Evidence of dietary feedback in a facultative association between deep-sea gastropods and sea anemones

While epibiotic associations between macrobenthic invertebrates are common, the role they play in the feeding ecology of intervening species is often incompletely understood. The diets of epibiotic sea anemones Allantactis parasitica and their gastropod hosts were analyzed using digestive tract contents, lipid biomarkers and observations of live specimens in an attempt to detect dietary feedback from the facultative association. Comparisons were made using symbiotic individuals and asymbiotic counterparts collected at depths of 191-627 m from three neighbouring areas in the northwest Atlantic. Gastropods carrying one or two epibionts had higher stomach indices than those harbouring three epibionts or no epibiont. The diet of symbiotic gastropods was also more diversified based on stomach contents and lipid analysis. Among other things, symbiotic gastropods contained four times more lipids and a greater proportion of Σn−3 fatty acids. Gastrovascular cavity content indices of asymbiotic sea anemones were generally lower than those of symbiotic counterparts. Their cavities were more often empty, and their diet less diversified with fewer benthic items, suggesting that foraging of gastropods through the sediments makes more food available to sea anemones living as epibionts. Lipid analysis showed some disparities between symbiotic and asymbiotic sea anemones at the regional scale, including in percent phospholipids and in the proportion of certain fatty acids. Together these findings indicate that mutual protection against predators leads to prolonged and more efficient foraging for gastropods and increased time spent deployed (feeding) in food-rich areas for sea anemones, thus enabling both partners to fully exploit food resources that may be limited at bathyal depths.     

Quantitative variability of 342 plasma proteins in a human twin population

The degree and the origins of quantitative variability of most human plasma proteins are largely unknown. Because the twin study design provides a natural opportunity to estimate the relative contribution of heritability and environment to different traits in human population, we applied here the highly accurate and reproducible SWATH mass spectrometry technique to quantify 1,904 peptides defining 342 unique plasma proteins in 232 plasma samples collected longitudinally from pairs of monozygotic and dizygotic twins at intervals of 2–7 years, and proportioned the observed total quantitative variability to its root causes, genes, and environmental and longitudinal factors. The data indicate that different proteins show vastly different patterns of abundance variability among humans and that genetic control and longitudinal variation affect protein levels and biological processes to different degrees. The data further strongly suggest that the plasma concentrations of clinical biomarkers need to be calibrated against genetic and temporal factors. Moreover, we identified 13 cis‐SNPs significantly influencing the level of specific plasma proteins. These results therefore have immediate implications for the effective design of blood‐based biomarker studies.     

Structural and functional analysis of the GABARAP interaction motif (GIM)

Through the canonical LC3 interaction motif (LIR), [W/F/Y]‐X₁‐X₂‐[I/L/V], protein complexes are recruited to autophagosomes to perform their functions as either autophagy adaptors or receptors. How these adaptors/receptors selectively interact with either LC3 or GABARAP families remains unclear. Herein, we determine the range of selectivity of 30 known core LIR motifs towards individual LC3s and GABARAPs. From these, we define a I nteraction 相似文献   

Fluorescent and radioactive solid phase dideoxy sequencing of pcr products in microtitre plates.

In this paper we describe a rapid method for the direct generation of DNA sequencing templates from phage or bacteria. Sequencing of these PCR products can be performed by radioactive and fluorescent methods. The non-radioactive method has been used to sequence a total of approximately 100 kb of human DNA fragments generated by digestion with HpaII and subsequent cloning. The method depends on direct small scale amplification using a biotinylated primer, and the binding of the product to streptavidin coated magnetic beads. All the procedures are carried out in a microtitre plate thus facilitating the handling of large numbers of clones and has potential for automation.     

Purification and some properties of Escherichia coli tRNA nucleotidyltransferase.

