Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermoregulation in the African side-necked Terrapin, Pelomedusa galeata.

Ectotherm body temperature (Tb) is influenced by the thermal environment, thus maintaining stable Tb requires adjustments to physiological and behavioural thermoregulation. There is an abundance of literature on thermoregulation in reptiles, however, little is known about the thermoregulatory behaviour of the recently taxonomically resurrected semi-aquatic, African side-necked terrapin, Pelomedusa galeata. Adult (n = 17) and hatchling (n = 16) P. galeata were evaluated for preferred body temperature (Tpref), set point range temperature (Tset) and associated thermoregulatory behaviours. Wild adult terrapins were captured and implanted with temperature data loggers (Thermochron iButton®, Dallas Semiconductor, Texas, USA), and observed for basking behaviour in a semi-natural environment. Captive bred hatchlings (neonates and yearlings) were evaluated for Tpref, Tset and thermophilic responses to an aquatic thermal gradient. All experiments were carried out in the Animal House, at the University of KwaZulu-Natal, Pietermaritzburg, South Africa. Adult Tb was weakly correlated with mass and ambient air temperature (Ta) in winter and only Ta in summer. Adults basked most frequently in summer and basking behaviours differed between seasons. Basking at the water surface in full sun was observed most often during summer and out the water in full sun during winter. Hatchling Tb was highly correlated with aquatic thermal gradient temperature (Tag), and was higher than acclimation temperature. Neonate and yearling Tpref were not significantly different and mass affected relocation between Tag sites. Adult P. galeata displayed ‘cooling’ behaviours during hot periods in summer and ‘warming’ behaviours during cold periods in winter, and Ta and Tb were good predictors for P. galeata thermoregulatory behaviour. Hatchling P. galeata are highly sensitive to the thermal environment. They selected for high Tb although this may not be possible in natural environments, owing to increased predation risk while basking at exposed sites. In light of increasing global temperature, P. galeata will be relatively unaffected by higher temperatures by making adjustments to basking behaviour to maintain Tpref. General climate change, however, may change the landscape and water bodies P. galeata depend on, thus affecting distribution and survival. Empirical data from species-specific studies contribute to the knowledge required for implementing conservation measures.
A Relationship between Competition and Sex Ratio of Shadscale

The sex ratio of shadscale populations within and outside grazing exclosures show significant departures from random expectations. Males are over represented within the ungrazed exclosures, while females are more prevalent in the grazed pastures. These unequal sex ratios could be the result of three factors: differences in genetic composition, differential grazing pressure on males and differences in water stress. Due to the increased plant cover within the ungrazed exclosures, we believe that plants inhabiting these sites are under greater water stress. Moreoever, it appears that females either tolerate water stress less well than males or change sex when stressed.
Comparison of Azolla mexicana and N and P fertilization on paddy taro (Colocasia esculenta) yield

The yields of taro intercropped with Azolla and under slowly flowing water (F) and taro intercropped with Azolla after incorporation of Azolla into mud (B) were compared with N and P fertilization and a control in Mangaia, The Cook Islands. Significantly, higher yields were obtained for treatments F and B than for the chemical fertilization treatment, which had a minimal effect on yield. The control produced 53.4 and 64.7% of yield of treatments F and B, respectively
A mucosa nasal como uma via estratégica de vacinação contra infecção por Leishmania (Viannia) braziliensis no modelo hamster dourado (Mesocricetus auratus)

