Parallel matrix inversion techniques

In this paper, we present techniques for inverting sparse, symmetric and positive definite matrices on parallel and distributed computers. We propose two algorithms, one for SIMD implementation and the other for MIMD implementation. These algorithms are modified versions of Gaussian elimination and they take into account the sparseness of the matrix. Our algorithms perform better than the general parallel Gaussian elimination algorithm. In order to demonstrate the usefulness of our technique, we implemented the snake problem using our sparse matrix algorithm. Our studies reveal that the proposed sparse matrix inversion algorithm significantly reduces the time taken for obtaining the solution of the snake problem. In this paper, we present the results of our experimental work.

Do drivers intentionally target wildlife on roads?

Despite frequent reliance on surveys to document public attitudes towards conservation issues (such as invasive-species control), only rarely do researchers assess the validity of statements made by the public in response to such surveys. Therefore, how well responses match actual behaviour remains an open question. We conducted a survey asking drivers if they had seen and/or run over (intentionally or not) snakes, native frogs or invasive cane toads (Rhinella marina) on roads in the Northern Territory of Australia. To compare actual driver behaviour to the survey responses, we also carried out field experiments where we quantified the rates at which model snakes, frogs and toads (and controls) were run over on a rural highway. Our results show a discrepancy between survey responses and driver behaviour: for example, 25% of the people we surveyed indicated that they intentionally run over cane toads, yet field experiments showed that model toads were run over no more frequently than expected by chance, or than any other type of model.

Impact of invasive cane toads on Australian birds

The cane toad (Bufo marinus), a large, toxic, American anuran, was introduced to Australia in 1935. Populations of many of Australia's reptiles (snakes, varanid lizards, crocodiles) and carnivorous mammals (dasyurid marsupials) have declined because these predators are killed by the toad's powerful toxins. In contrast to these well-studied species, little is known about the cane toads impacts on Australian birds. We reviewed published and unpublished data on behavioral interactions between Australian avian predators and cane toads and collated distributional and dietary information to identify avian taxa potentially at risk from cane toad invasion. Cane toads are sympatric with 172 frog-eating bird species in Australia, and an additional 8 bird species overlap with the predicted future range of the toad. Although many bird species thus are potentially at risk, behavioral observations suggest the risk level is generally low. Despite occasional reports of Australian birds being killed when they ingest cane toads, most birds either ignore toads or survive the predation event. The apparently higher tolerance of Australian birds to toad toxins, compared with Australian reptiles and marsupials, may reflect genetic exchange between Australian birds and Asian populations that encounter other bufonid species regularly and hence have evolved the capacity to recognize or tolerate this toxic prey. 

Climate-driven impacts of prey abundance on the population structure of a tropical aquatic predator

In the present study we explore how annual variation in climate (late wet-season rainfall) affects population demography in a gape-limited obligate piscivorous predator, the Arafura filesnake Acrochordus arafurae in the Australian tropics. These aquatic snakes display extreme sexual dimorphism, with body sizes and relative head sizes of females much larger than those of males. Two consecutive years with low rainfall during the late wet season reduced the abundance of small but not large sized fish. Although snake residual body mass (RBM, calculated from a general linear regression of ln-transformed mass to ln-SVL) decreased after the first year with low prey availability, it was not until the second year that reduced prey abundance caused a dramatic decline in filesnake survival, and hence in population numbers. Thus, our results suggest that most snakes survived the first year of reduced prey abundance, but a successive year with low prey availability proved fatal for many animals. However, the effects of prey scarcity on RBM and survival fell disproportionately on some size classes of snakes. Medium-sized animals (large males and intermediate-sized females) were affected more dramatically than were small or large snakes. We attribute the higher survival of small snakes to their lower energy needs compared to medium-sized individuals, and the higher survival of large snakes to the continued abundance of large prey (mainly large catfish). Two successive years with low abundance of smaller sized prey thus massively modified the size-structure of the filesnake population, virtually eliminating large males and intermediate-sized females. Our field data provide a clear demonstration of the ways in which stochastic variation in climatic conditions can have dramatic effects on predator population demography, mediated via effects on prey availability.

