Miracle-dz/UniFAR-FTUs huggingface dataset:
Numerical Taxonomic Study of Fast-Growing Soybean Rhizobia and a Proposal that Rhizobium fredii Be Assigned to Sinorhizobium gen. nov.

A total of 33 strains of fast-growing soybean rhizobia isolated from soil and soybean nodules collected in China and 25 strains belonging to the genera Rhizobium, Bradyrhizobium, and Agrobacterium were compared by numerical taxonomic techniques, using 240 different characters. Our results indicated that all of the strains of fast-growing soybean rhizobia which we examined are closely related (guanine-plus-cytosine content, 59.9 to 63.8 mol%) and are separated from Rhizobium and Bradyrhizobium at the generic level. Based on numerical taxonomy, deoxyribonucleic acid (DNA) base ratio determinations, DNA-DNA hybridization data, serological analysis data, the composition of extracellular gum, bacteriophage typing data, and soluble protein patterns, we propose that the fast-growing soybean rhizobia represent members of a new genus rather than a species of Rhizobium (Rhizobium fredii); we propose Sinorhizobium gen. nov. as an appropriate generic name. The type species of the new genus is Sinorhizobium fredii comb. nov. (basonym, Rhizobium fredii Scholla and Elkan 1984), and the type strain is strain ATCC 35423 (= USDA 205). For the other species we propose the name Sinorhizobium xinjiangensis sp. nov.; the type strain of this species is strain CCBAU 110, which has been deposited in the Beijing Agricultural University Culture Collection, Beijing, People's Republic of China.
Impacts of hypoxia on the structure and processes in pelagic communities (zooplankton, macro-invertebrates and fish)

Abstract. Dissolved oxygen (DO) concentration in the water column is an environmental parameter that is crucial for the successful development of many pelagic organisms. Hypoxia tolerance and threshold values are species- and stage-specific and can vary enormously. While some fish species may suffer from oxygen values of less than 3 mL O2 L−1 through impacted growth, development and behaviour, other organisms such as euphausiids may survive DO levels as low as 0.1 mL O2 L−1. A change in the average or the range of DO may have significant impacts on the survival of certain species and hence on the species composition in the ecosystem with consequent changes in trophic pathways and productivity. Evidence for the deleterious effects of oxygen depletion on pelagic species is scarce, particularly in terms of the effect of low oxygen on development, recruitment and patterns of migration and distribution. While planktonic organisms have to cope with variable DOs and exploit adaptive mechanisms, nektonic species may avoid areas of unfavourable DO and develop adapted migration strategies. Planktonic organisms may only be able to escape vertically, above or beneath the Oxygen Minimum Zone (OMZ). In shallow areas only the surface layer can serve as a refuge, but in deep waters many organisms have developed vertical migration strategies to use, pass through and cope with the OMZ. This paper elucidates the role of DO for different taxa in the pelagic realm and the consequences of low oxygen for foodweb structure and system productivity. We describe processes in two contrasting systems, the semi-enclosed Baltic Sea and the coastal upwelling system of the Benguela Current to demonstrate the consequences of increasing hypoxia on ecosystem functioning and services.
Performance of two red king crab pot designs

We conducted a laboratory experiment to compare effectiveness of two pot designs in reducing the bycatch of female and sublegal-sized male red king crabs (Paralithodes camtschaticus) while retaining legal males. One pot (pot A) was a simulated standard king crab pot; a newly designed pot (pot B) had smaller mesh size, lower and wider entrances, and one-way opening triggers. Pot B prevented crabs from inserting their chelipeds through the mesh, motivated crabs to search for the entrance, eased the entry for all crabs, and facilitated the escape for all crabs but legal-sized males. Given that crabs had approached the pot, the mean entry probability for all crabs was 0.63 for pot B and only 0.13 for pot A. The probability of escape for females and sublegal males averaged 0.72 for pot B compared with 0.28 for pot A. As a result, the new pot design reduced the catch probability of females and sublegal males by over 60% while it increased the catch probability of legal males by over 25%.
Fermentation kinetics of Lactobacillus plantarum at a rich culture medium as a potential probiotic.

