Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of DNA vaccine encoding koi herpesvirus glycoprotein GP-25in common carp juvenile by immersion

Koi herpesvirus (KHV) is a herpesvirus that particularly infects and causes mass mortality to koi and common carp. Therefore, the protection of common carp from KHV infection is urgently needed. In this study, we developed an application of DNA vaccine encoding KHV glycoprotein-25 by immersion method to increase survival of common carp against KHV infection. A total of 400 common carp juveniles at 30-day-old were immersed in 1-L water containing 1.3×10 8 CFU/mL of the killed Escherichia coli cells carrying DNA vaccine. Three frequencies and three duration of fish immersion were tested, namely: 1×30 minutes, 1×60 minutes, 1× 90 minutes, 2×90 minutes and 3×90 minutes by interval of 24 hours. Reversetranscription polymerase chain reaction analysis showed that DNA vaccine was successfully expressed in the vaccinated fish. Fish at twenty eight days post vaccination were challenged by injecting 10 -4 mL of KHV per fish. The result showed that vaccination by 1×30 minutes immersion allowed 61% of fish survived, and this was significantly higher (p 0.05). The relative percent survival of vaccinated fish were also similar among treatments (p>0.05). DNA vaccination has increased fish survival about two fold higher compared to unvaccinated fish control (26.67%). Thus, DNA vaccination was effectively delivered by immersion for 1×30 minutes, and this technique can be useful to level up the resistance of common carp juveniles against KHV infection. Keywords: DNA vaccine, KHV, glycoprotein, immersion, common carp
Structural studies of a membrane embedded chloride channel from E.Coli, a prokaryotic homologue of ClC channels

The ClC family of chloride channels are found throughout the eukaryotes and homologues are found among the prokaryotes. There are nine ClC chloride channels found in mammals that are expressed either ubiquitously or in specific tissues. They have a role in a broad spectrum of cellular functions, ranging from the control of electrical excitability of neurons and the maintenance of the balance of charge required in the acidification of organelles, to the regulation of cell volume. The physiological importance of these channels is often demonstrated by disease causing mutations. Mutations in ClC chloride channels cause myotonias, Becker’s Disease and have been implicated in the spread of cancer. The structural information on members of the ClC family is extremely limited. For this reason ClC prokaryotic homologues, ecClC1 and ecClC2 from E.coli, were cloned and expressed in the hope that this system would produce sufficient amounts of protein to grow crystals in order to obtain three-dimensional information. This information will provide a detailed mechanism of chloride conduction and molecular architecture of the channel necessary for the further physiological and pharmacological characterisation of this important family of chloride channels. The E.coli ClC chloride channel ecClC was cloned from E.coli genomic DNA and overexpressed in E.coli. The recombinant protein was purified from the E.coli membranes using detergents. Metal affinity and size exclusion chromatography were used to purify the protein to near homogeneity. Crystals of ecClC2 have been grown that diffract to 4A and structural analysis is underway. This thesis describes the development of the purification protocol, the crystallisation of the protein and the preliminary analysis of the X-ray diffraction data.
Effect of drying methods on volatile compounds, fatty acids and antioxidant property of Thai kaffir lime (Citrus hystrix D.C.)

Summary This study investigated the changes in colour, volatile compounds, fatty acids, total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity of kaffir lime leaves (makrud in Thai) Citrus hystrix D.C. after three drying treatments, namely hot-air (HA) drying, low relative humidity (LRH) air drying and far-infrared radiation (FIR) drying. Overall, when compared with fresh leaves, a slight decrease in L* values of the three dried samples was observed. TPC, TFC and ferric-reducing/antioxidant power (FRAP) values were increased by LRH and FIR drying (LRH: 39%, 43% and 28%; FIR: 62%, 39% and 39%), while HA drying decreased TPC, TFC and FRAP values (28%, 21% and 1%), compared with fresh leaves. The main volatile compounds in fresh leaves were citronellal, followed by linalool and viridiflorol. Drying brought about an increase in the concentrations of volatile components, such as citronellal with HA, LRH and FIR drying (79%, 83% and 64%, respectively), compared with the results for fresh leaves (56%). LRH and HA drying increased essential fatty acid alpha-linolenic acid (ALA, 18:3n-3), while linoleic acid (LA, 18:2n-6) was increased by FIR drying. The present study has provided useful information for the industrial use of dried kaffir lime production.
Algal-bacterial interactions:a study of Gymnodinium catenatumand its associated bacteria

