Miracle-dz/UniFAR-FTUs huggingface dataset:
Fish bacterial flora identification via rapid cellular fatty acid analysis

Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception o f Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon (Oncorhynchus gorbuscha) were determined by the rapid method. Fresh fish contained up to 7 genera in which the aerobic plate counts (APC) was 3.04 log colony-forming units (CFU)/cm2. As the fish spoiled, the APC increased to 6.60 log CFU/cm and the flora was composed o f P. fluorescens I putida, Psychrobacter immobilis and Shewanella putrefaciens. The Sherlock MIS rapidly and accurately identified seafood bacteria in fresh fish and can be used to monitor quality changes during iced storage o f fish.
A Biophysical Understanding of Mutations in the Human Thyroid Hormone Receptor Alpha

Thyroid Hormone Receptor alpha (TRα) is a transcription factor involved in the regulation of the T3 target genes expression in response to T3. TRα plays multiple critical roles in development and growth in addition to regulate the metabolism in adult organisms. TRα regulates the transcription of T3 target genes by recruiting corepressor or coactivator factors to the promoters of the target genes in response to T3. Corepressors such as SMRT are recruited by unliganded TRα, whereas coactivators such as GRIP1 are recruited in response to T3 binding to the receptors. Several mutations in the THRA1 gene have been recently identified in patients showing symptoms of tissue-specific hypothyroidism, delayed growth and development, and severe constipation. These mutations lead to a disorder called Resistance to Thyroid Hormone due to mutations in TRα (RTHα) whose degree of impairment depends on the location and severity of the mutation. Three mutations affecting the C-terminal or AF-2 domain of the TRα generate truncated TRα proteins that show aberrant interactions with coregulator proteins and a complete absence of T3 response. The aims of this thesis are to understand the molecular pathology of the mutant TRα as well as to obtain a deeper insight into the structural basis for repression by the mutant TRα using structural and biochemical approaches. The biophysical characterization demonstrates that mutant TRα impairment is mainly due to the inability of the mutant TRα to recruit coactivators in response to T3. Consequently, TRα mutants are constitutively bound to corepressors and repress T3 target gene transcription. X-rays structural data indicated that TRα mutants are able to bind and accommodate T3 in the hydrophobic pocket in an identical place and conformation as in the WT.
Atlantic mackerel daily spawning dynamics and implications for batch fecundity estimations

Atlantic mackerel daily spawning dynamics and implications for batch fecundity estimations K. Ganias*, D. Marmara, A. Solla, D. Garabana, and R. Dominguez-Petit School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece Spanish Institute of Oceanography (IEO), Oceanographic Centre of Vigo, Vigo, Spain Spanish Institute of Oceanography (IEO), Oceanographic Centre of A Coru~na, A Coru~na, Spain *Corresponding author: tel: þ3
Genetic divergence analysis in groundnut (Arachis Hypogaea l.) Under calcareous soil of northen Karnataka

Groundnut (Arachis hypogaea L.) is an important annual oilseed legume crop, valued as a rich source of proteins, minerals and vitamins. It is an unpredictable crop due to its underground pods development. For improvement of yield in groundnut direct selection is often misleading. The knowledge of existing variability is essential for developing high yielding genotypes in groundnut. An experiment was conducted with 43 gronudnut genotypes at college of agriculture, Vijayapura, UAS Dharwad, during kharif, 2013-14 to study the genetic diversity for IDC resistance related traits, yield and its component characters. The estimates of GCV and PCV were high for net plot yield (22.722 and 47.915) and low heritability with moderate GA as % mean was observed for net plot yield (22.5 and 22.197). The genotypes were highly diverse for IDC resistance and classified into 18 clusters. The diversity among the genotypes measured by intra-cluster & inter cluster distance in the present investigation was adequate for improvement of groundnut genotypes for IDC resistance by hybridization and selection. Seventeen clusters found to be solitary these can be used as promising parents for hybridization programme for obtaining high heterotic response for IDC resistance and thus better sergeants in groundnut.
Development of High-Order Organization of Guanine-Based Reflectors Underlies the Dual Functionality of the Zebrafish Iris