The objective to determine the kinetics of growth of Lactobacillus plantarum in culture medium enriched as potential probiotic. The strains of L. plantarum 1 were tested with MRS commercial medium, and 10 g/L white sugar, 15 g/L soy milk, 150 g/L whey, 15 g/L wheat bran (Medium 4). The variables were evaluated during the kinetics: determination of pH, plaque viability (CFU/ml), determination of total sugar, determination of organic acid production, and evaluation of biomass production. The best results for viability in the medium 4 (M4) were for L. plantarum 1 H1 and L. plantarum 1 H2 with values of 3.0 x 10 and 6.0 x 10 CFU/ml at 12 hours made the kinetics.The evolution of final pH was 4.21 and 4.07 respectively for each strain. The total sugar and lactic acid production in the medium 4 for L. plantarum 1 H1 showed values of 8.90 g/L and 17.66 g/L. For L. plantarum 1 H2 showed values of 10.8 g/L and 13.16 g/L respectively. During the fermentation process carried the two strains tested reach values greater than ofμh. However, it is of note that between the two bacteria the best μh was introduced in L. plantarum 1 H1 and hence, the cell doubling time is lower. L. plantarum 1 on the medium 4 shown to be optimal as probiotic inoculums can be evaluated in piglets as an alternative to antibiotics.
Elemental stoichiometry of marine particulate matter measured by wavelength dispersive X-ray fluorescence (WDXRF) spectroscopy

This paper describes the development of a method for quantitative measurement of the elemental composition of particulate matter (PM) in seawater. This method is based on use of wavelength dispersive X-ray fluorescence (WDXRF) analysing PM harvested on various filter types. As the amount of material is less than a monolayer of cells on the filters we reduced the need for absorption correction. Given the appropriate combination of filters and elements the detection limits are low: <1 µg/filter for carbon (C), nitrogen (N), and <0.1 µg/filter for silicon (Si), phosphorus (P), calcium (Ca) and iron (Fe). The analytical range used was 90–750 µg C, 23–116 µg N and 7–30 µg P, depending on the filters applied. Calibration constants for the elements included in this study were obtained from analysis of known quantities of chemical compounds on filters or silver plates. For carbon and nitrogen we also used comparative measurements of Synechococcus sp. cultures by CHN analyser and WDXRF. We harvested PM from 150 ml to 2000 ml on each filter in three replicates, obtaining less than 5% analytical variability between the replicates. One of the challenges using WDXRF as proposed here is the absorption of X-ray signals by the filter and variability of cell/particle sizes, and, consequentlyly, the variability of harvested PM on various filters. We find that an anodisc filter is best suited for C and N, while polycarbonate filters are best for heavier elements. Here we present analytical details and some data from field experiments related to C, N, P, Si, Ca and Fe in particles from seawater.
Pseudomonas aeruginosa Short-Range Signaling Protein Influence On Biofilm Phenotypic Expression

