Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Profile Assessment of Giant Clam Genus Tridacna as a Basis for Resource Management at Wakatobi National Park Waters

Giant clam population has been decreased in a few years. Resource management requires information from various aspects, such as ecological, population, and other aspects. This study was aimed at assessing the genetic profile of Tridacna giant clam in Wakatobi National Park waters using Cytochrome oxidase subunit I (COI) genetic marker. Sample collection was conducted around the three main islands, i.e., Wangi-wangi, Kaledupa, and Tomia. Genetic analysis using COI gene may contribute in identifying giant clams up to the species level and showed the relationship among species. The research found 41 specific nucleotide sites for the clams. T. crocea, T. squamosa and T. maxima had 2, 15 and 24 sites, respectively. COI gene as a biological marker was able to separate groups of giant clam by species. Nucleotide variation of T. crocea from Wakatobi was the highest among other locations, so it could be used as a genetic source for translocation and domestication. Keywords: cytochrome oxidase subunit I, specific nucleotide, Tridacna, Wakatobi National Park
Inhibition of UV-induced G1 arrest by exposure to 50 Hz magnetic fields in repair-proficient and -deficient yeast strains

We examined the gene conversion frequency at the ARG4 heteroallelic locus in DNA repair proficient and deficient strains of a budding yeast to assess the possibility that ELF magnetic fields obstructed the damage repair process. Diploid cells were exposed to magnetic fields after irradiation with sub-lethal doses of UV radiation. Gene conversion increased on exposure in DNA repair proficient cells, whereas it remained unchanged in the nucleotide excision repair (NER) deficient strain. The G1 cell cycle arrest which always follows UV irradiation was partly inhibited in both strains. These results suggest that exposure to ELF magnetic fields decreased the efficiency of NER by suppressing G1 arrest, which resulted in an enhancement of the UV induced
Degree of Polyembryony among the Accessions of Commiphora wightii Collected from Different Natural Habitats of India

Polyembryony, having more than one embryo in a single seed, was first discovered by Leeuwenhoek in 1719 in Citrus. Later, various researchers reported and described it in detail. The additional embryos in polyembryony are of either zygotic or non-zygotic origin and the latter is also known as adventitious polyembryony. Adventive polyembryony is reported from a number of tropical trees species, viz. Garcinia, Citrus, Shorea, Prunus and Commiphora. The degree of polyembryony varies greatly among species and also within the cultivars of the same species as revealed in Citrus. Nucellar originated polyembryony in guggul [Commiphora wightii (Arnott) Bhandari] was first reported by Gupta et al. Later, Prakash et al. reported morphological details of guggul seeds along with seed viability, test seed weight and seed germination in relation to seed maturity. Introduction of apomictic genes into hybrid plants has become a dream of present-day breeders all over the world. If the apomictic trait is associated with polyembryony, it would be an added advantage in increasing productivity of a genetically engineered apomictic hybrid. In the present paper we report the degree of polyembryony present within C. wightii germplasm. C. wightii belonging to the family Burseraceae is a slow growing, highly branched plant that grows wild mainly in the arid rocky tracts of Rajasthan and Gujarat, India, and in Sindh and Baluchistan, Pakistan. The oleo-gum-resin produced by the plant is antiarthritic, hypocholesterolaemic and hypolipidaemic. Overexploitation for resin extraction made the species status fall under the ‘data deficient’ category in the IUCN Red Data Book (1994). The present study was carried out at the Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat. Thirty-two accessions collected from Gujarat and 21 accessions collected from Rajasthan were maintained in the field gene bank of DMAPR. Mature fruits from these accessions were used for the study. The fruits are red when fully ripened and typically two-chambered drupes (occasionally three/four-chambered) with four ovules. Splitting of epicarp discloses the hard stone (putamen). The stone usually consists of a fertile one-seeded locule and a sterile locule, or both may be fertile and can easily be split into two halves (Figure 1 a–c). Well-developed seeds fill the entire cavity within the stony fruit wall and it is practically impossible to assess whether each half-fruit contains single or two seeds. Dissecting out the seeds often damages the thin testa and impedes germination. Hence in the present experiment, epicarp and mesocarp were removed by rubbing between the folds of cotton cloth and unfilled fruits (stones) were separated by floating on water. The stones settled at the bottom were considered filled and counted and expressed in percentage (Figure 1 d and e). Each filled stone was split into two halves and each stone half was
Effects of immunomodulatory supplementation with pre and probiotic on Th2-mediated airway inflammation in A/J and C57BL/6 mice

