Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of two isoenzymes of a-amylase of Araucaria araucana (Araucariaceae) on the digestion of starch

Starch is the principal reserve of Araucaria araucana seeds, and it is hydrolysed during germination mainly by a-amylase. There are several a-amylase iso enzymes whose patterns change in the embryo and in the megagametophyte from the one observed in quiescent seeds (T0) to a different one observed 90 h after imbibition (T90). The objective of this research was to study the roles of two purified a-amylase iso enzymes by in vitro digestion of starch granules extracted from the tissues at two times of imbibition: one is abundant in quiescent seeds and the other is abundant after 90 h of imbibition. The isoenzymes digested the starch granules of their own stage of ger mination better, since the isoenzyme T0 digested starch granules mainly from quiescent seeds, while the isoenzyme Tgo digested starch mainly at 90 h of imbibition. The sizes of the starch granule and the tissue from which these granules originated make a difference to digestion by the isoenzymes. Embryonic isoenzyme T0 digested large embryonic starch gran ules better than small and medium-sized granules, and better than those isolated from megaga metophytes. Similarly isoenzyme Tg0 digested small embryonic starch granules better than medium-sized and large granules, and better than those isolated from megagametophytes. However, a mixture of partially purified megagametophytic isoenzymes T0 and Tg0 digested the megagametophytic granules better than those isolated from embryos. Studies of in vitro sequential digestion of starch granules with these isoenzymes corroborated their specificity. The isoenzyme Tg0 digested starch granules previously digested by the isoenzyme T0. This suggests that in vivo these two isoenzymes may act sequentially in starch granule digestion.
Range extension of Hypostomus cochliodon Kner, 1854 (Siluriformes: Loricariidae) in Bermejo River, Salta, Argentina

Hypostomus cochliodon Kner, 1854 had been recorded from Paraguay and Parana rivers in Argentina. We recorded for the first time specimens of H. cochliodon to the Bermejo River basin. It is also the first record of this species to Salta province, Argentina.
Anti-Cancer Activity of Three Terminalia Species and Preliminary Phytochemical Screening

This study evaluated anticancer potential of three Terminalia species, Terminalia muelleri, Terminalia bellerica, and Terminalia laxiflora and also their phytochemical content were determined. Anticancer potential of the plant extracts was measured according to MTT assay. The results showed that T. muelleri methanolic extract was active against breast cancer cell line with IC50 40 µg/mL. T. bellerica methanolic extract exerted cytotoxic effects only against colon cancer and liver cancer cell lines with IC50 of 50 and 15µg/mL, respectively. While T. laxiflora methanolic extract did not inhibit the proliferation of all cancer cell lines tested. Phytochemical investigation of the three plant species proved the presence of carbohydrates, flavonoids, tannins, and triterpenes. The methanolic extracts of T. muelleri and T. bellerica had a significant anticancer activity and so further phytochemical study to isolate and identify the bioactive molecules responsible for the observed anticancer activity is necessary.
Natural occurrence of Pasteuria nishizawae in soybean areas

Soybean ( Glycine max (L.) Merrill) is a widely grown crop of economic prominence. Brazil is considered as the second largest worldwide producer and exporter. Soybean cyst nematode, Heterodera glycines Ichinohe, in one of the most serious threats for this crop, considered as its most destructive parasite. The first report of this disease in Brazil was recorded during the 1991/1992 harvest. Control of nematodes is more challenging if compared with other plant diseases control. Thus, there is a growing demand to search for alternative control practices that will not harm the environment nor the human being. Therefore, the highly specific bacteria Pasteuria spp. Metchnikoff, represents an auspicious biological control agent against nematodes. The biological control of the soybean cyst nematode with the bacterium Pasteuria nishizawae Sayre has proven an excellent choice and has been studied by different scientists. The objective of this work was to determine the natural occurrence of Pasteuria nishizawae in Brazilian soils. The experiment was performed under greenhouse conditions at the Research unit from Syngenta® in Uberlandia-MG, Brazil, with soil samples originated from soybean planted areas from the Brazilian states of Bahia, Goias, Mato Grosso and Parana. Fractions of 150 cm 3 of soil were withdrawn to be processed by the centrifugal flotation technique in sucrose solution. Aliquots of 1 mL from the obtained suspension were observed in Peters’ chamber with the aid of an inverted light microscope, in order to verify the absence or presence of bacterial endospores attached to the cuticle of the nematodes extracted from the soil samples. The frequency of Pasteuria nishizawae incidence was of 100% within the samples analyzed.
Productivity, metabolism and physiology of free-living Chemoautotrophic Epsilonproteobacteria

