The impact of reduced pH on the microbial community of the coral Acropora eurystoma

Rising concentrations of atmospheric carbon dioxide are acidifying the world''s oceans. Surface seawater pH is 0.1 units lower than pre-industrial values and is predicted to decrease by up to 0.4 units by the end of the century. This change in pH may result in changes in the physiology of ocean organisms, in particular, organisms that build their skeletons/shells from calcium carbonate, such as corals. This physiological change may also affect other members of the coral holobiont, for example, the microbial communities associated with the coral, which in turn may affect the coral physiology and health. In the present study, we examined changes in bacterial communities in the coral mucus, tissue and skeleton following exposure of the coral Acropora eurystoma to two different pH conditions: 7.3 and 8.2 (ambient seawater). The microbial community was different at the two pH values, as determined by denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis. Further analysis of the community in the corals maintained at the lower pH revealed an increase in bacteria associated with diseased and stressed corals, such as Vibrionaceae and Alteromonadaceae. In addition, an increase in the number of potential antibacterial activity was recorded among the bacteria isolated from the coral maintained at pH 7.3. Taken together, our findings highlight the impact that changes in the pH may have on the coral-associated bacterial community and their potential contribution to the coral host.     

Dynamics alignment: comparison of protein dynamics in the SCOP database

A novel methodology for comparison of protein dynamics is presented. Protein dynamics is calculated using the Gaussian network model and the modes of motion are globally aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. The alignment is fast and can be used to analyze large sets of proteins. The methodology is applied to the four major classes of the SCOP database: "all alpha proteins," "all beta proteins," "alpha and beta proteins," and "alpha/beta proteins". We show that different domains may have similar global dynamics. In addition, we report that the dynamics of "all alpha proteins" domains are less specific to structural variations within a given fold or superfamily compared with the other classes. We report that domain pairs with the most similar and the least similar global dynamics tend to be of similar length. The significance of the methodology is that it suggests a new and efficient way of mapping between the global structural features of protein families/subfamilies and their encoded dynamics.     

Multiple Gaussian network modes alignment reveals dynamically variable regions: The hemoglobin case

Gaussian network model (GNM) modes of motion are calculated to a dataset of h emoglobin (Hb) structures and modes with dynamics similarity to the T state are multiply aligned. The sole criterion for the alignment is the mode shape itself and not sequence or structural similarity. Standard deviation (SD) of the GNM value score along the alignment is calculated, regions with high SD are defined as dynamically variable. The analysis shows that the α1β1/α2β2 interface is a dynamically variable region but not the α1β2/α2β1 and the α1α2/β1β2 interfaces. The results are in accordance with the T → R2 transition of Hb. We suggest that dynamically variable regions are regions that are likely to undergo structural change in the protein upon binding, conformational transition, or any other relevant chemical event. The represented technique of multiple dynamics ‐ based alignment of modes is novel and may offer a new insight in proteins ' dynamics to function relation. Proteins 2014; 82:2097–2105. © 2014 Wiley Periodicals, Inc.     

Order parameters of unsaturated phospholipids in membranes and the effect of cholesterol: a 1H–13C solid-state NMR study at natural abundance

Most biological phospholipids contain at least one unsaturated alkyl chain. However, few order parameters of unsaturated lipids have been determined because of the difficulty associated with isotopic labeling of a double bond. Dipolar recoupling on axis with scaling and shape preservation (DROSS) is a solid-state nuclear magnetic resonance technique optimized for measuring ¹H–¹³C dipolar couplings and order parameters in lipid membranes in the fluid phase. It has been used to determine the order profile of 1,2-dimyristoyl-sn-glycero-3-phosphocholine hydrated membranes. Here, we show an application for the measurement of local order parameters in multilamellar vesicles containing unsaturated lipids. Taking advantage of the very good ¹³C chemical shift dispersion, one can easily follow the segmental order along the acyl chains and, particularly, around the double bonds where we have been able to determine the previously misassigned order parameters of each acyl chain of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We have followed the variation of such order profiles with temperature, unsaturation content and cholesterol addition. We have found that the phase formed by DOPC with 30% cholesterol is analogous to the liquid-ordered (l_o) phase. Because these experiments do not require isotopic enrichment, this technique can, in principle, be applied to natural lipids and biomembranes.Electronic Supplementary Material Supplementary material is available for this article at .     

