The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters

As novel SARS-CoV-2 variants continue to emerge, it is critical that their potential to cause severe disease and evade vaccine-induced immunity is rapidly assessed in humans and studied in animal models. In early January 2021, a novel SARS-CoV-2 variant designated B.1.429 comprising 2 lineages, B.1.427 and B.1.429, was originally detected in California (CA) and it was shown to have enhanced infectivity in vitro and decreased antibody neutralization by plasma from convalescent patients and vaccine recipients. Here we examine the virulence, transmissibility, and susceptibility to pre-existing immunity for B 1.427 and B 1.429 in the Syrian hamster model. We find that both variants exhibit enhanced virulence as measured by increased body weight loss compared to hamsters infected with ancestral B.1 (614G), with B.1.429 causing the most marked body weight loss among the 3 variants. Faster dissemination from airways to parenchyma and more severe lung pathology at both early and late stages were also observed with B.1.429 infections relative to B.1. (614G) and B.1.427 infections. In addition, subgenomic viral RNA (sgRNA) levels were highest in oral swabs of hamsters infected with B.1.429, however sgRNA levels in lungs were similar in all three variants. This demonstrates that B.1.429 replicates to higher levels than ancestral B.1 (614G) or B.1.427 in the oropharynx but not in the lungs. In multi-virus in-vivo competition experiments, we found that B.1. (614G), epsilon (B.1.427/B.1.429) and gamma (P.1) dramatically outcompete alpha (B.1.1.7), beta (B.1.351) and zeta (P.2) in the lungs. In the nasal cavity, B.1. (614G), gamma, and epsilon dominate, but the highly infectious alpha variant also maintains a moderate size niche. We did not observe significant differences in airborne transmission efficiency among the B.1.427, B.1.429 and ancestral B.1 (614G) and WA-1 variants in hamsters. These results demonstrate enhanced virulence and high relative oropharyngeal replication of the epsilon (B.1.427/B.1.429) variant in Syrian hamsters compared to an ancestral B.1 (614G) variant.     

Planning and Implementing a Reintroduction of Wolves to Yellowstone National Park and Central Idaho

The Northern Rocky Mountain Wolf Recovery plan proposed reintroduction of Canis lupus (gray wolf) to Yellowstone National Park and central Idaho as part of a wolf restoration plan for the northern Rocky Mountains of the United States. Strong opposition from some factions within the region forestalled the action for two decades. An environmental impact statement, conducted in 1992–1994 with extensive public input, culminated in a proposal to reintroduce wolves designated as “non-essential—experimental” under Section 10 (j) of the federal Endangered Species Act. This approach, approved by the Secretary of the Interior in 1994, provided for wolf restoration while allowing management flexibility to deal with concerns of the local public. A reintroduction plan was developed in the summer and fall of 1994. Acquiring, holding, transporting, and releasing suitable wolves for reintroduction presented a myriad of technical and logistical challenges that required effective planning and coordination by all participants. In January 1995, 29 wolves were captured in Alberta and transported to Yellowstone National Park (14) and central Idaho (15). Idaho wolves were freed immediately upon arrival; Yellowstone wolves (three family groups) were held in acclimation pens in the park until late March. Most Idaho wolves traveled extensively within the area intended for them, averaging 82 km net distance away from release sites after 5 months (range = 30–220 km), and three male-female pairs formed by July. After 5 months in the wild, at least 13 of 15 Idaho-released wolves were alive within the intended area, as were 13 of 14 Yellowstone wolves; one wolf was known to have been illegally killed in each area. No livestock were killed. Wolves released into Yellowstone Park continued to live as packs, stayed closer to their release sites (x = 22 km at end of June), and settled into home ranges; two packs produced a total of nine pups. The progress of the reintroduction program in its first year far exceeded expectations. Reintroductions of about 15 wolves to each area for 2–4 more years are scheduled, but the project may be shortened because of early successes. Future reintroduction planners can expect sociocultural issues to pervade the effort, but they can be optimistic that, from a biological standpoint, reintroduction of wolves has strong potential as a restoration technique.     

