Assemblage structure,vertical distributions and stable-isotope compositions of anguilliform leptocephali in the Gulf of Mexico

In August 2007, October 2008 and September–October 2010, 241 Tucker trawl and plankton net tows were conducted at the surface to depths of 1377 m at six locations in the northern and eastern Gulf of Mexico (GOM) to document leptocephalus diversity and determine how assemblage structure, larval size, abundance and isotopic signatures differ across the region and with depth. Overall, 2696 leptocephali representing 59 distinct taxa from 10 families were collected. Five families accounted for 96% of the total catch with Congridae and Ophichthidae being the most abundant. The top four most abundant species composed 59% of the total catch and included: Ariosoma balearicum, Paraconger caudilimbatus, Rhynchoconger flavus and Ophichthus gomesii. Four anguilliform species not previously documented in the GOM as adults or leptocephali were collected in this study, including Monopenchelys acuta, Quassiremus ascensionis, Saurenchelys stylura and one leptocephalus only known from its larval stage, Leptocephalus proboscideus. Leptocephalus catches were significantly greater at night than during the day. Catches at night were concentrated in the upper 200 m of the water column and significantly declined with increasing depth. Leptocephali abundances and assemblages were significantly different between sites on the upper continental slope (c. 500 m depth) and sites on the middle to lower continental slope (c. 1500–2300 m). Sites on the lower continental slope had a mixture of deep-sea demersal, bathypelagic and coastal species, whereas upper-slope sites contained several numerically dominant species (e.g., A. balearicum, P. caudilimbatus) that probably spawn over the continental shelf and upper slope of the GOM. Standard lengths of the four dominant species differed between sites and years, indicating heterochronic reproduction and potential larval source pools within and outside of the GOM. Stable-isotope analyses (δ¹³C and δ¹⁵N) conducted on 185 specimens from six families revealed that leptocephali had a wide range of isotopic values at the family and size-class levels. Species in the families Muraenidae, Congridae and Ophichthidae had similar δ¹⁵N values compared with the broad range of δ¹⁵N values seen in the deep-sea families Nemichthyidae, Nettastomatidae and Synaphobranchidae. Stable-isotope values were variably related to length, with δ¹⁵N values being positively size correlated in ophichthids and δ¹³C values being negatively size correlated in A. balearicum and P. caudilimbatus. Results suggest that leptocephali feed in various water depths and masses, and on different components of POM, which could lead to niche partitioning. Ecological aspects of these important members of the plankton community provide insight into larval connectivity in the GOM as well as the early life history of Anguilliformes.     

Localized structural effects of electrostatic interactions in a thermostable enzyme

The sequence and resolved structure of thermotrophic isopropylmalate dehydrogenase (IPMDH) and a related protein, mesotrophic isocitrate dehydrogenase (IDH), were compared emphasizing clusters of charged residues identified from X-ray crystallographic studies (Wallon, G., Kryger, G., Lovett, S. T., Oshima, T., Ringe, D., and Petsko, G. A. (1997) J. Mol. Biol. 266, 1016-1031). Mesotrophic isocitrate dehydrogenase was used for comparison because crystallographic data for a mesotrophic form of IPMDH was not available in the database. The structural features in the region of these clusters were compared and localized conformational differences were found in the thermotroph compared to the mesotroph. Because the overall topology of the two proteins is similar, it was concluded that these localized structural differences induced by electrostatic interactions between charged residues in the thermotrophic enzyme were responsible for the enhanced thermal stability of proteins from thermotroph.     

Fast Waves at the Base of the Cochlea

Georg von Békésy observed that the onset times of responses to brief-duration stimuli vary as a function of distance from the stapes, with basal regions starting to move earlier than apical ones. He noticed that the speed of signal propagation along the cochlea is slow when compared with the speed of sound in water. Fast traveling waves have been recorded in the cochlea, but their existence is interpreted as the result of an experiment artifact. Accounts of the timing of vibration onsets at the base of the cochlea generally agree with Békésy’s results. Some authors, however, have argued that the measured delays are too short for consistency with Békésy’s theory. To investigate the speed of the traveling wave at the base of the cochlea, we analyzed basilar membrane (BM) responses to clicks recorded at several locations in the base of the chinchilla cochlea. The initial component of the BM response matches remarkably well the initial component of the stapes response, after a 4-μs delay of the latter. A similar conclusion is reached by analyzing onset times of time-domain gain functions, which correspond to BM click responses normalized by middle-ear input. Our results suggest that BM responses to clicks arise from a combination of fast and slow traveling waves.     