Studies have demonstrated that some probiotics and prebiotics could improve Th2 airway inflammation, such as asthma disease. However, it is unclear if a specific probiotic and prebiotic could regulate asthma disease independent of genetic host and gut microbiota composition. Our objective is to elucidate if the habitual probiotic and prebiotic consumption can affect Th2-mediated airway inflammation in two inbred mice, A/J and C57BL/6 (B6). It is known that A/J have a greater Th2 airway inflammation predisposition than B6 and this fact was attributed to genetic difference. The purpose of this study is to examine the role of gut microbiota composition on Th2 inflammation predisposition and the effects of the probiotic (Bifidobacterium longum) and the prebiotic (pectin fiber) on experimental asthma on both mouse strains. Before treatment, an Ion-Torrent 16S rRNA gene-based amplification and sequencing protocol was used to determine the fecal microbiota profile. Ten days before sensitization, they were treated with probiotic or prebiotic. Experimental asthma was performed by sensitization and challenges with ovalbumin. Twenty-four hours after the last challenge, pulmonary inflammation and lung function were analyzed. Our results show that A/J mice have lower microbiota diversity than B6. Interestingly, probiotic and prebiotic treatment reduced lung inflammation and airway hyperresponsiveness, only on A/J mice. The results suggest that low microbiota diversity and genetic background can predispose Th2 airway inflammation. Moreover, high gut microbiota diversity can to strengthen the barrier function of the mucous membrane and to interfere with the effects of pre and probiotics, such as we observed in B6 mice.
Climate change projections for the surface ocean around New Zealand

ABSTRACT The future status of the surface ocean around New Zealand was projected using two Earth System Models and four emission scenarios. By 2100 mean changes are largest under Representative Concentration Pathway 8.5 (RCP8.5), with a +2.5°C increase in sea surface temperature, and decreases in surface mixed layer depth (15%), macronutrients (7.5–20%), primary production (4.5%) and particle flux (12%). Largest macronutrient declines occur in the eastern Chatham Rise and subantarctic waters to the south, whereas dissolved iron increases in subtropical waters. Surface pH projections, validated against subantarctic time-series data, indicate a 0.335 decline to ∼7.77 by 2100. However, projected pH is sensitive to future CO2 emissions, remaining within the current range under RCP2.6, but decreasing below it by 2040 with all other scenarios. Sub-regions vulnerable to climate change include the Chatham Rise, polar waters south of 50°S, and subtropical waters north of New Zealand, whereas the central Tasman Sea is least affected.
Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance

Evolved resistance to one antibiotic may be associated with “collateral” sensitivity to other drugs. Here we provide an extensive quantitative characterization of collateral effects in E. faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are per-vasive but difficult to predict, as independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity. Despite this apparent complexity, however, the sensitivity profiles cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. Using a simple mathematical framework, we leverage these phenotypic pro-files to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. Fi-nally, we performed whole-genome sequencing on single isolates from each population and identified candidate genes statistically associated with increased sensitivity to particular drugs.
Analysis of Mycoplasma gallisepticum Infection Factors in Commercial Layer Chicken Farm Using Analytical Hierarchy Process

