Miracle-dz/UniFAR-FTUs huggingface dataset:
Diazotroph community structure and the role of nitrogen fixation in the nitrogen cycle in the Chukchi Sea (western Arctic Ocean)

Marine nitrogen fixation occurs not only in subtropical and tropical regions but also in colder regions. However, the distribution of diazotrophs, nitrogen fixation rate, and its contribution to the nitrogen cycle in the Arctic Ocean remain poorly understood. We examined the diazotroph community structure and activity in the shelf and off‐shelf regions of the Chukchi Sea, western Arctic Ocean, during late summer 2015. The nitrate and ammonium assimilation rates were determined simultaneously to gain insights into the role of nitrogen fixation in the nitrogen cycle of the region. The diazotroph community determined by Illumina sequencing was mainly composed of Cluster III nifH phylotypes (putative anaerobes), accounting for > 80% of the total sequences examined, except for one surface sample. This result is strikingly different from previous findings in other oceanic regions. The nifH sequences other than those from Cluster III were mostly affiliated with UCYN‐A2 (symbiotic cyanobacteria), which accounted for < 15% of the total sequences. UCYN‐A2 tended to be abundant (maximum 2.9 × 103 copies L−1) in the high‐temperature low‐salinity water mass that is characteristic of Pacific‐originating water. Nitrogen fixation rate was detectable at most stations, with a range of 0.08–3.60 nmol L−1 d−1, displaying no clear relationship with depth (light intensity) or nitrate or ammonium concentration. Nitrogen fixation locally exceeded nitrate assimilation, but accounted for 1.00% at most in the total nitrogen assimilation in the euphotic zone.
Assessment of Genetic Diversity for the Properties Related to the Quality of Hexaploid Bread Wheat (SeriM82 / Babax) under Drought Stress

In order to study the diversity of related characteristics of bakery quality in 167 bread wheat genotypes (SeriM82 / Babax), along with their parents, were evaluated based on two replications. The measured traits including protein content, zeolite sediment volume, bread volume, moisture content, grain hardness, water absorption, wet gluten, gluten index, gluten elasticity, Sodium dodecyl sulfate (SDS) sedimentation volume and quantitative trait of 1000 seed weight according to standards International. After analysis of variance, the data of the experiments and the comparison of the meanings were performed using multivariate methods, cluster analysis and factor analysis, genotyping grouping and the relationship between the variables (traits). The result of variance Original Research Article Tabatabai et al.; ARRB, 24(5): 1-12, 2018; Article no.ARRB. 38989 2 showed that genotype was significant for protein, bread volume, wet gluten, gluten index, sedimentation of sodium dodecyl sulfate and 1000 grain weight at 1% level. Factor analysis from 11 traits examined, 4 factors with 60% variance, the first factor with variance of 27.48% including traits of protein content, zeolite sediment volume, bread volume, moisture content and water absorption, the second factor with variance of 4.8% Includes wet gluten characteristics, gluten elasticity, SDS sedimentation volume, third factor with 10.16% variance, including seed hardness and gluten index, and fourth factor with variance of 9.85% of 1000 seed weight. The results of factor coefficient evaluation indicate the importance of protein content traits, zeolite sediment volume, bread volume, moisture content and water absorption in selection of suitable genotypes for drought conditions. Based on cluster analysis (intra-group variance algorithm), genotypes were divided into eight groups, the fifth group had high baking quality and could be used in breeding programs to improve the quality of baking.
Unraveling host and parasite pathways in human innate immunity to Toxoplasma gondii