Over the last decades, harmful algal blooms (HABs) have increased globally in both frequency and extent, leading to intensified efforts to determine the primary factors that are controlling the population and toxin dynamics of bloom-forming algal species. One poorly understood factor in HAB ecology, yet shown to be of great importance, is that of algal-bacterial interactions. Efforts to investigate the relationships and mechanisms of interaction are often hindered by the complex composition of the algal-associated bacterial communities, wherefore this present study used simplified algal-bacterial experimental model systems. The model systems are based on the toxin producing dinoflagellate Gymnodinium catenatum and two of its associated bacteria, Marinobacter sp. DG879 and Alcanivorax sp. DG881, both known to support growth and survival of G. catenatum in culture. Using the experimental model systems, the work presented in this thesis examined the growth dynamics of G. catenatum and its associated bacteria, and studied the effect of bacteria on the toxicity of G. catenatum. The abundance of Alcanivorax and Marinobacter genotypes associated with natural populations of G. catenatum in the Derwent Estuary and D’Entrecasteaux Channel, south-east Tasmania was also investigated. This thesis demonstrates that the bacterial community is important for growth of G. catenatum and showed that different bacteria, in particular Marinobacter sp. DG879, have a significant effect on the growth dynamics and toxicity of G. catenatum laboratory cultures. When grown with Marinobacter sp. DG879, G. catenatum was found to remain viable in culture for a period longer than ever recorded, suggesting that Marinobacter sp. DG879 produce a compound inducing a positive growth response in G. catenatum, or that it plays a role in carbon recycling or nitrogen fixation. Toxin analysis of the G. catenatum / Marinobacter sp. DG879 cultures revealed a toxin profile significantly different to other analysed treatments containing different bacteria. As the experimental design of the study sought to minimise genetic variation among treatments, and with biotransformation generally operating on extracellular toxins (this study focussed on intracellular toxins), the differing toxin profile seen in the G. catenatum with Marinobacter sp. DG879 is most likely a response to Marinobacter sp. DG879 influencing toxin synthesis indirectly through its effect on dinoflagellate physiology. The field studies also suggest that Marinobacter sp. may have an important role in natural populations of G. catenatum, preceding G. catenatum blooms. With the use of molecular detection methods becoming more widespread, and with more research on naturally occurring blooms, there is potential that specific elements of the bacterial population, such as Marinobacter sp. DG879 could be employed as indicator species of G. catenatum and other algal blooms, ultimately allowing for early detection and management of potentially harmful blooms.
Biogeographic determinants of Australian freshwater fish life‐history indices assessed within a spatio‐phylogenetic framework

Aim This study aims (1) to quantify the broad-scale patterns of functional diversity and life-history strategies of freshwater fish in relation to environmental variation across Australian river basins and (2) to identify key life-history traits associated with species extinction risk in order to determine how fish communities and extinction-prone species may respond to future environmental change. Location One hundred and twenty-three river basins across eastern Australia. Methods Based on 10 key life-history traits for 194 freshwater fish we used a novel analytical approach to quantify multivariate life-history indices in relation to environmental variation within a spatio-phylogenetic framework. We assessed the utility of our analytical framework by contrasting final models against all candidate models, both with and without an eigenvector filtering procedure, and quantified the degree of autocorrelation in all model residuals. Results Temperature, habitat heterogeneity/availability, flow variability and primary productivity accounted for between 55 and 80% of the variation in life-history indices. Best-performing models were all derived from the addition of spatial and phylogenetic covariates to the analytical framework which consistently produced more parsimonious final models with higher explanatory power and insignificant levels of autocorrelation in the model residuals. Main conclusion The life-history functional diversity of fish assemblages and the composition of life-history strategies across Australian river basins is in part determined by environmental variability, stability and seasonality, highlighting both the importance of environmentally driven community assembly processes and the potential changes to freshwater fish biodiversity in response to climate change. A spatio-phylogenetic analytical framework is a key component in the effective management of autocorrelation in ecological data and the derivation of more rigorous trait–environment relationships.
β-Arrestin/AP-2 Interaction in G Protein-coupled Receptor Internalization

