Development of microsatellite markers for Permit (Trachinotus falcatus), cross-amplification in Florida Pompano (T. carolinus) and Palometa (T. goodei), and species delineation using microsatellite markers

Three of the 20 species in the genus Trachinotus, in the jack family, Carangidae, are found in Florida waters. These are Florida Pompano (T. carolinus), Permit (T. falcatus), and Palometa (T. goodei). Florida Pompano is a coastal pelagic species found in estuarine and marine waters; it spawns in multiple batches in offshore waters. Permit is the largest and longest lived of the three species and also spawns offshore in multiple batches, near reefs. As adults, Permit can be found nearshore and offshore and are often associated with reefs, but as juveniles they are common estuarine inhabitants. Palometa is a marine species, similar in size to Florida Pompano, and has the widest latitudinal distribution of the three species. Palometa spawn in offshore waters throughout the year with two peaks of activity. All three species support commercial or recreational fisheries on both the Gulf of Mexico coast and Atlantic coast of Florida. Very little has been done to evaluate movement patterns of Trachinotus species. Based on a few tagging studies, it appears that Pompano do not travel far from coastal waters. The only preliminary investigation of genetic stock structure for the Florida Pompano population from Tampa Bay, FL, and Puerto Rico was based on microsatellite markers developed for the Pompano. The report’s key conclusion was that Pompano from Puerto Rico and from Florida belong to two highly distinct genetic stocks. This study was conducted to re-examine, using different microsatellite markers, the genetic status of Pompano stocks in Florida and Puerto Rico. The objectives of this study, therefore, were the following: 1) to develop microsatellite markers for Permit; 2) to cross-amplify the markers in Pompano and Palometa; and 3) to use these markers to confirm the status of Puerto Rico Pompano as a novel genetic stock using the methods of Bayesian population assignment, phylogenetic clustering, and factorial correspondence analysis. ... Three methods were used to investigate the relationship among the taxa using the microsatellite genotype data obtained from the samples. The results from the three analytical methods, based on Bayesian population assignment tests, phylogenetic clustering, and factorial correspondence analysis of genetic relationships among the four Trachinotus samples, showed that Florida and Puerto Rico Pompano samples belong to two highly distinct gene pools. But other multiple molecular tools, particularly nuclear-DNA sequences from many introns, and nonmolecular tools, such as morphological and meristic data, should be used together to determine species-level categorical designation for the Puerto Rico Pompano

Disturbance and Predictability of Flowering Patterns in Bird-Pollinated Cloud Forest Plants

The distribution and flowering patterns of hummingbird—pollinated plants were compared from July 1981 to June 1983 in three patch types in cloud forest at Monteverde, Costa Rica. Study plots were: (1) four recent, large (1100—2500 m2) disturbances ("cutovers") produced by cutting vegetation, (2) six recent, smaller (200—600 m2) disturbances caused by treefalls, and (3) four plots (1600—1800 m2) of canopied forest. Based on published literature dealing with communities that characterize different regimes of disturbance, we tested one assumption and two hypotheses. Assumption: Plant species composition differs among the three patch types. Hypothesis 1: Phenotypic specialization by plants for co—evolved interactions with hummingbirds will be lowest in large gaps, highest in forest, and intermediate in treefalls. Hypothesis 2: Predictability of flowering phenologies and nectar production will be lowest in large gaps, highest in forest, intermediate in treefalls. Neither the assumption nor the hypotheses were supported by the results. The patch mosaic in this cloud forest was not associated with major differences in species composition of bird—pollinated plants. Most species studied were self—compatible. Most abundant in cutovers were species with long corollas, relatively specialized for attracting long—billed hummingbirds. Species with short corollas, which can be visited by many hummingbird species and some insects, were most abundant in treefalls and forest. Variation in phenological patterns showed no consistent trends among patch types. Predictability of flower and nectar production tended to be greatest in treefalls, which are foci of concentrated flowering activity by all species. Discrepancies between our results and previous studies can be ascribed to two facts. (1) Much of the literature dealing with ecological consequences of disturbance has dealt with large—scale anthropogenic disturbances such as old fields of the eastern USA, whereas we studied small, natural, or quasi—natural disturbances. (2) Studies of forest disturbance have focused on the tree layer, whereas we studied the understory herbs, shrubs, and epiphytes. Natural disturbance usually involves death and replacement of one or more trees, whereas individuals of other life forms may persist through the disturbance

