Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening for bioactivity and optimization of process parameters affecting growth of soil Fungi

Soil has proven to behold an immense diversity of microbes, which are considered as miniatures of chemical factories. Till now only a tiny fraction of soil microbes has been isolated and cultured. This makes soil an untapped source for novel chemistry (Jain and Pundir, 2011). Soil offers a zone of intensified microbial bioactivity due to secretion of root exudates including sugars, amino acids, vitamins and minerals. According to Bertrand (2004), the microenvironment due to elevated amounts of nutrients in soil favors the growth of a plethora of species of microbes for secreting effective bioactive metabolites.
Bayesian analysis of random regression models to model test-day somatic cell score of primiparous Holstein cattle in Iran

ABSTRACT Several functions (Ali-Schaeffer curve, Legendre polynomials, and the combination of Legendre polynomial and the Wilmink function) were used to adjust the lactation curve of somatic cell score (SCS) of primiparous Holstein cows in Iran. Data included 204,374 test-day records collected on 29,215 animals over 10 freshening years, from 2002 to 2011. The model included herd-year of calving (HY), additive genetic (AG), permanent environmental (PE) and residual effects as random and age-season of calving (A-S) as fixed regression effects. In addition, contemporary group effect (herd-year-month of test-day) was included as fixed effect. Residual variances were modelled considering 1, 4, 7, 10 or 20 classes of days in milk (DIM). Estimates of residual variance were quite similar, rating from 1.30 to 1.56. Estimates of daily heritability were practically constant until DIM 250 of lactation (around 0.03) and increased toward the end of lactation (0.07), thereby indicating the presence of low AG variation for SCS in this population of Holstein cattle. Regarding low heritabilities, a relatively low genetic progress will be expected following selection. The chosen model (according to the deviance- and Bayesian-information criterion) had Legendre polynomials with six coefficients for A-S effect, four coefficients for HY effect, five coefficients for additive effect, and six coefficients for PE effect with a homogeneous error structure.
Warm northern river temperatures increase post-exercise fatigue in an Arctic migratory salmonid but not in a temperate relative

The Arctic is warming at twice the global average rate; how native and non-native anadromous fishes will respond remains largely unknown. Some native Arctic salmonids are already experiencing warm (>21°C), physically challenging migratory river conditions and large diurnal temperature fluctuations (>10°C). We conducted field and laboratory experiments to determine how these extreme conditions may affect the capacity for migration in Arctic and temperate salmonids. In adult migratory Arctic char, reflex impairment following a handling challenge increased with temperature, indicating more extensive fatigue. In Arctic char smolts, temperature did not affect initial critical swimming performance (Umax1), however, there was a threshold for repeat swimming performance (Umax2) near 20°C, above which recovery was impaired. Following a simulated diurnal warming scenario (11–21°C), Umax1 increased in rainbow trout and remained constant in Arctic char as in the field while Umax2 remained constant in rainbow trout it was drastically reduced in Arctic char. Furthermore, at warm temperatures, Arctic char were unable to recover to routine levels of oxygen uptake after exercise, while rainbow trout were. Warming also had more pronounced effects on blood composition and plasma glucose and lactate concentration in Arctic char than in rainbow trout. In general, rainbow trout, a temperate salmonid, had superior swimming performance, aerobic capacity, and warm tolerance than Arctic char, an Arctic salmonid. The present flow and temperature regimes in some Arctic rivers may restrict migration of native salmonids by limiting their ability to recover from fatiguing exercise. Non-native, temperate salmonids are likely better suited to overcome these particular physical and thermal challenges. A plain language summary is available for this article.
Effect of dietary amino acid composition from proteins alternative to fishmeal on the growth of juveniles of the common snook, Centropomus undecimalis

ABSTRACT This study investigated the effect of dietary amino acid composition from proteins alternative to fishmeal on the growth performance of the common snook, Centropomus undecimalis. Fish of 10.79±0.71 g (n = 150) were stocked in 15 shaded outdoor tanks of 1 m3. The basal diet contained 643.4 g kg−1 salmon byproduct meal (SML) and 200.0 g kg−1 soy protein concentrate (SPC). Two other diets replaced 39 and 29% of the SML with poultry byproduct meal (PBM, 170.1 g kg−1) [. ]
Tension and contractile activity during adult muscle formation in Drosophila

