Miracle-dz/UniFAR-FTUs huggingface dataset:
CORRELATED MORPHOLOGICAL AND ALLOZYME VARIATION IN THE HYBRIDIZING TOADS BUFO AMERICANUS AND BUFO HEMIOPHRYS

Morphological and genetic variation were highly correlated in the hybrid zone between the toads Bufo hemiophrys and B. americanus in southeastern Manitoba. We subjected 30 morphological traits to discriminant function analysis and compared the results with a genetic index of hybridization constructed from five diagnostic isozyme loci (Pgdh, Mpi, Ldh-1, Icdh-2, and Sod) from the same specimens. The loci did not exhibit identical clines in allele frequencies. Both morphological and genetic scores for individuals demonstrated increased individual variation within the hybrid zone. Compared to morphological evidence taken 11 or more years prior, the hybrid zone shifted westward by about 9.6 km while maintaining the same width. Fluctuating population sizes may influence such dynamics. Selection against hybrids could not be demonstrated. Interspecies taxonomic boundaries are rendered vague by hybrid zones, creating difficulties for species delineation. Because hybridization may imply only the plesiomorphic lack of isolation mechanisms, evidence that the taxa involved maintain their historic identities outside of the hybrid zone despite a restricted exchange of genes within it argues for the existence of phylogenetic species.
Southern Hemisphere biodiversity and global change: Data gaps and strategies

Long-term datasets needed to detect the impacts of global change on southern biodiversity are still scarce and often incomplete, challenging adaptation planning and conservation management. Biological data are probably most limited in arid countries and from the oceans, where natural environmental variability (‘noise’) means that long time series are required to detect the ‘signal’ of directional change. Significant national and international investment and collaboration are needed for most southern nations to reliably track biodiversity trends and improve conservation adaptation to rapid climate change. Emerging early warning systems for biodiversity, incorporating regional environmental change drivers, citizen science and regional partnerships, can all help to compensate for existing information gaps and contribute to adaptation planning.
Investigating the mechanisms of silver nanoparticle toxicity in Daphnia magna: a multi-omics approach

The work presented in this thesis tests the hypothesis that AgNP toxicity is induced through the release of ionic silver (Ag) and therefore, that the mechanism of AgNP and Ag+ toxicity is identical. This hypothesis was tested through the comparison of molecular-level changes in Daphnia magna, a global keystone species of freshwater ecosystems, induced by AgNP and AgN03. Through use of Agilent microarray transcriptomics and direct-infusion mass spectrometry metabolomics, the same molecular profile changes were observed in D. magna exposed to AgNPs and to the dissolved Ag fraction alone. However, a greater magnitude of effect was observed in AgNP exposures. The measurement of the uptake and depuration of both forms of silver in D. magna suggested the increased magnitude of molecular response to AgNP exposure fit a Trojan-horse type mechanism. Whereby AgNPs absorbed by D. magna, resulted in higher internal concentration of toxic Ag+. Further investigation into the mechanism of AgNP toxicity revealed significant changes to constituents of the purine metabolism pathway and an absence of a traditional oxidative stress response. Overall, this research advances the mechanistic understanding of AgNP toxicity to aquatic organisms, and highlights the ability of omics technologies to provide unique insights into mechanisms of toxicity.
In vitro growth inhibition of microbes by human placental extract

Human placental extract that is used as a wound healer, acts as a stimulating agent for tissue repair. It has an effective inhibitory role on the growth of different microbes like bacteria, e.g. Escherichia coli, Staphylococcus aureus and fungi, e.g. Saccharomyces cerevisiae, Kluyveromyces fragilis and Candida albicans. It also prevents growth of clinically isolated bacteria, e.g. E. coli from urine and blood culture and S. aureus from pus. Drug-resistant strains such as E. coli DH5α Pet-16 Amp R and Pseudomonus aeruginosa Cam R were also significantly inhibited by the extract. The extract has both bacteriostatic and fungistatic activities. Dose-dependent response of the extract was observed. Antimicrobial activity was retained after heating but was lost after dialysis. The MIC of the extract varies between 200 and 8000 mg/l. No antimicrobial activity was observed with human serum and aqueous extract of mouse muscle serving as control. A mixture of polydeoxyribonucleotides appears to be the causative agent. Partial protection of the wound from secondary microbial infection is thus indicated.
Extraction and Quantification of Polyphosphate in the Budding Yeast Saccharomyces cerevisiae

