Miracle-dz/UniFAR-FTUs huggingface dataset:
GmFW1 expression decreased in GmSymRK knockdown transgenic soybean roots

ABSTRACT SymRK and GmFWL1 both play important roles in nodulation. However, during symbiotic development, the details of Nod factor signaling association with the regulation of cell division in nodules are unknown. SymRK, the immediately downstream component of these Nod factor receptors, is central to the Nod factor signaling cascade. In this study, specified RNAi plasmid of GmSymRK was constructed and transformed into soybean roots by agrobacterium rhizogenes-mediated hairy root transformation. We found that the nodule number decreased substantially in GmSymRK knockdown soybean transgenic roots. Further to study the relationship between GmFWL1 and Nod factor signaling, we analyzed the GmFWL1 expression levels in the GmSymRK RNAi soybean transgenic roots and found that rhizobia inoculation led to substantially reduced GmFWL1 expression in GmSymRK RNAi soybean transgenic roots. Our studies showed that the regulation of cell division was affected by Nod factor signaling during nodule development in soybean, which provides important information toward understanding the functions of GmSymRK and GmFWL1 in symbiotic signaling and nodule development.
Brood size manipulation in mallard ducks: Effects on duckling survival and brooding efficiency

Abstract:Parental care occurring after hatching of eggs in precocial birds has been assumed to have no effect on offspring survival because young feed themselves, and behaviour such as vigilance or defence benefits all young regardless of brood size. We tested this assumption by manipulating clutch and brood size of wild mallards (Anas platyrhynchos) and subsequently monitoring survival of ducklings. Offspring survival in enlarged broods tended to be lower than in control broods. By 14 days after hatching, enlarged broods had no more ducklings surviving than did controls. Brooding efficiency (i.e., the effectiveness of heat transfer from a care-giving female to her young) was evaluated with captive mallards in an environmental chamber where we manipulated ambient temperature and brood size, and monitored duckling temperature (Td). There was no difference in Td in broods of different sizes, but variation in Td increased with brood size. Under natural conditions, the female’s inability to effectively cover .
Molecular Characterization of Biosynthetic Genes of an Antifungal Compound Produced by Pseudomonas fluorescens MC07

Pseudomonas fluorescens MC07 is a growth-promoting rhizobacterium that suppresses mycelial growth in fungi such as Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Phytophthora capsici. To determine the role of the bacterium's antifungal activity in disease suppression, we screened 2,500 colonies generated by Tn5lacZ insertions, and isolated a mutant 157 that had lost antifungal activity. The EcoRI fragment carrying Tn5lacZ was cloned into pBluescript II SK(+) and used as a probe to isolate wild-type clones from a genomic library of the parent strain, MC07. Two overlapping cosmid clones, pEH4 and pEH5, that had hybridized with the mutant clone were isolated. pEH4 conferred antifungal activity to the heterologous host P. fluorescens strain 1855.344, whereas pEH5 did not. Through transposon mutagenesis of pEH4 and complementation analyses, we delineated the 14.7-kb DNA region that is responsible for the biosynthesis of an antifungal compound. DNA sequence analysis of the region identified 11 possible open reading frames (ORF), OR 1 through ORF11. A BLAST search of each putative protein implied that the proteins may be involved in an antifungal activity similar to polyketides.
Phylogeny and taxonomy of the genus Vuilleminia (Basidiomycota) based on molecular and morphological evidence, with new insights into Corticiales