Chemoautotrophic ecosystems at deep-sea hydrothermal vents were discovered in 1977, but not until 1995 were free-living autotrophic Epsilonproteobacteria identified as important microbial community members. Because the deep-sea is food-starved, the autotrophic metabolism of hydrothermal vent Epsilonproteobacteria may be very important for deep-sea consumers. However, quantifying their metabolic activities in situ has remained difficult, and biochemical mechanisms underlying their autotrophic physiology are poorly described. To gain insight into environmental processes, an approach was developed for incubations of microbes at in situ pressure and temperature (25 MPa, 24C) with various combinations of electron donors/acceptors (H2, O2 and NO3 – and 13HCO3 – ) as a tracer to track carbon fixation. During short (18-24 h) incubations of low-temperature vent fluids from Crab Spa (9N East Pacific Rise), the concentration of electron donors/acceptors and cell numbers were monitored to quantify microbial processes. Measured rates were generally higher than previous studies, and the stoichiometry of microbially-catalyzed redox reactions revealed new insights into sulfur and nitrogen cycling. Single-cell, taxonomically-resolved tracer incorporation showed Epsilonproteobacteria dominated carbon fixation, and their growth efficiency was calculated based on electron acceptor consumption. Using these data, in situ primary productivity, microbial standing stock, and average biomass residence time of the deep-sea vent subseafloor biosphere were estimated. Finally, the population structures of the most abundant genera Sulfurimonas and Thioreductor were shown to be strongly influenced by pO2 and temperature respectively, providing a mechanism for niche differentiation in situ. To gain insights into the core biochemical reactions underlying autotrophy in Epsilonprotebacteria, a theoretical metabolic model of Sulfurimonas denitrificans was developed. Validated iteratively by comparing in silico yields with data from chemostat experiments, the model generated hypotheses explaining critical, yet so far unresolved reactions supporting chemoautotrophy in Epsilonproteobacteria. For example, it provides insight into how energy is conserved during sulfur oxidation coupled to denitrification, how reverse electron transport produces ferredoxin for carbon fixation, and why aerobic growth yields are only slightly higher compared to denitrification. As a whole, this thesis provides important contributions towards understanding core mechanisms of chemoautrophy, as well as the in situ productivity, physiology and ecology of autotrophic Epsilonproteobacteria. Thesis Supervisor: Dr. Stefan Sievert Title: Associate Scientist with Tenure, Department of Biology Woods Hole Oceanographic Institution
Discovery of calcium enrichment in cutting teeth of parasitic wasp ovipositors (Hymenoptera: Ichneumonoidea)

Energy dispersion X-ray spectrometry of the ovipositor tips of two species of parasitic wasps, Gabunia sp. (Ichneumonidae : Cryptinae) from Uganda and the cosmopolitan Heterospilus prosopidis (Braconidae : Doryctinae) show that they have high concentrations of calcium as well as of manganese associated with the apex of the lower ovipositor valve and in the former, specifically with the lower valve teeth. Previous studies had revealed only manganese in the ovipositors of ichneumonoids, and the discovery of highly calcium-enriched cutting teeth might indicate the involvement of biomineralization, in addition to transition metal-protein complexes, in cuticular hardening in these parasitic wasps. Comparisons with related taxa indicate that the calcium enrichment is not present in all members of their groups.
Estimating the heritability of virulence in HIV