[Abstract] Inorganic polyphosphate (polyP) is a linear polymer present in both prokaryotic and eukaryotic organisms and made from three to hundreds of orthophosphate residues linked by phosphoanhydride bonds. The biological role of this molecule goes beyond serving as Pi store or energy source to replace ATP. For instance, in yeast polyP levels have been related to stress adaptation and this molecule has been shown to be the substrate for polyphosphorylation of proteins. Here we describe two different methods to purify polyP from the yeast Saccharomyces cerevisiae and the subsequent protocol to quantify polyP levels by spectrophotometrically measuring the Pi generated upon enzymatic hydrolysis of purified polyP. It must be noted that the purification protocol used greatly influences the polyP values obtained.
Effects of nitrogen-fixing symbiotic cyanobacteria on the microbial ecology of the coral, Montastraea cavernosa

Corals form the physical structure of coral reefs, one of the most ecologically and economically important ecosystems in the world. The abundant and broadly distributed Caribbean coral Montastraea cavernosa forms a symbiosis with intracellular nitrogen-fixing cyanobacteria in some, but not all colonies, which make up approximately 30% of the population and display a characteristic orange fluorescence. Diverse and functionally important microbial communities of dinoflagellates, bacteria, Archaea, viruses, fungi, and other organisms are also associated with corals and together with the host compose what is termed the coral holobiont. Whether the cyanobacteria are mutualists, commensals, or parasites, and their effects on the coral holobiont, are unknown. The influence of the cyanobacteria on the microbial ecology of M. cavernosa and overall holobiont fitness were investigated using sequencing of ribosomal RNA PCR amplicons, metatranscriptomic sequencing of rRNA and mRNA from the holobiont, and experimental tests of various fitness metrics. The cyanobacterial symbionts appear to be diverse, but many are Pleurocapsa-like and related to nitrogen-fixing cyanobacterial symbionts of diatoms. Their presence does not affect the taxonomic composition of the diverse coral-associated prokaryotic community, but such communities do exhibit significant geographic differences. Metatranscriptomic analysis of mRNA indicates that coral-associated prokaryotes, including cyanobacteria, are transcriptionally active, although few transcripts related to nitrogen fixation were recovered. There were no significant fitness differences between colonies with and without cyanobacteria for any of the metrics tested, including coral growth, response to thermal stress, and the ability to deter predators and produce cyanobacterial toxins. Genotyping of coral hosts revealed that colonies with and without cyanobacteria form two genetically distinct populations at small spatial scales, providing evidence for selection. The cyanobacteria do not appear to be parasitic to the coral host, but any potential benefits they may convey remain unknown. Analysis of metatranscriptomic data to investigate differences in the functional activity of coral hosts and associated microbial communities is ongoing.
Quantitative sampling of the benthic fauna in a large, fast flowing river (Austrian Danube)

The free flowing Austrian Danube is a 9th order gravel stream, deep and fast flowing and under these conditions obtaining quantitative samples is still proble­ matic. Four methods (Slurp Gun, Petersen Grab, Deep Water Freeze Corer and Air Lift) have been tested against each other and against a freeze corer with in situ electro positioning. The evaluation has to be a relative one, because the absolute population descriptors are unknown. Test criteria were therefore: the qualitative composition and the relative and absolute abundances of the stream fauna, in addition to the purely technical performance of the equipment. A multivariate discriminant analysis revealed constant performance traits for all four methods, regardless of variations in sediments and fauna, at least to the extent that there are variations in the stretch of the Danube that was sampled. All test criteria proved the 'Air Lift' sampler to be the best method. Second was the 'Deep Water Freeze Corer', which is the only available method for studying the vertical distribution of the stream fauna within the sediment, although with certain limitations. The 'Slurp Gun' and 'Petersen Grab' are very poor methods for quantitative sampling in these circumstances.
Troublesome tropical mints: re-examining generic limits of Vitex and relations (Lamiaceae) in South East Asia