Vuilleminia is a corticioid genus common in Europe whose species inhabit decaying and dead attached wood of angiosperms. To examine the circumscription of the genus and the phylogenetic relationships among its species, we analyzed nuclear ribosomal sequence data from the ITS region and the LSU gene with maximum parsimony and Bayesian methods and also studied morphological characters. Our results challenge the notion that spore size and host specificity are critically important factors in delimiting species of Vuilleminia. A taxonomic summary of the accepted species in Vuilleminia is provided. Vuilleminia species described from the South America and Africa are demonstrated to be distinct from those of the north temperate region. Australovuilleminia coccinea gen. & sp. nov. is proposed for the taxon previously reported as V. comedens from New Zealand. Punctulariopsis gen. nov. is proposed for V. subglobispora described from Argentina (= Punctulariopsis subglobispora) and V. obducens from Ethiopia (= Punctulariopsis obducens). Vuilleminia is shown to be a monophyletic genus, apparently north hemispheric, and currently comprises six species. Vuilleminia together with the closely related genera Cytidia and Australovuilleminia form a well-supported clade (Vuilleminia clade) and the family name Vuilleminiaceae is resurrected to recognize this clade. Vuilleminia quercina (= Corticium quercicola) is not closely related to the other Vuilleminia species and is instead nested in a completely different clade (Corticium clade). A new genus Marchandiopsis is erected for this taxon.
Calf Diarrhea: Epidemiological Prevalence and Bacterial Load in Oyo and Ogun States, Nigeria -

Diarrhea in calves is one of the most important causes of calf morbidity, mortality and economic losses. The prevalence of diarrhea in calves was studied in 12 farms in Oyo and Ogun states in South Western Nigeria. A total of 825 calves up to 6-months old were sampled over a period of 12 months with 120 (14.5%) of the calves showing signs of diarrhea. Faecal samples of diarrheic calves (n=120) were collected, and screened for bacterial pathogens using standard laboratory procedures. In Oyo and Ogun States, highest prevalence rates of calves with diarrhea were noticed in two farms of Oyo State 50% (25 out of 50 calves) and Ogun State 23% (12 out of 52 calves) were recorded respectively. Only 19 (15.8%) of the 120 calves had bacterial pathogens; Of the calves (n=19) where bacteria were isolated Escherichia coli was isolated from 12 calves (63.2%), Salmonella species was isolated from 10 calves (52.6%) and Campylobacter species was isolated from 1 calf (5.3%). The lowest levels of bacterial detection were seen in diarrheic samples from White Fulani calves (8.9%) with the highest levels seen in samples from Jersey calves (50%). Calves of 0-2 months had positivity bacterial cause of diarrhea of 18.4%, calves between 3 and 4 months had positivity of 8.8% and calves of 5-6 months had positivity of 20%. Bull calves had 17.0% positivity while heifers had 14.8% positivity among diarrheic calves. Calves having severe diarrhea had highest percentage positivity (26.1%) of bacterial isolates while calves with moderate diarrhea had the least percentage positivity (13.6%). Calves reared in semi intensive system of management were the most susceptible (18.0%) while those reared under extensive system were least susceptible (13.6%) to bacterial scours. Therefore, Escherichia coli, Salmonella and Campylobacter organisms were most prevalent in calf scours. Age, breeds, sex, severity of diarrhea and system of management are predisposing factors of calf diarrhea.
Characterization of goat production systems and trait preferences of goat keepers in Bench Maji zone, south western Ethiopia

Studies to characterize goat production system and identify breeding practices and trait preferences of goat keepers were conducted in three districts (Sheko, Shey Bench and Meanit Shasha) of Bench Maji zone, southwestern Ethiopia. Semi-structured questionnaires and own-flock ranking experiments were employed for data collection. The results of the analyses revealed that the average goat flock size was 9.8±9.3. The flock structure constituted females (42.7%), intact males (19.0%), castrates (1.9%) and kids of both sex (36.5%). Goat production was rated highest for income and then as source of meat, with lowest rating as a means of saving. Most of respondents practiced selection for breeding does than bucks. Mating was predominantly uncontrolled. Twinning ability (I=0.29) for female and body size (I= 0.35) for male were the most highly rated traits at own flock ranking. The goat production system in Sheko and Shey Bench districts was characterized by mixed crop-livestock, while in Meanit Shasha, agro-pastoralism was dominant. Thus, the breeding objectives of the communities are to improve meat production and increase income through increased number of goat flocks. Key words: Agro-pastoralism, breeding objectives, breeding practices, mixed crop-livestock.
Phylogenetic variation in hind-limb bone scaling of flightless theropods

