High-throughput sequencing to decipher the genetic heterogeneity of deafness

Identifying genes causing non-syndromic hearing loss has been challenging using traditional approaches. We describe the impact that high-throughput sequencing approaches are having in discovery of genes related to hearing loss and the implications for clinical diagnosis.     

Coils in the membrane core are conserved and functionally important

With the increasing number of available α-helical transmembrane (TM) protein structures, the traditional picture of membrane proteins has been challenged. For example, reentrant regions, which enter and exit the membrane at the same side, and interface helices, which lie parallel with the membrane in the membrane-water interface, are common. Furthermore, TM helices are frequently kinked, and their length and tilt angle vary. Here, we systematically analyze 7% of all residues within the deep membrane core that are in coil state. These coils can be found in TM-helix kinks as major breaks in TM helices and as parts of reentrant regions.Coil residues are significantly more conserved than other residues. Due to the polar character of the coil backbone, they are either buried or located near aqueous channels. Coil residues are frequently found within channels and transporters, where they introduce the flexibility and polarity required for transport across the membrane. Therefore, we believe that coil residues in the membrane core, while constituting a structural anomaly, are essential for the function of proteins.     

Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins

Proline residues play a fundamental and subtle role in the dynamics, structure, and function in many membrane proteins. Temperature derivative spectroscopy and differential scanning calorimetry have been used to determine the effect of proline substitution in the structural stability of the active site and transmembrane arrangement of bacteriorhodopsin. We have analyzed the Pro-to-Ala mutation for the helix-embedded prolines Pro⁵⁰, Pro⁹¹, and Pro¹⁸⁶ in the native membrane environment. This information has been complemented with the analysis of the respective crystallographic structures by the FoldX force field. Differential scanning calorimetry allowed us to determine distorted membrane arrangement for P50A and P186A. The protein stability was severely affected for P186A and P91A. In the case of Pro⁹¹, a single point mutation is capable of strongly slowing down the conformational diffusion along the denaturation coordinate, becoming a barrier-free downhill process above 371 K. Temperature derivative spectroscopy, applied for first time to study thermal stability of proteins, has been used to monitor the stability of the active site of bacteriorhodopsin. The mutation of Pro⁹¹ and Pro¹⁸⁶ showed the most striking effects on the retinal binding pocket. These residues are the Pro in closer contact to the active site (activation energies for retinal release of 60.1 and 76.8 kcal/mol, respectively, compared to 115.8 kcal/mol for WT). FoldX analysis of the protein crystal structures indicates that the Pro-to-Ala mutations have both local and long-range effects on the structural stability of residues involved in the architecture of the protein and the active site and in the proton pumping function. Thus, this study provides a complete overview of the substitution effect of helix-embedded prolines in the thermodynamic and dynamic stability of a membrane protein, also related to its structure and function.     

Connecting species richness, abundance and body size in deep-sea gastropods

Aim This paper examines species richness, abundance, and body size in deep‐sea gastropods and how they vary over depth, which is a strong correlate of nutrient input. Previous studies have documented the empirical relationships among these properties in terrestrial and coastal ecosystems, but a full understanding of how these patterns arise has yet to be obtained. Examining the relationships among macroecological variables is a logical progression in deep‐sea ecology, where patterns of body size, diversity, and abundance have been quantified separately but not linked together. Location 196–5042 m depth in the western North Atlantic. Method Individuals analysed represent all Vetigastropoda and Caenogastropoda (Class Gastropoda) with intact shells, excluding Ptenoglossa, collected by the Woods Hole Benthic Sampling Program (3424 individuals representing 80 species). Biovolume was measured for every individual separately (i.e. allowing the same species to occupy multiple size classes) and divided into log₂ body size bins. Analyses were conducted for all gastropods together and separated into orders and depth regions (representing different nutrient inputs). A kernel smoothing technique, Kolmogorov‐Smirnov test of fit, and OLS and RMA were used to characterize the patterns. Results Overall, the relationship between the number of individuals and species is right skewed. There is also a positive linear relationship between the number of individuals and the number of species, which is independent of body size. Variation among these relationships is seen among the three depth regions. At depths inferred to correspond with intermediate nutrient input levels, species are accumulated faster given the number of individuals and shift from a right‐skewed to a log‐normal distribution. Conclusion A strong link between body size, abundance, and species richness appears to be ubiquitous over a variety of taxa and environments, including the deep sea. However, the nature of these relationships is affected by the productivity regime and scale at which they are examined.     