The rate that HIV-infected individuals progress to AIDS and death varies greatly. Viral load taken during the asymptomatic phase of the disease is one of the best-known predictors of HIV progression rate and transmission risk, and is known to be influenced by both host and environmental factors. However, the role that the virus itself plays in determining the viral load is less clear. Previous studies have attempted to quantify the amount the viral genome influences viral load, or the heritability of viral load, using transmission pairs and phylogenetic signal in small sample sizes, but have produced highly disparate estimates. Efficient and accurate methods to estimate heritability have been utilised by quantitative geneticists for years, but are rarely applied to non-pedigree data. Here, I present a novel application of a population-scale method based in quantitative genetics to estimate the heritability of viral load in HIV using a viral phylogeny. This new phylogenetic method allows the inclusion of more samples than ever previously used, and avoids confounding effects associated with transmission pair studies. This new method was applied to the two largest HIV subtypes found in the UK, subtypes B and C, using sequences and clinical data from UK-wide HIV databases. For subtype B (n=8,483) and C (n=1,821), I estimated that 5.7% (CI 2.8–8.6%) and 29.7% (CI 14.8–44.7%) of the variance in viral load is determined by the viral genome, respectively. These estimates suggest that viral influence on viral load varies greatly between subtypes, with subtype C having much larger viral control over viral load than subtype B. I expanded the phylogenetic method to test whether the component of the viral load determined by the virus has changed over time. In subtype B, I found evidence of a small but significant decrease in the viral component of viral load of -0.05 log10 copies/mL/yr. I built a stochastic, individual-based model capable of simulating a realistic HIV epidemic, with heritable viral loads that influence transmission and disease progression, capable of generating data sets to assess the accuracy of phylogenetic methods. This was successfully used to generate epidemics approximating those in a small African village and a Western ‘men who have sex with men’ community under a variety of conditions. To test the accuracy of the new phylogenetic heritability estimation method, simulated datasets were generated with the heritability of viral load set at values of 30%, 50%, 70%, and 90%. Unfortunately, complications in the heritability equation used prevented full assessment of the new phylogenetic method on the simulated data. Future development of the model will enable simulation of realistic viral loads under varying heritability values, enabling simulation of data sets that can be used to test this and other heritability estimation methods. This new phylogenetic method allows accurate estimation of heritability in large datasets, and has provided valuable insight into the viral influence on viral load in HIV.
Effect of cryopreservation using slow freezing or vitrification on viability and metabolic activity of mesenchymal stromal cells encapsulated within alginate spheres with diameter of 1 mm and more

The aim of the study was to evaluate the effect of exposure duration of alginate encapsulated mesenchymal stromal cells (MSCs) in multicomponent cryoprotective solution DEPS-1 (10% dimethyl sulfoxide, 20% ethylene glycol, 1,2-propane diol and 0.5 M sucrose) on survival and metabolic activity following cryopreservation using vitrification. The spheres of 1mm diameter obtained by dropwise addition of sodium alginate into calcium chloride were used in the experiments. Alginate spheres derived by this method contained more cells as compared to the spheres of (0.5 ± 0.2) mm derived by pulverizing the alginate into calcium chloride. It was shown that using of multicomponent cryoprotective solution DEPS-1 allowed achieving successful cryopreservation of MSCs encapsulated in alginate spheres of different sizes. It was found that saturation with cryoprotective solution of MSCs encapsulated in spheres with 1.2 mm size needed a longer exposure with CPA if compared with spheres of 0.6 mm size. Probl Cryobiol Cryomed 2014; 24(3):222-230.
Who is killing the tiger Panthera tigris and why?

Abstract We investigated the range of people involved in killing tigers Panthera tigris in the Bangladesh Sundarbans, their motives and methods, and their links to the commercial trade. Using snowball sampling we conducted 141 qualitative interviews with local people. We identified five categories (village residents, poachers, shikaris, trappers and pirates), each with different motives, methods and networks. Village residents kill tigers predominantly for safety, whereas others kill in the forest professionally or opportunistically. Poachers kill tigers for money, but for others the motives are more complex. The motives of local hunters are multifaceted, encompassing excitement, profit, and esteem and status arising from providing tiger parts for local medicine. Pirates kill tigers for profit and safety but also as a protection service to the community. The emerging international trade in tiger bones, introduced to the area by non-local Bangladeshi traders, provides opportunities to sell tiger parts in the commercial trade and is a motive for tiger killing across all groups.
Etude expérimentale sur les premiers stades du développement du membre antérieur chez l'embryon du Chélonien Emys orbicularis L.: détermination en mosaïque et régulation