Abstract. The robusticity of the weight-bearing limbs of large terrestrial animals is expected to increase at a more rapid rate than in their smaller relatives. This scaling has been hypothesized to allow large species to maintain stresses in the limb bones that are similar to those seen in smaller ones. Curvilinear scaling has previously been found in mammals and nonavian theropods but has not been demonstrated in birds. In this study, polynomial regressions of leg-bone length and circumference in terrestrial flightless birds were carried out to test for a relationship similar to that seen in nonavian theropods. Flightless birds exhibit curvilinear scaling, with the femora of large taxa becoming thicker relative to length at a greater rate than in smaller taxa. Evidence was found for nonlinear scaling in the leg bones of nonavian theropods. However, unlike in avians, there is also phylogenetic variation between taxonomic groups, with tyrannosaur leg bones in particular scaling differently than other groups. Phylogenetically corrected quadratic regressions and separate analyses of taxonomic groupings found little phylogenetic variation in flightless birds. It is suggested here that the nonlinear scaling seen in avian femora is due to the need to maintain the position of the knee under a more anterior center of mass, thereby restricting femoral length. The femur of nonavian theropods is not so constrained, with greater variability of the linear scaling relationships between clades. Phylogenetic variation in limb-bone scaling may broaden the errors for mass-predictive scaling equations based on limb-bone measurements of nonavian theropods.
Salt tolerance of five varieties of wheatgrass during seedling growth.

Highlight: The salt tolerance of five relatively recently released varieties of wheatgrass was evaluated in a 6-week greenhouse study. Barton western wheatgrass (Agropyron smithii Rydb.) tended to be more sensitive to salinity than Arriba or Rosana western wheatgrass. Critana thickspike wheatgrass (A. dasystuchyum [Hook.] Scribn.) tended to be more salt tolerant than the western wheatgrasses but was not as salt tolerant as Jose tall wheatgrass (A. efongatum [Host] Beauv.).
Investigation of volumetric, micro-structural and functional MRI brain changes in Friedreich ataxia

Friedreich ataxia (FRDA) is caused by mutations in the FXN gene leading to inadequate expression of the protein frataxin. In addition to proximal spinal cord and brain stem atrophy in the early stages of FRDA, mild to moderate atrophy of the cerebellum has been reported in advanced FRDA. Despite recent advancements of neuroimaging in assessment of progression and severity of neurodegenerative diseases as well as utilisation as a biomarker tool, the neuroimaging studies on FRDA are scarce. In this PhD project, I used multi-modal MRI techniques including volumetric, micro-structural and functional methods to investigate in vivo characteristics and changes in FRDA.
Effects of multispecies and density-dependent factors on MSY reference points: example of the Baltic Sea sprat

In this paper, maximum sustainable yield (MSY) parameters for the Baltic Sea sprat (Sprattus sprattus) are estimated in relation to pressure from cod (Gadus morhua) predation and the influence of density dependence on sprat growth. This study is based on long-term deterministic and stochastic simulations in which sprat density-dependent growth and predation mortality are considered. The resultant model is a relatively simple tool that allows for streamlined analyses of problems typically approached using complex multispecies models. The analysis indicates that estimates of the MSY parameters (i.e., MSY and FMSY) and equilibrium biomass differ significantly between approaches that hold growth and natural mortality constant and those that allow for density-dependent growth and natural mortality. Based on the cod biomass observed in the 1980s, the MSY parameters estimated by a model that accounts for density-dependent growth and by a model assuming constant growth may differ by a factor of 2. As such, the MS.
Isolation and characterisation of bacteriophages infecting environmental strains of Clostridium difficile