Molecular and morphological description of a Hepatozoon species in reptiles and their ticks in the Northern Territory, Australia

Ticks, representing 3 species of Amblyomma, were collected from the water python (Liasis fuscus) and 3 additional reptile species in the Northern Territory, Australia, and tested for the presence of Hepatozoon sp., the most common blood parasites of snakes. In addition, blood smears were collected from 5 reptiles, including the water python, and examined for the presence of the parasite. Hepatozoon sp. DNA was detected in all tick and reptile species, with 57.7% of tick samples (n = 187) and 35.6% of blood smears (n=35) showing evidence of infection. Phylogenetic analysis of the 18S rRNA gene demonstrated that half of the sequences obtained from positive tick samples matched closest with a Hepatozoon species previously identified in the water python population. The remaining sequences were found to be more closely related to mammalian and amphibian Hepatozoon species. This study confirms that species of Amblyomma harbor DNA of the same Hepatozoon species detected in the water pythons. The detection of an additional genotype suggests the ticks may be exposed to 2 Hepatozoon species, providing further opportunity to study multiple host-vector-parasite relationships

Protected species use of a coastal marine migratory corridor connecting marine protected areas

The establishment of protected corridors linking the breeding and foraging grounds of many migratory species remains deficient, particularly in the world's oceans. For example, Australia has recently established a network of Commonwealth Marine Reserves, supplementing existing State reserves, to protect a wide range of resident and migratory marine species; however, the routes used by mobile species to access these sites are often unknown. The flatback marine turtle (Natator depressus) is endemic to the continental shelf of Australia, yet information is not available about how this species uses the marine area. We used a geospatial approach to delineate a coastal corridor from 73 adult female flatback postnesting migratory tracks from four rookeries along the north-west coast of Australia. A core corridor of 1,150 km length and 30,800 km2 area was defined, of which 52 % fell within 11 reserves, leaving 48 % (of equivalent size to several Commonwealth Reserves) of the corridor outside of the reserve network. Despite limited data being available for other marine wildlife in this region, humpback whale migratory tracks overlapped with 96 % of the core corridor, while the tracks of three other species overlapped by 5-10 % (blue whales, olive ridley turtles, whale sharks). The overlap in the distribution ranges of at least 20 other marine vertebrates (dugong, cetaceans, marine turtles, sea snakes, crocodiles, sharks) with the corridor also imply potential use. In conclusion, this study provides valuable information towards proposing new locations requiring protection, as well as identifying high-priority network linkages between existing marine protected areas. © 2014 Springer-Verlag Berlin Heidelberg.

Do the numbers and locations of road-killed anuran carcasses accurately reflect impacts of vehicular traffic?

Road-killed animals are easy and inexpensive to survey, and may provide information about species distributions, abundances, and mortality rates. As with any sampling method, however, we need to explore methodological biases in such data. First, how does an animal's behavior (e.g., use of the center vs. periphery of the road) influence its vulnerability to vehicular traffic? Second, how rapidly do post-mortem processes (scavenging by other animals, destruction or displacement by subsequent vehicles) change the numbers and locations of roadkills? Our surveys of anurans on a highway in tropical Australia show that different anuran species are distributed in different ways across the width of the road, and that locations of live versus dead animals sometimes differ within a species. Experimental trials show that location on the road affects the probability of being hit by a vehicle, with anurans in the middle of the road begin hit 35% more often than anurans on the edges; thus, center-using species are more likely to be hit than edge-using taxa. The magnitude of post-mortem displacement and destruction by subsequent vehicles depended on anuran species and body size. The mean parallel displacement distance was 122.7 cm, and carcasses of thin-skinned species exhibited greater post-mortem destruction. Scavenging raptors removed 73% of carcasses, most within a few hours of sunrise. Removal rates were biased with respect to size and species. Overall, our studies suggest that investigators should carefully evaluate potential biases before using roadkill counts to estimate underlying animal abundances or mortality rates.