Adenylyl (cytidylyl)-tRNA nucleotidyltransferase (ATP (CTP): tRNA adenylyl (cytidylyl)transferase, EC2.7.7.25) has been purified 11,800-fold from a crude extract of Escherichia coli B in an overall yield of 23%. The key step in this purification is the use of a tRNA-Sepharose affinity column. The purified enzyme has a specific activity of approximately 280 mumol of AMP incorporated/min/mg of protein at 37 degrees and has a molecular weight of 52,000 as determined by sodium dodecyl sulfate gel electrophoresis of Sephadex chromatography. The turnover number of the pure enzyme, under optimal assay conditions, is estimated as 21,000, and we believe it constitutes only o.oo6% of the total cellular protein. Both AMP- and CMP-incorporating activities have an identical isoelectric point of 5.85. The AMP-incorporating activity of the enzyme is inhibitied by some transition metal chelating agents but not by others.     

The inhibitor thiomandelic acid binds to both metal ions in metallo-beta-lactamase and induces positive cooperativity in metal binding

Thiomandelic acid is a simple, broad spectrum, and reasonably potent inhibitor of metallo-beta-lactamases, enzymes that mediate resistance to beta-lactam antibiotics. We report studies by NMR and perturbed angular correlation (PAC) spectroscopy of the mode of binding of the R and S enantiomers of thiomandelic acid, focusing on their interaction with the two metal ions in cadmium-substituted Bacillus cereus metallo-beta-lactamase. The 113Cd resonances are specifically assigned to the metals in the two individual sites on the protein by using 113Cd-edited 1H NMR spectra. Each enantiomer of thiomandelate produces large downfield shifts of both 113Cd resonances and changes in the PAC spectra, which indicate that they bind such that the thiol of the inhibitor bridges between the two metals. For R-thiomandelate, this is unambiguously confirmed by the observation of scalar coupling between Halpha of the inhibitor and both cadmium ions. The NMR and PAC spectra reveal that the two chiral forms of the inhibitor differ in the details of their coordination geometry. The complex with R-thiomandelate, but not that with the S-enantiomer, shows evidence in the PAC spectra of a dynamic process in the nanosecond time regime, the possible nature of which is discussed. The thiomandelate complex of the mononuclear enzyme can be detected only at low metal to enzyme stoichiometry; the relative populations of mononuclear and binuclear enzyme as a function of cadmium concentration provide clear evidence for positive cooperativity in metal ion binding in the presence of the inhibitor, in contrast to the negative cooperativity observed in the free enzyme.     

Requirement for Phe36 for DNA binding and mismatch repair by Escherichia coli MutS protein

The MutS family of DNA repair proteins recognizes base pair mismatches and insertion/deletion mismatches and targets them for repair in a strand-specific manner. Photocrosslinking and mutational studies previously identified a highly conserved Phe residue at the N-terminus of Thermus aquaticus MutS protein that is critical for mismatch recognition in vitro. Here, a mutant Escherichia coli MutS protein harboring a substitution of Ala for the corresponding Phe36 residue is assessed for proficiency in mismatch repair in vivo and DNA binding and ATP hydrolysis in vitro. The F36A protein is unable to restore mismatch repair proficiency to a mutS strain as judged by mutation to rifampicin or reversion of a specific point mutation in lacZ. The F36A protein is also severely deficient for binding to heteroduplexes containing an unpaired thymidine or a G:T mismatch although its intrinsic ATPase activity and subunit oligomerization are very similar to that of the wild-type MutS protein. Thus, the F36A mutation appears to confer a defect specific for recognition of insertion/deletion and base pair mismatches.     

Quirks of dye nomenclature. 5. Rhodamines

Rhodamines were first produced in the late 19^th century, when they constituted a new class of synthetic dyes. These compounds since have been used to color many things including cosmetics, inks, textiles, and in some countries, food products. Certain rhodamine dyes also have been used to stain biological specimens and currently are widely used as fluorescent probes for mitochondria in living cells. The early history and current biological applications are sketched briefly and an account of the ambiguities, complications and confusions concerning dye identification and nomenclature are discussed.