Many marine organisms have evolved a reflective iris to prevent unfocused light from reaching the retina. The fish iris has a dual function, both to camouflage the eye and serving as a light barrier. Yet, the mechanism that enables this dual functionality and the benefits of using a reflective iris have remained unclear. Using synchrotron micro-focused diffraction, cryo-SEM imaging and optical analyses on zebrafish at different stages of development, we show that the complex optical response of the iris is facilitated by the development a high-order organization of multilayered guanine-based crystal reflectors and pigments. We further demonstrates how the efficient light reflector is established during development to allow the optical functionality of the eye, already at early developmental stages. These results shed light on the evolutionary drive for developing a compact reflective iris, which are widely used by many animal species. One Sentence Summary The dual function of the zebrafish iris as a light barrier and camouflage reflector is enabled by the high-order organization of intracellular guanine crystals and pigments.
Climate changes and wildfire alter vegetation of Yellowstone National Park, but forest cover persists

We present landscape simulation results contrasting effects of changing climates on forest vegetation and fire regimes in Yellowstone National Park, USA, by mid-21st century. We simulated potential changes to fire dynamics and forest characteristics under three future climate projections representing a range of potential future conditions using the FireBGCv2 model. Under the future climate scenarios with moderate warming (>2°C) and moderate increases in precipitation (3–5%), model simulations resulted in 1.2–4.2 times more burned area, decreases in forest cover (10–44%), and reductions in basal area (14–60%). In these same scenarios, lodgepole pine (Pinus contorta) decreased in basal area (18–41%), while Douglas-fir (Pseudotsuga menziesii) basal area increased (21–58%). Conversely, mild warming (<2°C) coupled with greater increases in precipitation (12–13%) suggested an increase in forest cover and basal area by mid-century, with spruce and subalpine fir increasing in abundance. Overall, we found changes in forest tree species compositions were caused by the climate-mediated changes in fire regime (56–315% increase in annual area burned). Simulated changes in forest composition and fire regime under warming climates portray a landscape that shifts from lodgepole pine to Douglas-fir caused by the interaction between the magnitude and seasonality of future climate changes, by climate-induced changes in the frequency and intensity of wildfires, and by tree species response.
Early Exposure to Polycyclic Aromatic Hydrocarbons (PAHs) and Cardiac Toxicity in a Species (Xenopus laevis) with Low Aryl Hydrocarbon Receptor (AHR) Responsiveness

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous, persistent environmental contaminants, of which 16 are EPA-designated priority pollutants. Cardiotoxicity is observed in fish with developmental exposures to certain PAHs; however, the mechanism of toxicity can differ. Phenanthrene (PHE) and benzo(a)pyrene (BaP) are both cardiotoxic to fish, but PHE acts independently of aryl hydrocarbon receptor (AHR) activation while BaP-associated cardiotoxicity is AHR-dependent. To further understanding of mechanisms of toxicity, we compared the effects of early exposure to the priority PAHs pyrene (PYR), fluoranthene (FLA), PHE and BaP on cardiac function and cytochrome P450 type 1A (cyp1a) mRNA expression, an indicator of AHR activation, in a model system with lower AHR sensitivity than that of fish, the embryos and larvae of Xenopus laevis. Exposure to PYR, PHE, and FLA (0.25 – 25 μM) caused ventricular tachycardia early in heart development, but bradycardia and atrioventricular (AV) block in later stages. Elevated cyp1a mRNA levels indicate that FLA and BaP, but not PHE or PYR, are AHR agonists. The finding of FLA-induced cardiotoxicity and cyp1a expression (35-fold) is particularly surprising as FLA inhibits CYP1A activity in fish and, as a single compound, is not cardiotoxic. Our results suggest that early exposure to PHE, PYR, and FLA, but not to BaP, compromises cardiac function by altering normal pacemaker activity and conduction in Xenopus, effects associated with increased mortality. Our findings also reveal a considerable degree of species specificity between fish and frog regarding cardiac sensitivity to developmental PAH exposures and have implications for the cardiovascular health of PAH-exposed humans and wild amphibians.
Ecology of Microfungi in Mangrove Sediments at the Ganges River Estuary in India

