Characterization of the Neurospora Varkud Satellite Plasmid and Transcript in vivo

The Varkud satellite (VS) plasmid is found in the mitochondria of some strains of Neurospora, and exhibits properties that may allow it to be developed as a genetic transformation vector to study mitochondrial molecular biology. An ideal transformation vector would not confer a phenotype. The overall goal of my thesis was to examine interactions of VS with its Neurospora host to identify possible phenotypes, using biochemical and proteomic approaches. Biochemical experiments provided evidence consistent with the plasmid transcript, VS RNA, being present as a ribonucleoprotein particle that can be separated from ribosomal subunits by sucrose density gradient centrifugation; however, no VS-specific proteins were identified under the purification conditions examined. During the analyses of proteomic data I obtained new insights into the consequences of the statistical methods commonly used to normalize quantitative 2D gel data. However, irrespective of the method used, the fraction of the proteome amenable to 2D gel-based proteomics revealed, at most, subtle effects of VS on the abundance of a few proteins. I also observed no differences in growth rate between strains differing by the presence or absence of VS when grown in the presence of inhibitors and stressors affecting a wide range of mitochondrial and other cellular functions. Overall, despite VS RNA being as abundant as the large and small mitochondrial ribosomal RNAs, my genetic, biochemical and proteomic investigations of the effect of VS on its host strain provides evidence that VS is a phenotypically neutral element.Ph

DOI: 10.1093/nar/gkg049 Database for mobile group II introns

Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We have initiated an ongoing web site database for mobile group II introns in order to provide correct information on the introns, particularly in bacteria. Information in the web site includes: (1) introductory information on group II introns; (2) detailed information on subfamilies of intron RNA structures and intron-encoded proteins; (3) a listing of identified introns with correct boundaries, RNA secondary structures and other detailed information; and (4) phylogenetic and evolutionary information. The comparative data should facilitate study of the function, spread and evolution of group II introns. The database can be accessed a

The distribution and numbers of cheetah (Acinonyx jubatus) in southern Africa

Assessing the numbers and distribution of threatened species is a central challenge in conservation, often made difficult because the species of concern are rare and elusive. For some predators, this may be compounded by their being sparsely distributed over large areas. Such is the case with the cheetah Acinonyx jubatus. The IUCN Red List process solicits comments, is democratic, transparent, widely-used, and has recently assessed the species. Here, we present additional methods to that process and provide quantitative approaches that may afford greater detail and a benchmark against which to compare future assessments. The cheetah poses challenges, but also affords unique opportunities. It is photogenic, allowing the compilation of thousands of crowd-sourced data. It is also persecuted for killing livestock, enabling estimation of local population densities from the numbers persecuted. Documented instances of persecution in areas with known human and livestock density mean that these data can provide an estimate of where the species may or may not occur in areas without observational data. Compilations of extensive telemetry data coupled with nearly 20,000 additional observations from 39 sources show that free-ranging cheetahs were present across approximately 789,700 km2 of Namibia, Botswana, South Africa, and Zimbabwe (56%, 22%, 12% and 10% respectively) from 2010 to 2016, with an estimated adult population of 3,577 animals. We identified a further 742,800 km2 of potential cheetah habitat within the study region with low human and livestock densities, where another ∼3,250 cheetahs may occur. Unlike many previous estimates, we make the data available and provide explicit information on exactly where cheetahs occur, or are unlikely to occur. We stress the value of gathering data from public sources though these data were mostly from well-visited protected areas. There is a contiguous, transboundary population of cheetah in southern Africa, known to be the largest in the world. We suggest that this population is more threatened than believed due to the concentration of about 55% of free-ranging individuals in two ecoregions. This area overlaps with commercial farmland with high persecution risk; adult cheetahs were removed at the rate of 0.3 individuals per 100 km2 per year. Our population estimate for confirmed cheetah presence areas is 11% lower than the IUCN’s current assessment for the same region, lending additional support to the recent call for the up-listing of this species from vulnerable to endangered status