Previous results have shown that oral and intranasa l administration of crude Leishmania (Leishmania) amazonensis antigens (LaAg) partially protects mice against L. amazonensis infection. However, vaccination studies on species of the subgenus Viannia , the main causative species of cutaneous and mucos al leishmaniasis in the Americas, have been hampered b y the lack of easy-to-handle bio-models that accurately mimic the human disease. Recently, we demonstrated that the golden hamster is an appropriate model for studying the immunopathogenesis of cutaneous leishmaniasis cause d by L. (Viannia) braziliensis. Using the golden hamster model, we investigated whe ther the protective effect of intranasal immunisation with LaAg can be extended t o L. braziliensis infection. Golden hamsters vaccinated with either two intranas al (IN) doses of LaAg (10 μ g) or two intramuscular doses of LaAg (20 μ g) were challenged 2 weeks post-vaccination with L. braziliensis. The results showed that IN immunisation with LaAg s ignificantly reduced lesion growth and parasitic load as well as serum IgG and IgG2 levels. At the experimental endpoint on day 114 post-infection , IN-immunised hamsters that were considered protected expressed IFN- γ and IL10 mRNA at similar levels as uninfected skin. Unlike what was observed in animal s not protected. In contrast to the nasal route, intramuscular (IM) immunisation failed to provide protection. These results demonstrate for the first time that the nas al route of immunisation can induce cross protection against L. braziliensis infection.
The use of microorganisms in environmental remediation

Due to their high metabolic diversity and high adaptability, microorganisms are able to live in the most varied of natural and artificial habitats created by environmental contamination. Different microbes can use a great variety of refractory pollutants, thus permitting their use in ex and in situ bioremediation. The implementation of biotreatment processes requires the use of evaluation methods of pollution and the success of bioremediation. The microorganisms can also be used as biosensors. Laboratory microcosm experiments would allow isolation of new microorganisms, assessment of the methods for evaluating pollution and the risk of implementation of non- and recombinant microorganisms. Bioremediation technologies have an open future linked to multidisciplinary scientific work.
Indirect estimates reveal the potential of transgene flow in the crop–wild–weed Sorghum bicolor complex in its centre of origin, Ethiopia

Abstract A study was carried out between 2008 and 2011 to investigate the potential risks of gene flow and its consequences in the crop–wild–weed S. bicolor complex in Ethiopia to aid efforts to conserve genetic diversity. Morphological measurements and genomic DNA samples were taken in situ from 30 wild and eight cultivated populations representing a total of 760 samples from five regions. Genetic diversity, gene flow, population structure and outcrossing rates of wild populations were computed using phenotypic measurements and/or polymorphic simple sequence repeat (SSR) markers. Moreover, morphological analyses of fitness of crop–wild hybrids were studied. High diversity was observed among the wild/weedy sorghum populations for phenotypic traits and SSRs. SSR diversity was high in both wild and cultivated populations, but the magnitude was greater in the former. Gene flow between the wild and the cultivated sorghum was observed to be higher than that within either pool. Wild sorghums exhibited variation in the multilocus outcrossing rate (range = 0.31–0.65) and fitness was not compromised in most wild × crop hybrids. The study indicated that crop-to-wild gene flow is possible in Ethiopia. Thus, genes from transgenic sorghum are expected to enter into the wild and non-transgenic cultivated populations and may spread and persist, if transgenic sorghum is deployed in Ethiopia and in other countries of Africa, which may pose risk of introduction of unwanted effects, which in turn may lead to loss of genetic diversity.
Molecular cloning and expression of the stress gene HSP70 in the marine crab Charybdis japonica (A. Milne-Edwards, 1861) (Decapoda: Brachyura: Portunidae) in response to ammonia-N, nitrite-N, and sulfide exposure

A full-length complementary DNA sequence of heat-shock protein 70 (HSP70) was cloned from the hepatopancreas of Charybdis japonica (A. Milne-Edwards, 1861) through reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends. The expression profile of HSP70 in different tissues of C. japonica and its expression upon exposure to ammonia-N, nitrite-N, and sulfide was also investigated. The full-length cDNA of HSP70 was 2203 bp long and contained a 107 bp 5′ untranslated region (UTR), a 143 bp 3′ UTR, and a 1953 bp open reading frame, which distributed 108-2060 bp and encoded a polypeptide of 650 amino acids (aa) with a calculated molecular mass of 71.24 kDa and an isoelectric point of 5.34. Three signature sequences of the HSP70 family, IDLGTT-S-V (residues 9-18), IFDLGGGTFDVSIL (197-210 aa), and IVLVGGSTRIPKIQK (334-348 aa) were detected in the predicted amino-acid sequence. The HSP70 gene of C. japonica showed the highest similarity (>90%) to HSP70 from other crustacean species. The HSP70 gene was expressed in all tissues tested, and its abundance in these tissues can be arranged as hepatopancreas > stomach > gill > heart > ova > muscle. The expression of HSP70 was significantly induced after the stress of ammonia-N, nitrite-N, and sulfide, and the induced degree showed a positively correlation with increasing concentrations. The HSP70 expression reached a peak after 3 or 6 h of stress, which suggests that the HSP70 expression was affected quickly by the changes of environmental factors.
The factors in prenatal and perinatal sensory input