Purification, characterization, crystallization and theoretical molecular modeling of gyroxin fraction from Crotalus durissus terrificus venom (Laurenti, 1768)

The venom of Crotalus durissus terrificus snakes presents various substances, including a serine protease with thrombin-like activity, called gyroxin, that clots plasmatic fibrinogen and promote the fibrin formation. The aim of this study was to purify and structurally characterize the gyroxin enzyme from Crotalus durissus terrificus venom. For isolation and purification, the following methods were employed: gel filtration on Sephadex G75 column and affinity chromatography on benzamidine Sepharose 6B; 12% SDS-PAGE under reducing conditions; N-terminal sequence analysis; cDNA cloning and expression through RT-PCR and crystallization tests. Theoretical molecular modeling was performed using bioinformatics tools based on comparative analysis of other serine proteases deposited in the NCBI (National Center for Biotechnology Information) database. Protein N-terminal sequencing produced a single chain with a molecular mass of similar to 30 kDa while its full-length cDNA had 714 bp which encoded a mature protein containing 238 amino acids. Crystals were obtained from the solutions 2 and 5 of the Crystal Screen Kit (R), two and one respectively, that reveal the protein constitution of the sample. For multiple sequence alignments of gyroxin-like B2.1 with six other serine proteases obtained from snake venoms (SVSPs), the preservation of cysteine residues and their main structural elements (alpha-helices, beta-barrel and loops) was indicated. The localization of the catalytic triad in His57, Asp102 and Ser198 as well as S1 and S2 specific activity sites in Thr193 and Gli215 amino acids was pointed. The area of recognition and cleavage of fibrinogen in SVSPs for modeling gyroxin B2.1 sequence was located at Arg60, Arg72, Gln75, Arg81, Arg82, Lis85, Glu86 and Lis87 residues. Theoretical modeling of gyroxin fraction generated a classical structure consisting of two alpha-helices, two beta-barrel structures, five disulfide bridges and loops in positions 37, 60, 70, 99, 148, 174 and 218. These results provided information about the functional structure of gyroxin allowing its application in the design of new drugs.

Occurrence of Cryptosporidium (Apicomplexa, Cryptosporidiidae) in Crotalus durissus terrificus (Serpentes, Viperidae) in Brazil

The objective of the present study was to investigate the prevalence of Cryptosporidium (Apicomplexa, Cryptosporidiidae) in the snake Crotalus durissus terrificus (Serpentes, Viperidae). Fifty animals were evaluated for the presence of oocysts of Cryptosporidium sp. at the time of arrival and 30 and 60 days later. Intestinal washings with saline solution (1% body weight), fecal samples, and organ scrapings were collected during the study. Oocysts were concentrated by an ether-phosphate-buffered saline sedimentation technique and then separated by a density gradient centrifugation technique. Smears were made with the sediment and submitted to modified acid-fast and auramine-rhodamine staining. Cryptosporidium-positive smears were used as controls for the experimental findings. The overall prevalence of Cryptosporidium sp. oocysts was 14%. Among the positive snakes, oocysts were detected only in the intestinal washing in two specimens, only in the feces in four specimens, and in both materials at least once in one specimen. The positive snakes were predominantly from Santa Maria da Serra city State of São Paulo (57.1%). We also observed that all of the examinations that presented positive results were obtained at least 27 days after the capture of the animals.

