Investigating molecular recognition and biological function at interfaces using piscidins, antimicrobial peptides from fish

We studied amidated and non-amidated piscidins 1 and 3, amphipathic cationic antimicrobial peptides from fish, to characterize functional and structural similarities and differences between these peptides and better understand the structural motifs involved in biological activity and functional diversity among amidated and non-amidated isoforms. Antimicrobial and hemolytic assays were carried out to assess their potency and toxicity, respectively. Site-specific high-resolution solid-state NMR orientational restraints were obtained from ¹⁵N-labeled amidated and non-amidated piscidins 1 and 3 in the presence of hydrated oriented lipid bilayers. Solid-state NMR and circular dichroism results indicate that the peptides are α-helical and oriented parallel to the membrane surface. This orientation was expected since peptide-lipid interactions are enhanced at the water-bilayer interface for amphipathic cationic antimicrobial peptides. ¹⁵N solid-state NMR performed on oriented samples demonstrate that piscidin experiences fast, large amplitude backbone motions around an axis parallel to the bilayer normal. Under the conditions tested here, piscidin 1 was confirmed to be more antimicrobially potent than piscidin 3 and antimicrobial activity was not affected by amidation. In light of functional and structural similarities between piscidins 1 and 3, we propose that their topology and fast dynamics are related to their mechanism of action.     

IL-10 Production Is Critical for Sustaining the Expansion of CD5+ B and NKT Cells and Restraining Autoantibody Production in Congenic Lupus-Prone Mice

The development and progression of systemic lupus erythematosus is mediated by the complex interaction of genetic and environmental factors. To decipher the genetics that contribute to pathogenesis and the production of pathogenic autoantibodies, our lab has focused on the generation of congenic lupus-prone mice derived from the New Zealand Black (NZB) strain. Previous work has shown that an NZB-derived chromosome 4 interval spanning 32 to 151 Mb led to expansion of CD5⁺ B and Natural Killer T (NKT) cells, and could suppress autoimmunity when crossed with a lupus-prone mouse strain. Subsequently, it was shown that CD5⁺ B cells but not NKT cells derived from these mice could suppress the development of pro-inflammatory T cells. In this paper, we aimed to further resolve the genetics that leads to expansion of these two innate-like populations through the creation of additional sub-congenic mice and to characterize the role of IL-10 in the suppression of autoimmunity through the generation of IL-10 knockout mice. We show that expansion of CD5⁺ B cells and NKT cells localizes to a chromosome 4 interval spanning 91 to 123 Mb, which is distinct from the region that mediates the majority of the suppressive phenotype. We also demonstrate that IL-10 is critical to restraining autoantibody production and surprisingly plays a vital role in supporting the expansion of innate-like populations.     

Ribosomal RNA sequence phylogeny is not congruent with ascospore morphology among species in Ceratocystis sensu stricto

The genus Ceratocystis sensu stricto includes important fungal pathogens of woody and herbaceous plants. This genus is distinguished from species in Ceratocystis sensu lato by the presence of Chalara anamorphs. Ascospore shape has been used extensively in delineating Ceratocystis taxa, which show a large variety of ascospore shapes. Sequence analysis of one region of he 18S ribosomal RNA subunit and two regions of the 28S ribosomal RNA subunit showed that there was a majority of multiple substitutions at nucleotide sites and that there was a low transition/transversion ratio, T = 0.72. Both of these results suggest that these are well established, old species. Ascospore morphology, for the most part, was not congruent with the molecular phylogeny, and the use of morphological characters may be misleading in the taxonomy of these species.      

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database

The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible resources and maintenance of a local database. The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results. The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page.     

Nuclear staining with alum hematoxylin

The hematoxylin and eosin stain is the most common method used in anatomic pathology, yet it is a method about which technologists ask numerous questions. Hematoxylin is a natural dye obtained from a tree originally found in Central America, and is easily converted into the dye hematein. This dye forms coordination compounds with mordant metals, such as aluminum, and the resulting lake attaches to cell nuclei. Regressive formulations contain a higher concentration of dye than progressive formulations and may also contain a lower concentration of mordant. The presence of an acid increases the life of the solution and in progressive solutions may also affect selectivity of staining. An appendix lists more than 60 hemalum formulations and the ratio of dye to mordant for each.     

Itch WW Domains Inhibit Its E3 Ubiquitin Ligase Activity by Blocking E2-E3 Ligase Trans-thiolation

Nedd4-family E3 ubiquitin ligases regulate an array of biologic processes. Autoinhibition maintains these catalytic ligases in an inactive state through several mechanisms. However, although some Nedd4 family members are activated by binding to Nedd4 family-interacting proteins (Ndfips), how binding activates E3 function remains unclear. Our data reveal how these two regulatory processes are linked functionally. In the absence of Ndfip1, the Nedd4 family member Itch can bind an E2 but cannot accept ubiquitin onto its catalytic cysteine. This is because Itch is autoinhibited by an intramolecular interaction between its HECT (homologous to the E6-AP carboxy terminus domain) and two central WW domains. Ndfip1 binds these WW domains to release the HECT, allowing trans-thiolation and Itch catalytic activity. This molecular switch also regulates the closely related family member WWP2. Importantly, multiple PY motifs are required for Ndfip1 to activate Itch, functionally distinguishing Ndfips from single PY-containing substrates. These data establish a novel mechanism for control of the function of a subfamily of Nedd4 E3 ligases at the level of E2-E3 trans-thiolation.     