The relationships of vitex and genera historically placed in Lamiaceae subfamily Viticoideae were investigated. Particular focus was given to some South East Asian genera traditionally allied to Vitex (Paravitex, Tsoongia, Viticipremna, Teijsmanniodendron) since progress with South East Asian Floras is being hampered by a lack of clarity in current generic delimitation. On the basis of maximum parsimony and Bayesian phylogenetic analyses of ITS and ndhF sequence data we provide evidence that the Viticoideae is not monophyletic, its members being spread between a number of clades which include genera currently recognised as incertae sedis (Peronema, Hymenopyramis, Petraeovitex, Tectona). The most well supported clade, the Vitex group, contains Vitex, Paravitex, Tsoongia, Viticipremna, Petitia and Teijsmanniodendron. Morphological similarities of the genera included in this group are also discussed. In light of this evidence Paravitex, Viticipremna and Tsoongia are reduced to synonymy with Vitex, the new combinations being made here. The position of Teijsmanniodendron is not resolved and its generic status is therefore upheld. Similarly, Petitia is upheld due to a lack of neotropical taxa within the sample.
Local and landscape drivers of arthropod diversity and decomposition processes in oil palm leaf axils

Oil palm expansion results in a loss of biodiversity and associated ecosystem services. However, there are factors that influence the severity of these impacts and enhancing biodiversity within plantations is important. In the present study, we examined the role of epiphytes for supporting arthropod communities in oil palm plantations in Sumatra, Indonesia. We considered the effects of landscape context and local characteristics (epiphyte cover, herbicide use and local microclimate) on arthropod communities and litter decomposition in oil palm leaf axils. We surveyed arthropods and measured decomposition rates at two different heights on 80 oil palms located at the centre and edge of eight plantations. We found that oil palms at the edge of plantations hosted a higher abundance and more arthropod taxa than oil palms in the centre of plantations. Moreover, organic matter mass and height of the leaf axil were important for arthropod communities, and the decomposition rate was negatively related to ant abundance. However, epiphyte cover did not influence arthropod communities. The results of the present study show that leaf axils with more organic matter and at a higher location on the oil palm promote arthropod biodiversity. Furthermore, oil palm plantations adjacent to different land‐use systems have enhanced biodiversity.
Down-regulation of PINCH-1 Reduces Expression of EGFR, ERK1/2 and c-Myc, and Leads to Loss of Cell Viability in Colon Cancer Cells

Particularly interesting new cysteine-histidine rich protein (PINCH) is related to poor outcome in colorectal cancers. Here, the relationship between PINCH-1 and cell survival in colon cancer cells was analyzed and the signaling pathways regulated by PINCH-1 by using PINCH-1 siRNA. KM12C cells were treated with PINCH-1 siRNA or control siRNA. Cell number was analyzed by crystal violet staining and caspase-3 activity was assessed using a fluorescent substrate. PINCH-1 extra- and intracellular pathways in KM12C cells were investigated, using phospho-kinase/phospho-receptor tyrosine kinase (RTK) antibody arrays. The expression of c-Myc was evaluated by Quantitative real-time PCR (qPCR) and Western blot analysis. Cell number was significantly decreased ( P =0.003) and the caspase-3 activity increased ( P =0.019) in PINCH-1 depleted KM12C cultures compared to siRNA cultures. In PINCH-1 silenced KM12C cells, the levels of EGFR and ERK1/2 were significantly decreased ( P =0.008, P= 0.003, respectively) compared to their controls, as were the c-Myc mRNA and protein expressions ( P =0.0073, P= 0.0002, respectively). Down-regulation of PINCH-1 reduced the cell survival and lowers the levels of EGFR, ERK1/2 and c-Myc in colon cancer cells. PINCH-1 is essential for cell survival, and may be a future target for anticancer therapy.
The complete mitochondrial genome of Leiocassis argentivittatus (Siluriformes: Bagridae)

Abstract In this study, the complete mitochondrial genome of Leiocassis argentivittatus has been determined by polymerase chain reaction methods for the first time. The overall base composition of Leiocassis argentivittatus mitogenome is 31.7% for A, 26.4% for C, 14.9% for G and 27.0% for T. The percentage of G + C content is 41.3%. The mitogenome is a circular DNA molecule of 16,534 bp in length with a D-loop region and contains 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 13 protein-coding genes. The mitochondrial genome sequencing for Leiocassis argentivittatus in this study provides important molecular data for further evolutionary analysis of Siluriformes.
Atividade antifúngica in vitro de compostos naftoquinoidais contra cepas de Candida tropicalis resistentes ao fluconazol