Digenetic trematodes infection in a Bothrops moojeni (Viperidae) population from a fauna rescue in Porto Primavera, São Paulo State

No presente estudo é descrita a infecção por trematódeos digenéticos parasitas da cavidade oral e esôfago em uma população de serpentes Bothrops moojeni provenientes de resgate de fauna em Porto Primavera, Estado de São Paulo. Foi observada prevalência de infecção de 68%. O grau de infecção (número de trematódeos por serpente) variou de 2 a 51 helmintos. Os trematódeos encontrados foram Ophisthogonimus spp. e Sticholecitha serpentis. A alta prevalência de infecção foi associada com a drástica alteração ambiental e o estresse multi-fatorial aos quais os animais foram submetidos, que poderiam ter favorecido o ciclo dos parasitas.

Antibacterial and antiparasitic effects of Bothrops marajoensis venom and its fractions: Phospholipase A(2) and L-amino acid oxidase

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Venous tone and cardiac function in the South American rattlesnake Crotalus durissus: mean circulatory filling pressure during adrenergic stimulation in anaesthetised and fully recovered animals

The effects of adrenergic stimulation on mean circulatory filling pressure (MCFP), central venous pressure (P-CV) and stroke volume (Vs), as well as the effects of altered MCFP through changes of blood volume were investigated in rattlesnakes (Crotalus durissus). MCFP is an estimate of the upstream pressure driving blood towards the heart and is determined by blood volume and the activity of the smooth muscle cells in the veins (venous tone). MCFP can be determined as the plateau in P-CV during a total occlusion of blood flow from the heart.Vs decreased significantly when MCFP was lowered by reducing blood volume in anaesthetised snakes, whereas increased MCFP through infusion of blood (up to 3 ml kg(-1)) only led to a small rise in Vs. Thus, it seems that end-diastolic volume is not affected by an elevated MCFP in rattlesnakes. To investigate adrenergic regulation on venous tone, adrenaline as well as phenylephrine and isoproterenol (alpha- and beta-adrenergic agonists, respectively) were infused as bolus injections (2 and 10 mu g kg(-1)). Adrenaline and phenylephrine caused large increases in MCFP and P-CV, whereas isoproterenol decreased both parameters. This was also the case in fully recovered snakes. Therefore, adrenaline affects venous tone through both alpha- and beta-adrenergic receptors, but the alpha-adrenergic receptor dominates at the dosages used in the present study. Injection of the nitric oxide donor SNP caused a significant decrease in P-CV and MCFP. Thus, nitric oxide seems to affect venous tone.

Perfil eletroforético das proteínas séricas de serpentes Crotalus durissus terrificus (cascavel) criadas em cativeiro

As serpentes peçonhentas dos gêneros Bothrops e Crotalus têm sido mantidas em cativeiro visando à extração de venenos para a produção de imunobiológicos. O conhecimento da fisiologia desses animais e as alterações na concentração de proteínas e suas frações séricas são importantes para a identificação precoce de importantes enfermidades que cursam com estados de hipoproteinemia e hiperproteinemia. O objetivo do trabalho foi determinar a concentração de proteína total e o perfil eletroforético das proteínas séricas de serpentes Crotalus durissus terrificus (cascavel) criadas em cativeiro. Foram colhidas amostras de sangue da veia coccígea ventral de 21 serpentes adultas e sadias, divididas em dois grupos: Grupo 1 de 12 machos com peso médio de 588,89±193,55g, e Grupo 2 de nove fêmeas com peso médio de 708,33±194,04g. A proteína total sérica foi determinada pelo método de refratometria e a eletroforese em gel de agarose. Obtiveram-se valores da proteína total sérica (g/dL) de 4,51±0,50 para machos e de 4,82±0,72 para fêmeas, e para machos e fêmeas de 4,64±0,61. Foram identificadas pela eletroforese quatro frações protéicas (g/dL): albumina, a, b, g-globulinas e calculada a relação albumina:globulina. As serpentes fêmeas apresentaram maiores valores para as variáveis, albumina e para a relação albumina/globulina (AG) diferindo significativamente (P<0,05) do grupo de machos, porém sem significado clínico.

Seasonal influence on biochemical profile and serum protein electrophoresis for Boa constrictor amarali in captivity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)