Author(s): Gov, Lanny | Advisor(s): Lodoen, Melissa B | Abstract: Toxoplasma gondii is a pathogen of global importance. Innate immunity is critical for control of acute infection. In vivo mouse models have shown that monocytes are rapidly recruited to sites of T. gondii infection and MCP-1 and CCR2 knock-out mice that fail to do so succumb to infection, underscoring the importance of monocytes in host defense. However, the role of human monocytes in immunity to T. gondii and their specific interactions with T. gondii are not well understood.Human monocytes are actively infected by T. gondii and permissive to parasite replication. Infected human monocytes release interleukin-1beta (IL-1beta), a "master regulator" of inflammation that has been shown to be protective against T. gondii in vivo. However, the host and parasite factors regulating T. gondii-induced IL-1beta production in human monocytes were unknown. We found that T. gondii induces IL-1beta transcript, post-translational processing, and release from human monocytes. We demonstrate a role for host inflammasome components caspase-1 and ASC and the parasite protein GRA15 in the induction and release of IL-1beta. This work provides important mechanistic insight into the regulation of a key mediator of inflammation and is the first to identify a T. gondii factor that drives innate immune responses in human cells.Recently, there has been increasing appreciation for the heterogeneity of circulating monocytes. Three phenotypically and functionally distinct subpopulations have been defined in humans based on CD14 and CD16 expression. However, the interactions of specific monocyte subsets with T. gondii and their functional outcomes have not been elucidated. We found that T. gondii preferentially invades classical (CD14+CD16-) and intermediate (CD14+CD16+) monocytes and that these subsets are more permissive to intracellular parasite survival. All monocyte subsets were capable of phagocytosing and degrading Mycalolide B-treated parasites. T. gondii infection induces IL-1beta in all three monocyte subsets, but the resident monocytes (CD14loCD16+) showed an enhanced IL-1beta response. These data suggest that resident monocytes are less permissive to infection and may play a critical role in parasite control. Collectively, our work defines host and parasite pathways driving innate immunity and contributes to a better understanding of the role of human monocytes in parasite control.
Effect of breed and finishing diet on growth performance, carcass and meat quality characteristics of Mos young hens

Mos breed is a Spanish authoctonus breed linked to raising and natural food, with a growing market niche in the restoration due to their meat is associated with high quality products. The effect of breed (Mos and Sasso X44) on growth performance, carcass characteristics and meat quality of breast and drumsticks was examined in young hens reared 20 weeks in free-range system. The effect of finishing feeding (fodder, corn and linseed) was also evaluated on the aforementioned parameters. The Sasso group grew faster and the maximum weights were higher ( p <0.001), but there was no effect of genotype or feed on final weight or growth efficiency. With the exception of breast piece, the highest percentages of commercial cuts were achieved in Mos birds, when breed was the studied effect. On the other hand, color parameters were not affected by breed. However, significant differences were found among feeding, since animals fed with corn achieved the highest redness values in drumstick (11.94 vs . 10.09 for corn and fodder, respectively; p <0.05). Regarding chemical composition, intramuscular fat (IMF) displayed significant differences between breeds ( p <0.05), showing higher values in Sasso X-44. On the contrary, with the exception of IMF, significant differences ( p <0.05) on chemical composition were observed among feeding groups. Finally, fatty acid profile was significantly affected by breed and feeding since animals fed with linseed presented better nutritional indices (lower SFA, n-6/n-3 ratio and higher PUFA and P/S ratio). The results show the suitability of Mos breed to produce high quality poultry products.
Plant gene silencing: molecular mechanisms of RNA interference and biotechnological applications