Bacterial biofilms are communities of bacteria which grow on various surfaces. They are composed of the bacteria themselves and an extracellular polymeric slime (EPS) matrix which they encase themselves within. Biofilms can be found in any environment where there is persistent water, such as oceans, pipes, and the human body. Biofilms are formed when freefloating, planktonic bacteria attach to a surface and grow. Cells in a biofilm use communication via cell signaling bacteria to coordinate the behavior of the whole biofilm population for a diverse array of functions, including expression of virulence factors, proliferation and dispersal. In cell signaling, diffusible chemicals are released by individual bacteria which can be “sensed” by others in the biofilm. A short-range cell signaling protein in Myxococcus was discovered to be responsible for social motility in biofilms. We have identified a single potential protein homolog in Pseudomonas aeruginosa, PA4079, for which we are testing to determine social motility differences between a wild-type strain of P. aeruginosa versus a strain with a knockout of the PA4079 gene. Biofilms of both a wild-type strain tagged with green fluorescent protein (GFP) and a PA4079 transposon knockout strain tagged with GFP are grown under various media and temperature conditions. Images have been collected to compare phenotypic differences among the biofilms. In current experiments, we are using time-lapse photography to determine if dispersal rates and motility are affected by the absence of this protein. We are also utilizing a flow cell system to manipulate biofilms under shear stress. We believe the PA4079 gene and homologs may be responsible for dispersal from pathogenic biofilms and could represent a possible target for treating problematic biofilm infections. With
RESEARCH Imperilled phylogenetic endemism of Malagasy lemuriformes

Aim To highlight where in Madagascar the phylogenetically and spatially rare lemur species at risk of extinction are concentrated. Location Madagascar. Methods Phylogenetic endemism (PE) is a combined measure for apportioning a phylogenetic tree across a landscape used to identify those geographical locations that contain spatially rare phylogenetic diversity (Rosauer et al., 2009). We present a simple extension (imperilled phylogenetic endemism) that scales this phylogenetic diversity by the probability of its loss to extinction. We apply these measures to a composite phylogeny of all confirmed Malagasy lemuriform species using International Union for Conservation of Nature (IUCN) extent of occurrence and threat status data. Results We find that, because nonimperilled species are scattered about the lemuriform tree, interior branches of the tree are still quite secure: this also means that areas of high phylogenetic endemism for Madagascar lemuriformes are often the same areas as those of high imperilled PE (IPE), as both are heavily weighted by branches nearer the tips. However, although the North of Madagascar holds the largest amount of spatially rare evolutionary history using both PE and IPE, there are additional pockets of imperilled history in the south and west. Main Conclusions Correlations of endemism and threat status with phylogenetic isolation are modest across lemurs and so are not substitutable conservation values. They might best be integrated on the landscape using IPE. As illustrated here, IPE successfully highlights areas containing species which are at once threatened with extinction and that are phylogenetically and spatially rare.
Changes of Immunoglobulins and Lymphocyte Subpopulations in Peripheral Blood from Holstein Calves Challenged with Escherichia coli Lipopolysaccharide

The objective of this study was to characterize serum immunoglobulins and lymphocytes subpopulations in the peripheral blood mononuclear cells (PBMCs) of Holstein calves in response to lipopolysaccharide (LPS) challenge from Escherichia coli. Fourteen calves received subcutaneous injections of E. coli LPS at 10 weeks of age, and six calves were injected with saline as a control. The concentrations of total serum IgG and the relative amount of LPS-specific IgG in calves challenged with LPS were significantly higher (p<0.05) compared to control animals and LPS challenge significantly increased (p<0.05) the percentage of CD5 + and CD21 + T cells in PBMCs. Meanwhile, LPS challenge significantly increased (p<0.05, p<0.01) the percentage of CD8 + and CD25 + T cells in peripheral blood mononuclear cells (PBMC) at 7 and 14 Day-post LPS challenge (DPLC), respectively. The composition of CD4 + CD25 + T cells and CD8 + CD25 + T cells from calves challenged with LPS was also higher (p<0.05 and p = 0.562, respectively) than those of control calves at 14 DPLC. In conclusion, LPS challenge not only induces production of IgG with expression of B-cell immune response related cell surface molecules, but also stimulates activation of T-lymphocytes in PBMC. Our results suggest that LPS
Changes in the lease and permanent sale quota markets of a rock lobster fishery in response to stock abundance