β-Arrestins, proteins involved in the turn-off of G protein-coupled receptor (GPCR) activation, bind to the β2-adaptin subunit of the clathrin adaptor AP-2. The interaction of β2-adaptin with β-arrestin involves critical arginine residues in the C-terminal domain of β-arrestin and plays an important role in initiating clathrin-mediated endocytosis of the β2-adrenergic receptor (β2AR) (Laporte, S. A., Oakley, R. H., Holt, J. A., Barak, L. S., and Caron, M. G. (2000)J. Biol. Chem. 275, 23120–23126). However, the β-arrestin-binding site in β2-adaptin has not been identified, and little is known about the role of β-arrestin/AP-2 interaction in the endocytosis of other GPCRs. Using in vitro binding assays, we have identified two glutamate residues (Glu-849 and Glu-902) in β2-adaptin that are important in β-arrestin binding. These residues are located in the platform subdomain of the C terminus of β2-adaptin, where accessory/adapter endocytic proteins for other classes of receptors interact, distinct from the main site where clathrin interacts. The functional significance of the β-arrestin/AP-2/clathrin complex in the endocytosis of GPCRs such as the β2AR and vasopressin type II receptor was evaluated using mutant constructs of the β2-adaptin C terminus containing either the clathrin and the β-arrestin binding domains or the β-arrestin-binding domain alone. When expressed in human embryonic kidney 293 cells, both constructs acted as dominant negatives inhibiting the agonist-induced internalization of the β2AR and the vasopressin type II receptor. In addition, although the β2-adaptin construct containing both the clathrin and β-arrestin binding domains was able to block the endocytosis of transferrin receptors, a β2-adaptin construct capable of associating with β-arrestin but lacking its high affinity clathrin interaction did not interfere with transferrin receptor endocytosis. These results suggest that the interaction of β-arrestin with β2-adaptin represents a selective endocytic trigger for several members of the GPCR family.
Growers Adaptation Strategic Alleviation of Climate Variability in Peri-Urban Agriculture for Food Security in Calabar – Nigeria

all the study, the of the and relevant empirical work. the methodology, the protocol and review the first Author AEO performed the statistical analysis, carried out mapping and description of the study area and the ABSTRACT This study examined the adaptive mechanisms employed by farmers in stabilizing crop yield against the wave of climate variability in Calabar, Nigeria. The study adopts a participatory approach based on focused group discussion and questionnaire survey to examine the farmers’ perception of climate variability, adaptation strategies and the influence of the strategies on crop yield. A total of 180 farmers were randomly selected for the study. The results revealed that in response to climate variability 16 strategies were adopted by farmers to stabilize crop yield in line with their indigenous knowledge systems. On indexing and ranking of the strategies based on their priorities, six strategies were predominant which include multiple cropping, use of improved crop varieties, soil conservation, planting cultivars that suit climate, intercropping, changing planting pattern. Multiple cropping with adaptation index of 638 and 94 5 response on climate and land criteria as well as use of improved varieties with adaptation index of 500 and 100% response on mixed criteria of climate and land were outstanding. Crop combination including vegetables, cereals, spices and roots were preferred. Though cassava is highly cultivated, pumpkin has the highest preference due to its market value and demand. The driving factors behind farmers’ choices of adaptation were informed by yields and availability of land. Farmers considered yields and income as the factor in selecting resilience crops. Undoubtedly, 80% of farmers that have adopted these practices no longer experience the persistence of the various environmental problems arising climatic variability. The implication is that indigenous knowledge system on the use of improved varieties and suitable cultivars as well as soil management is essential for improved and bountiful harvest to feed the teeming population amidst climate change. The paper reveals that adaptive measures taken by crop farmers to cushion the effect of climate on crop yield are effective. Hence, it is recommended that indigenous knowledge should be considered alongside other scientific knowledge to combat the impact of climate variability on agriculture while improving crop yield.
Identification of stripe rust resistant genes in resistant synthetic hexaploid wheat accessions using linked markers