A incidencia de infeccoes oportunistas causadas por fungos, com destaque para as leveduras do genero Candida vem aumentando substancialmente. Estudos relatam que tem sido observado um notavel crescimento de infeccoes por especies nao albicans (Candida tropicalis, Candida glabrata, Candida parapsilosis e Candida krusei). Isolados clinicos resistentes aos azolicos, em especial ao fluconazol, sao cada vez mais relatados. As naftoquinonas sao uma importante classe de moleculas biologicamente ativas, apresentando atividades antibacteriana, antifungica, antiviral, anti-inflamatoria, antipiretica, anticancerigena e tripanocida e tem sido amplamente testadas em varios estudos farmacologicos. Nos ultimos anos intensificou-se o interesse nestas substâncias, nao so devido a sua importância em processos bioquimicos vitais, como tambem ao destaque cada vez maior que apresentam em variados estudos farmacologicos. O presente trabalho buscou avaliar e comparar o efeito antifungico de naftoquinonas frente a cepas de Candida tropicalis resistentes e sensiveis ao fluconazol, utilizando diferentes tecnicas tais como metodos de microdiluicao em caldo, procedimentos de citometria de fluxo e ensaio do Cometa. Utilizamos sete cepas de Candida tropicalis resistentes ao fluconazol para esse estudo, as quais foram isoladas de sangue e faziam parte da coleccao de leveduras do Laboratorio de Bioprospeccao Experimental em leveduras (LABEL), afiliado com a Faculdade de Farmacia da Universidade Federal do Ceara . Foi utilizado tres compostos de naftoquinonas frente a 07 cepas de Candida tropicalis e foram submetidas aos testes de Sensibilidade in vitro , onde apresentaram uma potente atividade antifungica. Atraves da Citometria de Fluxo, foi possivel avaliar alteracoes morfologicas e de integridade da membrana significativas desses compostos frentes as cepas, alem de disfuncao mitocondrial e producao de especies reativas de oxigenio. Atraves do ensaio do Cometa foi possivel encontrar danos significativos ao DNA. Em sintese, os resultados sugerem que estes compostos podem ser usados como agentes antifungicos para o tratamento de candidemias.
Hummingbird Conservation in Mexico: The Natural Protected Areas System

ABSTRACT: Hummingbirds represent an avian family restricted to the Americas that feeds mainly on nectar obtained from ornithophilous plants. In North America (Mexico-USA-Canada), 58 species have been reported out of the 330 total hummingbird species, all of them occurring in Mexico. In this work we analyzed the distribution of hummingbirds in relation to the coverage of the natural protected area system in Mexico using a complementarity analysis to assess the minimum set of areas needed to protect all species. We focused our search mainly to biosphere reserves, as these areas have complete bird lists. Six biosphere reserves included 93% of the hummingbird species. Four species were not included in any biosphere reserve or other natural protected area. To preserve those species, three important bird areas (AICAs as they are known in Spanish) are needed. With these nine areas, all hummingbird species are included. Hummingbird distributions can be classified in six groups that distribute following the major biogeographic regions described for Mexico, including groups using; (1) the main mountain ranges, (2) the Pacific tropical dry forests, (3) the Gulf of Mexico slopes with tropical dry forest, (4) the humid tropical forest in southern Mexico, and both (5) Yucatan and (6) Baja California peninsulas.
Effects of grain variability and processing on starch utilization by lactating dairy cattle

Variation in site of digestion and lactation performance among lactating dairy cows fed different grain sources was evaluated and reviewed. The enzymatic assay for starch contributes to variation among and possibly even within experiments. Genetic differences within grain source affect digestibility, but effects of grain processing are considerable. When quantifying response criteria among numerous experiments with varying experimental procedures, the variation among experiments is very high and should be considered in regressions used to evaluate treatment responses. Some of the variation among experiments could be explained by variable DMI (positive relationship with milk production and microbial N flow to the duodenum but negative relationship with milk fat percentage and ruminal digestibility of starch) and other chemical measurements of dietary composition (especially forage and NDF percentages of the diet). Other sources of variation that could not be quantified among experiments were accounted for in regression models as experiment effects. After these adjustments, least squares means were calculated as the average of all effects remaining in the models. Our results documented that processing
ISOLATION AND IDENTIFICATION OF FUNGI INVOLVED IN THE POST-HARVEST SPOILAGE OF GUAVA (Psidium guajava) IN AWKA METROPOLIS