Effective individual transferable quotas (ITQ) systems rebuild stocks and allow transfer of quotas to more efficient operators. This process requires functional markets for both quota sales and temporary quota leases. These markets are expected to respond to changes in economic rent from the fishery, which is influenced by stock abundance and the international rock lobster price. This research used multistate Markov modelling and Granger causality test to examine changes in the permanent and temporary quota trade in the Tasmanian rock lobster fishery quota market, during periods of both increasing and decreasing stock abundance. The permanent quota trade market was more active during the period of stock growth, while the quota lease market was active in both periods of stock growth and decline. In contrast to theoretical trends in ITQ fisheries, trades in both markets were not linked to the technical efficiency (i.e. catching capability) of operators, but were more driven by the quota owners' financial capacity (i.e. number of owned quotas). Prolonged and unexpected stock decline affected the quota market so that it deviated from the theoretical pattern of ITQ fisheries. Operators previously active in the market reduced their activity, while smaller operators and firms that previously had not traded became more active, so the fleet expanded with smaller operators entering.
Simulated effects of seagrass loss and restoration on settlement and recruitment of blue crab postlarvae and juveniles in the York River, Chesapeake Bay

Seagrass meadows provide important settlement habitat, food and refuge for postlarvae and young juveniles of the blue crab, Callinectes sapidus. In the York River, Chesapeake Bay, areal cover and distribution of seagrass beds has declined historically. Beds which existed 12-25 km upriver from the mouth disappeared and have not recovered. A model for planktonic postlarval behavior, coupled with a 3-dimensional hydrodynamic transport model for the York River, was used to investigate potential effects of the decline in seagrass abundance, and hypothetical restoration, on blue crab settlement and recruitment to the benthos, both in seagrass and to unvegetated bottom. Effects of habitat loss were investigated in model simulations using two historic patterns of seagrass cover (ca. 1965 and ca. 1996), five patterns with intermediate loss of cover, and three settlement rates. Declines of crab settlement in seagrass (<40%) and total settlement (<25%) were not as great as the reduction in seagrass cover (70%). Although settlement was higher when seagrass cover was greater, a settlement shadow created by seagrass near the river mouth reduced settlement in historic upstream seagrass beds and ameliorated effects associated with the loss of those beds. Increases in recruitment associated with restored seagrass beds differed significantly with restoration location, such that seagrass restoration in some locations enhanced recruitment substantially more than equivalent restoration in other locations, due to spatial variation in transport processes. Thus, landscape-level spatial patterns of existing and lost seagrass habitat across the landscape interact with transport processes and postlarval behavior to determine settlement and recruitment, and should be considered when evaluating population impacts of habitat loss or restoration.
Improving cold tolerance and insect resistance in chickpea and the use of AFLPs for the identification of molecular markers for these traits

Selection for shorter time to flowering and maturity has been highly successful in chickpea in environments where terminal drought is likely, such as southern Australia. However, like many tropical and subtropical species, chickpea is highly susceptible to mean temperatures below 15 °C at flowering. Hence any advantage derived from early flowering and the avoidance of drought stress during pod development is negated by flower and pod loss due to low temperature. Another limiting factor to yield and seed quality in chickpea is susceptibility to native budworm (Helicoverpa spp.). In this study increased cold tolerance in chickpea at flowering was achieved through an accelerated breeding programme based on haploid selection. Controlled environment assessments of the cross breeds show that the mean daily temperature at which pod set occurs is improved from 15 °C to 13 °C after only one cycle of pollen selection. Initial trials indicate that flowering and pod set also occurred earlier in the field. Selective genotyping for cold tolerance and insect resistance are being investigated to identify putative genomic segments that contribute to these traits. The use of Amplified Fragment Length Polymorphisms (AFLPs), a Polymerase Chain Reaction (PCR) based technique, is described for the identification of molecular genetic markers that potentially span the genome of chickpea.
Artificial neural networks for simulating wind effects on sprinkler distribution patterns.