Background : Mycoplasma galliseptium (MG) is a pathogenic microbial often found in poultry farm industry. In Indonesia there are rarely data of MG research. There are some factors increased the risk of MG infection. Purpose : This research aimed to determine the factors involved in the transmission of MG in commercial layer chicken farm. Methods : This was a descriptive research with the data was collected from pairwise comparison questionnaire distributed to poultry expert. The Data was analyzed using Analytical Hierarchy Process (AHP) supported by computer programme “Expert Choice”. Results : The results showed that risk value of rearing management (0.425), health management (0.312), feed management (0.088), and biosecurity of farm (0.175) to the transmission of MG. The results of AHP analysis to the risk factor variables of MG infection in commercial layer chicken farm showed that the highest risk value of MG infection was the number of bird in house (0.277), followed by antibiotic administration (0.276), while the other variables only have risk value under 0.100. Conclusion : The highest risk value of MG infection was rearing management factor especially on the variable of the population number of poultry in house.
The Effect of Social Media on Supply Chain Sensing Capability: An Environmental Scanning Perspective

Supply chain management relies on sufficient and relevant information. To acquire and supplement such information, organization’s sensing capability of business environments becomes a core aspect of the organization. A burgeoning avenue to sense surrounding environments is through social media. Researchers are beginning to recognize the ability of social media in environmental scanning (ES) activities and witness its impact on business performance. However, published evidence detailing the effect of social-media-enabled ES on firms’ sensing capabilities is sparse. From ES perspective, we propose a research model to bridge this gap under the supply chain background. Results from 117 survey responses indicate that turbulent environments increase a firm’s scanning activities on supply market, while intense competition increases the firm’s scanning on both supply and customer markets via social media. The social-media-enabled ES on both markets boosts the sensing capability of firms’ supply chain management. Research implications and limitations are also discussed.
Phytochemical analysis of leaf, bark and fruit extracts of Baccaurea courtallensis Muell. Arg

Baccaurea courtallensis Muell. Arg is an evergreen tree of Euphorbiaceae family endemic to the Western Ghats. The bark of the plant is used as a tonic in disorders of mucous membrane and to heal wounds and its root is used in controlling diabetes. The present study was aimed to investigate the phytochemical profile of Baccaurea courtallensis Muell. Arg. The leaf, bark and fruit powder was extracted with methanol and hexane. Phytochemical analysis showed the presence of tannins, saponins, terpenoids and phenolic compounds. The present study provides evidence that solvent extract of this plant contains medicinally important bioactive compounds. The phytochemical analysis of the plants is very important commercially and for the production of the new drugs for curing of various diseases.
Role of aquaporins in the improvement of adiposity and non-alcoholic fatty liver disease after bariatric surgery

The regulation of aquaglyceroporins in metabolic tissues is important for the control of fat accumulation, glucose homeostasis and insulin secretion. Obesity and insulin resistance are associated with changes in the expression of adipose tissue aquaglyceroporins, one of the main sources of plasma glycerol. Moreover, the coordinated regulation of aquaglyceroporins in adipose tissue and liver is impaired in both pathologies. The overall aim of the present thesis was to analyze whether the altered expression of aquaglyceroporins in adipose tissue, liver and pancreas is recovered in diet-induced obese rats submitted to two different bariatric surgery techniques, namely sleeve gastrectomy or gastric plication.
The use of Thrombospondin-1 Mimetic Peptides for the Treatment of Epithelial Ovarian Cancer