Experimental study on the early stages of development of the front limbs of the embryo of the chelonian Emys orbicularis L. : mosaic determination and regulation Ablation of postotic somites 6–13 on one side in embryos of Emys orbicularis L. or injury to the adjacent somatopleure at the developmental stage when 15–21 somite pairs were present, led to arrest of forelimb-bud development in this part of the somatopleure on the operated side. Limb development in the remaining part of prospective somatopleure on the operated side was investigated 5–11 days after the operation. When this part of somatopleure was adjacent to cranial somites 6–9 or 6–10, the development stopped at the start of the apical crest as in Anguis or Scelotes forelimb-buds. A part of somatopleure adjacent to caudal somites 8–12, 9–12 or 10–12 developed into a normal limb with three segments; a part of somatopleure adjacent to 1–2 somites only, developed into a reduced limb, scarcely swelling. Each somitic level developed in relation to its initial regional determination dependent on position in the cephalocaudal axis; to its environment (cranial or caudal bud) and to the quantity of somatopleural material in the bud.
CDF Checklist of Galapagos Mammals

This Checklist of Galapagos Mammals includes a total of all 59 taxa reported from the Galapagos Islands. For each name, detailed information is provided: its Galapagos distribution in islands groups or bioregions generated from the specimen records, comments about the taxonomy (especially synonyms), the origin (native and introduced), taxon status (accepted vs. rejected records) and relevant literature references.
A Practical Field Extraction Method for Non-invasive Monitoring of Hormone Activity in Animals

Researchers are gaining an insight into the reproductive and adrenal activity of a wide variety of species [1,2] by monitoring specific hormone levels. Investigating the relationship between hormone levels and animal behaviour [3-5] gives an insight into reproductive processes [1,6], indices of stress [7,8], life-history traits [9], as well as understanding the evolution of physical and behavioural traits [10], and how individuals respond to both natural and anthropomorphic changes in their environment [11-13]. For endangered species both in the wild and captivity, these approaches can be hugely beneficial to gain a better understanding of species biology, optimise welfare and aid conservation [14,15].
Neuromorphic Models of the Amygdala with Applications to Spike Based Computing and Robotics

Computational neural simulations do not match the functionality and operation of the brain processes they attempt to model. This gap exists due to both our incomplete understanding of brain function and the technological limitations of computers. Moreover, given that the shrinking of transistors has reached its physical limit, fundamentally different computer paradigms are needed to help bridge this gap. Neuromorphic hardware technologies attempt to abstract the form of brain function to provide a computational solution post-Moore’s Law, and neuromorphic algorithms provide software frameworks to increase biological plausibility within neural models. This thesis focuses on utilizing neuromorphic frameworks to better understand how the brain processes social and emotional stimuli. It describes the creation of a spiking-neuron computational model of the amygdala, the brain region behind our social interactions, and the simulation of the model using brain-inspired computer hardware, as well as the implementations of other spike-based computations on these hardwares. Although scientists agree that the amygdala is the main component of the social brain, few models exist to explain amygdala function beyond “fight or flight”. ii
The availability of cavity trees along an age gradient in fresh pine forests

Given their importance as a resource for many forest organisms, tree cavities were inventoried in the managed pine forests of north-east Poland, in relation to the: 70–100, 101–130 and >130 year age-classes within the clear-cutting system. The densities at which cavities were present was found to depend on forest age, given that stands 70–100 years old were characterised by an average density of 0.62 trees ha–1, while forests older than 130 years reported 3.28 trees ha–1. Stands aged 70–100 years differed from those aged 130+ in having just 0.27 trees ha–1 of cavity trees, as compared with 2.91 trees ha–1. The total volume of cavity trees in stands up to 100 years old was 0.37 m3 ha–1 on average, as compared with 5.42 m3 ha–1 in stands over 130 years old. The cavities created by woodpeckers constituted 76% of all of those found, and included 53% excavated by great spotted woodpeckers (Dendrocopos major L.) and 23% by black woodpeckers (Dryocopus martius L.) The proportion of cavities excavated by D. major was highest in the youngest age class of stands. There, cavities made by D. martius constituted only 8% of the total, as compared with 31% in the oldest stands. The abundance of cavity trees thus differed along an age gradient, though in any event the availability of cavity trees appears to be too limited to provide for the needs of hole-nesting birds. Forest managers must thus take more account than hitherto of the need to protect cavity trees.
Cryopreservation Protocol for Chlamydomonas reinhardtii