A new approach based on Artificial Neural Networks (ANNs) is presented to simulate the effects of wind on the distribution pattern of a single sprinkler under a center pivot or block irrigation system. Field experiments were performed under various wind conditions (speed and direction). An experimental data from different distribution patterns using a Nelson R3000 Rotator® sprinkler have been split into three and used for model training, validation and testing. Parameters affecting the distribution pattern were defined. To find an optimal structure, various networks with different architectures have been trained using an Early Stopping method. The selected structure produced R2= 0.929 and RMSE = 6.69 mL for the test subset, consisting of a Multi-Layer Perceptron (MLP) neural network with a backpropagation training algorithm; two hidden layers (twenty neurons in the first hidden layer and six neurons in the second hidden layer) and a tangent-sigmoid transfer function. This optimal network was implemented in MATLAB® to develop a model termed ISSP (Intelligent Simulator of Sprinkler Pattern). ISSP uses wind speed and direction as input variables and is able to simulate the distorted distribution pattern from a R3000 Rotator® sprinkler with reasonable accuracy (R2> 0.935). Results of model evaluation confirm the accuracy and robustness of ANNs for simulation of a single sprinkler distribution pattern under real field conditions.
MYCN downregulates integrin α1 to promote invasion of human neuroblastoma cells

Neuroblastoma is a childhood tumor thought to arise through improper differentiation of neural crest cells. MYCN amplification is a prognostic factor that indicates a highly malignant disease and poor patient prognosis. Integrins are important regulators of neuroblastoma attachment and migration and participate in many aspects of metastasis. However, the role of integrins in neuroblastoma metastasis, the leading cause of death from this disease, remains less well understood. Screening of neuroblastoma cell lines for integrin mRNA expression showed that integrin alpha1 expression was higher in lines such as SK-N-SH and NB69 that do not have MYCN amplification than in cell lines such as IMR32, NB1, NB9 and NB19 that have MYCN amplification. A knockdown of MYCN in NB1 and NB19 cells resulted in increased expression of integrin alpha1, which correlated with enhanced attachment to the extracellular matrix and reduced migratory activity. In contrast, the overexpression of MYCN in SK-N-SH and NB69 cells resulted in decreased expression of integrin alpha1, which correlated with reduced attachment to the extracellular matrix and enhanced migratory activity. These results show that MYCN may limit cell adhesion to the extracellular matrix and promote cell migration by downregulating integrin alpha1.
Dispersion of traits related to competitive ability in an old‐field plant community

1 We investigated patterns in the dispersion (i.e. spread and spacing) of plant species traits that are frequently associated with competitive ability, in an old‐field plant community. In contrast with previous studies, we found no evidence for significant over‐ or under‐dispersion of maximum plant height, maximum plant biomass, or seed mass. 2 These findings hold across three plot sizes (10 × 10 cm, 30 × 30 cm, 50 × 50 cm), and when plot size is measured in terms of number of ramets (50 ramets, 250 ramets or 500 ramets) rather than per unit area. Plot size, however, significantly affected the direction of dispersion observed across test statistics, supporting previous studies that have observed that trait dispersion patterns are sensitive to plot size. 3 While no significant dispersion was detected, dispersion direction, measured as the tendency for a two‐tailed test to indicate trends for a given trait, was more frequently observed when analyses were weighted by abundance. Abundance weighted analyses had significantly different dispersion directions compared with presence/absence analyses for one of three traits considered. These findings suggest that abundance weighted analyses may yield more consistent trait dispersion patterns. 4 Synthesis. Our results may be interpreted as evidence for limited, if any, functional niche partitioning between co‐occurring species via size‐mediated differences in rooting depth or physical space niches (i.e. limiting similarity). Alternatively, some species with large differences in competitive traits may avoid competition through niche separation, while others may simply compete asymmetrically, leading to overall patterns of dispersion that cannot be distinguished from random. This interpretation supports recent perspectives that niche and neutral theoretical concepts are not mutually exclusive; both, working together, can be applied to the interpretation of plant community assembly and structure.