During its embryonic formation the brain develops its lower centers and large neural trunks by genetic mandate. While, the upper neural growth is dependent to a large part on the sensory input provided during growth and maturation. The various types of sensory and extrasensory input are reviewed. Post birth factors having effect on intellectual development are presented. A comparison of human process with animal imprinting is made. The way in which the environment imprints and alters genetic expression is explored.
Main potential drivers of trout population dynamics in bypassed stream sections

The key role of hydrological variability in structuring brown trout populations is well established. However, the influence of additional drivers is more difficult to identify. The implementation of long-term monitoring and the development of reliable tools can help to reveal fine local drivers structuring fish populations in contrasted flow regimes. This study used data series for nine reaches monitored for nine to nineteen years in four French salmonid streams. Study reaches were within five bypassed sections influenced by instream flow. A deterministic trout population dynamics model was applied on each reach, with calibration and validation procedures. Results revealed that biological drivers structured all reaches similarly. In addition, seven other drivers were identified. Among these additional drivers, hydrology mainly explained temporal fluctuations in trout density, regardless of reach. Three drivers independent of hydrology were also revealed: poor water quality, limited spawning area and the effect of power plant operations (overtopping, flushing or plant shutdown). All drivers influenced the whole bypassed section and were never limited to the scale of the reach (sampling area). Further analyses of each driver are now needed, to regionalise and quantify their respective impact precisely. Thus, assessment of trout population status would be simplified , enabling implementation of efficient management rules.
Novel Peptide Nucleic Acid Melting Array for the Detection and Genotyping of Toxoplasma gondii

Peptide nucleic acid (PNA) probes, developed in the early 1990s, are DNA mimics, in which the negatively charged sugar-phosphate backbone is replaced by an achiral, neutral polyamide backbone formed by repetitive N-(2-aminoethyl) glycine units [1]. PNA can hybridize to complementary nucleic acid targets according to the Watson-Crick base-pairing rules [2]. Their unique chemical characteristics have been studied extensively owing to their research and diagnostic applications, e.g., in genomics, human pathology, virology, mycology, and bacteriology [3]. PNA molecules have unique hybridization characteristics; they exhibit rapid and strong binding to complementary targets and a lack of electrostatic repulsion [4]. Toxoplasma gondii, an opportunistic intracellular parasite, has the ability to infect any eukaryotic cell. It can infect all warm-blooded mammals, including humans [5]. Felids are the definitive hosts of T. gondii. Environmental contamination is commonly caused by the secretion of oocysts, which become infective upon sporulation, by felids. Intermediate hosts can be infected by T. gondii and produce tissue cysts in a number of organs, such as the skeletal muscle and central nervous system. When ingested in raw or uncooked food, these tissue cysts are Despite differences in virulence between strains of Toxoplasma gondii, rapid and accurate genotyping methods are lacking. In this study, a method was developed to detect and genotype T. gondii in food and environmental samples using PCR and a novel peptide nucleic acid (PNA) melting array. An alignment of genome sequences for T. gondii type I, II, and III obtained from NCBI was generated, and a single nucleotide polymorphism analysis was performed to identify targets for PCR amplification and a PNA melting array. Prior to the PNA melting array, conventional PCR was used to amplify GRA6 of T. gondii. After amplification, the PNA melting array was performed using two different PNA hybridization probes with fluorescent labels (FAM and HEX) and quenchers. Melting curves for each probe were used to determine genotypes and identify mutations. A 214-bp region of the GRA6 gene of T. gondii was successfully amplified by PCR. For all T. gondii strains (type I, II, and III) used to evaluate specificity, the correct genotypes were determined by the PNA melting array. Non-T. gondii strains, including 14 foodborne pathogens and 3 protozoan parasites, such as Giardia lamblia, Cryptosporidium parvum, and Entamoeba histolytica, showed no signal, suggesting that the assay has a high specificity. Although this is only a proof-of-concept study, the assay is promising for the fast and reliable genotyping of T. gondii from food and environmental samples.
Molecular characterization and expression pattern of tobacco (Nicotiana tabacum) ascorbate oxidase gene

