Matrix‐glycoprotein interactions required for budding of a plant nucleorhabdovirus and induction of inner nuclear membrane invagination

Nucleorhabdoviruses such as Sonchus yellow net virus (SYNV) replicate in the nuclei and undergo morphogenesis at the inner nuclear membrane (IM) in plant cells. Mature particles are presumed to form by budding of the Matrix (M) protein‐nucleocapsid complexes through host IMs to acquire host phospholipids and the surface glycoproteins (G). To address mechanisms underlying nucleorhabdovirus budding, we generated recombinant SYNV G mutants containing a truncated amino‐terminal (NT) or carboxyl‐terminal (CT) domain. Electron microscopy and sucrose gradient centrifugation analyses showed that the CT domain is essential for virion morphogenesis whereas the NT domain is also required for efficient budding. SYNV infection induces IM invaginations that are thought to provide membrane sites for virus budding. We found that in the context of viral infections, interactions of the M protein with the CT domain of the membrane‐anchored G protein mediate M protein translocation and IM invagination. Interestingly, tethering the M protein to endomembranes, either by co‐expression with a transmembrane G protein CT domain or by artificial fusion with the G protein membrane targeting sequence, induces IM invagination in uninfected cells. Further evidence to support functions of G‐M interactions in virus budding came from dominant negative effects on SYNV‐induced IM invagination and viral infections that were elicited by expression of a soluble version of the G protein CT domain. Based on these data, we propose that cooperative G‐M interactions promote efficient SYNV budding.     

Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling

Detecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult‐to‐detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management. In this study, we set out to determine the impacts of imperfect detection, and decisions about thresholds for inclusion in occupancy, on estimates of species richness and community structure. We collected data from a stream fish assemblage in Algonquin Provincial Park to be used as a representation of ecological communities. We then used multispecies occupancy modeling to estimate species‐specific occurrence probabilities while accounting for imperfect detection, thus creating a more informed dataset. This dataset was then compared to the original to see where differences occurred. In our analyses, we demonstrated that imperfect detection can lead to large changes in estimates of species richness at the site level and summarized differences in the community structure and sampling locations, represented through correspondence analyses.     

A machine‐learning approach for extending classical wildlife resource selection analyses

Resource selection functions (RSFs) are tremendously valuable for ecologists and resource managers because they quantify spatial patterns in resource utilization by wildlife, thereby facilitating identification of critical habitat areas and characterizing specific habitat features that are selected or avoided. RSFs discriminate between known‐use resource units (e.g., telemetry locations) and available (or randomly selected) resource units based on an array of environmental features, and in their standard form are performed using logistic regression. As generalized linear models, standard RSFs have some notable limitations, such as difficulties in accommodating nonlinear (e.g., humped or threshold) relationships and complex interactions. Increasingly, ecologists are using flexible machine‐learning methods (e.g., random forests, neural networks) to overcome these limitations. Herein, we investigate the seasonal resource selection patterns of mule deer (Odocoileus hemionus) by comparing a logistic regression framework with random forest (RF), a popular machine‐learning algorithm. Random forest (RF) models detected nonlinear relationships (e.g., optimal ranges for slope and elevation) and complex interactions which would have been very challenging to discover and characterize using standard model‐based approaches. Compared with standard RSF models, RF models exhibited improved predictive skill, provided novel insights about resource selection patterns of mule deer, and, when projected across a relevant geographic space, manifested notable differences in predicted habitat suitability. We recommend that wildlife researchers harness the strengths of machine‐learning tools like RF in addition to “classical” tools (e.g., mixed‐effects logistic regression) for evaluating resource selection, especially in cases where extensive telemetry data sets are available.     

Small Interfering RNA-Mediated Control of Virus Replication in the CNS Is Therapeutic and Enables Natural Immunity to West Nile Virus

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A new genus and species of turtle blood fluke (Digenea: Schistosomatoidea) from the Mekong snail-eating turtle, <Emphasis Type="Italic">Malayemys subtrijuga</Emphasis> (Schlegel &amp; Müller) (Testudines: Geoemydidae) in Vietnam,with a reassessment of related Asiatic turtle blood flukes and molecular phylogeny