Population values of micro fungi in plant associated sediments of the four successional stages of mangrove vegetation at the Ganges river estuary in India showed an apparent inverse relationship with the levels of soil-water salinity. The highly saline formative and developed mangrove swamps had higher proportional population of more halotolerant fungi. Thirty eight species of filamentous fungi belonging to fourteen genera, with predominance of Aspergillus and Penicillium spp. , were isolated from these sediments where species diversity was reduced with increasing concentrations of soil-water salinity. The fungi isolated varied in their nature and extent of halotolerance, with a few tolerating upto 15% in-vitro NaCl concentration. Leaves, roots and pneumatophores of Avicennia officinalis showed association of fungi similar in quality and diversity to that observed for sediments. Results established the presence of some ecologically adapted common decomposer species of microfungi in soil and plant association in the ecosystem which might have some role in detritus decomposition there.
Facilitation between plants shapes pollination networks

Although it is known that plant–plant and plant–pollinator interactions can strongly influence biodiversity and its effects on ecosystem functioning, the details of how competition and facili-tation among plants scale up to mutualistic interactions with pollinators and thus affect pollina-tion networks are poorly understood. We introduce a simple experimental system in which we control local plant interactions, measure pollinator responses and characterize plant–pollinator networks. We find that facilitation among plants produces synergistic and antagonistic effects on the pollinator community affecting the architecture and robustness of plant–pollinator net-works. Our results provide evidence for bottom-up non-additive effects of plant interactions on pollination networks and have implications for the way we study and manage ecosystems.
Above-ground growth and temporal plant–soil relations in midterm hybrid aspen (Populus tremula L. × P. tremuloides Michx.) plantations on former arable lands in hemiboreal Estonia

ABSTRACT Short-rotation forestry with hybrid aspen is a novel silvicultural system in northern Europe on former arable lands. However, knowledge about hybrid aspen growth potential in different soil types and the impact of soil physico-chemical properties on tree productivity in the long term is still scanty. We used repeated monitoring of soil properties and tree growth in young (5-year) and midterm (15-year) hybrid aspen plantations in various soil types (corresponding to four forest site types) to determine the temporal changes in tree growth–soil relationships. Growth of midterm hybrid aspen plantations exceeded same-aged native European aspen stands about two-fold. Growth had improved on Aegopodium, remained moderate on moist Dryopteris and was increasingly suppressed on dry Hepatica soils. The pHKCl, available Ca, content of clay and layer thickness of the soil A-horizon had a significant effect on tree growth in young plantations, but these effects disappeared in the midterm age. The soil water-holding capacity and available P in the A-horizon had a significant growth-controlling effect on tree growth in both ages. We concluded that former arable soils provide a sufficient supply of major nutrients in midterm hybrid aspen plantations whereas minor changes have occurred in growth–soil relationships between young and midterm age.
Yield Potentiality of Maize as Relay Crop with T. Aman Rice under Different Agronomic Management

Abstract The experiment was conducted at the Regional Agricultural Research Station, BARI, Ishwardi, Pabna, Bangladesh, during 2013-2014 and 2014-2015 to introduce maize as relay crop with T. Aman rice under different agronomic practices for determine the production potentials. The experiment was design split plot with three replications. The agronomic management practices included four plant spacing viz. S1=75 cm×20 cm (66666 plants/ha), S2=60 cm×20 cm (83333 plants/ha), S3=50 cm×20 cm (100000 plants/ha) and S4=40 cm×20 cm (125000 plants/ha) and four soil management practices viz. M1=soil mulching at 25 DAE, M2=earthing up at 25 DAE, M3=straw mulching at 25 DAE and M4= without earthing up and mulching (control). Seeds were relayed by dibbling manually in 10 days before the harvest of T. Aman rice. Results showed that an increasing plant spacing increased leaf area Index (LAI), total dry matter (TDM), crop growth rate (CGR) and light energy interception (LEI). Grain yield was higher in S3 spacing (8.44 t/ha) than others (S4 8.11 t/ha, S2 7.34 t/ha and S1 6.89 t/ha). Among the soil management practices, M2 increased LAI, TDM, CGR, LEI as well as grain yield. Moreover, M2 and M1 gave similar grain yield (8.22 t/ha and 8.02 t/ha), that were significantly greater than other two soil management practices (M3 7.55 t/ha and M4 6.98 t/ha). From the economic point of view, combination of S3M1 gave better performance with gross margin of Tk. 95000/ha and BCR of 2.17. On the basis of results, S3M1 combination was suitable for growing maize under relay sowing with T. Aman rice.
Bioefficacy of Newer and Biorational Insecticides against Shoot and Fruit Borer, Earias spp. on Okra