Mapping of citrullinated fibrinogen B-cell epitopes in rheumatoid arthritis by imaging surface plasmon resonance

Introduction  

Rheumatoid arthritis (RA) frequently involves the loss of tolerance to citrullinated antigens, which may play a role in pathogenicity. Citrullinated fibrinogen is commonly found in inflamed synovial tissue and is a frequent target of autoantibodies in RA patients. To obtain insight into the B-cell response to citrullinated fibrinogen in RA, its autoepitopes were systematically mapped using a new methodology.     

Aerenchyma development and elevated alcohol dehydrogenase activity as alternative responses to hypoxic soils in the Piriqueta caroliniana complex

The ability of plants to make morphological or physiological adjustments in response to environmental cues allows them to survive and reproduce under a wide range of conditions. One stress that plants are often exposed to is soil oxygen depletion due to flooding. Plants can respond to hypoxic soils by producing oxygen-conducting aerenchymous tissue or through induction of enzymes in the ethanolic fermentation pathway. Here we use greenhouse experiments to examine flood responses in plants of the Piriqueta caroliniana (Turneraceae) complex, which occupy a range of moisture regimes. Morphotypes and hybrids in this complex exhibited contrasting responses to hypoxic conditions. Genotypes from flooded habitats developed aerenchyma and did not substantially elevate levels of alcohol dehydrogenase (ADH) activity, an enzyme associated with anaerobic respiration. Plants from drier sites, on the other hand, did not develop aerenchyma but had much higher levels of ADH activity. Plants with aerenchymous tissue had substantially higher rates of growth under sustained flooding. Results are consistent with the hypothesis that aerenchyma development is an effective strategy in habitats subject to persistent flooding, while elevating activity of enzymes for ethanolic fermentation is effective only under ephemeral flooding. The range of phenotypic responses observed illustrates contrasting adaptive strategies that can lead to habitat isolation and evolutionary divergence.     

Turbo-mixing in microplates

How to effectively mix small volumes of liquids within microplate wells is a still underestimated and often neglected challenge. The method the authors introduce here relies on violent turbulent motion within a liquid caused by spotting an organic solvent drop onto its surface. The amount needed, less than 1 to 3 microL, is generally small enough not to alter bioactive molecules. Moreover, a solvent may be selected for its compatibility with assay components. The method was tested with layers of aqueous liquids that differ in pH and concentration of a pH-dependent dye, allowing mixing to be monitored optically. Rapid mixing was caused by spotting drops of alcohols, acetone, acetonitrile, and aqueous solutions of these, as long as the difference of surface tension between the drop and the uppermost layer of the bulk liquid surpassed 30 dynes/cm. Along with this difference, position and velocity of spotting, as well as viscosity and geometry of the bulk liquid volume, may influence the turbulence evoked. No significant difference was found for the activity of aspartate aminotransferase, alanine aminotransferase, and alkaline phosphatase when measured after mixing by shaking and after mixing by spotting 1 microL of methanol onto assays within 96-well microplates.     

Association of 25-Hydroxyvitamin D status and genetic variation in the vitamin D metabolic pathway with FEV1 in the Framingham Heart Study

Background

Vitamin D is associated with lung function in cross-sectional studies, and vitamin D inadequacy is hypothesized to play a role in the pathogenesis of chronic obstructive pulmonary disease. Further data are needed to clarify the relation between vitamin D status, genetic variation in vitamin D metabolic genes, and cross-sectional and longitudinal changes in lung function in healthy adults.

Methods

We estimated the association between serum 25-hydroxyvitamin D [25(OH)D] and cross-sectional forced expiratory volume in the first second (FEV₁) in Framingham Heart Study (FHS) Offspring and Third Generation participants and the association between serum 25(OH)D and longitudinal change in FEV₁ in Third Generation participants using linear mixed-effects models. Using a gene-based approach, we investigated the association between 241 SNPs in 6 select vitamin D metabolic genes in relation to longitudinal change in FEV₁ in Offspring participants and pursued replication of these findings in a meta-analyzed set of 4 independent cohorts.