低温对植物叶片中超氧物歧化酶、过氧化氢酶和过氧化氢水平的影响

番茄和鸡蛋果叶片中可提取的SOD活性不受低温的影响。在电泳谱带上SOD主同工酶带被氰化物而不被低温抑制,次同工酶带在低温下不稳定,且活性很低,它的变化不影响总的SOD活性。一些冷敏感植物叶片中CAT活性被低温抑制,而H_2O_3水平在低温下稳定或有增加,这可能使毒性更强的羟基离子(OH·)易于形成。     

Quantification of total iodine in intact granular starches of different botanical origin exposed to iodine vapor at various water activities

Iodine has been used as an effective tool for studying both the structure and composition of dispersed starch and starch granules. In addition to being employed to assess relative amylose contents for starch samples, it has been used to look at the molecular mobility of the glucose polymers within intact starch granules based on exposure to iodine vapor equilibrated at different water activities. Starches of different botanical origin including corn, high amylose corn, waxy corn, potato, waxy potato, tapioca, wheat, rice, waxy rice, chick pea and mung bean were equilibrated to 0.33, 0.75, 0.97 water activities, exposed to iodine vapor and then absorbance spectra and LAB color were determined. In addition, a new iodine quantification method sensitive to <0.1% iodine (w/w) was employed to measure bound iodine within intact granular starch. Amylose content, particle size distribution of granules, and the density of the starch were also determined to explore whether high levels of long linear glucose chains and the surface area-to-volume ratio were important factors relating to the granular iodine binding. Results showed, in all cases, starches complexed more iodine as water content increased and waxy starches bound less iodine than their normal starch counterparts. However, much more bound iodine could be measured chemically with waxy starches than was expected based on colorimetric determination. Surface area appeared to be a factor as smaller rice and waxy rice starch granules complexed more iodine, while the larger potato and waxy potato granules complexed less than would be expected based on measured amylose contents. Corn, high amylose corn, and wheat, known to have starch granules with extensive surface pores, bound higher levels of iodine suggesting pores and channels may be an important factor giving iodine vapor greater access to bind within the granules. Exposing iodine vapor to moisture-equilibrated native starches is an effective tool to explore starch granule architecture.     

Improving biodiversity surrogates for conservation assessment: A test of methods and the value of targeted biological surveys

Aim

Conservation assessment and planning across extensive regions rely on the use of mapped or modelled surrogates because direct field‐based inventories of biodiversity rarely provide complete spatial coverage. Surrogates are assumed to represent spatial patterns in the distribution of biodiversity, yet the validity of this assumption is rarely evaluated. Here, we use data from new biological surveys targeting poorly known taxonomic groups across sparsely surveyed landscapes to test: (1) the performance of established and novel surrogates; and (2) the value of targeted survey data in further improving surrogate effectiveness.

Location

Continental Australia.

Methods

Surrogates were derived from either mapped land classifications (bioregions, vegetation types), or models of spatial turnover in biodiversity composition. Models were derived by linking best‐available biological observations to high‐resolution mapped climate, terrain and soil attributes using generalized dissimilarity modelling (GDM). The performance of surrogates was evaluated using survey data for eight biological groups collected as part of the Bush Blitz programme ( http://bushblitz.org ). For the GDM‐based surrogates, within‐ and cross‐taxon performance was first evaluated for models fitted to biological data available prior to Bush Blitz, and then for models enhanced through the addition of the Bush Blitz data.

Results

All of the tested surrogates performed significantly better than random across all eight biological groups. GDM‐based surrogates performed over 10% better on average than the best performing combination of mapped land classifications. The addition of Bush Blitz targeted data in GDM‐based surrogates led to further improvements in surrogate performance.

Main conclusions

Our results support continued investment in targeted biological survey programmes to enhance the performance of surrogates and ensure that surrogates represent a wider breadth of biodiversity. The strong performance of compositional turnover modelling, relative to mapped land classifications, suggests that this surrogate strategy deserves greater consideration in future conservation assessments and has potential for use in continental‐scale monitoring of biodiversity.