In India, it is cultivated throughout the country occupying an area of 507 thousand hectares with an annual production of 5853 thousand metric tones during 2014-15 (Anonymous, 2015). In Rajasthan, it is grown in an area of 4.21 thousand hectares with an annual production to the tune of 16.64 thousand metric tonnes (Anonymous, 2015). The crop, right from germination to harvesting is attacked by about 72 species of insect pests (Rao and Rajendran, 2003). Among them, the shoot and fruit borer (E. insulana and E. vittella) is one of the most serious pests of okra. The larvae bore into the terminal growing shoots, floral buds, flowers and fruits of okra, resulting in cessation, withering and drying of infested shoots, tender leaves and heavy shedding of floral buds and flowers. The infested fruits become malformed and are rendered unfit for human consumption as well as for procurement of the seeds. The borer has been reported to cause 24.6 to 26.0 per cent damage to okra shoots (Pareek et al., 1986; Zala et al., 1999) and 40 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 7 (2017) pp. 1035-1044 Journal homepage: http://www.ijcmas. com
Effects on egg quality traits of crossing Egyptian Golden Montazah with White Leghorn chickens

A crossbreeding experiment was executed between an Egyptian strain of Golden Montazah (M) and a foreign breed of White Leghorn (L). Data on 996 pullets fathered by 79 sires and mothered by 441 dams produced from five genetic groups of M, L, ½M½L, (½M½L) 2 and ((½M½L) 2 ) 2 were used to evaluate these genetic groups and to estimate the crossbreeding effects of direct additive effects (D I (ML) ), direct (H I ) and maternal heterosis (H M ) for some egg quality characteristics related to egg weight (EW), yolk weight (YW), albumen weight (AW), Haugh units (HU), shell weight (SW), egg shape index (ESI), albumen index (AI), yolk index (YI) and shell thickness (STH). Single-trait animal model analysis was used to analyze the data of these traits. Results showed that eggs of crossbreds were generally better in egg quality traits than eggs in purebreds. Eggs of L breed were significantly better than M strain in most traits (p<0.05), while eggs of M strain were better in HU, ESI and STH compared to eggs of L breed. Eggs of (½M½L) 2 cross had the heaviest EW, AW, YW and SW compared to both ½M½L and ((½M½L) 2 ) 2 crosses (P<0.05), while eggs of ((½M½L) 2 ) 2 cross recorded the superiority in HU . Estimates of D I (M-L) were significantly in favor of M chickens for EW, YW and SW; the percentages were in favor of M chickens by 3.9, 6.9 and 6.8 % relative to the mid-parents, respectively. The estimates were negatively in favor of L favorable for HU, ESI, AI and STH, but in favor of M by 0.5% for YI. Estimates of H I were favourable and better for EW, AW, YW, SW, HU, AI and YI relative to the mid-parents. Estimates of maternal heterosis in actual units (H M ) were favourable for EW, AW, YW, SW, AI, YI and STH relative to the mid-parent.
"IN VITRO" GROWTH AND MULTIPLICATION OF HYPERICUM CANARIENSE L.

