In vitro establishment of Cryptomeria japonica (Taxocidaceae)

In this work, it was achieved to establish in vitro shoots of Cryptomeria japonica from 20 year old trees. The shoots were disinfected and treated with six different concentrations of kinetin and belciladenine in order to induce their development and budding. It was evaluated the effect of quality and lighting intensity on these using for this orange light at 20 microEs-1 m-2 and white light at 30 microEs-1 m-2. For shoots rooting it was used different concentrations of NAA (naftalen acetic acid) and IBA (indolbutiric acid) alone or combined. BA and KIN induced the bud formation in Cryptomeria but it was observed the best budding with BA at 9.1 microM. White light and orange light promoved the growth of explants as well as the growth of new buds but it was higher with orange light. The bud rooting was observed but it was not possible to find the best auxin concentration for rooting because of the plentiful callus formation on the base of explants and the root formation was very sporadic. The rooted shoots were placed on a substrate for their acclimation in greenhouse conditions.     

Pedigree-based assignment tests for reversing coyote (Canis latrans) introgression into the wild red wolf (Canis rufus) population

The principal threat to the persistence of the endangered red wolf (Canis rufus) in the wild is hybridization with the coyote (Canis latrans). To facilitate idengification and removal of hybrids, assignment tests are developed which use genotype data to estimate identity as coyote, 1/4, 1/2, 3/4 or full red wolf. The tests use genotypes from the red wolves that founded the surviving population and the resulting pedigree, rather than a contemporary red wolf sample. The tests are evaluated by analysing both captive red wolves at 18 microsatellite loci, and data simulated under a highly parameterized, biologically reasonable model. The accuracy of assignment rates are generally high, with over 95% of known red wolves idengified correctly. There are, however, tradeoffs between ambiguous assignments and misassignments, and between misidengifying red wolves as hybrids and hybrids as red wolves. These result in a compromise between limiting introgression and avoiding demographic losses. The management priorities and level of introgression determine the combination of test and removal strategy that best balances these tradeoffs. Ultimately, we conclude that the use of the assignment tests has the capacity to arrest and reverse introgression. To our knowledge, the presented approach is novel in that it accounts for genetic drift when the genotypes under analysis are temporally separated from the reference populations to which they are being assigned. These methods may be valuable in cases where reference databases for small populations have aged substantially, pedigree information is available or data are generated from historical samples.     

Identification of SpyA, a novel ADP-ribosyltransferase of Streptococcus pyogenes

Streptococcus pyogenes, the aetiological agent of both respiratory and skin infections, produces numerous exotoxins to establish infection. This report identifies a new exotoxin produced by this organism, termed SpyA, for S. pyogenesADP-ribosylating toxin. SpyA, MW 24.9, has amino acid identity with the ADP-riboslytransferases (ADPRTs) Staphylococcus aureus EDIN and Clostridium botulinum C3. Recombinant SpyA was able to hydrolyse beta-NAD(+), and this activity was dependent on a glutamate at position 187. SpyA has a putative biglutamate active site, and similar to most biglutamate ADPRTs, was able to ADP-ribosylate poly-l-arginine. SpyA modified numerous proteins in both CHO and HeLa cell lysates. Two-dimesional gel analysis and MALDI-TOF MS analysis of modified proteins indicated that vimentin, tropomyosin and actin, all cytoskeletal proteins, are targets. Expression of spyA in HeLa cells resulted in loss of actin microfilaments. We hypothesize that SpyA is produced by S. pyogenes to disrupt cytoskeletal structures and promote colonization of the host.     

A new method for estimating the size of small populations from genetic mark-recapture data

The use of non-invasive genetic sampling to estimate population size in elusive or rare species is increasing. The data generated from this sampling differ from traditional mark-recapture data in that individuals may be captured multiple times within a session or there may only be a single sampling event. To accommodate this type of data, we develop a method, named capwire, based on a simple urn model containing individuals of two capture probabilities. The method is evaluated using simulations of an urn and of a more biologically realistic system where individuals occupy space, and display heterogeneous movement and DNA deposition patterns. We also analyse a small number of real data sets. The results indicate that when the data contain capture heterogeneity the method provides estimates with small bias and good coverage, along with high accuracy and precision. Performance is not as consistent when capture rates are homogeneous and when dealing with populations substantially larger than 100. For the few real data sets where N is approximately known, capwire's estimates are very good. We compare capwire's performance to commonly used rarefaction methods and to two heterogeneity estimators in program capture: Mh-Chao and Mh-jackknife. No method works best in all situations. While less precise, the Chao estimator is very robust. We also examine how large samples should be to achieve a given level of accuracy using capwire. We conclude that capwire provides an improved way to estimate N for some DNA-based data sets.     

Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites

The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error-checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.     

Caveolae and caveolae-like membrane domains in cellular signaling and disease: identification of downstream targets for the tumor suppressor protein caveolin-1

Caveolae are small, flask-shaped invaginations of the plasma membrane present on a large number of mammalian cells. Recent results obtained with knock-out mice for the gene caveolin-1 demonstrate that expression of caveolin-1 protein is essential for caveolae formation in vivo. Caveolae are implicated in a wide variety of cellular events including transcytosis, cholesterol trafficking and as cellular centers important in coordinating signalling events. Caveolae share this role and the property of detergent insolubility with plasma membrane assemblies rich in glycosphingolipids and cholesterol, often called lipid rafts, but preferably referred to here as caveolae-like membrane domains. Due to such widespread presence and usage in cellular function, caveolae and related domains are implicated in human diseases, including cancer. In particular, the protein caveolin-1 is suggested to function as a tumor suppressor protein. Evidence demonstrating such a role for caveolin-1 in human colon carcinoma cells will be discussed together with data from microarray experiments seeking to identify caveolin-1 target genes responsible for such behavior.     

Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late pleistocene cave bears

Cave bears (Ursus spelaeus) existed in Europe and western Asiauntil the end of the last glaciation some 10,000 years ago.To investigate the genetic diversity, population history, andrelationship among different cave bear populations, we havedetermined mitochondrial DNA sequences from 12 cave bears thatrange in age from about 26,500 to at least 49,000 years andoriginate from nine caves. The samples include one individualfrom the type specimen population, as well as two small-sizedhigh-Alpine bears. The results show that about 49,000 yearsago, the mtDNA diversity among cave bears was about 1.8-foldlower than the current species-wide diversity of brown bears(Ursus arctos). However, the current brown bear mtDNA gene poolconsists of three clades, and cave bear mtDNA diversity is similarto the diversity observed within each of these clades. The resultsalso show that geographically separated populations of the high-Alpinecave bear form were polyphyletic with respect to their mtDNA.This suggests that small size may have been an ancestral traitin cave bears and that large size evolved at least twice independently.