Las moléculas de ácido ribonucleico de cadena corta, que forman parte del mecanismo de ARN de interferencia (RNAi), son secuencias de ribonucleótidos que regulan la expresión a nivel traduccional de genes eucariontes. El silenciamiento génico mediado por RNAi, se refiere al proceso que permite, mediante complementariedad entre una molécula de ARN de interferencia y un ARN transcrito, promover la degradación de este último así como la reducción de sus niveles de traducción. Existen dos clases principales de moléculas ARN reguladoras que llevan a cabo dicho fenómeno: ARN de interferencia corto (siRNA) y microARN (miRNA). Ambas son generadas a partir del rompimiento de monómeros de ARN de doble cadena por una enzima ribonucleasa denominada DICER perteneciente a la familia de las ARNasas III, que genera fragmentos entre 17-25 nucleótidos. A nivel transcripcional, el ARN de interferencia promueve un complejo proceso de metilación de ADN (adición de un grupo metilo a la molécula), el cual conduce a una transformación de la eucromatina en heterocromatina en una posición fija del cromosoma (locus). A nivel post-transcripcional, el fenómeno de silenciamiento se origina mediante la intervención de una molécula de RNAi. El complejo de silenciamiento ARN-inducido (RISC) resultante permite la vinculación al ARN mensajero (mRNA) diana. En plantas, las secuencias RNAi reguladoras en posición cis se encuentran involucradas en mecanismos de defensa contra organismos antagonistas y transposones, mientras que aquéllas en posición trans, interceden en la expresión de genes relacionados con su crecimiento. De igual manera, algunas respuestas adaptativas a estrés se regulan por el miRNA. La presente revisión recopila de forma detallada algunos de los avances más importantes en el conocimiento del RNAi, e incluye antecedentes sobre su relación con el metabolismo de las plantas. Asimismo, se discuten progresos recientes en el entendimiento de su mecanismo molecular al igual que algunas aplicaciones biotecnológicas.
Evaluation of Weeds as Virus Reservoirs in Watermelon Crops

ABSTRACT: Watermelon is one of the most important vegetable crops in Brazil, which is grouped among the greatest producers worldwide. Viruses stand out among the most damaging disease agents, which can drastically reduce fruit production. In this context, weeds present in the field can also interfere in crop production, acting as reservoirs for viruses. Thus, this study aimed to investigate virus occurrence in weeds at the main watermelon-growing regions in the State of Tocantins. Viruses identification (e.g. potyviruses: Watermelon mosaic virus - WMV; Papaya ring spot virus - type watermelon -PRSV-W; Zucchini yellow mosaic virus- ZYMV; the cucumovirus Cucumber mosaic virus - CMV, and the orthotospovirus Zucchini lethal chlorosis virus - ZLCV) infecting weeds was performed by serology and confirmed by RT-PCR tests. Serological and molecular test results indicate that Amaranthus spinosus, Nicandra physaloides, Physalis angulata and Heliotropium indicum were infected by at least one virus species. The highest infection rate was represented by ZYMV (52.7%), followed by PRSV-W (22.2%); CMV, WMV, and ZLCV that showed the same infection rate (8.3%) each. Plants of P. angulata were infected by all five viruses, singly or in mixed infection, and represented 50% of the total number of infected samples. The highest virus infection rates, 50% and 44.4%, occurred in weeds collected at Lagoa da Confusão and Formoso do Araguaia, respectively. The results on occurrence and distribution of viruses infecting weeds in watermelon commercial plantations in the State of Tocantins provide important information about the role of weeds as virus reservoirs contribute to the knowledge of the epidemiology of these diseases, and enable a proper weed management aiming at reducing the secondary spreading control of viruses by insect vectors.
Predation risk-induced adjustments in provisioning behavior for Horned Lark (Eremophila alpestris) in British Columbia

ABSTRACT Parental provisioning rates influence nestling development with consequences for their survival and fitness as adults, but provisioning behavior can be disrupted by predation risk. For an alpine population of Horned Lark (Eremophila alpestris) on Hudson Bay Mountain, British Columbia, we tested the effects of perceived predation risk on parental provisioning behavior. Using a repeated measures experimental design, we presented nests with decoys representing 3 levels of predation risk: (1) a scent-oriented predator (red fox; Vulpes vulpes), (2) a visually oriented predator (Common Raven; Corvus corax), and (3) a noncompetitive sympatric species (Savannah Sparrow; Passerculus sandwichensis) as a control. We found that elevated perceived predation risk decreased parental nest visitation rate by 65.6% compared to the control rate (mean 0.64 [SE 0.04] visits per 10 min), with no difference in response to predators that use visual (raven: 0.17 [0.03]) or olfactory (fox: 0.27 [0.04]) cues after controlling for zero inflation. Although background levels of provisioning behavior differed between sexes, we found no evidence for sex-specific responses to perceived predation risk. Horned Larks did not compensate for reduced visitation rates by increasing prey bill-load size, and thus an overall decrease in biomass delivery occurred during predator presentations. Females increased nest visitation rates immediately (30 min period) following fox decoy presentations, however, such that the net biomass delivery rate was comparable to control rates. This immediate compensatory behavior was not observed for females following raven treatments or for males. We showed that Horned Lark parents can assess and respond to increased perceived predation risk and provide evidence for compensatory provisioning behavior, which may indicate the potential to cope with habitats experiencing elevated mesopredator densities.
Visual biology of salmonids with special reference to polarised-light sensitivity