Clostridium difficile is a leading cause of nosocomial infections associated with antibiotic treatment. Despite its’ pathogenic role, the bacterium can be carried asymptomatically in the GI tract and has an ubiquitous presence in the environment. The ecology of C. difficile outside clinical settings is not fully understood, but the evolution of pathogenic strains may occur in its zoonotic and environmental reservoirs. A major driver of bacterial genome evolution is bacteriophages. This project has investigated the prevalence and diversity of phages associated with strains from these reservoirs. A large and diverse collection of C. difficile isolates was established in order to isolate and characterise the phages associated with them. 27 phages were isolated. These were characterised according to their particle morphology, genome size and plaque morphology which showed they could be sub-grouped according to morphology. Host range analyses showed there is a complex network of phage-host interactions within this species. To characterise to a genetic level, the genomes of seven phages were sequenced and annotated. Their genomes show they are related to known C. difficile phages. However, genes which are unusual or novel to phage genomes were also identified. Comparative genomics identified distinct lineages within C. difficile phages, which correspond to their morphological sub-grouping. Also the bioinformatic analyses provide evidence of genetic exchange occurring between them, presumably during co-infection as multiple prophage carriage is common in this species. Interestingly, analysis of the C. difficile CRISPR system showed that in addition to the bacterial arrays, several prophages encode CRISPR arrays that target phage sequences. Evidence of their co-evolution suggests phage infection impacts both genome evolution of their host and other C. difficile phages. In summary, a diverse C. difficile phage collection has been established which has the potential for development to allow their exploitation.
Isolation, identification and in vitro evaluation of Bacillus spp. in control of Magnaporthe oryzae comparing evaluation methods.

Environmentally friendly technologies, such as the use of bacteria (e.g. Bacillus spp.) to control fungal diseases of rice (Oryza sativa L.), represent a promising alternative for the sustainability of agricultural ecosystems. The present work aimed to isolate, identify, and evaluate (in vitro) various Bacillus spp. from the rice phylloplane for their potential to control the rice fungus Magnaporthe oryzae. Samples were taken from the phylloplane of healthy young rice plants growing in commercial fields in ten municipalities of Maranhao (Brazil), and Bacillus spp. were subsequently isolated and molecularly identified. Both experiments utilized a randomized design, and data were submitted to analysis of variance as well as means comparison by the Tukey test. Twelve bacterial isolates were obtained and identified. Using a control isolate (B25), four in vitro M. oryzae-inhibition methods were compared, with the ? circle? method ultimately providing the highest mycelium growth inhibition. The most promising experimental isolates for biological control were then identified as B. methylotrophicus isolates B41, B31, and B22, which achieved 90.41, 69.47, and 67.55% inhibition, respectively. This study demonstrates the potential of Maranhao Bacillus spp. isolates for use as biological fungal-control agents.
The Division of the Human Claustrum Based on Anatomical Landmarks

The subdivisions of claustrum into parts exist in literature. The aim of this study was the division of the human claustrum based on anatomical landmarks to facilitate its future study. Ten human brains, which died of non-neurological causes and after fixation and embedding, were coronally cut into 25-µm-thick serial sections and stained with Kluver-Barrera. The human claustrum was divided using anatomical landmarks into three parts in both dorsoventral and anteroposterior directions. We also estimated the density, number, and volume of neurons as well as volume of each part by using stereological methods. We distinguished three parts cap, dorsal and ventral in dorsoventral direction. The circular insular and inferior end of insula, are the upper and lower borders of dorsal part. The cap and ventral parts are the smallest and largest parts, respectively. We have also found three parts anterior, central, and posterior in anteroposterior direction. The central part is alongside of globus pallidus nucleus, whereas anterior and posterior parts are referred to parts of claustrum that lie in front and behind of this nucleus, respectively. The central and posterior parts are the largest and smallest parts, respectively. The neuronal density decreased both dorsoventrally and anteroposteriorly. This study demonstrates that human claustrum consists of three anatomical parts in both dorsoventral and anteroposterior directions. Each part has its specific shape, neuron density, neuron number and neuron size.
Two New Members of Freshwater Red Algae in Taiwan: Compsopogon tenellus Ling et Xie and C. chalybeus Kützing (Compsopogonaceae, Rhodophyta)