For the investigation of in vivo adult muscle development in Drosophila , a custom built nanodissection device was used to optically sever developing muscles of two structurally and functionally different groups: dorsal-longitudinal muscles (DLMs) and dorsal abdominal muscles (DAMs). Based on the knowledge that tension contributes to DLM development, its verification in DAMs demonstrated a universal role for tension in Drosophila adult muscle development. From investigations of contractile DAM activity it was found that this precedes sarcomeric order, indicating a causal chain.
Combining ability × environment interaction and genetic analysis for agronomic traits in safflower (Carthamus tinctorius L.): biplot as a tool for diallel data

Combining ability × environment interaction is considerable to identify the effect of environment on the combining ability and gene action of the traits to select appropriate parents for safflower hybrid production. The 36 genotype (28 F 2 progenies of eight-parent half-diallel crosses across 8 parental genotypes) of safflower were studied to investigate the mentioned parameters across different geographical regions of Iran. The results indicated significant differences among parents for general and specific combining ability, except for seeds per capitulum across three environments. The overall results indicated that K 21 and Mex.22-191 were excellent parents with greater general combining ability for the improvement of seed yield in safflower. The K 21 × Mex.22-191 hybrid could be, therefore, employed for the production of high seed yield in safflower breeding. The estimates of genetic variance components recommended the importance of additive- dominance genetic effects that contributed to variation in yield per plant. Such gene action expression for seed yield needs auxiliary methods based on hybridization and selection for seed yield advancement in safflower.
On the female plumage of Glow-throated Hummingbird Selasphorus ardens Salvin, 1870

Summary. Glow-throated Hummingbird Selasphorus ardens is a poorly known trochilid described from the highlands of western Panama. It is documented by no more than 12 putative specimens of which the last was collected in 1924. Most specimens have ambiguous or untraceable localities. There are few recent reports, and the lack of reliable diagnostic criteria has limited efforts to understand the status, distribution and life history of S. ardens. We reviewed the extant specimen material and demonstrate that published descriptions of female plumage cannot be verified and that female plumage is unknown.
Torymidae (Hymenoptera, Chalcidoidea) revised: molecular phylogeny, circumscription and reclassification of the family with discussion of its biogeography and evolution of life‐history traits

A phylogeny of the Torymidae (Chalcidoidea) is estimated using 4734 nucleotides from five genes. Twelve outgroups and 235 ingroup taxa are used, representing about 70% of the recognized genera. Our analyses do not recover Torymidae as monophyletic and we recognize instead two families: Megastigmidae (stat. rev.) and Torymidae s.s. (stat. rev.). Within Torymidae s.s. , we recognize six subfamilies and six tribes, including Chalcimerinae, Glyphomerinae and Microdontomerinae (subf. nov.), and two new tribes: Boucekinini and Propalachiini (trib. nov.). Seven unclassified genera (i.e. Cryptopristus, Echthrodape, Exopristoides, Exopristus, part of Glyphomerus, Thaumatorymus, Zaglyptonotus) are assigned to tribes within our new classification. Five genera are restored from synonymy—Ameromicrus and Didactyliocerus from under Torymoides (stat. rev.), Iridophaga and Iridophagoides from under Podagrionella (stat. rev.) and Nannocerus from under Torymus (stat. rev.)—and three genera are synonymized—Allotorymus under Torymussyn. nov., Ditropinotus under Eridontomerussyn. nov. and Pseuderimerus under Erimerussyn. nov. A Palaearctic or Eurasian origin for Torymidae is proposed. The ancestral area of Megastigmidae is indicated as the Australian region. The most probable ancestral life strategy for Torymidae s.s. is ectoparasitism on gall‐forming Cynipidae. The life strategy and putative hosts of the common ancestor of Megastigmidae remain uncertain.
Antioxidant properties and Flavonoids-Phenolic content of citrullus colocynthis (L.) schrad growing in Khuzestan, Iran