Radiation Campaign of HPK Prototype LGAD sensors for the High-Granularity Timing Detector (HGTD)

We report on the results of a radiation campaign with neutrons and protons of Low Gain Avalanche Detectors (LGAD) produced by Hamamatsu (HPK) as prototypes for the High-Granularity Timing Detector (HGTD) in ATLAS. Sensors with an active thickness of 50~$\mu$m were irradiated in steps of roughly 2$\times$ up to a fluence of $3\times10^{15}~\mathrm{n_{eq}cm^{-2}}$. As a function of the fluence, the collected charge and time resolution of the irradiated sensors will be reported for operation at $-30^{\circ}$

Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations

PURPOSE: Predicting the phenotypic effects of mutations has become an important application in clinical genetic diagnostics. Computational tools evaluate the behavior of the variant over evolutionary time and assume that variations seen during the course of evolution are probably benign in humans. However, current tools do not take into account orthologous/paralogous relationships. Paralogs have dramatically different roles in Mendelian diseases. For example, whereas inactivating mutations in the NPC1 gene cause the neurodegenerative disorder Niemann-Pick C, inactivating mutations in its paralog NPC1L1 are not disease-causing and, moreover, are implicated in protection from coronary heart disease. METHODS: We identified major events in NPC1 evolution and revealed and compared orthologs and paralogs of the human NPC1 gene through phylogenetic and protein sequence analyses. We predicted whether an amino acid substitution affects protein function by reducing the organism’s fitness. RESULTS: Removing the paralogs and distant homologs improved the overall performance of categorizing disease-causing and benign amino acid substitutions. CONCLUSION: The results show that a thorough evolutionary analysis followed by identification of orthologs improves the accuracy in predicting disease-causing missense mutations. We anticipate that this approach will be used as a reference in the interpretation of variants in other genetic diseases as well. Genet Med 18 10, 1029–1036

Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies

© The Author(s) 2017 This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The attached file is the published version of the article

Pseudo-Response Regulator (PRR) Homologues of the Moss Physcomitrella patens: Insights into the Evolution of the PRR Family in Land Plants

The pseudo-response regulators (PRRs) are the circadian clock component proteins in the model dicot Arabidopsis thaliana. They contain a receiver-like domain (RLD) similar to the receiver domains of the RRs in the His–Asp phosphorelay system, but the RLDs lack the phosphoacceptor aspartic acid residue invariably conserved in the receiver domains. To study the evolution of PRR genes in plants, here we characterize their homologue genes, PpPRR1, PpPRR2, PpPRR3 and PpPRR4, from the moss Physcomitrella patens. In the phylogenetic analysis, PpPRRs cluster together, sister to an angiosperm PRR gene subfamily, illustrating their close relationships with the angiosperm PRRs. However, distinct from the angiosperm sequences, the RLDs of PpPRR2/3/4 exhibit a potential phosphoacceptor aspartic acid–aspartic acid–lysine (DDK) motif. Consistently, the PpPRR2 RLD had phosphotransfer ability in vitro, suggesting that PpPRR2 functions as an RR. The PpPRR1 RLD, on the other hand, shows a partially diverged DDK motif, and it did not show phosphotransfer ability. All PpPRRs were expressed in a circadian and light-dependent manner, with differential regulation between PpPRR2/4 and PpPRR1/3. Altogether, our results illustrate that PRRs originated from an RR(s) and that there are intraspecific divergences among PpPRRs. Finally, we offer scenarios for the evolution of the PRR family in land plants

Epidemiology of vampire bat-transmitted rabies virus in Goiás, central Brazil: re-evaluation based on G-L intergenic region