The rotifer fauna of peat-swamps in southern Thailand

Different taxa have had different degrees of success in invading and proliferating in the deep sea. The reasons for these differences are not well known, and exemplars need to be studied to provide insight as to factors that lead to success in the deep sea. Because the abundance of the deep-sea fauna taken as a whole declines with depth, the absolute abundance of a taxon is not an appropriate metric of its success. Rather, a taxon whose abundance declines as rapidly as or less rapidly than the general trend should be considered successful. In this paper, I used the macrofauna to define the general trend of abundance change with depth. When I compared the trend of abundance of harpacticoids to that for macrofauna, I found that harpacticoid abundance decreased less rapidly. Thus, harpacticoids are unusually successful in the deep sea. The reasons for their success are unknown, but I discuss three possible explanations.     

Effects of the northern pocket gopher (Thomomys talpoides) on alpine soil characteristics, Niwot Ridge, CO

Effects of the northern pocket gopher (Thomomys talpoides) on surface soilcharacteristics were examined at the alpinesite of Niwot Ridge, CO. We measured erosionof soil from gopher mounds and compared thecharacteristics of gopher mound (disturbed) andundisturbed soils in two major plant communitytypes. Our measurements of erosion indicatelong-term susceptibility of gopher-disturbedsoils to redistribution by water and/or wind inthis ecosystem. Ecosystem heterogeneityintroduced by the gopher is reflected insignificantly lower SOM in gopher mounds thanin surrounding undisturbed soils, acharacteristic which appears to be causallyassociated with other effects of gopherdisturbance including changes in soil textureand significantly lower clays, total C, totalN, total P, and labile P. In contrast toplant-available P, NO₃ ^– was higherand steadily increased for the short term in both gopher mound soils and those beneath the mounds. These pools of NO₃ ^– thendecreased to pre-disturbance levels by thefollowing spring. Collectively our resultsindicate that, through the physicalmanipulation of soil and subsequent effects onsoil resources, the northern pocket gopherfunctions as an agent of increased ecosystemheterogeneity and soil mass and nutrientredistribution at Niwot Ridge.     

Identification of intramembrane hydrogen bonding between 13 keto group of bacteriochlorophyll and serine residue α27 in the LH2 light-harvesting complex

Intramembrane hydrogen bonding and its effect on the structural integrity of purple bacterial light-harvesting complex 2, LH2, have been assessed in the native membrane environment. A novel hydrogen bond has been identified by Raman resonance spectroscopy between a serine residue of the membrane-spanning region of LH2 α-subunit, and the C-13¹ keto carbonyl of bacteriochlorophyll (BChl) B850 bound to the β-subunit. Replacement of the serine by alanine disrupts this strong hydrogen bond, but this neither alters the strongly red-shifted absorption nor the structural arrangement of the BChls, as judged from circular dichroism. It also decreases only slightly the thermal stability of the mutated LH2 in the native membrane environment. The possibility is discussed that weak H-bonding between the C-13¹ keto carbonyl and a methyl hydrogen of the alanine replacing serine(−4) or the imidazole group of the nearby histidine maintains structural integrity in this very stable bacterial light-harvesting complex. A more widespread occurrence of H-bonding to C-13¹ not only in BChl, but also in chlorophyll proteins, is indicated by a theoretical analysis of chlorophyll/polypeptide contacts at <3.5 Å in the high-resolution structure of Photosystem I. Nearly half of the 96 chlorophylls have aa residues suitable as hydrogen bond donors to their keto groups.     

Functional diversity for body actions in the mesencephalic locomotor region

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Spatial and temporal patterns of genetic variation in the widespread antitropical deep‐sea coral Paragorgia arborea

Numerous deep‐sea species have apparent widespread and discontinuous distributions. Many of these are important foundation species, structuring hard‐bottom benthic ecosystems. Theoretically, differences in the genetic composition of their populations vary geographically and with depth. Previous studies have examined the genetic diversity of some of these taxa in a regional context, suggesting that genetic differentiation does not occur at scales of discrete features such as seamounts or canyons, but at larger scales (e.g. ocean basins). However, to date, few studies have evaluated such diversity throughout the known distribution of a putative deep‐sea species. We utilized sequences from seven mitochondrial gene regions and nuclear genetic variants of the deep‐sea coral Paragorgia arborea in a phylogeographic context to examine the global patterns of genetic variation and their possible correlation with the spatial variables of geographic position and depth. We also examined the compatibility of this morphospecies with the genealogical‐phylospecies concept by examining specimens collected worldwide. We show that the morphospecies P. arborea can be defined as a genealogical‐phylospecies, in contrast to the hypothesis that P. arborea represents a cryptic species complex. Genetic variation is correlated with geographic location at the basin‐scale level, but not with depth. Additionally, we present a phylogeographic hypothesis in which P. arborea originates from the North Pacific, followed by colonization of the Southern Hemisphere prior to migration to the North Atlantic. This hypothesis is consistent with the latest ocean circulation model for the Miocene.