Identification of Quantitative Trait Loci Associated with Resistance to Viral Haemorrhagic Septicaemia (VHS) in Turbot (Scophthalmus maximus): A Comparison Between Bacterium,Parasite and Virus Diseases

One of the main objectives of genetic breeding programs in turbot industry is to reduce disease-related mortality. In the present study, a genome scan to detect quantitative trait loci (QTL) affecting resistance and survival to viral haemorrhagic septicaemia (VHS) was carried out. Three full-sib families with approximately 90 individuals each were genotyped and evaluated by linear regression and maximum likelihood approaches. In addition, a comparison between QTL detected for resistance and survival time to other important bacterial and parasite diseases affecting turbot (furunculosis and scuticociliatosis) was also carried out. Finally, the relationship between QTL affecting resistance/survival time to the virus and growth-related QTL was also evaluated. Several genomic regions controlling resistance and survival time to VHS were detected. Also significant associations between the evaluated traits and genotypes at particular markers were identified, explaining up to 14 % of the phenotypic variance. Several genomic regions controlling general and specific resistance to different diseases in turbot were detected. A preliminary gene mining approach identified candidate genes related to general or specific immunity. This information will be valuable to develop marker-assisted selection programs and to discover candidate genes related to disease resistance to improve turbot production.     

Sequential invasions by fruit flies (Diptera: Tephritidae) in Pacific and Indian Ocean islands: A systematic review

The aim of our review was to examine the cases of Tephritidae invasions across island systems in order to determine whether they follow a hierarchical mode of invasion. We reviewed the literature on factors and mechanisms driving invasion sequences in Pacific and Southwest Indian Ocean islands and gathered every record of invasion by a polyphagous tephritid in island groups. From invasion date or period, we defined an invasion link when a new fruit fly established on an island where another polyphagous tephritid is already resident (that was indigenous or a previous invader). Across surveyed islands, we documented 67 invasion links, involving 24 tephritid species. All invasion links were directional, i.e., they involved a series of invasions by invaders that were closely related to a resident species but were increasingly more competitive. These sequential establishments of species are driven by interspecific competition between resident and exotic species but are also influenced by history, routes, and flows of commercial exchanges and the bridgehead effect. This information should be used to improve biosecurity measures. Interactions between trade flow, invasive routes, and the presence of invasive and resident species should be integrated into large‐scale studies.     

A new species of Nezumia (Gadiformes: Macrouridae) from Fieberling Guyot, eastern North Pacific Ocean

A new species of the macrourine genus Nezumia is described from specimens collected from the crest of Fieberling Guyot in the eastern North Pacific Ocean. The new species is distinguishable from all other Nezumia species chiefly on the basis of a high number of pelvic fin rays, a relatively high number of first dorsal fin soft rays, a steep blunt snout lacking scales ventrally, a relatively weak suborbital ridge, and a moderately long, thin barbel. Although possibly endemic to the Baja California Seamount Province, the new species appears to lack close relatives among the other Nezumia species of the eastern North Pacific Ocean. It might have arrived there either from a disjunct Tethyan distribution, thus retaining close relatives among the Atlantic Ocean species of Nezumia, or by way of stepping-stone dispersal from the Indo-west Pacific Ocean.     

The Last Frontier: Catch Records of White Sharks (Carcharodon carcharias) in the Northwest Pacific Ocean