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases affecting wheat. In this study, seven gene-linked markers were used to identify the presence of stripe rust resistant genes in 51 accessions of synthetic hexaploid of wheat which were found to be resistant at seedling plant stage. Molecular marker-based gene identification showed the presence of Yr5, Yr10 and Yr15 in three accessions, Yr36 in three accessions, Yr48 in seven accessions, YrR61 in four accessions, and YrTP1 in ten accessions of resistant hexaploid of wheat. These gene-linked markers were also used for the detection of genetic diversity. A total of 68 alleles were detected by these seven gene-linked markers. The mean number of allele was 11.3 alleles per locus. Genetic diversity values ranged from 0.34 to 0.93, with highest genetic diversity value of 0.93 detected for marker Xwm477. The lowest genetic diversity value was observed for marker Xbarc167. The polymorphic information content value ranged from 0.33 to 0.92 with an average of 0.54. The highest number of alleles (n= 24) were detected for marker Xwmc477. The evidence in this study on the basis of genetic diversity and presence of Yr genes in synthetic hexaploid wheat accessions will be useful in further breeding programmes.
Evaluating a multi-generational reintroduction program for threatened salmon using genetic parentage analysis

Dams, utilized for hydroelectric or flood control purposes, obstruct organism dispersal and have contributed to the decline of many migratory fish populations. For threatened Chinook salmon (Oncorhynchus tshawytscha) from the Willamette River Basin in Oregon, human-assisted reintroductions are being used to facilitate dispersal to historical habitats located above dams. However, little is known about the reproductive outcomes of reintroduced individuals or the efficacy of reintroductions towards the goal of population demographic viability. Using genetic parentage assignments to 3-, 4-, and 5-year-old adult recruits, we estimated the fitness of hatchery and wild Chinook salmon reintroduced above Foster Dam on the South Santiam River, a tributary of the Willamette River. Our parentage assignments indicated that the fitness of reintroduced salmon was highly variable, with individuals producing a range of 0–40 adult progeny. We also detected a possible trend towards reduced fitness in mate pairs composed of .
Impact of pest problems in Gmelina arborea Linn. plantations in Western Maharashtra.

Different age group plantations of Gmelina arborea Linn. In Western Maharashtra, were evaluated for monitoring the status of pests. These plantations have suffered due to mortality caused by some biotic factors i.e. grazing, hacking, faulty pruning, rab firing, diseases, insect pests viz. defoliators, leaf miner, bark eating caterpillar, phassus borer, sap suckers, canker grub, weevil, termites etc. In this study, the impact of different pest outbreaks was evaluated on Gmelina arborea mortality. In this regard, observations were recorded on the pest incidence, their relationship with soil nutrients and different girth and height classes. Additional scenarios included possible measures to counter the present problem are also suggested.
Avian richness and habitat characteristics in primary and logged hill dipterocarp tropical rainforest of Peninsular Malaysia

