Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family

BACKGROUND: The medical community requires computational tools that distinguish missense genetic differences having phenotypic impact within the vast number of sense mutations that do not. Tools that do this will become increasingly important for those seeking to use human genome sequence data to predict disease, make prognoses, and customize therapy to individual patients. RESULTS: An approach, termed DETECTER, is proposed to identify sites in a protein sequence where amino acid replacements are likely to have a significant effect on phenotype, including causing genetic disease. This approach uses a model-dependent tool to estimate the normalized replacement rate at individual sites in a protein sequence, based on a history of those sites extracted from an evolutionary analysis of the corresponding protein family. This tool identifies sites that have higher-than-average, average, or lower-than-average rates of change in the lineage leading to the sequence in the population of interest. The rates are then combined with sequence data to determine the likelihoods that particular amino acids were present at individual sites in the evolutionary history of the gene family. These likelihoods are used to predict whether any specific amino acid replacements, if introduced at the site in a modern human population, would have a significant impact on fitness. The DETECTER tool is used to analyze the cystic fibrosis transmembrane conductance regulator (CFTR) gene family. CONCLUSION: In this system, DETECTER retrodicts amino acid replacements associated with the cystic fibrosis disease with greater accuracy than alternative approaches. While this result validates this approach for this particular family of proteins only, the approach may be applicable to the analysis of polymorphisms generally, including SNPs in a human population

Mechanical Flip-Chip for Ultra-High Electron Mobility Devices

Electrostatic gates are of paramount importance for the physics of devices based on high-mobility two-dimensional electron gas (2DEG) since they allow depletion of electrons in selected areas. This field-effect gating enables the fabrication of a wide range of devices such as, for example, quantum point contacts (QPC), electron interferometers and quantum dots. To fabricate these gates, processing is usually performed on the 2DEG material, which is in many cases detrimental to its electron mobility. Here we propose an alternative process which does not require any processing of the 2DEG material other than for the ohmic contacts. This approach relies on processing a separate wafer that is then mechanically mounted on the 2DEG material in a flip-chip fashion. This technique proved successful to fabricate quantum point contacts on both GaAs/AlGaAs materials with both moderate and ultra-high electron mobility.Comment: 5 pages, 3 figure

Interchanging Functionality Among Homologous Elongation Factors Using Signatures of Heterotachy

Numerous models of molecular evolution have been formulated to describe the forces that shape sequence divergence among homologous proteins. These models have greatly enhanced our understanding of evolutionary processes. Rarely are such models empirically tested in the laboratory, and even more rare, are such models exploited to generate novel molecules useful for synthetic biology. Here, we experimentally demonstrate that the heterotachy model of evolution captures signatures of functional divergence among homologous elongation factors (EFs) between bacterial EF-Tu and eukaryotic eEF1A. These EFs are GTPases that participate in protein translation by presenting aminoacylated-tRNAs to the ribosome. Upon release from the ribosome, the EFs are recharged by nucleotide exchange factors EF-Ts in bacteria or eEF1B in eukaryotes. The two nucleotide exchange factors perform analogous functions despite not being homologous proteins. The heterotachy model was used to identify a set of sites in eEF1A/EF-Tu associated with eEF1B binding in eukaryotes and another reciprocal set associated with EF-Ts binding in bacteria. Introduction of bacterial EF-Tu residues at these sites into eEF1A protein efficiently disrupted binding of cognate eEF1B as well as endowed eEF1A with the novel ability to bind bacterial EF-Ts. We further demonstrate that eEF1A variants, unlike yeast wild-type, can function in a reconstituted in vitro bacterial translation system. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00239-013-9540-9) contains supplementary material, which is available to authorized users