Data from: The distribution and numbers of cheetah (Acinonyx jubatus) in southern Africa

Assessing the numbers and distribution of threatened species is a central challenge in conservation, often made difficult because the species of concern are rare and elusive. For some predators, this may be compounded by their being sparsely distributed over large areas. Such is the case with the cheetah Acinonyx jubatus. The IUCN Red List process solicits comments, is democratic, transparent, widely-used, and has recently assessed the species. Here, we present additional methods to that process and provide quantitative approaches that may afford greater detail and a benchmark against which to compare future assessments. The cheetah poses challenges, but also affords unique opportunities. It is photogenic, allowing the compilation of thousands of crowd-sourced data. It is also persecuted for killing livestock, enabling estimation of local population densities from the numbers persecuted. Documented instances of persecution in areas with known human and livestock density mean that these data can provide an estimate of where the species may or may not occur in areas without observational data. Compilations of extensive telemetry data coupled with nearly 20,000 additional observations from 39 sources show that free-ranging cheetahs were present across approximately 789,700 km2 of Namibia, Botswana, South Africa, and Zimbabwe (56%, 22%, 12% and 10% respectively) from 2010 to 2016, with an estimated adult population of 3,577 animals. We identified a further 742,800 km2 of potential cheetah habitat within the study region with low human and livestock densities, where another ∼3,250 cheetahs may occur. Unlike many previous estimates, we make the data available and provide explicit information on exactly where cheetahs occur, or are unlikely to occur. We stress the value of gathering data from public sources though these data were mostly from well-visited protected areas. There is a contiguous, transboundary population of cheetah in southern Africa, known to be the largest in the world. We suggest that this population is more threatened than believed due to the concentration of about 55% of free-ranging individuals in two ecoregions. This area overlaps with commercial farmland with high persecution risk; adult cheetahs were removed at the rate of 0.3 individuals per 100 km2 per year. Our population estimate for confirmed cheetah presence areas is 11% lower than the IUCN’s current assessment for the same region, lending additional support to the recent call for the up-listing of this species from vulnerable to endangered status

Cheetah Distribution and Population Data

Cheetah Distribution and Population Dat

Collaboration for conservation : assessing countrywide carnivore occupancy dynamics from sparse data

AIM : Assessing the distribution and persistence of species across their range is a crucial component of wildlife conservation. It demands data at adequate spatial scales and over extended periods of time, which may only be obtained through collaborative efforts, and the development of methods that integrate heterogeneous datasets. We aimed to combine existing data on large carnivores to evaluate population dynamics and improve knowledge on their distribution nationwide. LOCATION : Botswana. METHODS : Between 2010 and 2016, we collated data on African wild dog, cheetah, leopard, brown and spotted hyaena and lion gathered with different survey methods by independent researchers across Botswana. We used a multi-species, multi-method dynamic occupancy model to analyse factors influencing occupancy, persistence and colonization, while accounting for imperfect detection. Lastly, we used the gained knowledge to predict the probability of occurrence of each species countrywide. RESULTS : Wildlife areas and communal rangelands had similar occupancy probabilities for most species. Large carnivore occupancy was low in commercial farming areas and where livestock density was high, except for brown hyaena. Lion occupancy was negatively associated with human density; lion and spotted hyaena occupancy was high where rainfall was high, while the opposite applied to brown hyaena. Lion and leopard occupancy remained constant countrywide over the study period. African wild dog and cheetah occupancy declined over time in the south and north, respectively, whereas both hyaena species expanded their ranges. Countrywide predictions identified the highest occupancy for leopards and lowest for the two hyaena species. MAIN CONCLUSIONS : We highlight the necessity of data sharing and propose a generalizable analytical method that addresses the challenges of heterogeneous data common in ecology. Our approach, which enables a comprehensive multi-species assessment at large spatial and temporal scales, supports the development of data-driven conservation guidelines and the implementation of evidence-based management strategies nationally and internationally.http://www.wileyonlinelibrary.com/journal/ddihj2022Centre for Wildlife ManagementMammal Research InstituteZoology and Entomolog