Introduction: Free radicals cause several human diseases. Antioxidants decrease the risk of cardiovascular diseases and heart attack, and prevent the development of cancers through neutralization of free radicals. This study set out to determine the antioxidative properties of Citrullus colocynthis growing in Khuzestan. This plant is traditionally used for the treatment of type II diabetes. Methods: In this study, 2, 2-diphenyl-1-picrylhydrazyl (DPPH) and beta-carotene linoleic acid assays were used for the evaluation of antioxidative properties. In addition, the measurement of flavonoids and phenolic compounds was done based on the Gallic acid and quercetin reagents. Correspondence: Hamzeh Amiri, PhD. Biology Department Faculty of Science, Lorestan University. Khorramabad, Iran Tel:+98 9166634064 Email: amirihlu@yahoo.com Results: In the DPPH assay, the maximum and minimum scavenging activity of free radicals were found in the extractions of stem (IC50=12.4mg/ml) and leaves (IC50=5.46 mg/ml), respectively. With respect to the beta-carotene linoleic assay, the maximum and minimum antioxidative activities were observed in the extractions of leaves (79.78) and fruits (47.08), respectively. Moreover, the maximum content of flavonoids and phenolic compound were 22.15mg/ml in stem, and 4.09mg/ml in fruit. Conclusion: The methanol extracts from different organs of citrullus colocynthis (C. colocynthis) showed antioxidative activities at different levels. Therefore, they can be used as antioxidants in food industries and adjuvant treatments.
Flooding drives a macroinvertebrate biomass boom in ephemeral floodplain wetlands

Despite broad recognition of the importance of the Flood Pulse Concept to large river ecology, few studies have provided empirical evidence to support a number of its arguments. We compared and contrasted the responses of water quality, nutrients, and the macroinvertebrates of ephemeral and permanent wetlands to a 22-wk managed inundation. We hypothesized that inundation of ephemeral wetlands would mobilize higher concentrations of nutrients from floodplain sediments and C from organic matter, which would, in turn, fuel greater abundance and biomass of aquatic macroinvertebrates than in permanent wetlands. The response of ephemeral wetlands to flooding contrasted very strongly with that of permanent wetlands. Freshly inundated ephemeral wetlands had significantly higher dissolved nutrient and organic C concentrations than permanent wetlands and supported different aquatic macroinvertebrate communities. Macroinvertebrate diversity was higher in permanent wetlands, but ephemeral wetlands supported much greater macroinvertebrate abundance and biomass. Differences between macroinvertebrate communities in ephemeral and reference wetlands were driven primarily by Chironomidae. Chironomus tepperi was the dominant taxon among ephemeral wetlands, both numerically and by biomass. Early-colonizing Coleoptera contributed strongly to taxonomic richness among ephemeral wetlands. Analysis of functional feeding groups (FFGs) indicated that ephemeral wetlands contained a higher proportion of detritus-feeding collector–gatherers compared to permanent wetlands, suggesting an increased reliance on heterotrophic energy pathways. We showed that a managed flood pulse can mobilize latent terrestrial energy sources within ephemeral floodplain wetlands and support a boom of aquatic invertebrate biomass, with important implications for both terrestrial and aquatic food webs.
Differences in bioactive protein and vitamin status of milk from certified organic and conventional farms

The aim of the study was to determine differences in the status of selected bioactive whey proteins and lipophilic vitamins in milk obtained from certified organic farms as compared to conventional farms (using traditional and intensive production systems). Significant relationships were noted with regard to production system and individual bioactive milk compounds, that is β-lactoglobulin, lactoferrin, lysozyme, vitamins A, D3 and E, and β-carotene (P = 0.001) and bovine serum albumin (BSA) (P = 0.016). Milk obtained from extensive farms, especially certified organic ones, was a valuable source of certain antioxidant compounds: β-lactoglobulin (3.32 g/L), lactoferrin (123.8 mg/L), vitamin E (2.044 mg/L) and β-carotene (0.257 mg/L) in the case of organic farms.
Amendment of a hardwood biochar with compost tea: effects on plant growth, insect damage and the functional diversity of soil microbial communities

Abstract Biochar is an organic soil amendment that has been shown to improve plant growth and increase resistance to plant diseases and insect damage in certain soils. Organic growers have been known to use compost teas to amend biochar, claiming that this practice adds nutrients and beneficial microorganisms that can improve plant growth and resistance to pathogens and insect pests. However, few data exist to support this hypothesis. This study investigated the effects of a hardwood biochar amended with different types of compost teas and microbial enrichments (prepared from vermicompost) on eggplant (Solanum melongena var. Rosa Bianca) growth, flea beetle (Epitrix fuscula) damage, and soil microbial activity and functional diversity in two temperate soils. No positive short-term effects were observed on eggplant growth or flea beetle damage when biochar amended with compost teas prepared from horse manure, mushroom compost or vermicompost were added to a temperate agricultural soil. However, a second experiment suggested that biochar amended with microbial enrichments from vermicompost tea may improve eggplant growth if matched with the physical and chemical properties of a given soils. Results from Community Level Physiological Profiling (CLPP) revealed that biochar amended with compost teas altered soil microbial activity and functional diversity differently to that of biochar alone, and that these changes corresponded with plant growth and insect damage.
Genetic analysis of emotional memory in AMPA and NMDA receptor mutant mice

My goal was to study the role of AMPA and NMDA receptors in fear memory using genetic tools. In particular, I aimed to unravel the function of these glutamate receptors in the long-term retrieval of passive avoidance and fear conditioning, both in the brain in general and in the Basolateral Amygdala (BLA). Through the analysis of GluA3 knockout mice, I could show that the AMPA receptor subunit GluA3 is not necessary for the initial phases of cued fear learning, but is required for the normal attenuation of fear to a remote negative event, both in the passive-avoidance and fear-conditioning paradigms. In contrast, GluA1 is essential for the acquisition and short-term retrieval of cue- and context-induced fear. Two gene-targeted mouse lines were used, one with a global GluA1 knockout, and a ”loss of function“ mutant GluA1 (Q586R). Both lines showed impaired acquisition and reduced cue- and context-induced retrieval 24 h and 48 h after fear conditioning, supporting the hypothesis of involvement of GluA1-containing AMPA receptors in learning of emotional associations. Moreover, in a similar way as for GluA3, GluA1 is also required for the normal decrease of fear to remote events in the passive avoidance test, suggesting that both subunits play an important role in the normal destabilization of older memories such as those that no longer provide an advantage in survival. To study AMPA and NMDA receptor function specifically in the retrieval phase of fear conditioning, I used inducible recombinant adeno-associated virus (rAAV)-mediated gene manipulations in the amygdala. The efforts to generate a BLA-specific promoter for rAAV failed. Therefore a doxycycline-inducible neuron-specific system was used for synaptic silencing of neurons in the amygdala, and to inactivate NMDA and GluA1-containing AMPA receptors in the BLA. Altogether, the analysis of rAAV-injected mice provided strong evidence that retrieval of cued fear memory is dependent on the chronic expression of NMDA receptors in the BLA, whereas the contribution of the GluA1-containing AMPA receptors remains to be confirmed. In the second part of this thesis, I generated and analyzed a new rAAV vector for tissue-specific gene delivery. A new endogenous promoter was cloned from the murine lynx2 gene, a member of the Ly-6/neurotoxin superfamily, for overexpression of genes in dentate gyrus granule cells. This virus can be used to further restrict rAAV-mediated targeting to certain groups of cells.
Elicitor induction of defence genes and reduction of bacterial canker in kiwifruit

Pseudomonas syringae pv. actinidiae (Psa), which causes bacterial canker, is the most serious global pathogen of kiwifruit. Like most bacterial pathogens, control options are limited, but elicitors can reduce disease significantly, particularly those that induce the salicylic acid (SA) pathway. Acibenzolar-S-methyl (ASM), a SA analogue, is one of the most effective elicitors for Psa control. In this study, real-time PCR (qPCR) was used to measure the expression of 18 putative defence genes in Actinidia chinensis var. chinensis ‘Hort16A’ in response to Psa and ASM. Application of ASM led to up-regulation of RPM1 interacting protein 4 (RIN4), phenylalanine ammonia lyase (PAL), a hypersensitivity-induced response protein (HIRP), and I²-1,3-glucosidase. Expression of PAL and HIRP was further enhanced when elicitor application and Psa-inoculation were combined. Elevated gene expression was correlated with decreased disease expression, and supports the hypothesis that elicitor-treated plants are primed to react more rapidly and/or strongly to pathogens.
White matter correlates of hemi-face dominance in emotional expression