White sharks are highly migratory apex predators, globally distributed in temperate, sub-tropical, and tropical waters. Knowledge of white shark biology and ecology has increased recently based on research at known aggregation sites in the Indian, Atlantic, and Northeast Pacific Oceans; however, few data are available for the Northwest Pacific Ocean. This study provides a meta-analysis of 240 observations of white sharks from the Northwest Pacific Ocean between 1951 and 2012. Records comprise reports of bycatch in commercial fisheries, media accounts, personal communications, and documentation of shark-human interactions from Russia (n = 8), Republic of Korea (22), Japan (129), China (32), Taiwan (45), Philippines (1) and Vietnam (3). Observations occurred in all months, excluding October-January in the north (Russia and Republic of Korea) and July-August in the south (China, Taiwan, Philippines, and Vietnam). Population trend analysis indicated that the relative abundance of white sharks in the region has remained relatively stable, but parameterization of a 75% increase in observer effort found evidence of a minor decline since 2002. Reliably measured sharks ranged from 126–602 cm total length (TL) and 16–2530 kg total weight. The largest shark in this study (602 cm TL) represents the largest measured shark on record worldwide. For all countries combined the sex ratio was non-significantly biased towards females (1∶1.1; n = 113). Of 60 females examined, 11 were confirmed pregnant ranging from the beginning stages of pregnancy (egg cases) to near term (140 cm TL embryos). On average, 6.0±2.2 embryos were found per litter (maximum of 10) and gestation period was estimated to be 20 months. These observations confirm that white sharks are present in the Northwest Pacific Ocean year-round. While acknowledging the difficulties of studying little known populations of a naturally low abundance species, these results highlight the need for dedicated research to inform regional conservation and management planning.     

New species and new records of Callionymus from the Pacific Ocean (Teleostei: Callionymidae)

Recently obtained material of Callionymus from the Pacific Ocean includes: Callionymus marquesensis sp. n. (Marquesas Islands), characterized within the C. variegatus-group of the subgenus Calliurichthys by its preopercular spine formula of with an upcurved main tip and a bony keel between the points on the dorsal margin, and a spotted dorsal fin without filaments which is higher than the 1st D₂ ray in both sexes; C. pleurostictus Fricke, 1982, record from New Britain and Solomon Islands, with a discussion of competition with C. delicatulus; C.simplicicornis Valenciennes, 1837, record from Society Islands and Marquesas Islands, with a discussion of competition with C. marquesensis; C. obscurus sp. n. (Ambon, Indonesia) which is characterized within the subgenus Spini-capitichthys by its preopercular spine formula with an upcurved main tip and very small ventral serrae, its weakly armed head, and its 7 anal fin rays.     

A new species of anchovy,Encrasicholina auster (Clupeiformes: Engraulidae) from Fiji,southwestern Pacific Ocean

ABSTRACT

Encrasicholina auster sp. nov. (Clupeiformes: Engraulidae) is described on the basis of six specimens collected from Fiji, southwestern Pacific Ocean. The new species is distinguished from congeners by the following combination of characters: long upper jaw (posterior tip extending beyond posterior margin of preopercle) 20.8%–22.5% standard length (SL); long lower jaw 19.0%–20.7% SL; long head 29.1%–29.2% SL; three unbranched rays in the dorsal and anal fins; transverse scales 11; branched pectoral-fin rays 12–13; pseudobranchial filaments 19–21; gill rakers 45–49, 40–43, 26–31 and 22–25 on the first, second, third and fourth gill arches, respectively.     

Replication Protein A (RPA): The Eukaryotic SSB

Replication protein A (RPA) is a heterotrimeric single-stranded DNA-binding protein that is highly conserved in eukaryotes. RPA plays essential roles in many aspects of nucleic acid metabolism, including DNA replication, nucleotide excision repair, and homologous recombination. In this review, we provide a comprehensive overview of RPA structure and function and highlight the more recent developments in these areas. The last few years have seen major advances in our understanding of the mechanism of RPA binding to DNA, including the structural characterization of the primary DNA-binding domains (DBD) and the identification of two secondary DBDs. Moreover, evidence indicates that RPA utilizes a multistep pathway to bind single-stranded DNA involving a particular molecular polarity of RPA, a mechanism that is apparently used to facilitate origin denaturation. In addition to its mechanistic roles, RPA interacts with many key factors in nucleic acid metabolism, and we discuss the critical nature of many of these interactions to DNA metabolism. RPA is a phosphorylation target for DNA-dependent protein kinase (DNA-PK) and likely the ataxia telangiectasia-mutated gene (ATM) protein kinase, and recent observations are described that suggest that RPA phosphorylation plays a significant modulatory role in the cellular response to DNA damage.     