Topological analysis of a haloacid permease of a Burkholderia sp. bacterium with a PhoA-LacZ reporter

Background  

2-Haloacids can be found in the natural environment as degradative products of natural and synthetic halogenated compounds. They can also be generated by disinfection of water and have been shown to be mutagenic and to inhibit glyceraldehyde-3-phosphate dehydrogenase activity. We have recently identified a novel haloacid permease Deh4p from a bromoacetate-degrading bacterium Burkholderia sp. MBA4. Comparative analyses suggested that Deh4p is a member of the Major Facilitator Superfamily (MFS), which includes thousands of membrane transporter proteins. Members of the MFS usually possess twelve putative transmembrane segments (TMS). Deh4p was predicted to have twelve TMS. In this study we characterized the topology of Deh4p with a PhoA-LacZ dual reporters system.     

Lead poisoning in captive Andean condors (Vultur gryphus)

Elevated lead in the tissues of raptors, especially those that scavenge, is a common occurrence, and lead poisoning appears to be a significant problem in the ongoing recovery effort for California condors (Gymnogyps californianus). Elevated blood lead levels have been found in released birds, and a number of birds have died of lead poisoning. In earlier work, we dosed turkey vultures (Cathartes aura) with lead shot but found them to be a poor model for lead poisoning. In this study, we dosed four Andean condors (Vultur gryphus) with lead shot and found them to be quite sensitive, as two of the birds died and the other two exhibit signs of lead poisoning within 50 days. All lead-responsive parameters were affected, and regurgitation of dosed shot occurred only once. The response of the Andean condors appeared to mimic California condors, suggesting that once exposed to lead, the possibility of survival is poor. This is consistent with observations in the wild, where otherwise healthy birds exposed to metallic lead quickly succumb. At the very least, the release program has to maintain constant surveillance and an active lead monitoring program.     

Influence of climatic factors upon tree rings of Larix decidua and L. decidua × L. kaempferi from Pulawy,Poland

Summary Dendroclimatological techniques are used to assess the impact of climatic factors on tree-ring width of Larix decidua and L. decidua × L. kaempferi (= L. x eurolepis) growing in two experimental plots established in 1914 in south-west Poland. One plot included F₁ progeny grown from seeds of an artificial crossing between European and Japanese larch. The other plot included progeny from maternal trees of European larch. Total ring width, earlywood width and latewood widths were dated, standardized and related to monthly climatic data using response function and stepwise multiple regression analyses. Wide rings in larch are associated with high precipitation in May–July, cool conditions in July–September of the preceding year, and cool dry conditions in August. Ring widths in L. x eurolepis are more dependent upon precipitation than ring widths in L. decidua. Latewood widths in L. x eurolepis are more dependent on high temperatures in June and July than latewood in L. decidua as well as total width and earlywood measurements. Variations in latewood were relatively independent of variations in earlywood and total wood. The variability of ring widths in these larches was greater than the variability reported for larches in many alpine sites and for other conifer species in some regions of North America.     

Algorithms and software for support of gene identification experiments

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.      

Divergent and reticulate processes in evolution of Ethiopian Lophuromys flavopunctatus species complex: evidence from mitochondrial and nuclear DNA differentiation patterns

Molecular study of mitochondrial and nuclear genes and cytogenetic analysis were performed to examine possible patterns of speciation in the diverse Lophuromys flavopunctatus species complex of Ethiopia. Phylogenetic analysis of mtDNA data resulted in an unresolved bush of ten deeply diverged haplotype groups corresponding to potential species either well supported by various types of character or 'cryptic'. The cytogenetic analysis showed representatives of five of these mtDNA lineages to share an identical karyotype (2 n  = 70, NFa = 84), that has not been found previously in Ethiopia. One of them, L.  cf.  sikapusi , being a member of the L. flavopunctatus species complex, demonstrates remarkable morphological similarity to representatives of another species complex, L. sikapusi s.l ., which might be considered as a result of convergent evolution in analogous environments. Analysis of RAPD data suggests that at least two mtDNA types might have been subject to interspecific transfer due to hybridization. In the case of two sympatric haplotypes of L. brunneus we may assume that the contemporary pattern of variation between them can be explained by relatively recent hybridization with another distinct species, L. flavopunctatus . The formation of two groups belonging to distinct mitochondrial lineages within northern populations could be associated with more complex processes including ancient hybridization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 301–316.     

Anti-rotavirus Properties and Mechanisms of Selected Gram-Positive and Gram-Negative Probiotics on Polarized Human Colonic (HT-29) Cells

Probiotics and Antimicrobial Proteins - Probiotics have been investigated to improve the universal rotavirus (RV) vaccination as well as to ameliorate the RV infection. However, underlying...