Abstract Background Vampire bat related rabies harms both livestock industry and public health sector in central Brazil. The geographical distributions of vampire bat-transmitted rabies virus variants are delimited by mountain chains. These findings were elucidated by analyzing a high conserved nucleoprotein gene. This study aims to elucidate the detailed epidemiological characters of vampire bat-transmitted rabies virus by phylogenetic methods based on 619-nt sequence including unconserved G-L intergenic region. Findings The vampire bat-transmitted rabies virus isolates divided into 8 phylogenetic lineages in the previous nucleoprotein gene analysis were divided into 10 phylogenetic lineages with significant bootstrap values. The distributions of most variants were reconfirmed to be delimited by mountain chains. Furthermore, variants in undulating areas have narrow distributions and are apparently separated by mountain ridges. Conclusions This study demonstrates that the 619-nt sequence including G-L intergenic region is more useful for a state-level phylogenetic analysis of rabies virus than the partial nucleoprotein gene, and simultaneously that the distribution of vampire bat-transmitted RABV variants tends to be separated not only by mountain chains but also by mountain ridges, thus suggesting that the diversity of vampire bat-transmitted RABV variants was delimited by geographical undulations

Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)

PMCID: PMC3581519This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Identification of Giardia lamblia DHHC Proteins and the Role of Protein S-palmitoylation in the Encystation Process

Protein S-palmitoylation, a hydrophobic post-translational modification, is performed by protein acyltransferases that have a common DHHC Cys-rich domain (DHHC proteins), and provides a regulatory switch for protein membrane association. In this work, we analyzed the presence of DHHC proteins in the protozoa parasite Giardia lamblia and the function of the reversible S-palmitoylation of proteins during parasite differentiation into cyst. Two specific events were observed: encysting cells displayed a larger amount of palmitoylated proteins, and parasites treated with palmitoylation inhibitors produced a reduced number of mature cysts. With bioinformatics tools, we found nine DHHC proteins, potential protein acyltransferases, in the Giardia proteome. These proteins displayed a conserved structure when compared to different organisms and are distributed in different monophyletic clades. Although all Giardia DHHC proteins were found to be present in trophozoites and encysting cells, these proteins showed a different intracellular localization in trophozoites and seemed to be differently involved in the encystation process when they were overexpressed. dhhc transgenic parasites showed a different pattern of cyst wall protein expression and yielded different amounts of mature cysts when they were induced to encyst. Our findings disclosed some important issues regarding the role of DHHC proteins and palmitoylation during Giardia encystation.Fil: Merino, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Zamponi, Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Vranych, Cecilia Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Touz, Maria Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaFil: Ropolo, Andrea Silvana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentin

Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago

Turnip mosaic potyvirus (TuMV) is probably the most widespread and damaging virus that infects cultivated brassicas worldwide. Previous work has indicated that the virus originated in western Eurasia, with all of its closest relatives being viruses of monocotyledonous plants. Here we report that we have identified a sister lineage of TuMV-like potyviruses (TuMV-OM) from European orchids. The isolates of TuMV-OM form a monophyletic sister lineage to the brassica-infecting TuMVs (TuMV-BIs), and are nested within a clade of monocotyledon-infecting viruses. Extensive host-range tests showed that all of the TuMV-OMs are biologically similar to, but distinct from, TuMV-BIs and do not readily infect brassicas. We conclude that it is more likely that TuMV evolved from a TuMV-OM-like ancestor than the reverse. We did Bayesian coalescent analyses using a combination of novel and published sequence data from four TuMV genes [helper component-proteinase protein (HC-Pro), protein 3(P3), nuclear inclusion b protein (NIb), and coat protein (CP)]. Three genes (HC-Pro, P3, and NIb), but not the CP gene, gave results indicating that the TuMV-BI viruses diverged from TuMV-OMs around 1000 years ago. Only 150 years later, the four lineages of the present global population of TuMV-BIs diverged from one another. These dates are congruent with historical records of the spread of agriculture in Western Europe. From about 1200 years ago, there was a warming of the climate, and agriculture and the human population of the region greatly increased. Farming replaced woodlands, fostering viruses and aphid vectors that could invade the crops, which included several brassica cultivars and weeds. Later, starting 500 years ago, inter-continental maritime trade probably spread the TuMV-BIs to the remainder of the world