The biostratigraphy and paleobiology of Oligocene planktonic foraminifera from the equatorial Pacific Ocean (ODP Site 1218)

Planktonic foraminifera from a continuous Oligocene succession with clear magnetochronology and sediment cycles at Ocean Drilling Program Site 1218 (equatorial Pacific Ocean) were studied in the interval from 27 to 30 Ma. Paragloborotalia taxa are common and we examined their size, relative abundance, and stable isotopes. Multispecies stable isotope data indicate the depth habitats of Oligocene planktonic foraminifera and suggest that “Globoquadrina” venezuelana and Dentoglobigerina globularis were probably mixed-layer dwellers, with paragloborotaliids recording heavier δ¹⁸O signatures consistent with a thermocline habitat. Cyclic variations in the abundance of Paragloborotalia match eccentricity (100 kyr) variations in percent carbonate and δ¹³C, suggesting orbitally forced upwelling in the equatorial Pacific Ocean and that Paragloborotalia were responding directly to changes in surface water productivity. The high-resolution biostratigraphy calibrated to the magnetochronology constrains the extinction of Paragloborotalia opima which marks the top of Planktonic Foraminifera Biozone O5 (P21b) at 27.456 Ma. The highest occurrence of P. opima is associated with a 50% size decrease in Paragloborotalia pseudocontinuosa taxa within Chron 9n. In addition, we find the extinction of Chiloguembelina cubensis is consistent with other deep-sea sections within Chron 10n at 28.426 Ma marking the O4/O5 (P21a/P21b) boundary.     

The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development

The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB), AlphaFold, and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included.The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes.     

Vap (Vascular Associated Protein): a novel factor involved in erythropoiesis and angiogenesis

Both endothelial and erythroid cells are generated in the intermediate cell mass (ICM) during zebrafish embryogenesis, but the nature of the genes that contribute to the processes of erythrocyte maturation and blood vessel network formation is not fully understood. From our in situ-based screening, we have identified a novel factor, Vap (Vascular Associated Protein) that is predominantly expressed in the ICM, and subsequently enriched in endothelial cells. Vap expression in the ICM was drastically suppressed in the cloche mutant that has defects in both vasculogenesis and hematopoiesis, whereas Vap expression was not affected in the vlad tepes/gata1 mutant. Knockdown of Vap using anti-sense morpholinos (VAP-MO) not only resulted in decreased numbers of erythrocytes but also in the strong suppression of hemoglobin production. Further, we found that Vap knockdown caused the disorganization of the intersegmental vessels (ISVs), which show irregular branching. We propose that Vap plays an important role in the maturation of endothelial and erythroid cells in zebrafish.     

Quantitative Trait Loci Mapping for ChlorophyⅡ Fluorescence and Associated Traits in Wheat （ Triticum aestivum）

Parameters of chlorophyll fluorescence kinetics （PCFKs） under drought stress condition are generally used to characterize instincts for dehydration tolerance in wheat （Triticum aestivum L.）. Therefore, it is important to map quantitative trait loci （QTLs） for PCFKs in wheat genetic improvement for drought tolerance. A doubled haploid （DH） population with 150 lines, derived from a cross between two common wheat varieties, Hanxuan 10 and Lumai 14, was used to analyze the correlation between PCFKs and chlorophyll content （CHIC） and to map QTLs at the grainfilling stage under conditions of both rainfed （drought stress, DS） and well-watered （WW）, respectively. QTLs for these traits were detected by QTLMapper version 1.0 based on the composite Interval mapping method of the mixed-linear model. The results showed a very significant positive correlation between Fv, Fm, Fv/Fm and Fv/Fo. The correlation coefficients were generally higher under WW than under DS. Also, there was a significant or a highly significant positive correlation between Fv, Fm, Fv/Fm, Fv/Fo and CHIC. The correlation coefficients were higher in the DS group than the WW group. A total of 14 additive QTLs （nine QTLs detected under DS and five QTLs under WW） and 25 pairs of eplstatlc QTLs （15 pairs detected under DS and 10 pairs under WW） for PCFKs were mapped on chromosomes 6A, 7A, 1B, 3B, 4D and 7D. The contributions of additive QTLs for PCFKs to phenotype variation were from 8.40% to 72.72%. Four additive QTLs （two QTLs detected under DS and WW apiece） controlling Chic were mapped on chromosomes 1A, 5A and 7A. The contributions of these QTLs for ChIC to phenotype variation were from 7.27% to 11.68%. Several QTL clusters were detected on chromosomes 1B, 7A and 7D, but no shared chromosomal regions for them were identified under different water regimes, indicating that these QTLs performed different expression patterns under rainfed and well-watered conditions.     