Results

We found a positive cross-sectional association between 25(OH)D and FEV₁ in FHS Offspring and Third Generation participants (P = 0.004). There was little or no association between 25(OH)D and longitudinal change in FEV₁ in Third Generation participants (P = 0.97). In Offspring participants, the CYP2R1 gene, hypothesized to influence usual serum 25(OH)D status, was associated with longitudinal change in FEV₁ (gene-based P < 0.05). The most significantly associated SNP from CYP2R1 had a consistent direction of association with FEV₁ in the meta-analyzed set of replication cohorts, but the association did not reach statistical significance thresholds (P = 0.09).

Conclusions

Serum 25(OH)D status was associated with cross-sectional FEV₁, but not longitudinal change in FEV₁. The inconsistent associations may be driven by differences in the groups studied. CYP2R1 demonstrated a gene-based association with longitudinal change in FEV₁ and is a promising candidate gene for further studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0238-y) contains supplementary material, which is available to authorized users.     

青藏高原边缘地区史前遗址2009年调查试掘报告

2009年6月—7月,在青藏高原边缘地区调查、试掘了6处遗址,获得一批石制品、动物骨骼残片、火塘等材料。石制品多数个体较小,类型包括石核、石片、工具、断块、细石核、细石叶等。通过对比出土材料及部分遗址测年数据判断,6处遗址的年代处于13ka BP左右的晚更新世至全新世。此次调查试掘,丰富了该区域人类活动的证据,对研究青藏高原环境变化、古人类的适应生存过程及技术交流有一定意义。     

IL-15:IL-15 receptor alpha superagonist complex: high-level co-expression in recombinant mammalian cells, purification and characterization

IL-15, a promising cytokine for treating cancer and viral diseases, is presented in trans by the IL-15 receptor (IL-15R) alpha-chain to the IL-15Rβγc complex displayed on the surface of T cells and natural killer (NK) cells. We previously reported that an asparagine to aspartic acid substitution at amino acid 72 (N72D) of IL-15 provides a 4-5-fold increase in biological activity compared to the native molecule. In this report, we describe Chinese hamster ovary (CHO) cell expression of a soluble complex (IL-15 N72D:IL-15RαSu/Fc) consisting of the IL-15 N72D superagonist and a dimeric IL-15Rα sushi domain-IgG1 Fc fusion protein. A simple but readily scalable affinity and ion exchange chromatography method was developed to highly purify the complex having both IL-15 binding sites fully occupied. The immunostimulatory effects of this complex were confirmed using cell proliferation assays. Treatment of mice with a single intravenous dose of IL-15N72D:IL-15RαSu/Fc resulted in a significant increase in CD8+ T cells and NK cells that was not observed following IL-15 treatment. Pharmacokinetic analysis indicated that the complex has a 25-h half-life in mice which is considerably longer than <40-min half-life of IL-15. Thus, the enhanced activity of the IL-15N72D:IL-15RαSu/Fc complex is likely the result of the increased binding activity of IL-15N72D to IL-15Rβγc, optimized cytokine trans-presentation by the IL-15RαSu domain, the dimeric nature of the cytokine domain and its increased in vivo half-life compared to IL-15. These findings indicate that this IL-15 superagonist complex could serve as a superior immunostimulatory therapeutic agent.     

Visualization of p53(264-272)/HLA-A*0201 complexes naturally presented on tumor cell surface by a multimeric soluble single-chain T cell receptor

Intracellular Ags are processed into small peptides that are presented on cell surfaces in the context of HLA class I molecules. These peptides are recognized by TCRs displayed by CD8+ T lymphocytes (T cells). To date, direct identification and quantitation of these peptides has relied primarily on mass spectrometry analysis, which is expensive and requires large quantities of diseased tissues to obtain useful results. Here we demonstrate that multimerization of a soluble single-chain TCR (scTCR), recognizing a peptide from p53 presented in the context of HLA-A2.1, could be used to directly visualize and quantitate peptide/MHC complexes on unmanipulated human tumor cells. Tumor cells displaying as few as 500 peptide/MHC complexes were readily detectable by flow cytometry. The scTCR/multimers exhibited exquisite recognition capability and could distinguish peptides differing in as little as a single amino acid. We also demonstrate that scTCR/multimers could specifically stain human tumors generated in mice, as well as tumors obtained from patient biopsies. Thus, scTCR/multimers represent a novel class of immunostaining reagents that could be used to validate, quantitate, or monitor epitope presentation by cancer cells.