ABSTRACT The complete coding sequence of one tobacco (Nicotiana tabacum) gene, ascorbate oxidase (AO), was isolated by the application of reverse transcription-polymerase chain reaction. The tobacco AO gene consists of a 1722-bp open reading frame and encodes a protein of 573 amino acids. Sequence comparison analysis revealed that the tobacco AO protein shares high homology with the AO proteins of Lycopersicon esculentum (89%), Populus trichocarpa (75%), soybean (74%), castor bean (73%) and peach (73%). The prediction of transmembrane helices showed that tobacco AO might be a transmembrane protein. The expression profile was studied and the results indicated that the tobacco AO gene was diversely expressed in different tobacco tissues, including leaves, stem, roots and flowers. Our experiment laid the grounds for further research on this tobacco gene.
Use of Desmidiales flora for monitoring rivers : a case of South-Hungarian waters

The Desmidiales flora can be a very good indicator of ecological status of rivers and other water-bodies. Desmids found in rivers show the connections of the rivers with their dead- and sidearms. This seems especially important in determining the ecological status of slowly streaming waters (mainly lowland's rivers, canals, dead- and sidearms of rivers). The sample collection from these biotops cannot be omitted if we liked to know about their status. In the present study, a Dutch-system (COESEL 1998) was applied to the investigated South-Hungarian waters. The results of the rivers were compared to that of dead- and sidearms, lakes situated on these areas. The essence of the applied method is the determination of the Nature Conservation Value (NW by COESEL) based on desmid assemblages. The parameters chosen to determine NW are diversity (species richness), rarity (occurrence of rare taxa) and maturity (presence of species indicative of ecosystem maturity). The comparison of 15 water-bodies belonging to different types (canals, side-arms, dead-arms and lakes) is presented. There are 6 water-bodies that have a high natural conservation value according to their desmid flora. Experience shows that this method is well usable for Hungarian waters, too. In the present study, there are some suggested modifications for the indicator value based on the occurrences of the determined Desmidiales taxa in Hungary.
Comparative and reverse genetic analysis of the cytokinin response regulator gene family in Populus

of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy COMPARATIVE AND REVERSE GENETIC ANALYSIS OF THE CYTOKININ RESPONSE REGULATOR GENE FAMILY IN Populus By Gustavo A. Ramirez Carvajal May 2009 Chair: John Davis Major: Plant Molecular and Cellular Biology Cytokinins are important plant hormones that influence a diverse array of physiological and developmental processes such as root and shoot morphogenesis. However, little is known with respect to whether or how cytokinin action is connected to biomass distribution in any forest tree. A better understanding of the molecular mechanisms by which cytokinin signaling is connected to specific traits can provide the genetic tools to improve agronomic characteristics (e.g, stem wood production per unit root biomass). Cytokinin signaling resembles two-component systems from bacteria and yeast in which an external signal is sensed by a histidine kinase (HK) and then transferred to a response regulator (RR). Because of their ability to activate transcription and regulate protein activity, RRs have been proposed to coordinate most of physiological processes regulated by cytokinin. I identified, annotated and characterized at the transcript level 11 type-As, 11 type-Bs and 11 pseudo cytokinin response reulators (RRs) in Populus balsamifera ssp. trichocarpa (Torr. and Gray) genotype Nisqually-1. Developmental and cytokinin-responsive expression of the Populus RRs indicate that while the type-As and type-Bs are preferentially expressed in nodes, pseudoRRs are preferentially expressed in mature leaves.
Robust Multi-Agent Pickup and Delivery with Delays