Hypericum canariense L. is an endemic specie of the Canary Islands and belongs to the Hypericaceae family. Furthermore, this specie is extensively used in the pharmaceutical industry. During in vitro establishment of many species - including Hypericum canariense L. - brown exudates are detrimental to the future development of this plant material (1). The purpose of this work was to prevent the brown exudate that diffuses in the culture medium during in vitro establishment of shoots and furthermore to determine the culture medium for shoot development and proliferation. Initial explants issued from the shoot apex and axillary buds were taken from mature plants. The explants were collected from sprouts during the months of May and June. To avoid the oxidative browning of the explants and also of the culture media, the fragments were rinsed in a water solution or in a solutions containing a natural antioxidants -rosmanol or carnosic acid- for six, twelve and twenty four hours. On the other hand, the rosmanol and carnosic acid were added separately to the culture medium at the same concentrations that we used before. This natural products were isolated from Salvia canariensis L. (2) (Lamiaceae family). As well this specie is an endemic plant to the Canary Islands. Cultures were maintained under a 16 hr photoperiod (20 μExm-2xs-1) and at temperature of 24°C. All experiments were repeated twice. The results showed that the contamination was visible only in the explants rinsed by immersion prior to culture. Similar observations have been reported from other species (6). Soaking the explants in pretreatments with water solution; solutions containing rosmanol or carnosic acid was not effective and also it sem that the immersion of explants under this anaerobic conditions was detrimental for the in vitro culture of the explants. However, oxidative browning was supressed when the Almácigo medium (3) (5) was supplemented with rosmanol. The in vitro establishment from shoots of Hypericum canariense L. was achieved in Almácigo medium (3) (5).
Studies on cross compatibility in interspecific crosses of Vigna radiata × Vigna umbellata species

The present study was undertaken to study the crossability barriers in interspecific crosses of Vigna radiata × Vigna umbellata. The basic materials of this experiment comprising of five mungbean MYMV Susceptible genotypes and five rice bean MYMV resistant genotypes. Interspecific crosses were attempted by utilizing rice bean genotypes as male parents and mungbean genotypes as female parents. The successful pod set was observed on 12 crosses out of 25 interspecific crosses of Vigna radiata and Vigna umbellata. The results revealed that highest crossability per cent was recorded in the crosses Yellowmung × KBR-1 (17.30 %), DGGV-2× RBL-35 (16.0%), Selection-4×KBR-1 (11.80%), Chinamung × KBR-1 (11.0%) and BGS-9× RBL-35 (10.20%) which were considered as successful crosses. This suggests that the parents of these four interspecific cross combinations may be ideal for transfer of useful genes across the two divergent species and to broaden the genetic base of interspecific hybrid and further, the existence of moderate hybrid pollen fertility (78.24%) coupled with moderate seed germination percentage (36.84%), lower hybrid lethality (21.43%) and lower hybrid breakdown (7.14%) was observed in Chinamung × KBR-1 followed by cross Selection-4 ×KBR-1. In the present investigation prominent observation noticed are strong pre-fertilization as well as post fertilization barriers were present in the cross between V. radiata and V. umbellata, while, growth and lethality of interspecific hybrid seedlings were influenced by the genotypes of both the parental species.
Incorporating stand level risk management options into forest decision support systems

Aim of study: To examine methods of incorporating risk and uncertainty to stand level forest decisions. Area of study: A case study examines a small forest holding from Jonkoping, Sweden. Material and methods: We incorporate empirically estimated uncertainty into the simulation through a Monte Carlo approach when simulating the forest stands for the next 100 years. For the iterations of the Monte Carlo approach, errors were incorporated into the input data which was simulated according to the Heureka decision support system. Both the Value at Risk and the Conditional Value at Risk of the net present value are evaluated for each simulated stand. Main results: Visual representation of the errors can be used to highlight which decision would be most beneficial dependent on the decision maker’s opinion of the forest inventory results. At a stand level, risk preferences can be rather easily incorporated into the current forest decision support software. Research highlights: Forest management operates under uncertainty and risk. Methods are available to describe this risk in an understandable fashion for the decision maker.
UTILIZATION OF GRAFTED TOMATO SEEDLINGS FOR BACTERIAL WILT RESISTANCE IN OPEN FIELD PRODUCTION

U.S. growers have been dealing with increasing incidence of bacterial wilt (Ralstonia solanacearum) as well as other soil-borne diseases in tomato. In many cases decades of monoculture have aggravated the problem and growers often have few methods to deal with these issues. Preliminary research has illustrated the potential for the use of grafted in open field production. These experiments as well as ongoing research focus on the utility and implementation of using grafted tomato seedlings.