The visual biology and its relevance to orientation was examined in fishes in the subfamily Salmoninae (salmon, trout, and char) by characterising the spectral and polarisation sensitivity of their visual systems. In addition, the underlying neural mechanisms and biological relevance of polarisation sensitivity in the Salmoninae were examined with an emphasis on its role in orientation. Integrated spike activity of axons from the optic nerve was used as a measure to determine the polarised-light sensitive mechanism underlying the ability of rainbow trout (Oncorhynchus mykiss) to orient in down-welling, linearlypolarised light. Relative sensitivity curves were then obtained for the five types of photoreceptor cells in this trout’s retina: rods, ultraviolet sensitive cones (UV), short wavelength cones (blue-sensitive) (S), medium wavelength cones (greensensitive) (M), and long wavelength cones (red-sensitive) (L). Under scotopic conditions (dark adapted), no sensitivity to e-vector was apparent. Under photopic conditions (light adapted), trout parr exhibited onresponses with e-vector sensitivity in two orthogonal channels. No evidence of polarisation sensitivity was observed in the on-responses of larger fish (50-78 g smolts) under UV-isolating background conditions, whereas the off-responses were unchanged. M and L cones, in contrast, retained their unimodal response. The decrease in UV-polarisation sensitivity in larger fish was found not to be attributable to size-related changes in the ability of the ocular media of the eye to transmit polarised light. Rainbow trout was used as a model species and spectral and polarisation sensitivity were compared with steelhead (an anadromous form of O. mykiss), cutthroat trout (O. clarki), kokanee (land-locked form of O. nerka), and brook char {Salvelinus fontinalis). Visual pigment templates from rainbow trout were corrected for ocular media absorbance and overlaid on the spectral sensitivity
A descent subgradient method using Mifflin's line search for nonsmooth nonconvex optimization

We propose a descent subgradient algorithm for minimizing a real function, assumed to be locally Lipschitz, but not necessarily smooth or convex. To find an effective descent direction, the Goldstein subdifferential is approximated through an iterative process. The method enjoys a new two-point variant of Mifflin line search in which the subgradients are arbitrary. Thus, the line search procedure is easy to implement. Moreover, in comparison to bundle methods, the quadratic subproblems have a simple structure, and to handle nonconvexity the proposed method requires no algorithmic modification. We study the global convergence of the method and prove that any accumulation point of the generated sequence is Clarke stationary, assuming that the objective $f$ is weakly upper semismooth. We illustrate the efficiency and effectiveness of the proposed algorithm on a collection of academic and semi-academic test problems.
Evaluation of milk replacer supplemented with lysine and methionine in combination with glutamate and glutamine in dairy calves

ABSTRACT This study aimed to evaluate performance, gut health and metabolic changes in dairy calves receiving milk replacer supplemented with lysine and methionine with 0.6% or 1% AminoGut (10% Glutamate and 10% Glutamine). Forty-five Holstein calves were blocked and distributed in the treatments: (1) Control: no supplementation; (2) Lys, Met, AminoGut 0.6%; (3) Lys, Met, AminoGut 1%. Animals were individually housed, with free access to water and concentrate. Milk replacer (6 L/d) was fed until the eighth week of life. Feed intake and faecal score were monitored daily. Calves were weighted and measured weekly. Blood samples were collected every other week to determine metabolites. Supplementation did not affect the performance nor the metabolism of calves. There was no effect of supplementation for faecal score. An age effect was observed for most of the variables, mainly as a response of starter intake and consequent shift from a pre to a functional ruminant metabolism. The supplementation of the milk replacer with lysine and methionine in association with 0.6% or 1% AminoGut had no effect on performance, gut health nor metabolism of dairy calves. More important than the fine adjustment of amino acid requirements is the adoption of practices to improve starter intake.
Identification of Candida species by direct inoculation of cornmeal tween™ 80 agar from blood culture bottles: Rapid and cost-effective approach