     

Comparisons of CD8+ T Cells Specific for Human Immunodeficiency Virus,Hepatitis C Virus,and Cytomegalovirus Reveal Differences in Frequency,Immunodominance, Phenotype,and Interleukin-2 Responsiveness

To better understand the components of an effective immune response to human immunodeficiency virus (HIV), the CD8⁺ T-cell responses to HIV, hepatitis C virus (HCV), and cytomegalovirus (CMV) were compared with regard to frequency, immunodominance, phenotype, and interleukin-2 (IL-2) responsiveness. Responses were examined in rare patients exhibiting durable immune-mediated control over HIV, termed long-term nonprogressors (LTNP) or elite controllers, and patients with progressive HIV infection (progressors). The magnitude of the virus-specific CD8⁺ T-cell response targeting HIV, CMV, and HCV was not significantly different between LTNP and progressors, even though their capacity to proliferate to HIV antigens was preserved only in LTNP. In contrast to HIV-specific CD8⁺ T-cell responses of LTNP, HLA B5701-restricted responses within CMV pp65 were rare and did not dominate the total CMV-specific response. Virus-specific CD8⁺ T cells were predominantly CD27⁺45RO⁺ for HIV and CD27⁻45RA⁺ for CMV; however, these phenotypes were highly variable and heavily influenced by the degree of viremia. Although IL-2 induced significant expansions of CMV-specific CD8⁺ T cells in LTNP and progressors by increasing both the numbers of cells entering the proliferating pool and the number of divisions, the proliferative capacity of a significant proportion of HIV-specific CD8⁺ T cells was not restored with exogenous IL-2. These results suggest that immunodominance by HLA B5701-restricted cells is specific to HIV infection in LTNP and is not a feature of responses to other chronic viral infections. They also suggest that poor responsiveness to IL-2 is a property of HIV-specific CD8⁺ T cells of progressors that is not shared with responses to other viruses over which immunologic control is maintained.Gaining a better understanding of the immunologic control of human immunodeficiency virus type 1 (HIV-1) is among the most critical goals for the rational design of HIV vaccines and immunotherapies. Although most HIV-infected patients develop high-level viremia, CD4⁺ T-cell depletion, and progressive disease, a rare subgroup of patients variably termed long-term nonprogressors (LTNP) or elite controllers restrict HIV replication to below 50 copies of HIV RNA/ml plasma and remain disease free for up to 25 years without antiretroviral therapy (ART). Measurements of HIV-specific immune responses in these patients, in comparison with progressors, are providing insights into mechanisms that mediate immunologic control or loss of control in humans. Although the mechanisms of restriction of HIV replication remain incompletely understood, a number of lines of evidence suggest that it is mediated by HIV-specific CD8⁺ T cells (reviewed in reference 51). High frequencies of HIV-specific CD8⁺ T cells specific for the autologous virus are observed in both LTNP and untreated progressors, suggesting that differences in immunologic control are mediated not by quantitative but more likely by qualitative features of the immune response.A number of qualitative features of the HIV-specific CD8⁺ T-cell response of LTNP or progressors have recently been proposed as the cause of immunologic control or loss of control, respectively. HLA B*5701 is highly overrepresented in LTNP, and the HIV-specific CD8⁺ T-cell response is highly focused on B5701-restricted peptides in B*5701⁺ LTNP but not in B*5701⁺ progressors (19, 50). In addition, there is a difference in surface markers between HIV- and cytomegalovirus (CMV)-specific CD8⁺ T cells thought to represent differences in maturation of the T-cell response (8). The CD8⁺ T cells of progressors are diminished in proliferative capacity and perforin upregulation in response to autologous HIV-infected CD4⁺ T cells (49). Recently, it has been proposed that this diminished proliferative capacity is due to a lack of paracrine or autocrine interleukin-2 (IL-2) production by HIV-specific CD4⁺ T cells or CD8⁺ T cells (41, 42, 75). Interpretation of proliferation studies is complicated by the fact that the effects of IL-2 were measured on the basis of 5,6-carboxyfluorescein diacetate succinimidyl ester (CFSE) dye dilution of major histocompatibility complex (MHC) tetramer-positive cells. Because cell division over 6 days is an exponential function, IL-2 may induce small increases in the percentage of cells dividing or in the number of cell divisions that can result in large changes in the percent CFSE^lo cells, and yet the majority of antigen-specific cells may not proceed through the cell cycle. In addition, there are very limited data regarding whether the features of immunodominance, surface phenotype, and IL-2 responsiveness of HIV-specific CD8⁺ T cells extend to other chronic virus infections.In the present study, we examined these qualitative features within the response to HIV, CMV, or hepatitis C virus (HCV) across patient groups. We observed that the high degree of focus upon B5701-restricted peptides found in LTNP does not extend to the HCV- or CMV-specific responses. The phenotype of HIV- or CMV-specific CD8⁺ T cells was highly variable and heavily influenced by the degree of viremia. In addition, when both the number of divisions and the percentage of cells dividing were analyzed, proliferation of HIV-specific CD8⁺ T cells was refractory to IL-2 stimulation, unlike that of CMV-specific cells. These results offer important insights into qualitative features of the HIV-specific CD8⁺ T-cell response, whether they extend to responses to other viruses, and whether they are associated with the presence or absence of immunologic control.