[Abstract] Cryopreservation is commonly used for storing viable cells, tissues, organs or organisms at ultralow temperatures, and usually involves immersion in liquid nitrogen at -196 °C. Here we provide a detailed cryopreservation protocol for C. reinhardtii based on Crutchfield’s work (Crutchfield et al. , 1999), with minor changes (Yang and Li, 2016). In this study, we compared the cryoprotection effect of two common cryopreservation agents (CPAs), methanol and DMSO. Furthermore, the two-step cryopreservation process was divided into five stages to study the factors affecting the survival rate at each stage. We found that the use of methanol as the CPA, combined with the cooling process outlined here (cooling from 25 °C to -55 °C at a rate of 1 °C/min), were indispensable for cell survival after cryopreservation. The thawing process described here (thawing at 35 °C for 5 min) was also important for increasing the survival rate.
Effect of High Temperature and Drought Stress on Carbohydrate Translocation in Japanese Apricot ‘Nanko’ Trees

With the continuing trend of global warming, the adverse impact of high temperature and the inevitably accompanying drought stress on the growth of Japanese apricot trees (Prunus mume Siebold et Zucc.) are of concern. Therefore, the effects of these factors on photosynthesis and carbohydrate translocation were analyzed. An investigation was conducted at average daytime temperatures of 24°C, 30°C, and 34°C under both irrigated and drought conditions. The 34°C temperature was higher than the open air temperature by 5°C. Stable isotope 13C was administered to trees to determine carbohydrate positioning. Under the drought stress condition, the photosynthetic rate declined accompanied by temperature elevation, and at the highest temperature of 34°C, 13C concentrations in the twigs and roots were lower than those in the irrigated trees at 24°C. Two-way analysis of variance revealed a trend of 13C translocation to the young organs above ground, and old organs, while roots were affected by water status, temperature, and their combination, respectively. In the irrigated trees, the photosynthetic rate reduction was not detected, even at higher temperatures. However, translocation incompetence reflecting a decline in 13C concentration in the roots was observed at 34°C. These results indicate that the permissible diurnal average temperature during summer for the growth of Japanese apricot trees is approximately up to 30°C, and in the temperature range around this irrigation is helpful to facilitate regular functioning of carbohydrate translocation under drought stress conditions.
Conformational changes and drug action.

: Conformational changes induced or selected by drugs in receptors may be coupled to second sites on receptor molecules giving negative or positive cooperative binding. The structure-activity relationships may be changed depending on the predominant conformation. Some conformational changes can be identified by nuclear magnetic resonance spectroscopy. Conformational coupling between subunits is complex and provides a mechanism for modulation of receptor affinity.
EFFECT OF TEMPERATURE AND pH ON GROWTH AND ENTEROTOXIN PRODUCTION BY STAPHYLOCOCCUS AUREUS1

Four strains of Staphylococcus aureus producing enterotoxin types A, B, C, and D were inoculated into buffered Brain Heart Infusion (BHI) broth at a concentration of 106 cells/ml and incubated with agitation at temperatures ranging from 7 to 50 C for intervals extending to 4 weeks. At 45 C, strains 265 (type A), 493 (type C), and 315 (type D) grew and produced enterotoxin, but there was a rapid decrease in viable cells and no enterotoxin produced by strain 243 (type B). In the range of 19 to 39 C, all strains grew and produced enterotoxin. At 13 C, strains 265, 243, and 493 grew but only strain 243 produced enterotoxin. Strain 315 did not grow at 13 C and none of the strains grew at 7 or 50 C. The population of S. aureus varied from 1.3 × 107 to 5.5 × 108 cells/ml when enterotoxin was first detected. S. aureus strain 243 was inoculated at a concentration of 108 cells/ml into BHI broth with and without 0.2 M sodium phosphate buffer and incubated at 37 C for time intervals extending to 172 hr. The initial p.