mammals, and in birds, it can be explained by a positive relationship between species richness and skewness that is also present in clades that originated after the transition. Hence, we cannot infer from extant species whether the K‐Pg mass extinctions were size‐selective, but they are not the reason why most extant bird and mammal species are small‐bodied.     

The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours

Dispersal is a key ecological process that is strongly influenced by both phenotype and environment. Here, we show that juvenile environment influences dispersal not only by shaping individual phenotypes, but also by changing the phenotypes of neighbouring conspecifics, which influence how individuals disperse. We used a model system (Tribolium castaneum, red flour beetles) to test how the past environment of dispersing individuals and their neighbours influences how they disperse in their current environment. We found that individuals dispersed especially far when exposed to a poor environment as adults if their phenotype, or even one‐third of their neighbours’ phenotypes, were shaped by a poor environment as juveniles. Juvenile environment therefore shapes dispersal both directly, by influencing phenotype, as well as indirectly, by influencing the external social environment. Thus, the juvenile environment of even a minority of individuals in a group can influence the dispersal of the entire group.     

Effect of Electron‐Transport Material on Light‐Induced Degradation of Inverted Planar Junction Perovskite Solar Cells

This paper presents a systematic study of the influence of electron‐transport materials on the operation stability of the inverted perovskite solar cells under both laboratory indoor and the natural outdoor conditions in the Negev desert. It is shown that all devices incorporating a Phenyl C₆₁ Butyric Acid Methyl ester ([60]PCBM) layer undergo rapid degradation under illumination without exposure to oxygen and moisture. Time‐of‐flight secondary ion mass spectrometry depth profiling reveals that volatile products from the decomposition of methylammonium lead iodide (MAPbI₃) films diffuse through the [60]PCBM layer, go all the way toward the top metal electrode, and induce its severe corrosion with the formation of an interfacial AgI layer. On the contrary, alternative electron‐transport material based on the perylendiimide derivative provides good isolation for the MAPbI₃ films preventing their decomposition and resulting in significantly improved device operation stability. The obtained results strongly suggest that the current approach to design inverted perovskite solar cells should evolve with respect to the replacement of the commonly used fullerene‐based electron‐transport layers with other types of materials (e.g., functionalized perylene diimides). It is believed that these findings pave a way toward substantial improvements in the stability of the perovskite solar cells, which are essential for successful commercialization of this photovoltaic technology.     

Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network

Using a phenome-wide association study (PheWAS) approach, we comprehensively tested genetic variants for association with phenotypes available for 70,061 study participants in the Population Architecture using Genomics and Epidemiology (PAGE) network. Our aim was to better characterize the genetic architecture of complex traits and identify novel pleiotropic relationships. This PheWAS drew on five population-based studies representing four major racial/ethnic groups (European Americans (EA), African Americans (AA), Hispanics/Mexican-Americans, and Asian/Pacific Islanders) in PAGE, each site with measurements for multiple traits, associated laboratory measures, and intermediate biomarkers. A total of 83 single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) were genotyped across two or more PAGE study sites. Comprehensive tests of association, stratified by race/ethnicity, were performed, encompassing 4,706 phenotypes mapped to 105 phenotype-classes, and association results were compared across study sites. A total of 111 PheWAS results had significant associations for two or more PAGE study sites with consistent direction of effect with a significance threshold of p<0.01 for the same racial/ethnic group, SNP, and phenotype-class. Among results identified for SNPs previously associated with phenotypes such as lipid traits, type 2 diabetes, and body mass index, 52 replicated previously published genotype–phenotype associations, 26 represented phenotypes closely related to previously known genotype–phenotype associations, and 33 represented potentially novel genotype–phenotype associations with pleiotropic effects. The majority of the potentially novel results were for single PheWAS phenotype-classes, for example, for CDKN2A/B rs1333049 (previously associated with type 2 diabetes in EA) a PheWAS association was identified for hemoglobin levels in AA. Of note, however, GALNT2 rs2144300 (previously associated with high-density lipoprotein cholesterol levels in EA) had multiple potentially novel PheWAS associations, with hypertension related phenotypes in AA and with serum calcium levels and coronary artery disease phenotypes in EA. PheWAS identifies associations for hypothesis generation and exploration of the genetic architecture of complex traits.     

Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1

Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations that predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.     

Genetic and biological characterization of a T suppressor cell induced by anti-idiotypic antibody

The cellular and molecular characteristics of anti-idiotype-induced suppression have been investigated. We have shown that i.v. immunization of A/J or C.AL-20 mice with rabbit antibodies against the major cross-reactive idiotype on A/J anti-ABA antibodies induces splenic suppressor T cells (Ts) able to suppress T cell-mediated cytolytic and delayed-type hypersensitivity responses to ABA. In these studies, we compare the T suppressor activity manifested by anti-Id-induced suppressor cells with that described previously after conventional antigen priming. Results indicate that i.v. injection of anti-idiotypic antibodies primes for efferent level Ts; in contrast, i.v. administration of ABA-coupled cells induces afferent level suppressor cells. Soluble cell lysates, containing suppressor factor(s) derived from these anti-idiotype-induced Ts, can also mediate suppression of T cell immune responses in an efferent manner. Factor-mediated suppression is MHC-unrestricted and is also observed in mice pretreated with cyclophosphamide, suggesting that this activity is analogous to third-order suppression. Furthermore, this factor suppresses the T cell-mediated DTH and CTL responses in an antigen-nonspecific but Igh-restricted manner. These latter results suggest that the cellular elements conferring antigen specificity and Igh restriction are separate. The implications of these findings to the relationship between idiotypic elements, antigen-binding structures, and Igh restriction elements on immunoregulatory T cells are discussed.     

High sensitivity proteomics assisted discovery of a novel operon involved in the assembly of photosystem II, a membrane protein complex

Photosystem II (PSII) is a large membrane protein complex that performs the water oxidation reactions of photosynthesis in cyanobacteria, algae, and plants. The unusual redox reactions in PSII often lead to damage, degradation, and reassembly of this molecular machine. To identify novel assembly factors, high sensitivity proteomic analysis of PSII purified from the cyanobacterium Synechocystis sp. PCC 6803 was performed. This analysis identified six PSII-associated proteins that are encoded by an operon containing nine genes, slr0144 to slr0152. This operon encodes proteins that are not essential components of the PSII holocomplex but accumulate to high levels in pre-complexes lacking any of the lumenal proteins PsbP, PsbQ, or PsbV. The operon contains genes with putative binding domains for chlorophylls and bilins, suggesting these proteins may function as a reservoir for cofactors needed during the PSII lifecycle. Genetic deletion of this operon shows that removal of these protein products does not alter photoautotrophic growth or PSII fluorescence properties. However, the deletion does result in decreased PSII-mediated oxygen evolution and an altered distribution of the S states of the catalytic manganese cluster. These data demonstrate that the proteins encoded by the genes in this operon are necessary for optimal function of PSII and function as accessory proteins during assembly of the PSII complex. Thus, we have named the products of the slr0144-slr0152 operon Pap (Photosystem II assembly proteins).     

Epstein-Barr virus-positive and -negative B-cell lines can be infected with human immunodeficiency virus types 1 and 2.

Human immunodeficiency virus type 1 (HIV-1) can infect CD4+ lymphocytes, monocytes-macrophages, and various other cell lines, including B-cell lines. To study the parameters of B-cell infections, we examined the susceptibility of 24 B-lymphoid cell lines to both HIV-1 and HIV-2 infections. These cell lines included a series of Epstein-Barr virus (EBV) genome-negative Burkitt's lymphoma cell lines and their EBV-converted counterparts. To infect these cells we used two HIV-1 isolates and one HIV-2 isolate. Infections were monitored with a cytoplasmic RNA dot-blot and a syncytium assay. HIV infection was also studied by a novel method based on electrophoresis of DNA liberated from cells that were lysed in situ in the well of an agarose gel. All human B-cell lines could be infected with HIV-1, regardless of the presence of EBV genomes; thus, EBV infection had no major effect on HIV susceptibility of B-cell lines. Integrated proviral HIV genomes could be detected by Southern blot analysis of DNA extracted from long-term, non-HIV-producing B-cell lines. This study suggests that B-lymphoid cells may serve as reservoirs for latent or persistent HIV infections in vivo, even in the absence of EBV infection.