Platt sinuosus Roberts & Bullard n. g., n. sp. (type-species) infects the kidney and mesenteric blood vessels of Mekong snail-eating turtles, Malayemys subtrijuga (Schlegel & Müller), in the Mekong River Basin. Species of Platt Roberts & Bullard n. g. are unique by the combination of having a papillate ventral sucker, vasa efferentia that are dorsal to the gonads, a massive cirrus-sac that is directed anteriad or laterad, and a vitellarium that surrounds the intestinal caeca. The new species resembles Platt ocadiae (Takeuti, 1942) Roberts & Bullard n. comb. but differs from it by having an external seminal vesicle that overlaps with or is immediately posterior to the level of the ventral sucker. Seven species previously of Hapalorhynchus Stunkard, 1922 are reassigned herein to Platt: P. odhnerensis (Mehra, 1933) Roberts & Bullard n. comb.; P. yoshidai (Ozaki, 1939) Roberts & Bullard n. comb.; P. ocadiae; P. oschmarini (Belous, 1963) Roberts & Bullard n. comb.; P. sutlejensis (Mehrotra, 1973) Roberts & Bullard n. comb.; P. synderi (Platt & Sharma, 2012) Roberts & Bullard n. comb.; and P. tkachi (Platt & Sharma, 2012) Roberts & Bullard n. comb. A dichotomous key to Platt spp. is provided. Hapalorhynchus sheilae (Mehrotra, 1973) Bourgat, 1990 and Hapalorhynchus mica (Oshmarin, 1971) Bourgat, 1990 are considered as species inquirendae, and Hapalorhynchus indicus (Thapar, 1933) Price, 1934 and Hapalorhynchus macrotesticularis (Rohde, Lee, & Lim, 1968) Brooks & Sullivan, 1981 are considered as species incertae sedis. Phylogenetic analysis of the large subunit rDNA (28S) showed P. sinuosus and P. snyderi to be sister taxa distinct from a monophyletic Hapalorhynchus and Coeuritrema platti Roberts & Bullard, 2016.     

Age, growth and maturation of the deepwater squid Moroteuthis ingens (Cephalopoda: Onychoteuthidae) in New Zealand waters

 Individuals of the deepwater squid Moro- teuthis ingens were obtained from New Zealand waters at depths between 500 and 1452 m. Depth distribution suggested that there was an ontogenetic migration to deeper water by females in association with maturity. Males did not show any clear pattern in their depth distribution. Statolith increment analysis was also undertaken to obtain putative age and life span information. Based on statolith age estimates, M. ingens appears to be predominantly an annual species with the oldest individuals aged at 358 and 393 days for males and females respectively. The form of growth over the size range sampled was linear with females having a growth rate almost twice that of males. Back-calculated hatching dates revealed a peak in hatching in the austral winter between June and August. Maturation in males was more closely related to size rather than age whereas in females the pattern in ovary growth in relation to both mantle length and age was similar. Received: 23 January 1996/Accepted: 29 May 1996     

Multiple independent molecular etiology for limb-girdle muscular dystrophy type 2A patients from various geographical origins.

Limb-girdle muscular dystrophies (LGMDs) are a group of neuromuscular diseases presenting great clinical heterogeneity. Mutations in CANP3, the gene encoding muscle-specific calpain, were used to identify this gene as the genetic site responsible for autosomal recessive LGMD type 2A (LGMD2A; MIM 253600). Analyses of the segregation of markers flanking the LGMD2A locus and a search for CANP3 mutations were performed for 21 LGMD2 pedigrees from various origins. In addition to the 16 mutations described previously, we report 19 novel mutations. These data indicate that muscular dystrophy caused by mutations in CANP3 are found in patients from all countries examined so far and further support the wide heterogeneity of molecular defects in this rare disease.     

The activin receptor-like kinase 1 gene: genomic structure and mutations in hereditary hemorrhagic telangiectasia type 2.

The activin receptor-like kinase 1 gene (ALK-1) is the second locus for the autosomal dominant vascular disease hereditary hemorrhagic telangiectasia (HHT). In this paper we present the genomic structure of the ALK-1 gene, a type I serine-threonine kinase receptor expressed predominantly in endothelial cells. The coding region is contained within nine exons, spanning < 15 kb of genomic DNA. All introns follow the GT-AG rule, except for intron 6, which has a TAG/gcaag 5' splice junction. The positions of introns in the intracellular domain are almost identical to those of the mouse serine-threonine kinase receptor TSK-7L. By sequencing ALK-1 from genomic DNA, mutations were found in six of six families with HHT either shown to link to chromosome 12q13 or in which linkage of HHT to chromosome 9q33 had been excluded. Mutations were also found in three of six patients from families in which available linkage data were insufficient to allow certainty with regard to the locus involved. The high rate of detection of mutations by genomic sequencing of ALK-1 suggests that this will be a useful diagnostic test for HHT2, particularly where preliminary linkage to chromosome 12q13 can be established. In two cases in which premature termination codons were found in genomic DNA, the mutant mRNA was either not present or present at barely detectable levels. These data suggest that mutations in ALK-1 are functionally null alleles.     

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates.

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five polymorphisms differed by the presence of two to six copies of the 12-bp tandem repeat 5'-CAATATCAACAA-3'. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations.