Miracle-dz/UniFAR-FTUs huggingface dataset:
Postemergence Grass Control with Herbicides Applied at ULV in Paraffinic Oil

Variables affecting ultra-low-volume (ULV) application of herbicides for postemergence grass control in soybeans were evaluated in field experiments from 1988 to 1990. Air-assist applications of clethodim at 2.3 and 4.7 L ha–1 were compared with 94 and 187 L ha–1 applications with a conventional hydraulic sprayer. Rate of herbicide, volume of diluent, type of diluent, air pressure, and four other herbicides were evaluated. Clethodim at 28, 56, and 112 g ha–1 applied in paraffinic oil at 2.3 L ha–1 controlled johnsongrass better 10 wk after treatment than equivalent rates applied at 2.3 or 187 L ha–1 in water. At 2.3 L ha–1, barnyardgrass control was improved by applying clethodim in paraffinic oil rather than water. Johnsongrass control 10 wk after treatment was better with clethodim at 28 g ha–1 applied in paraffinic oil than when applied in soybean oil, cottonseed oil, No. 2 diesel fuel, kerosene, or jet A fuel. Low air pressures of 14 or 28 kPa resulted in better control of johnsongrass and barnyardgrass than higher pressures of 56 and 112 kPa. Clethodim, fluazifop-P, haloxyfop, quizalofop, or sethoxydim were more effective on johnsongrass and barnyardgrass when applied in paraffinic oil than in water at 2.3 and 4.7 L ha–1 with an air-assist sprayer.
Spatiotemporal distribution of Ascochyta pinodes and Ascochyta pinodella during the winter growing season in France

C. Le May*, M. I. Chilvers, A. L. Saucereau, M. Guibert and T. L. Peever Institut de G en etique, Environnement et Protection des Plantes (IGEPP), INRA, UMR 1349, Domaine de la Motte, Le Rheu, 35653; Agrocampus Ouest, Laboratoire Ecologie et Sant e des Plantes (ESP), 65 rue de Saint Brieuc, Rennes, 35042; Universit e de Rennes I, 9 rue Jean Mac e, Rennes, 35700, France; Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430; and Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
Developmental and evolutionary consequences of mutation to transcription factor Gli3

Gli3 is a zinc-finger transcription factor homologous to the Drosophila segment polarity gene Cubitus interruptus. It is expressed early in mouse development in mesoderm and ectoderm, and continues to be expressed during organogenesis of brain, limb, and other structures. In mouse, mutation in Gli3 produces the extra-toe (Xt) phenotype. In man, mutation in GLI3 produces isolate preand post-axial polydactylys, and polydactyl complexes associated with craniofacial and neurological abnormalities (Greig's Cephalopolysyndactyly and Pallister-Hall syndrome). GU3 function has been well studied in the limb and spinal cord, but little is known about its mode of action in brain. In this thesis, I examined the function of Gli3 in murine forebrain development. I employed a primary culture technique to test the survival and gene expression characteristics of neocortical cells from Xt/Xt, Xt/+, and +/+ mice during midneurogenesis (embryonic days (E)14.5, 15.5, and 16.5). I found that the survival of neocortical cells is age and density dependent, and that Xt/Xt cells exhibit greater viability than their +/+ counterparts. Furthermore, I found that E16.5 Xt/+ cells exhibit greater viability than +/+ cells, indicating that a murine Xt/+ neurological phenotype might exist. I tested Xt/Xt and Xt/+ telencephalon for disruption to normal cell-type composition using markers of preand post-mitotic cell types. Acutely dissociated neocortical and ganglionic eminence cells from E14.5 and E15.5 embryos were immunoreacted with neuronal markers (3-tubulin III and microtubule associated protein 2. Proliferating pre-mitotic cell types were labelled with RC2 and nestin. A further BrDU incorporation technique was employed to test for cells in active cell cycle. The results from these experiments suggest that the cell-type composition of Xt/Xt
Adaptability and stability of cotton cultivars (Gossypium hirsutum L. race latifolium H.) using factor analytic model

To build up efficient strategies in plant breeding programs, it is requested a certain level of knowledge about the genotype–by-environments interaction (GEI) effects over the crop to be improved. One efficient way to gather this information is using linear mixed models using a parsimonious structure of GEI pattern such as factor analytic (FA) structure. In this work, we applied a multivariate analysis using the FA structure on a dataset composed of 11 cotton genotypes (Gossypium hirsutum) which were evaluated in seven environments in Mozambique, to identify stable and wide/specific adapted genotypes. Using the FA structure, it has been possible to select genotypes with specific and broad adaptability for the environmental network. The results indicated that FK37, Flash, BA525 and BA919 were the most productive genotypes, reaching the highest scores for first Factor. Nevertheless, the FK37 genotype presented Factor 2 close to zero classifying it as the most stable followed by Flash cultivar. The genotypes ISA205, QM301 and Albar SZ9314 were considered the less productive, although QM301 presented good stability. These findings suggest that the FK37 genotype might be recommended for Mozambique, since it had good yield and potential stability when compared to the most cultivated varieties, CA324 and Albar SZ9314.
Molecular Verification of Cryptops hortensis (Scolopendromorpha: Cryptopidae) in the Nearctic Region

ABSTRACT: Cryptops hortensis is a successful invasive species probably of Palearctic origin. However, recent molecular studies in Europe identified multiple similar species previously misidentified as C. hortensis. In the Nearctic Region, C. hortensis is presumably an exotic species with well-established populations in the northeastern USA. After molecular and morphological identification, C. hortensis from Ohio, USA, were identified as the same species in Europe. The molecular data supported the hypothesis that C. hortensis was introduced from Europe.
Pattern formation in clonal plants

The precise dynamical features emerging from meadows of seagrasses (marine clonal plants) are not well understood. Research on modeling clonal plants tries to define the relative contribution of the different natural components on the global development of a meadow as well as on its extinction. To this day, no model is providing a simple, analytically tractable, comprehensive description of the dynamical features emerging from seagrasses. In the following thesis we approach this gap, inspired by the numerical results of a recent model (ABD model) (Ruiz et al., 2016). Specifically, starting from the numerical bifurcation and phase diagrams of the ABD model we build a single partial differential equation reproducing the behavior. In particular, we expose the analytical and numerical arguments verifying the compatibility of the two models. Overall, we show that the complex dynamical behavior emerging in the growth of seagrass meadows can be reduced to a single equation, thus providing a possible predictive tool for designing effective re-population strategies and prevent extinctions.
An isotopic analysis of the phytoplankton–zooplankton link in a highly eutrophic tropical reservoir dominated by cyanobacteria

YESHIEMEBET MAJOR, DEMEKE KIFLE, GEORG H. NIEDRIST AND RUBEN SOMMARUGA*  SCHOOL OF APPLIED NATURAL SCIENCE, APPLIED BIOLOGICAL PROGRAM, ADAMA SCIENCE AND TECHNOLOGY UNIVERSITY, PO BOX , ADAMA, ETHIOPIA,  FISHERIES AND AQUATIC SCIENCES STREAM, DEPARTMENT OF ZOOLOGICAL SCIENCES, ADDIS ABABA UNIVERSITY, PO BOX , ADDIS ABABA, ETHIOPIA AND  INSTITUTE OF ECOLOGY, UNIVERSITY OF INNSBRUCK, TECHNIKERSTRAßE , INNSBRUCK , AUSTRIA
ISOLASI DNA GENOM DAN IDENTIFIKASI KEKERABATAN GENETIK NANAS MENGGUNAKAN RAPD (RANDOM AMPLIFIED POLIMORFIC DNA)

Beberapa jenis nanas lokal di Indonesia umumnya diberi nama berdasarkan nama daerah atau lokasi, sehingga klon yang secara genetik sama kemungkinan dapat berbeda namanya. Dengan demikian identifikasi nanas berdasarkan marka biokimia maupun molekuler sangat dibutuhkan. Penelitian ini bertujuan memperoleh informasi mengenai teknik isolasi DNA daun nanas dengan metode CTAB dan kekerabatan genetik nanas lokal dengan metode yang lebih valid yaitu dengan RAPD ( Random Amplified Polimorfic DNA ). Hasil isolasi DNA daun nanas menggunakan metode CTAB menunjukkan kemurnian yang bagus yaitu diantara 1,8 – 1,9. Hasil analisis RAPD dan dendogram menunjukkan bahwa kisaran kekerabatan antara kedua kelompok nanas tersebut berkisar antara 0.95 - 1.00. Hal ini menunjukkan bahwa keragaman antara ketiga jenis nanas kode 1, 2 dan 4 sangat rendah meskipun memiliki fenotip yang berbeda. Kata Kunci: RAPD, Kekerabatan Genetik, Nanas, Ananas sp.
Hypocholesterolemic effect of Cymbopogon citratus in Rabbits.

The current study was designed to examine the effect of an aqueous extract of Cymbopogon citratus leaves on the level of total serum cholesterol for normal and hypercholesterolemic rabbits. The results showed that the treatment of rabbits with an aqueous extract of Cymbopogon citratus leaves in concentration of 100 mg / ml and therapeutic dose of 5 ml/ kg / day via oral administration and for ten days, reduced significantly (P ‹ 0.05) the total serum cholesterol ( TC) level in induced hypercholesterolemic rabbits ( group D ) from (501.67±28.81) mg/100ml to ( 441.59±29.78 ) mg/100ml ,While no significant reduction was observed in the level of total serum cholesterol for treated healthy( normal ) rabbits ( group B ) were about from ( 127. 33 ± 9.44 ) mg/100ml befor treated to(130.09±0.23 ) mg/100ml after treated with the aqueous extract for ten days .
Formulation of a peach ice cream as potential symbiotic food

Today’s population increasingly demands and consumes healthy products. For this reason, the food industry has been developing and marketing food with added bioactive components. The aim of this work was to formulate a peach ice cream reduced in calories with an added probiotic (Bifidobacterium lactis Bb-12) and prebiotics (inulin), and to evaluate its sensory quality and acceptability as potential symbiotic food. The moisture content was 76.47%; 7.14% protein; 0.15% fat; 6.37%; carbohydrates; 9.87% inulin; 1.22% ash; 0.201% calcium, 0.155% phosphorus and 0.168% sodium. On the first and 21th day of storage counts of B. lactis Bb – 12 was 4 x 108 CFU/mL and 1.5 x 107 CFU/mL, respectively. It was possible to formulate a peach ice cream reduced in calories, fat, and sugar and with potential symbiotic effect, by addition of B. lactis Bb – 12. A product with suitable organoleptic characteristics, creamy texture, peachy colour, taste and flavour, and no ice crystals was obtained. This ice cream would be a suitable food matrix to incorporate prebiotic and probiotic ingredients as a potential symbiotic food.
Alpha brain oscillations, approach attitude, and locus of control affect self-perception of social efficacy in cooperative joint-action

ABSTRACT The neurophysiological basis of social ranking perception underlying the execution of cooperative joint-actions was explored in the present study. Self-perception of social ranking, personality trait (Behavioral Activation System (BAS) and locus of control (LoC)) and alpha brain oscillations were considered. Subjects were required to match their cognitive performance in terms of accuracy (error rate) and response time. A positive feedback condition of a better joint-performance was provided and compared to absence of feedback. It was found that higher BAS participants and higher internal LoC responded in greater measure to post-feedback condition with better real performance probably based on their sensitivity to rewarding for high-BAS and the increased sense of self-efficacy. Moreover, higher-BAS showed an increased frontal left activity when they perceived increased cooperative efficacy. The present results confirmed the tendency to modulate both self-perceived social position and real performance based on the personal attitudes and the frontal.
miRge 2.0: An updated tool to comprehensively analyze microRNA sequencing data

miRNAs play important roles in the regulation of gene expression. The rapidly developing field of microRNA sequencing (miRNA-seq; small RNA-seq) needs comprehensive bioinformatics tools to analyze these large datasets. We present the second iteration of miRge, miRge 2.0, with multiple enhancements. miRge 2.0 adds new functionality including novel miRNA detection, A-to-I editing analysis, better output files, and improved alignment to miRNAs. Our novel miRNA detection method is the first to use both miRNA hairpin sequence structure and composition of isomiRs resulting in a more specific capture of potential miRNAs. Using known miRNA data, our support vector machine (SVM) model predicted miRNAs with an average Matthews correlation coefficient (MCC) of 0.939 over 32 human cell datasets and outperformed miRDeep2 and miRAnalyzer regarding phylogenetic conservation. The A-to-I editing analysis implementation strongly correlated with a reference dataset’s prior analysis with adjusted R2 = 0.96. miRge 2.0 comes with alignment libraries to both miRBase v21 and MirGeneDB for 6 species: human, mouse, rat, fruit fly, nematode and zebrafish; and has a tool to create custom libraries. With the redevelopment of the tool in Python, it is now incorporated into bcbio-nextgen and implementable through Bioconda. miRge 2.0 is freely available at: https://github.com/mhalushka/miRge.
Avoiding misinterpretation of regression lines in allometry: is sexual dimorphism in digit ratio spurious?

The statistical analysis of allometry (size-dependence of traits) is fraught with difficulty that is often underestimated. In light of some recent controversies about statistical methods and the resulting biological conclusions, I here discuss the interpretation of regression lines and show how to avoid spurious effects. General linear models based on ordinary least square (OLS) regression are often used to quantify sexual dimorphism in a trait of interest that is modelled as a function of sex while controlling for size as a covariate. However, an analysis of artificially generated data where males and females differ in size only, but are otherwise built according to the same principles, shows that the OLS method induces a spurious dimorphism where there is none. Hence, OLS-based general linear models should not be regarded as a fail-proof tool that automatically provides the correct answer to whatever question one has in mind. Here I show how to avoid misinterpretation and how to best proceed with answering the recent debate about sexual dimorphism in digit ratio, a trait that is thought to reflect sex-hormone levels during development. The limited data, currently available to me, suggests that the widely accepted sexual dimorphism in digit ratio might well be only a by-product of an allometric shift in shape, urgently calling for a re-examination in larger data sets on humans and other vertebrates.
Whole-genome sequencing of parvoviruses from wild and domestic animals in Brazil provides new insights into parvovirus distribution and diversity

Parvoviruses (family Parvoviridae) are small, single-stranded DNA viruses. Many parvoviral pathogens of medical, veterinary and ecological importance have been identified. In this study, we used high-throughput sequencing (HTS) to investigate the diversity of parvoviruses infecting wild and domestic animals in Brazil. We identified 21 parvovirus sequences (including twelve nearly complete genomes and nine partial genomes) in samples derived from rodents, bats, opossums, birds and cattle in Pernambuco, São Paulo, Paraná and Rio Grande do Sul states. These sequences were investigated using phylogenetic and distance-based approaches, and were thereby classified into eight parvovirus species (six of which have not been described previously), representing six distinct genera in the subfamily Parvovirinae. Our findings extend the known biogeographic range of previously characterized parvovirus species, and the known host range of three parvovirus genera (Dependovirus, Aveparvovirus, and Tetraparvovirus). Moreover, our investigation provides a window into the ecological dynamics of parvovirus infections in vertebrates, revealing that many parvovirus genera contain well-defined sub-lineages that circulate widely throughout the world within particular taxonomic groups of hosts.
Multiple Small RNAs Alter Membrane Lipid Composition via Post-Transcriptional Regulation of Cyclopropane Fatty Acid Synthase

Microbial membranes are the first line of defense against environmental stress as well as the site of many metabolic processes. As such, maintenance of membrane integrity and homeostasis is key to cell survival. Altering membrane protein and lipid composition is an important strategy for maintaining membrane integrity in response to many environmental stresses. There are now numerous examples of small RNA (sRNA)-mediated regulation of membrane protein production, but less is known about how sRNAs regulate the types and relative proportions of different fatty acids in the membrane. The only sRNA known to regulate membrane fatty acid composition is RydC, which stabilizes cfa mRNA, encoding cyclopropane fatty acid (CFA) synthase, resulting in increased production of the synthase and higher levels of cyclopropane fatty acids (CFAs) in the cell membrane. Here, we report that three additional sRNAs, ArrS, CpxQ, and GadF also alter cfa translation and thus the amount of CFAs in cell membranes. RydC, ArrS, and GadF bind at sites that overlap a known RNase E cleavage site in the cfa mRNA 5′-untranslated region (UTR), resulting in increased cfa mRNA stability and translation. In contrast, CpxQ binds to a different site in the cfa mRNA 5′-UTR, and acts to reduce cfa translation. The physiological role of CFAs in membrane lipids is poorly understood, but CFAs have been shown to promote bacterial resistance to acid stress. We show that cfa translation increases in an sRNA-dependent manner when cells are subjected to mild acid stress. RydC is necessary for an increase in cfa translation at pH 5.0 and a rydC mutant is more sensitive to acid shock than the rydC+ strain. Alteration of membrane lipid composition is a key mechanism for bacterial responses to many environmental stresses, including acid stress. This work suggests an important role for sRNAs in these responses through their regulation of cfa mRNA.
Host Diet Influences Lethal and Sublethal Responses of Hosts to Amphibian Pathogen Exposure

The severity of the impacts of pathogens on hosts may be driven by environmental factors like resource availability that create tradeoffs on energetic demands for immune responses and basal metabolic activity within the host. These responses can vary among species from sublethal to lethal effects, which can have consequences for the host population trajectories within a community. Chytridiomycosis, caused by the pathogen Batrachochytrium dendrobatidis (or Bd), has been associated with global amphibian population declines. However, it also occurs in populations without appearing to cause mass mortality; the effect of Bd in these situations is not well understood and environmental factors like food abundance that impact host conditions could play an important role in the magnitude of the pathogen’s impact. In the present study, we exposed American toad (Anaxyrus americanus), northern leopard frog (Lithobates pipiens), and Blanchard’s cricket frog (Acris blanchardi) metamorphs to Bd and then reared them in the terrestrial habitat under low or high food environments. We found additive effects of Bd and reduced food abundance on host growth and survival that varied according to species. For instance, Bd-induced reductions in American toad survival were greater under low food conditions compared to high food conditions but survival of northern leopard frogs and Blanchard’s cricket frogs was not affected by Bd. For northern leopard frogs and Blanchard’s cricket frogs, low food abundance resulted in the lower growth rates under Bd exposure compared to high food abundance. Additionally, we developed stage-structured population models for American toads to assess if reduced survival of metamorphs exposed to Bd under conditions of low and high food abundance could influence population trajectories; models indicated that Bd exposure would reduce annual population growth rates by 14% under conditions of high food abundance and 21% under conditions of low food abundance. Our results suggest that environmental conditions that influence resource availability for species that are sensitive or tolerant to Bd may increase the negative effects of Bd on host growth and survival, which could have important implications for how populations and communities with infected members respond over time.
Detection of a Hop-Tolerance Gene horA Insertion Variant in Lactic Acid Bacteria That Results in a Truncated HorA Lacking the Walker B Motif Necessary for Transport Function

The hop-tolerance gene horA frequently found in beer-spoilage lactic acid bacteria (LAB) was investigated for sequence variability. Although the horA gene was found to have less sequence variability relative to the LAB hop-tolerance gene horC, a sequence insertion in horA in some isolates resulted in early truncation of HorA translation. This truncated HorA was found in LAB both capable and incapable of growth in beer. Protein modeling revealed that the truncated HorA may retain some capacity to bind and sequester hop iso-α-acids but lacks the transport function essential for moving hop compounds out of the cell. Sequence analysis of LAB plasmids that contain horA revealed a high level of conservation in all of the genes comprising the horA gene cassette. Assessing whether a LAB isolated in a brewery setting is capable of making a full-length protein with intact hop transport function or a truncated HorA requires redesign of commonly used horA polymerase chain reaction primers to target detection of horA both with and without the sequence insertion.
Sequence diversity of two chloroplast genes: rps4 and tRNAGly (UCC), in the liverwort Marchantia polymorpha, an emerging plant model system

The primary purpose of this study is to evaluate the sequence variation for two regions of chloroplast DNA in a collection of 27 taxonomically well-annotated clonal lines of Marchantia polymorpha sensu lato derived from European populations. We attempted to develop molecular markers so as to identify three taxa usually recognized as subspecies. We sequenced two regions: the rps4 gene along with the rps4-trnT intergenic spacer and an intron of the tRNA Gly (UCC) gene. Samples of Marchantia paleacea ssp. diptera from Japan were used for comparative purposes. Three haplotypes (MA, MB, and MC) were identified for the species, and almost all sequence divergence between subspecies was found to occur at the level of 0.0023–0.0032 substitutions per site. The sequence divergence between M. polymorpha and M. paleacea was tenfold greater (0.0331–0.0340). We did not detect any differences between M. paleacea and homologous sequences from the reference chloroplast genome of M. polymorpha obtained from the GeneBank (NC_001319). It was confirmed that the cell suspension line A-18 used for the sequencing of the full chloroplast genome in 1986 was incorrectly taxonomically annotated.