THE USE OF THROMBOSPONDIN-1 MIMETIC PEPTIDES FOR THE TREATMENT OF EPITHELIAL OVARIAN CANCER Nicole Campbell Advisor: University of Guelph, 2012 Professor Jim Petrik This thesis is an investigation of the use of thrombospondin-1 mimetic peptides for the treatment of epithelial ovarian cancer. The current standard of care for women diagnosed with ovarian cancer is surgical de-bulking followed by chemotherapeutics. Initially, this treatment regimen results in a reduction in the primary tumor, unfortunately chemoresistance and disease recurrence are problematic. Recent data has suggested a potential role for anti-angiogenic therapy for the treatment of various cancers. Therefore, the purpose of this study was to investigate the use of mimetics consisting of the anti-angiogenic domain of thrombospondin-1 (TSP-1) for the treatment of epithelial ovarian cancer (EOC) using a mouse model of the disease. The peptides were applied at various stages of tumor progression and a significant reduction in tumor size following treatment was observed. We found that not only were the peptides capable of slowing down tumor progression but they also played a role in reducing the size of established tumors. Treatment with TSP-1 mimetics also resulted in a significant reduction in secondary lesions and ascites fluid in the peritoneal cavity of animals. A significant increase in disease-free survival was also identified following long-term treatment with the peptide. Various histological studies revealed that the antiangiogenic peptide was in fact inducing apoptosis of the endothelial cells and also reorganizing the vasculature. To determine whether this resulted in increased blood vessel profusion we applied standard chemotherapeutics in combination with TSP-1 mimetics. Experiments with radiolabelled and fluorescent chemotherapeutics demonstrated that pre-treating with TSP-1 mimetics allowed the vasculature to become normalized and resulted in an increased uptake of chemotherapeutics. Lastly, we investigated the mechanism of action of anti-angiogenic peptides. Most of the antitumor effects appeared to be due to the apoptotic effects of TSP-1 mimetics on the vasculature. A direct apoptotic effect on epithelial cells also was observed; however, it is uncertain how much of a role this plays. In conclusion, this study was important for identifying TSP-1 mimetic peptides as a potential therapeutic treatment for women suffering from EOC.
Community composition and Biogeography of northern Canadian Ephemeroptera, Plecoptera and Trichoptera

Climate change has a disproportionately effect on northern ecosystems. To measure this impact we need to understand the structure of northern communities and the influence of current and historical climate events. Insect of the orders Ephemeroptera, Plecoptera and Trichoptera (EPTs) are excellent subjects for study because they are widespread and good bioindicators. The objectives of this study are: (1) Determine patterns of distribution and community composition of northern EPTs. (2) Understand the role of historical events (i.e., Pleistocene glaciations). We found that northern EPT communities are influenced by temperature and precipitation. Also, community composition and population structure of EPT exhibit a similar geographical pattern, with differences on either side of Hudson Bay, suggesting the influence of glaciations in shaping communities of EPTs in northern Canada. The COI barcode approach provided a reliable means for identifying specimens to produce the first wide-scale study of community structure and biogeography of northern EPTs.
The Forests of the Amazon and Cerrado Moderate Regional Climate and Are the Key to the Future

The role of tropical forests in climate is most often expressed in terms of the carbon they keep out of the atmosphere if deforestation is avoided or the carbon they remove from the atmosphere as they grow. The direct role of forests, particularly in the tropics, in maintaining low surface temperatures and relatively high precipitation has been underappreciated. Recent studies in the Brazilian agricultural frontier indicate that tropical deforestation, for pasture and crop production, has led to significant regional climate change in the last 40 years of a scale much larger than that attributed to the carbon released from deforestation. Deforestation reduces net surface radiation and evapotranspiration, thus increasing sensible heat flux and land surface temperature. In Mato Grosso state, the temperature of the forested Xingu Indigenous Park is 3℃ cooler than the surrounding mosaic of pasturelands, croplands, and remaining forest fragments. In the neighboring state of Rondônia, rainfall has significantly decreased and the dry season lengthened as deforestation occurred. Numerical model studies strongly suggest that Brazil’s agricultural frontier will be much warmer and dryer in coming decades as greenhouse gas concentrations increase. Thus, in Brazil, it is becoming clear that, because of their capacity to moderate regional climate, preserving tropical forests will be a key component of mitigating exogenously driven future climate change.
Biodiversity of ostracod communities (Crustacea, Ostracoda) in a tropical floodplain