Background: This study aimed to compare the accuracy of Candida species identification by direct inoculation of positive blood culture specimens into CornMeal Tween™ (CMT) 80 agar with the conventional methods. Methods: This study was performed in two phases: Phase 1: Inoculation of direct CMT from artificially spiked blood culture bottles with identified Candida species. Phase 2: Direct inoculation of smear-positive bottles on CMT agar for identification. Routine identification method was carried out using urease production, sensitivity to cycloheximide, CMT inoculation, and colony morphology on BiGGY agar. All isolates were also evaluated for sugar assimilation on the biochemical test panel Analytical profile index (API) 20C AUX (BioMerieux). Statistical Analysis Used: The correlation between both methods was determined as percentage agreement rate using kappa score. Results: In the first phase 50 artificially spiked blood culture bottles were included in the study. The sample set consisted of 24% C albicans, 38% C tropicalis, and 22% C glabrata isolates. There was 100% agreement between the directly inoculated and CMT inoculated from colonies at 48 hours. Phase 2: The overall agreement between directly inoculated CMT and conventional method of identification at 72 h was 92%. Conclusion: Direct inoculation of CMT agar can easily differentiate common Candida species microscopically on the basis of chlamydospores, blastopores, and arrangement of pseudo hyphae. However, identification of rare species from specimens containing two different species using direct method is challenging. Therefore, conventional methods including macroscopic/microscopic characteristics and biochemical profile with the aid of API with API 20 AUX would be a better choice for such cases.
Effects of some green leafy vegetables on the haematological parameters ofdiabetic rats

The effect of some green leafy vegetable diets on haematological parameters of streptozotocin-induced diabetic rats was investigated. 16% vegetable inclusion (Occimum gratissimum,Pterocarpus soyauxii,Corchorus olitorius and Vernonia amygdalina) in the basal diets of streptocotozin-induced diabetic rats for 21 days resulted in modulation of haematological parameters. The results showed that there was a significant decrease (p<0.05) in the levels of Packed cell volume(PCV), Haemoglobin (Hb),white blood cell(WBC), red blood cell(RBC), platelets and neutrophils counts of the diabetic rats without vegetable-formulated diets when compared to the control. However, a significant increase of these hematological indices was observed in the groups fed with vegetable-diet. Lymphocytes, eosinophils, monocytes and basophils also showed significant difference(p<0.05) with increase in lymphocyte count. Among these vegetables, Pterocarpus soyauxii seems to be most promising. These results therefore suggest that green leafy vegetables are capable of normalising the hematological abnormalities associated with pathophysiology of diabetes mellitus.
Combination of trophic group habitat preferences determines coral reef fish assemblages

: We conducted an underwater survey to collect quantitative data on fish assemblages and various environmental factors on extensive reef slopes of Okinawa Island, southern Japan, and examined the relative influence of environmental factors on 6 trophic groups. Abundance and richness of most of the trophic groups were primarily affected by 1 of 2 factors, either percentage areal cover of bedrock or current velocity. For omnivores and mobile invertivores, abundance was relatively consistent across habitat types. Based on counts of fish species across 4 distinct habitat types, omnivores included more environmental generalist species occurring in multiple habitat types. In contrast, the consistent occurrence of mobile invertivores across habitat types was probably attributable to interspecific compensation, since species of this trophic function exhibited greater environmental specialization than omnivores did. Both species richness and abundance of herbivores and planktivores were more dependent on habitat type, and species included in these 2 trophic groups exhibited more consistent responses to environmental variation. Our results highlight the similarities and differences in responses to environmental variation among trophic groups, and the potential for environmental conditions to explain community structure and diversity in coral reef fishes. The realized niche width of species within each trophic group with respect to their habitat preference should be taken into consideration when developing effective conservation management strategies for coral reef fish communities.