Multi-Agent Pickup and Delivery (MAPD) is the problem of computing collision-free paths for a group of agents such that they can safely reach delivery locations from pickup ones. These locations are provided at runtime, making MAPD a combination between classical Multi-Agent Path Finding (MAPF) and online task assignment. Current algorithms for MAPD do not consider many of the practical issues encountered in real applications: real agents often do not follow the planned paths perfectly, and may be subject to delays and failures. In this paper, we study the problem of MAPD with delays, and we present two solution approaches that provide robustness guarantees by planning paths that limit the effects of imperfect execution. In particular, we introduce two algorithms, $k-\mathbf{TP}$ and $p-\mathbf{TP}$, both based on a decentralized algorithm typically used to solve MAPD, Token Passing (TP), which offer deterministic and probabilistic guarantees, respectively. Experimentally, we compare our algorithms against a version of TP enriched with online replanning. $k-\mathbf{TP}$ and $p-\mathbf{TP}$ provide robust solutions, significantly reducing the number of replans caused by delays, with little or no increase in solution cost and running time.
Biotecnologia vegetal: da clonagem de plantas à transformação genética

Na medida em que todas as obras da UC Digitalis se encontram protegidas pelo Código do Direito de Autor e Direitos Conexos e demais legislação aplicável, toda a cópia, parcial ou total, deste documento, nos casos em que é legalmente admitida, deverá conter ou fazer-se acompanhar por este aviso. Biotecnologia vegetal: da clonagem de plantas à transformação genética Autor(es): Canhoto, Jorge M. Publicado por: Imprensa da Universidade de Coimbra URL persistente: URI:http://hdl.handle. net/10316.2/2586 DOI: DOI:http://dx.doi. org/10.14195/978-989-26-0404-6
Long term selection for oil concentration in five maize populations

Five maize populations with different genetic backgrounds were subjected to long term recurrent selection for oil concentration. These populations were: BHO, AIHO, Syn.D. O. RYD, and KYHO. By the end of 2001, seven to eighteen cycles of selection had been completed. Selection procedures used in the program were very effective. Within the selection period, total oil increase was from 6.32% to 9.95% among the five populations. The average genetic gain per cycle was 0.77%. KYHO was the highest, at 1.18%. The average realized heritability was 0.42, with KYHO again the highest, at 0.67. Correlation analysis indicated that except for KYHO, oil% was not negatively correlated with kernel weight but was positively correlated with protein and lysine. Regression analysis indicated that with each 1% oil increase, protein would increase by 0.25% to 0.56% and lysine would increase by 0.01% to 0.015%. Oil% was highly but negatively correlated with starch%. With each 1% oil increase, starch would decrease by 1.48% to 1.83%.
Microhabitats of brown trout when feeding on drift and when resting in a lowland salmonid brook : effects on Weighted Usable Area

Summer habitat preferences by brown trout (10-20 cm fork length) were determined by daylight and night dive sampling in the Saint Sauveur brook, a tributary of the River Scorff (Brittany, France). Habitat change was analyzed from night and day sampling. At the geomorphological unit scale, fish preferred riffles during daylight hours and pools at night. According to behavioural data, night and day locations in the channel depended on the two activities: resting (night samples) and feeding on drift (daylight samples). Suitability curves drawn at the microhabitat scale showed differences between day and night, in terms of water depth (25-45 cm by daylight, 40-55 cm at night), velocity (15-45 cm/s by daylight, 0-15 cm/s at night) and substrate particle size (gravel, cobble and stones by daylight, silt and sand at night). Based on these habitat suitability curves, Weighted Usable Area was computed by EVHA, the French version for the Physical Habitat Simulation system. Results show that WUA varied in magnitude from 1 to 9 between night and day, depending on stream discharge. In addition, the need to modify the Standard Habitat Suitability Indices (HSI) is emphazised, owing to the differences in the shape of the suitability curves between Standard HSI and Feeding HSI according to water velocity.