Hill dipterocarp tropical rainforest provides a variety of habitats for understorey bird species. These habitats are under severe pressure due to deforestation and logging activities which adversely affect the understorey bird species directly or indirectly through habitat fragmentation, reduced food resources and increase risk of predation. This study examined the effects of habitat disturbance on understorey bird species due to logging in hill dipterocarp tropical rainforest in Peninsular Malaysia. Understorey bird species richness and habitat characteristics between primary and logged forest were determined using mist-netting and plot quadrant method respectively. A total of 431 individuals of 60 bird species representing 23 families was captured in both logged and primary forests (212 individuals of 34 species from primary forest and 219 individuals of 42 species from logged forest). Spectacled Bulbul and Cream-vented Bulbul (each 3.48%) were the two most dominant understorey bird species captured in logged forest. In contrast, Rufous-Collared Kingfisher (4.64%) and Grey-Headed Babbler (3.71%) were the most abundant bird species of primary forest. The results indicated that understorey bird species of primary forest was significantly different from the logged forest (F1, 120 = 1.95, P < 0.05). In addition, a total of 66 tree species representing 22 families was recorded from primary and logged forest. Out of the total, 53 tree species belong to 22 families were sampled from primary forest and 14 species belong to 10 families from logged forest. Primary forest was dominated with White Skin and Great Woolly Nutmeg (3.57%) while logged forest with Pigeon Wood/Indian Nettle Tree (17.86%) and Ant Plant (12.50%). Comparison analysis indicated that the mean vegetation relative abundance of primary forest was significantly different from the logged forest (F1, 134 = 10.5, P < 0.005). Selective logging has also altered the microclimate characteristics. The findings of this study revealed that primary forest may harbour a higher understorey bird species diversity and richness than logged forest. This study indicated that forest logging affects the understorey birds and the effects may vary from species to species.
Pharmacological Studies of a Novel Inhibitor of the Mammalian Target of Rapamycin (mTOR) Signaling Pathway

The apoptotic mode of cell death (programmed cell death) is an active and defined process that plays an important role in the development of multicellular organisms and in the regulation and maintenance of cell populations in tissues under physiologic and pathologic conditions. Since dysregulation of apoptosis is associated with the progress of many diseases, induction of apoptosis is an interesting pharmacological target for the therapy of many diseases. Our study shows that the novel semisynthetic pentacyclic triterpenoid C-KβBA has a profound antiproliferative effect on different tumor cell lines and that it induces apoptosis of tumor cells in vitro and vivo. Previous studies have shown that the mammalian target of rapamycin (mTOR) is a key regulator for many cells activities, and that the perturbation of this signaling pathway is implicated in many diseases and metabolic disorders. Accordingly targeting the mTOR signaling pathway seems to be a promising therapeutic approach for the treatment of various diseases and metabolic disorders. We have shown in our study that C-KβBA downregulates the mTOR signaling pathway in vitro and vivo, which leads to the induction of cell cycle arrest in the G0 cell cycle phase as well as downregulation of the protein translation machinery. Together, the presented data strongly suggest that C-KβBA could serve as a lead compound for the development of novel treatment modalities for diseases and disorders associated with defects in the apoptosis machinery, or the mTOR signaling pathway, or both.
New combinations and range extension for Neotropical mosses

Abstract New combinations are proposed for three Neotropical moss species following the transfer of Barbula uncinicoma to Gertrudiella and of Cyrto-hypnum sharpii to Pelekium. Furthermore Gertrudia validinervis is considered a synonym of G. uncinicoma and its variety serratopungens (Herzog) is maintained within the latter as Gertrudiella uncinicoma var. serratopungens (Herzog) G. Suárez & M. Schiavone. Pelekium sharpii, a Central American species is recorded for the first time for South America from Bolivia and Argentina.
Penta-coordinated phosphorus structure analysis on kinases

In this paper, based on the known crystal structures of Square Pyramid (SP) and Trigonal Bipyramid (TBP) penta-coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software designed to survey the P(5)-Structure of phosphorylated proteins. By this software, it was found that 382 of 398 phosphorus-related kinases (96%) from current PDB could go through the penta-coordinated phosphorus transition state or intermediate. For example, in protein 1HE8, amino group in Lysine16 was within 3.58 A from the phosphorus atom, and a potential TBP structure consisting GNP2 and N Z could be overlapped with an authentic TBP with an RMSD value of 0.71 A.
Introduced or glacial relict? Phylogeography of the cryptogenic tunicate Molgula manhattensis (Ascidiacea, Pleurogona)

Aim The tunicate Molgula manhattensis has a disjunct amphi‐Atlantic distribution and a recent history of world‐wide introductions. Its distribution could be the result of regional extinctions followed by post‐glacial recolonization, or anthropogenic dispersal. To determine whether the North Atlantic distribution of M. manhattensis is natural or human‐mediated, we analysed mtDNA cytochrome c oxidase subunit I (COI) sequence variation in individuals from cryptogenic and introduced ranges.