Expression of the Opc protein correlates with invasion of epithelial and endothelial cells by Neisseria meningitidis

Whereas capsulate strains of Neisseria meningitidis are dependent on pili for adhesion to human endothelial and epithelial cells, strains which lacked assembled pili and were partially capsule-deficient adhered to and invaded human endothelial and epithelial cells if they expressed the Opc protein. Bacteria expressing low or undetectable levels of Opc protein failed to adhere to or invade eukaryotic cells. In addition, the presence of OpaAC751 protein on the surface of bacteria did not increase bacterial interactions with host cells. Association of Opc-expressing bacteria was inhibited by antibodies against Opc. Invasion was dependent on the host-cell cytoskeletal activity and was inhibited by cytochalasin D. In some cells, infected at the apical surface, bacteria emerging from basal surface were detected by electron microscopy. Opc is found in diverse meningococci and may represent a common virulence factor which facilitates adherence and invasion by these bacteria.     

MHC-linked Ir gene control of T cell responses: GAT-specific proliferating T cells and helper T cells are elicited in nonresponder mice immunized with soluble GAT

The immune response to the synthetic terpolymer GAT is controlled by MHC-linked Ir gene(s). We show in this paper that antigen-presenting cells and T cells from mice belonging to two nonresponder strains (SJL and DBA/1) can present and recognize GAT, respectively. This has been measured with a T cell proliferation assay of GAT-primed lymph node cells. In order to detect T cell proliferation among GAT-primed lymph node cells from DBA/1 mice, it is necessary to treat the cells with monoclonal anti-Lyt-2 antibodies and complement (C) before the assay. These conclusions were further verified with SJL mice, when a T cell line derived from LN cells was used. We have shown that after immunization with GAT, specific T helper cells can be generated in the lymph nodes of SJL mice but not in the lymph nodes of DBA/1 mice. Furthermore, GAT-specific T helper cells can be detected in the spleen of SJL mice after immunizations with GAT, provided these spleen cells are pretreated with monoclonal anti-Lyt-2 antibodies + C or mild irradiation. Together, these results support the general idea that nonresponsiveness can be explained by a regulatory imbalance rather than by discrete cellular "defects."     

Mixed Layer Depth Seasonality within the Coral Sea Based on Argo Data

The worldwide deployment of Argo floats has enabled much more detailed studies of global and regional seas over the last decade. Here, the seasonal variability of the mixed layer depth (MLD) within the Coral Sea was examined with CTD profiles from Argo floats. Multiple threshold values for both temperature and density have been employed to determine the most suitable threshold values for the Coral Sea. A threshold value of 0.04 kg/m³ for density and 0.2°C for temperature appear the most fitting for this region. Although MLD and isothermal layer depth (ILD) coincide quite well in most cases, the relatively common presence of temporary, non-seasonal barrier layers induces an ILD that is significantly deeper than the MLD. Consequently, an MLD estimation based on density is more appropriate. A distinct seasonality in the MLD is evident throughout the Coral Sea, but is generally more pronounced in higher southern latitudes (20–30°S). Salinity inversions are rare and mainly occur in the south-eastern Coral Sea, while barrier layers are more commonly associated with the north-eastern Coral Sea, a region characterised by high rainfall. The significance of regional currents is evident in the north-western Coral Sea, where temperature and ocean heat content is relatively low due to a northward moving boundary current. Shallow bathymetry, in turn, is linked to the absence of Argo data on the continental shelf and in the central Coral Sea.     