The neural underpinnings of human emotional expression are thought to be unevenly distributed among brain hemispheres. However, little is known on the anatomy supporting this claim, particularly in the cerebral white matter. Here we explored the relationship between hemi-face dominance in emotional expression and cerebral white matter asymmetries in 33 participants. Measures of emotional expression were derived from picture of their faces in a ‘happy smiling’ and a ‘sad frowning’ conditions. Chimeric faces were constructed by assembling right and left hemi-faces – respectively – with their mirrored version. These faces were presented in competition at the extremities of a 155 mm segment to be marked according to the emotional intensity. A jury made of 10 additional participants evaluated the set of chimeric facial stimuli. Hemispheric asymmetry of the uncinate, the cingulum and the three branches of superior longitudinal fasciculi were derived from diffusion weighted imaging tractography dissections. Group effect analyses indicated that the degree of asymmetry in emotional expression was not as prominent as reported in the literature with a large inter-individual variability. Secondly, anatomical dissections replicated previous finding in white matter anatomical lateralisation. Lastly, a strong relationship was revealed between SLF I and happy hemi-face dominance so that the greater the hemispheric lateralisation of SLF I, the more the expression of happiness in the contralateral half of the face. This result brings up interesting hypotheses on the relationship of the SLF I and emotional expression, especially its role in mood disorders.
Variación morfológica en Opuntia jaliscana (Cactaceae)

espanolEn este estudio se describe la variacion morfologica de Opuntia jaliscana en 5 poblaciones del estado de Jalisco (Mexico). Se seleccionaron las poblaciones a lo largo de un gradiente ambiental de aridez y se midieron 61 caracteres vegetativos y reproductivos de 25 individuos por poblacion. Los caracteres cuantitativos se analizaron de forma independiente mediante una prueba de ANDEVA de una via utilizando como factor de variacion el sitio. Posteriormente se realizo un analisis discriminante. Los resultados revelaron que el analisis discriminante explico el 46% de la variacion total en las cuatro primeras funciones discriminantes. El analisis de asignacion general entre poblaciones indico que los individuos fueron clasificados correctamente en el 87% de los casos. La correlacion lineal de Pearson entre las variables mas significativas y el indice de aridez demostro una relacion positiva para grosor de cladodio y diametro de tronco. La poblacion de Tierra Blanca mostro tendencia hacia la separacion por variaciones en el grosor del cladodio y tamano del fruto, caracteres que podrian estar relacionados a la plasticidad fenotipica de los individuos mayor disponibilidad de agua, mientras que en Los Vallejo la separacion podria ser debido al manejo y aprovechamiento. El resto de las poblaciones exhibio cierta variabilidad morfologica, pero sin tendencias a la separacion. EnglishThe aim of this study was to describe morphological variations of Opuntia jaliscana in 5 wild populations in the state of Jalisco (Mexico). Populations were selected along an environmental aridity gradient, and 61 vegetative and reproductive characters from 25 individuals were measured per population. Quantitative characters were analyzed independently by a one-way ANOVA test using the site as variation factor. Subsequently, a discriminant analysis was performed. The discriminant analysis results showed that the 46% of the total variation was explained by the first four discriminant functions. The analysis of overall membership between populations indicated that individuals were correctly classified in 87% of cases. Pearson linear correlation between the most significant variables and the aridity index, showed a positive relationship to cladode thickness and diameter of the trunk. The population from Tierra Blanca shows an outlier behavior because of variation in cladode thickness and fruit size, which might be related to plasticity of individuals to have a greater availability of water, while in Los Vallejo the separation might be due to selection by management and use. The remaining populations exhibited some morphological variability without separation.