Dental Abnormalities and Early Diagnosis of Hyperphosphatasemia

Dental hard tissue abnormalities have never been described as part of the symptoms associated with hyperphosphatasemia. Fourteen teeth obtained from a young man, who had a mild form of hyperphosphatasemia, were analyzed using scanning electron microscopy (SEM), secondary ion mass spectroscopy (SIMS), X-ray diffraction (XRD), and infrared (IR) spectroscopy. SEM revealed a thin enamel, presenting a prismatic structure with many pits, and atypical cementum and dentin showing numerous resorption areas. The X-ray diffractograms revealed poorly crystallinehydroxyapatite associated with α-tricalcium phosphate and magnesium hydroxide phases. SIMS data showed high Ca concentrations: 40.5 weight % {wt%; standard deviation (SD) = 0.13) and 42.5 wt% (SD = 1.03) in enamel and dentin respectively, and high Ca/P weight ratios: 2.28 in the enamel, 2.65 in the dentin. The lack of crystallinity may be linked to the high content of proteins and magnesium adsorbed onto apatite. This study demonstrates the need for thorough radiographical and biological investigations for skeletal abnormalities, even in the absence of systemic symptoms, when generalized dental abnormalities of both enamel and dentin are observed

Estimativas populacionais de Dendrobates tinctorius (Anura: Dendrobatidae) em três áreas da Guiana Francesa e primeiro relato de quitridiomicose.

A região Neotropical abriga o maior número de espécies de anuros da Terra e é também uma das regiões em que os anfíbios estão mais ameaçados. No entanto, poucos dados estão atualmente disponíveis para avaliar a situação daspopulações de anfíbios neotropicais. Estudamos três populações de Dendrobates tinctorius na Guiana Francesa (Tresor, Favard e Nouragues) usando o modelo de Captura-Marcação-Recaptura (CMR) para a realização de estimativas robustas da densidade da espécie nesses três locais. Além disso, avaliamos a prevalência do fungo patogênico Batrachochytrium dendrobatidis (Bd) em duaspopulações (Favard and Nouragues). O uso do modelo CMR revelou uma densidade de 4,67 indivíduos/100 m² para Tresor, 8,43 indivíduos/100 m² para Favard e 4,28 indivíduos/100 m² para Nouragues, fornecendo estimativas das densidades populacionais de D. tinctorius na Guiana Francesa com as quais estimativas populacionais futuras poderão ser comparadas. Constatamos que 25 ocasiões de encontro podem ser suficientes para estimativas de uma população estável se as capturas forem concentradas no tempo. Bd foi detectado em ambas as áreas (Favard 7/152, Nouragues 3/18). Propomos, portanto, o início de um acompanhamento de longa-duração dessa espécie em vários locais (dentro e fora de áreas protegidas) da Guiana Francesa, combinando estudos de CMR com ocasiões de encontros concentrados em um curto período de tempo e o monitoramento de Bd.The Neotropics shelter the highest number of frog species on Earth and is also one of the regions where anurans aremost threatened. Nonetheless, few data are available to assess the population status of Neotropical anurans. We studied three populations (Tresor, Favard, and Nouragues) of the poison frog, Dendrobates tinctorius, in French Guiana and used Capture-Mark-Recapture (CMR) to make robust estimations of the species’ density at these three sites. In addition, we assessed the prevalence of the pathogen fungal Batrachochytrium dendrobatidis (Bd) in two populations (Favard and Nouragues). Based on the CMR protocol, the densities of frogs was 8.43 individuals/100 m² at Favard, 4.28 individuals/100 m² at Nouragues and from 2.30 to 4.67 individuals/100 m² at Tresor (depending on the CMR model used); these data provide a baseline for population densities of D. tinctorius in French Guiana, against which future population estimates can be compared. We found that 25 encounter events may be sufficient for stable population estimates, if the captures are concentrated in time. Bd was detected at both sites (Favard 7/152; Nouragues 3/18)

Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics

BACKGROUND: The exchange of nucleotides at synonymous sites in a gene encoding a protein is believed to have little impact on the fitness of a host organism. This should be especially true for synonymous transitions, where a pyrimidine nucleotide is replaced by another pyrimidine, or a purine is replaced by another purine. This suggests that transition redundant exchange (TREx) processes at the third position of conserved two-fold codon systems might offer the best approximation for a neutral molecular clock, serving to examine, within coding regions, theories that require neutrality, determine whether transition rate constants differ within genes in a single lineage, and correlate dates of events recorded in genomes with dates in the geological and paleontological records. To date, TREx analysis of the yeast genome has recognized correlated duplications that established a new metabolic strategies in fungi, and supported analyses of functional change in aromatases in pigs. TREx dating has limitations, however. Multiple transitions at synonymous sites may cause equilibration and loss of information. Further, to be useful to correlate events in the genomic record, different genes within a genome must suffer transitions at similar rates. RESULTS: A formalism to analyze divergence at two fold redundant codon systems is presented. This formalism exploits two-state approach-to-equilibrium kinetics from chemistry. This formalism captures, in a single equation, the possibility of multiple substitutions at individual sites, avoiding any need to "correct" for these. The formalism also connects specific rate constants for transitions to specific approximations in an underlying evolutionary model, including assumptions that transition rate constants are invariant at different sites, in different genes, in different lineages, and at different times. Therefore, the formalism supports analyses that evaluate these approximations. Transitions at synonymous sites within two-fold redundant coding systems were examined in the mouse, rat, and human genomes. The key metric (f(2)), the fraction of those sites that holds the same nucleotide, was measured for putative ortholog pairs. A transition redundant exchange (TREx) distance was calculated from f(2 )for these pairs. Pyrimidine-pyrimidine transitions at these sites occur approximately 14% faster than purine-purine transitions in various lineages. Transition rate constants were similar in different genes within the same lineages; within a set of orthologs, the f(2 )distribution is only modest overdispersed. No correlation between disparity and overdispersion is observed. In rodents, evidence was found for greater conservation of TREx sites in genes on the X chromosome, accounting for a small part of the overdispersion, however. CONCLUSION: The TREx metric is useful to analyze the history of transition rate constants within these mammals over the past 100 million years. The TREx metric estimates the extent to which silent nucleotide substitutions accumulate in different genes, on different chromosomes, with different compositions, in different lineages, and at different times

Explosive breeding in tropical anurans: Environmental triggers, community composition and acoustic structure

Background: Anurans largely rely on acoustic communication for sexual selection and reproduction. While multiple studies have focused on the calling activity patterns of prolonged breeding assemblages, species that concentrate their reproduction in short-time windows, explosive breeders, are still largely unknown, probably because of their ephemeral nature. In tropical regions, multiple species of explosive breeders may simultaneously aggregate leading to massive, mixed and dynamic choruses. To understand the environmental triggers, the phenology and composition of these choruses, we collected acoustic and environmental data at five ponds in French Guiana during a rainy season, assessing acoustic communities before and during explosive breeding events. Results: We detected in each pond two explosive breeding events, lasting between 24 and 70 h. The rainfall during the previous 48 h was the most important factor predicting the emergence of these events. During explosive breeding events, we identified a temporal factor that clearly distinguished pre- A nd mid-explosive communities. A common pool of explosive breeders co-occurred in most of the events, namely Chiasmocleis shudikarensis, Trachycephalus coriaceus and Ceratophrys cornuta. Nevertheless, the species composition was remarkably variable between ponds and for each pond between the first and the second events. The acoustic structure of explosive breeding communities had outlying levels of amplitude and unexpected low acoustic diversity, significantly lower than the communities preceding explosive breeding events. Conclusions: Explosive breeding communities were tightly linked with specific rainfall patterns. With climate change increasing rainfall variability in tropical regions, such communities may experience significant shifts in their timing, distribution and composition. In structurally similar habitats, located in the same region without obvious barriers, our results highlight the variation in composition across explosive breeding events. The characteristic acoustic structure of explosive breeding events stands out from the circadian acoustic environment being easily detected at long distance, probably reflecting behavioural singularities and conveying heterospecific information announcing the availability of short-lived breeding sites. Our data provides a baseline against which future changes, possibly linked to climate change, can be measured, contributing to a better understanding on the causes, patterns and consequences of these unique assemblagesThis research was supported by the Labex CEBA (Centre d’Étude de la Biodiversité Amazonienne), which provided fnancial and logistic support for the data collection. JSU was supported by COLCIENCIAS (Doctoral Scholarship of the Colombian government, 2014 call #646). DLL was supported by a Global Marie S. Curie fellowship (European Commission, program H2020, EAVESTROP–661408), a postdoctoral grant Atracción de Talento Investigador (Comunidad de Madrid, CAM, Spain, 2016-T2/AMB-1722), and acknowledges funding provided by the Ministerio de Economía, Industria y Competitividad (CGL2017-88764-R, MINECO/AEI/FEDER, Spain). None of the funders had any role in the design, analysis, interpretation of results or writing the manuscrip