Two freshwater red algae, Compsopogon tenellus Ling et Xie and C. chalybeus Kutzing, are first reported to the freshwater algal flora of Taiwan. In this study, we describe in detail the morphology of them and compare the ecological differences of their habitats. Both of them were found in clear, warm (24-27 °C) and running stream in low altitude plain areas of southern Taiwan.
Protocol for the in vitro rearing of honey bee (Apis mellifera L.) workers

The in vitro rearing of worker honey bees (Apis mellifera L.) has become an increasingly important method in honey bee research in general, and in pesticide risk assessment specifically. Authorities from the European Organization for Economic Co-operation and Development and the United States Environmental Protection Agency are requesting data on pesticide impacts on immature bee survivorship prior to registering new crop protection products. Those using the current in vitro rearing protocols have had variable success with immature bee survival and protocol repeatability. Here, we present an improved method for the in vitro rearing of worker honey bees from larvae to adult emergence. We have achieved consistently high survival (>95%) in our control and solvent-control rearing trials. Changes in the proportion of diet components, royal jelly source, maintenance of the developing bee, and rearing environment are the main contributors for our high rearing success and are discussed herein. Our in vitro rearing protocol can be implemented as the standard protocol to determine the impact of pesticides on immature bees because of the protocol’s high control survivability, ease in end point determination, and high overall repeatability.
The influence of coastal zonation and meteorological variables on terrestrial isopod populations: a case study in western Sicily (Italy)

Abstract Because of their biological and ecological characteristics terrestrial isopods are considered as bioindicators of ecosystem health and several studies have shown that their distribution and abundance are influenced by environmental factors, such as weather, soil texture, composition and vegetation structure. However, few quantitative data are available on the relationship between single species of terrestrial isopods, meteorological variables and coastal zonation. This study aims to clarify relationships between terrestrial isopod populations, coastal zones and weather conditions of a protected area in Sicily. The terrestrial isopods were sampled using pitfall traps, and we verified the association between each species abundance and three different (lower, medium and upper) coastal zones. Furthermore, we analyzed correlations between isopod abundances and meteorological conditions (temperature and precipitation). The results showed a close relationship between some isopod species and coastal zone types, as well as a positive correlation of most of the species abundances with temperature and a negative one with precipitation.
Diet and Pollinator Role of the Long-Snouted Bat Platalina genovensium in Lomas Ecosystem of Peru

The long-snouted bat (Platalina genovensium) is an endemic nectar-feeding bat from arid regions in western Peru and Chile. In certain areas of its distribution, it is likely the only bat pollinator and seed disperser of plants, and it is currently highly endangered. However, some aspects of its ecology, diet, and pollinator role remain unknown, especially in the unique and endangered lomas ecosystem. We conducted monthly evaluations of bats and plants over 15 months in the lomas of the National Reserve of Lachay (Peru) by sampling in three different plant communities along the Guayabito gorge. We collected fecal and pollen fur samples from 16 individuals of P. genovensium and recorded the phenology of its potential plant food resources. We differentiated fecal sample components and then identified and counted all pollen morphotypes in order to estimate their frequency and abundance in the samples. We also analyzed the niche breadth. Our results showed that the dietary components of P. genovensium included nectar, pollen, fruits, and insects, and that it utilized the cacti community for feeding. Pollen of the genus Haageocereus (Cactaceae) was the most frequent and abundant resource recorded, which was available all year long; moreover, the niche breadth analysis revealed that P. genovensium has a specialized diet on the Haageocereus cactus in Lachay. Finally, we suggest that P. genovensium could serve as a pollinator for Haageocereus acranthus, Haageocereus pseudomelanostele, and Puya ferruginea (Bromeliaceae) due to the large pollen loads it carries and the specific placement of pollen on different body zones.