The postharvest spoilage of Guava fruit (Psidium guajava Linn.) from four selected markets in Awka, Anambra State, Nigeria was investigated. Isolation of associated fungi from guava fruits was carried out on Sabouraud dextrose agar (SDA). A total of seven (7) fungi were isolated namely Colletotrichum gloeosporioides, Fusarium oxysporum, Mucor sp. , Rhizopus stolonifer, Aspergillus niger, A. fumigatus and A. parasiticus. F. oxysporum was the most prevalent of the seven fungi isolated and appeared in all the four locations. Guava fruit spoilage was most severe under humid environment and was enhanced by wounds on fruit surfaces. Pathogenicity test carried out revealed that of the seven isolates four proved pathogenic when artificially inoculated into healthy guava fruits. These were F. oxysporum, A. niger, A. fumigatus and A. parasiticus. These organisms are, therefore, the causal agents of guava fruit rot under the conditions of this study. The rest isolates did not reproduce fruit rot following artificial inoculation.
Growth and reproductive biology of the amphidromous shrimp Palaemon pandaliformis (Decapoda: Caridea) in a Neotropical river from northeastern Brazil

Population biology, growth and reproductive aspects of the amphidromous shrimp Palaemon pandaliformis (Stimpson, 1871) were investigated in a Neotropical river of northeastern Brazil. The specimens were collected every month from September 2009 to August 2010. Total and monthly sex ratios deviated in favour of males. Von Bertalanffy growth parameters indicated that the females grew more rapidly, reached larger sizes, and had a longer life span than males. We also observed continuous reproductive activity and juvenile recruitment throughout the year. Relations between the number of eggs (fecundity) and body size indicated that fecundity in females increase with size. Compared with previous results, some population biology parameters of the freshwater population of P. pandaliformis differ from estuarine populations. The reproductive aspects analyzed here and their comparison with other marine species were consistent with the hypothesis that Palaemonidae species are undergoing an adaptation process and colonizing fresh water environments.
Diversity in the diet of the predator Octopus cyanea in the coral reef system of Moorea, French Polynesia

ABSTRACT This study examines interactions among behavioural and environmental influences on individual octopus diet. Octopus cyanea were surveyed in July 2014 in Moorea, French Polynesia (17°29ʹ S, 149°50ʹ W) and the diversity of their diets – revealed by prey species remains – were combined with data on octopus personality, habitat complexity, prey size and octopus density to test hypotheses on three different levels: individuals, study sites and population. Diets were more diverse for octopuses that exhibited more approach behaviours during a disturbance test of personality, than for those that were more withdrawn. Octopus diets were more diverse within areas of greater substrate type diversity, suggesting that on a local scale, substrate type diversity influences biodiversity. Octopus diets were also more diverse when prey were smaller and where octopuses were more abundant, suggesting an effect of prey abundance (or conversely of competition among octopuses). For the Moorea population overall, dietary diversity was high (richness = 64 taxa of Bivalvia, Crustacea, and Gastropoda), with low dominance. This study confirms that to better understand the variation in octopus diet we should look from the individuals to populations, taking into account environmental and behavioural factors, such as individual personality, habitat diversity, prey sizes (energy) and octopus abundance.
Factors affecting protein digestibility in soybean foods

Factors affecting protein digestibility in soybean foods were studied. There was no significant correlation between protein digestibility of the soybean foods examined and their levels of inhibitory activity against trypsin and α-chymotrypsin. On the other hand, a variation in protein digestibility among soybean foods examined was noted : the protein of yuba (soy protein-lipid film) was more digestible by protease, but the protein of kinako (roasted soy meal) was less digestible. Kinetic analysis revealed a difference in susceptibility of proteins to proteolytic action between yuba and kinako. The present study concludes that the chemical form of proteins of soybean foods may be an important factor in their protein digestibility.