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Analyses of publicly available structural data reveal interesting insights into the impact of the three‐dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G‐protein‐coupled receptors, voltage‐gated ion channels, ligand‐gated ion channels, transporters, and E3 ubiquitin ligases). The Protein Data Bank (PDB) archive currently holds > 155,000 atomic‐level 3D structures of biomolecules experimentally determined using crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy. The PDB was established in 1971 as the first open‐access, digital‐data resource in biology, and is now managed by the Worldwide PDB partnership (wwPDB; wwPDB.org ). US PDB operations are the responsibility of the Research Collaboratory for Structural Bioinformatics PDB (RCSB PDB). The RCSB PDB serves millions of RCSB.org users worldwide by delivering PDB data integrated with ～40 external biodata resources, providing rich structural views of fundamental biology, biomedicine, and energy sciences. Recently published work showed that the PDB archival holdings facilitated discovery of ～90% of the 210 new drugs approved by the US Food and Drug Administration 2010–2016. We review user‐driven development of RCSB PDB services, examine growth of the PDB archive in terms of size and complexity, and present examples and opportunities for structure‐guided drug discovery for challenging targets (e.g., integral membrane proteins).     

Confidently identifying the correct K value using the ΔK method: When does K = 2?

Populations delineated based on genetic data are commonly used for wildlife conservation and management. Many studies use the program structure combined with the ΔK method to identify the most probable number of populations (K). We recently found K = 2 was identified more often when studies used ΔK compared to studies that did not. We suggested two reasons for this: hierarchical population structure leads to underestimation, or the ΔK method does not evaluate K = 1 causing an overestimation. The present contribution aims to develop a better understanding of the limits of the method using one, two and three population simulations across migration scenarios. From these simulations we identified the “best K” using model likelihood and ΔK. Our findings show that mean probability plots and ΔK are unable to resolve the correct number of populations once migration rate exceeds 0.005. We also found a strong bias towards selecting K = 2 using the ΔK method. We used these data to identify the range of values where the ΔK statistic identifies a value of K that is not well supported. Finally, using the simulations and a review of empirical data, we found that the magnitude of ΔK corresponds to the level of divergence between populations. Based on our findings, we suggest researchers should use the ΔK method cautiously; they need to report all relevant data, including the magnitude of ΔK, and an estimate of connectivity for the research community to assess whether meaningful genetic structure exists within the context of management and conservation.     

Methylation Status of Arabidopsis DNA Repair Gene Promoters During Agrobacterium Infection Reveals Epigenetic Changes in Three Generations

Agrobacterium tumefaciens is a unique pathogen with the ability to transfer a portion of its DNA, the T-DNA, to other organisms. The role of DNA repair genes in Agrobacterium transformation remains controversial. In order to understand if the host DNA repair response and dynamics was specific to bacterial factors such as Vir proteins, T-DNA, and oncogenes, we profiled the expression and promoter methylation of various DNA repair genes. These genes belonged to nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), homologous recombination (HR), and non-homologous end joining (NHEJ) pathways. We infected Arabidopsis plants with different Agrobacterium strains that lacked one or more of the above components so that the influence of the respective factors could be analysed. Our results revealed that the expression and promoter methylation of most DNA repair genes was affected by Agrobacterium, and it was specific to Vir proteins, T-DNA, oncogenes, or the mere presence of bacteria. In order to determine if Agrobacterium induced any transgenerational epigenetic effect on the DNA repair gene promoters, we studied the promoter methylation in two subsequent generations of the infected plants. Promoters of at least three genes, CEN2, RAD51, and LIG4 exhibited transgenerational memory in response to different bacterial factors. We believe that this is the first report of Agrobacterium-induced transgenerational epigenetic memory of DNA repair genes in plants. In addition, we show that Agrobacterium induces short-lived DNA strand breaks in Arabidopsis cells, irrespective of the presence or absence of virulence genes and T-DNA.

     

At Palmyra Atoll,the fish-community environmental DNA signal changes across habitats but not with tides

At Palmyra Atoll, the environmental DNA (eDNA) signal on tidal sand flats was associated with fish biomass density and captured 98%–100% of the expected species diversity there. Although eDNA spilled over across habitats, species associated with reef habitat contributed more eDNA to reef sites than to sand-flat sites, and species associated with sand-flat habitat contributed more eDNA to sand-flat sites than to reef sites. Tides did not disrupt the sand-flat habitat signal. At least 25 samples give a coverage >97.5% at this diverse, tropical, marine system.