The warm interglacial Marine Isotope Stage 31: Evidences from the calcareous nannofossil assemblages at Site 1090 (Southern Ocean)

Calcareous nannofossil assemblages have been investigated at Ocean Drilling Program (ODP) Site 1090 located in the modern Subantarctic Zone, through the Pleistocene Marine Isotope Stages (MIS) 34–29, between 1150 and 1000 ka. A previously developed age model and new biostratigraphic constraints provide a reliable chronological framework for the studied section and allow correlation with other records. Two relevant biostratigraphic events have been identified: the First Common Occurrence of Reticulofenestra asanoi, distinctly correlated to MIS 31–32; the re-entry of medium Gephyrocapsa at MIS 29, unexpectedly similar to what was observed at low latitude sites.The composition of the calcareous nannofossil assemblage permits identification of three intervals (I–III). Intervals I and III, correlated to MIS 34–32 and MIS 30–29 respectively, are identified as characteristic of water masses located south of the Subtropical Front and reflecting the southern border of Subantarctic Zone, at the transition with the Polar Front Zone. This evidence is consistent with the hypothesis of a northward shift of the frontal system in the early Pleistocene with respect to the present position and therefore a northernmost location of the Subantarctic Front. During interval II, which is correlated to MIS 31, calcareous nannofossil assemblages display the most significant change, characterized by a distinct increase of Syracosphaera spp. and Helicosphaera carteri, lasting about 20 ky. An integrated analysis of calcareous nannofossil abundances and few mineralogical proxies suggests that during interval II, Site 1090 experienced the influence of subtropical waters, possibly related to a southward migration of the Subtropical Front, coupled with an expansion of the warmer Agulhas Current at the core location. This pronounced warming event is associated to a minimum in the austral summer insolation. The present results provide a broader framework on the Mid-Pleistocene dynamic of the ocean frontal system in the Atlantic sector of the Southern Ocean, as well as additional evidence on the variability of the Indian–Atlantic ocean exchange.     

New Resources for Marine Genomics: Bacterial Artificial Chromosome Libraries for the Eastern and Pacific Oysters (Crassostrea virginica and C. gigas)

Large-insert genomic bacterial artificial chromosome (BAC) libraries of two culturally and economically important oyster species, Crassostrea virginica and C. gigas, have been developed as part of an international effort to develop tools and reagents that will advance our ability to conduct genetic and genomic research. A total of 73,728 C. gigas clones with an average insert size of 152 kb were picked and arrayed representing an 11.8-fold genome coverage. A total of 55,296 clones with an average insert size of 150 kb were picked and arrayed for C. virginica, also representing an 11.8-fold genome coverage. The C. gigas and C. virginica libraries were screened with probes derived from selected oyster genes using high-density BAC colony filter arrays. The probes identified 4 to 25 clones per gene for C. virginica and 5 to 50 clones per gene for C. gigas. We conducted a preliminary analysis of genetic polymorphism represented in the C. gigas library. The results suggest that the degree of divergence among similar sequences is highly variable and concentrated in intronic regions. Evidence supporting allelic polymorphism is reported for two genes and allelic and/or locus specific polymorphism for several others. Classical inheritance studies are needed to confirm the nature of these polymorphisms. The oyster BAC libraries are publicly available to the research community on a cost-recovery basis at