Abstract Neotropical floodplains harbour both floating and rooted plants and are associated with rich ostracod communities. After dry seasons, flooding causes recruitment in 2 ways: floods bring in allochthonous macrophytes with associated pleuston communities, and these rising water levels rehydrate plants and attached (ostracod) eggs that dried at the onset of the dry season. We analysed the ostracods communities in the Araguaia River floodplain (Brazil) during 2 hydrological periods (dry and rainy) and evaluated the species distribution in relation to abiotic and biotic factors. We compared the ostracod fauna of 6 lakes in the dry and rainy period and 17 lakes in the rainy period. We tested the hypothesis that the highest values of ostracod community attributes (richness, density, and evenness) occur in the rainy season owing to the influx of allochthonous individuals and the rehydration of the dried autochthonous macrophytes. We indeed observed the highest richness and diversity of ostracods in the rainy season; the homogenizing effect of the flood pulse at the onset of the rainy season caused a more homogeneous fauna (lower beta diversity) during that hydrological period. The distribution of species showed a significant effect of both abiotic factors (local) and hydrological period (regional).
Increased trapping efficiency for the peach fruit moth Carposina sasakii (Matsumura) with synthetic sex pheromone

Carposina sasakii Matsumura is one of the most serious fruit‐damaging pests in Southern East Asia. The management of C. sasakii using sex pheromones has proven to be simple, effective and environmentally friendly with respect to monitoring and controlling this pest. To apply sex pheromone‐based pest control techniques effectively, we characterized a range of application parameters, as well as the effects of synthetic sex pheromones, in jujube orchards. Trapping radius was determined by comparing the mean number of trapped individuals at different inter‐trap distances, and mating disruption parameters were inferred by comparing the rate of trapping efficiency reduction and the infestation ratio of fruits in the experimental fields by uniformly placing different number/types of lures/100 m2. These studies revealed capture rates with significant differences across 10–50‐m inter‐trap distances: for example, a 30‐m or greater inter‐trap distance was suitable for monitoring and mass trapping, whereas distances <20 m significantly decreased the trapping efficiency in the testing area. The studies lay the foundation for the implementation of these technologies within the context of a well‐conceived control strategy against this significant agricultural pest.
Provisional method for detecting endosulfan resistance in coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

Cet article décrit et compare trois méthodes de mesure de la résistance à I'endosulfan du scolyte du café, Hypothenemus hampe? la pulvérisation directe des femelles avec la tour de Potter et l'exposition directe ou indirecte à un papier filtre préalablement traité. La similarité des résultats obtenus suggère que la tour de Potter sera utilisée pour toutes les études toxicologiques et que la méthode d'exposition indirecte aux insecticides conviendra aux programmes visant à détecter précocement de nouveaux cas de résistance ou à gérer une résistance déjà établie.
The effects of light intensity on oxygen production in CC 3913 pf9-3 mutant and CC-1690 mt+21 gr wild-type Chlamydomonas reinhardtii

The purpose of our study was to examine if wild type strain CC-1690 mt+21 gr and mutant strain CC 3913 pf9-3 Chlamydomonas reinhardtii exhibit different photosynthetic activities under different light intensities, as measured by oxygen production. Oxygen production of the wild-type and mutant C. reinhardtii was measured at average light intensities of 442 lux, 3055 lux, and 13300 lux. A two-way ANOVA indicated that there was a statistically significant relationship between light intensity and oxygen production in C. reinhardtii (p = 0.00016) . Furthermore, it was determined that oxygen production of the mutant was different than the wild type (p = 6.62 x 10 -7 ), and that the wild type and mutant responded differently to changes in light intensity (p = 0.01354). Oxygen production increased as the light intensity increased due the greater availability of light energy for photosynthesis. The mutant strain of C. reinhardtii has impaired flagellar movement and is observed to produce significantly less oxygen than the wild-type strain, thus suggesting that flagellar movement is important for detecting light and producing oxygen.