Atrophic thyroid follicles and inner ear defects reminiscent of cochlear hypothyroidism in Slc26a4-related deafness

Thyroid hormone is essential for inner ear development and is required for auditory system maturation. Human mutations in SLC26A4 lead to a syndromic form of deafness with enlargement of the thyroid gland (Pendred syndrome) and non-syndromic deafness (DFNB4). We describe mice with an Slc26a4 mutation, Slc26a4 ^loop/loop , which are profoundly deaf but show a normal sized thyroid gland, mimicking non-syndromic clinical signs. Histological analysis of the thyroid gland revealed defective morphology, with a majority of atrophic microfollicles, while measurable thyroid hormone in blood serum was within the normal range. Characterization of the inner ear showed a spectrum of morphological and molecular defects consistent with inner ear pathology, as seen in hypothyroidism or disrupted thyroid hormone action. The pathological inner ear hallmarks included thicker tectorial membrane with reduced β-tectorin protein expression, the absence of BK channel expression of inner hair cells, and reduced inner ear bone calcification. Our study demonstrates that deafness in Slc26a4 ^loop/loop mice correlates with thyroid pathology, postulating that sub-clinical thyroid morphological defects may be present in some DFNB4 individuals with a normal sized thyroid gland. We propose that insufficient availability of thyroid hormone during inner ear development plays an important role in the mechanism underlying deafness as a result of SLC26A4 mutations.     

The olfactory receptor gene superfamily: data mining, classification, and nomenclature

The vertebrate olfactory receptor (OR) subgenome harbors the largest known gene family, which has been expanded by the need to provide recognition capacity for millions of potential odorants. We implemented an automated procedure to identify all OR coding regions from published sequences. This led us to the identification of 831 OR coding regions (including pseudogenes) from 24 vertebrate species. The resulting dataset was subjected to neighbor-joining phylogenetic analysis and classified into 32 distinct families, 14 of which include only genes from tetrapodan species (Class II ORs). We also report here the first identification of OR sequences from a marsupial (koala) and a monotreme (platypus). Analysis of these OR sequences suggests that the ancestral mammal had a small OR repertoire, which expanded independently in all three mammalian subclasses. Classification of ``fish-like' (Class I) ORs indicates that some of these ancient ORs were maintained and even expanded in mammals. A nomenclature system for the OR gene superfamily is proposed, based on a divergence evolutionary model. The nomenclature consists of the root symbol `OR', followed by a family numeral, subfamily letter(s), and a numeral representing the individual gene within the subfamily. For example, OR3A1 is an OR gene of family 3, subfamily A, and OR7E12P is an OR pseudogene of family 7, subfamily E. The symbol is to be preceded by a species indicator. We have assigned the proposed nomenclature symbols for all 330 human OR genes in the database. A WWW tool for automated name assignment is provided. Received: / Accepted:     

Bird predation alters infestation of desert lizards by parasitic mites

Theory predicts that predators can reduce parasite abundance on prey by reducing prey density and through disproportionate predation on heavily infested individuals. We experimentally tested this prediction by examining the effects of bird predation on parasitic mite infestation of the prey lizard Acanthodactylus beershebensis. We manipulated predation by adding perches to arid scrubland, allowing avian predators to hunt for lizards in a habitat the birds would not normally use. Host density influenced parasite abundance in hatchlings, but not in older aged individuals and parasite abundance did not affect lizard host survival. Contrary to expectation mite abundance on adult lizards increased under low predation intensities. We explain these results by suggesting a novel hypothesis based on the assumption that the two components of predation, i.e. actual removal of prey and risk, exert contradictory effects on macroparasite abundance.     

The eukaryote chaperonin CCT is a cold shock protein in Saccharomyces cerevisiae

The eukaryotic Hsp60 cytoplasmic chaperonin CCT (chaperonin containing the T-complex polypeptide-1) is essential for growth in budding yeast, and mutations in individual CCT subunits have been shown to affect assembly of tubulin and actin. The present research focused mainly on the expression of the CCT subunits, CCTalpha and CCTbeta, in yeast (Saccharomyces cerevisiae). Previous studies showed that, unlike most other chaperones, CCT in yeast does not undergo induction following heat shock. In this study, messenger ribonucleic acid (mRNA) and protein levels of CCT subunits following exposure to low temperatures, were examined. The Northern blot analysis indicated a 3- to 4-fold increase in mRNA levels of CCTalpha and CCTbeta genes after cold shock at 4 degrees C. Interestingly, Western blot analysis showed that cold shock induces an increase in the CCTalpha protein, which is expressed at 10 degrees C, but not at 4 degrees C. Transfer of 4 degrees C cold-shocked cells to 10 degrees C induced a 5-fold increase in the CCTalpha protein level. By means of fluorescent immunostaining and confocal microscopy, we found CCTalpha to be localized in the cortex and the cell cytoplasm of S. cerevisiae. Localization of CCTalpha was not affected at low temperatures. Co-localization of CCT and filaments of actin and tubulin was not observed by microscopy. The induction pattern of the CCTalpha protein suggests that expression of the chaperonin may be primarily important during the recovery from low temperatures and the transition to growth at higher temperatures, as found for other Hsps during the recovery phase from heat shock.