Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Aflatoxin B1 Producing Aspergillus flavus Genes from Maize Feed Using Loop-Mediated Isothermal Amplification (LAMP) Technique

Aflatoxin contamination in maize feed, one of several agriculture crops grown for livestock feeding, is still a problem throughout the world mainly under hot and humid weather conditions like Thailand. In this study Aspergillus flavus (A. flavus), the key fungus for aflatoxin production especially aflatoxin B1 (AFB1), isolated from naturally infected maize were identified and characterized according to colony morphology and PCR detected on ITS, β-tubulin and calmodulin genes. The isolates were analysed for the presence of four aflatoxigenic biosynthesis genes in relation to their capability to produce AFB1, Ver1, Omt1, Nor1, and aflR. AFB1 production of the isolates was then confirmed using high performance liquid chromatography (HPLC) technique. A loopmediated isothermal amplification (LAMP) was applied as an innovative technique for rapid detection of target nucleic acid. The reaction condition was optimized at 65C for 60 min and calcein fluorescent reagent was added before amplification. The LAMP results showed clear differences between positive and negative reactions in end point analysis under daylight and UV light by the naked eye. In daylight, the samples with AFB1 producing A. flavus genes developed a yellow color, but those without the genes retained the orange color. When excited with UV light, the positive samples become visible by bright green fluorescence. LAMP reactions were positive after addition of purified target DNA until dilutions of 10 (89 pg/μl) whereas PCR reactions were positive after addition of purified target DNA until dilutions of 10 (0.0089 ng/μl). The reaction products were then confirmed and visualized with 1% agarose gel electrophoresis. To test the LAMP utility, 50 maize samples were collected from livestock farms and tested for the presence of four aflatoxigenic biosynthesis genes. The results were positive in 18 samples (36%) but negative in 32 samples (64%). All of the samples were rechecked by multiplex PCR and the results were the same as LAMP, indicating 100% specificity. Additionally, when assessing LAMP results with the HPLC aflatoxin analysis results using correlation coefficient, there was a significant correlation between the two methods (r = 0.83, P<0.05) which suggested that positive maize samples were likely to be a highrisk feed. In conclusion, the LAMP technique in this study can provide a simple and rapid approach for detecting AFB1 producing A. flavus genes from maize and appeared to be a promising tool for the prediction of potential aflatoxigenic risk in livestock feedings.
The three-dimensional crystal structure of cholera toxin

The clinical manifestations of cholera are largely attributable to the actions of a secreted hexameric AB{sub 5} enterotoxin (choleragen). We have solved the three-dimensional structure of choleragen at 2.5 {Angstrom} resolution and compared the refined coordinates with those of choleragenoid (isolated B pentamer) and the heat-labile enterotoxin from Escherichia coli (LT). The crystalline coordinates provide a detailed view of the stereochemistry implicated in binding to GM1 gangliosides and in carrying out ADP-ribosylation. The A2 chain of choleragen, in contrast to that of LT, is a nearly continuous {alpha}-helix with an interpretable carboxyl tail.
Optimization of Nitrogen Acquisition, and Metabolism, by Potassium in Rice, and Barley

N radiotracing showed that increased K supply reduces futile NH4 cycling at the plasma membrane, diminishing the excessive rates of both unidirectional influx and efflux. Pharmacological testing showed that low-affinity NH4 influx may be mediated by both K and non-selective cation channels. Suppression of NH4 influx by K occurred within minutes of increasing K supply. Increased K reduced free [NH4] in roots and shoots by 50-75%. Plant biomass was maximized on 10 mM NH4 and 5 mM K, with growth 160% higher than 10 mM NO3-grown plants, and 220% higher than plants grown at 10 mM NH4 and 0.1 mM K. Unlike NH4-sensitive barley, growth optimization was not attributed to a reduced energy cost of futile NH4 cycling at the plasma membrane. Activities of both glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC) enzymes were strongly stimulated by elevated K, mirroring plant growth and
Observation of a Spider, Ancylometes bogotensis (Ctenidae), Preying on the Frog Rhinella beebei (Bufonidae) in Trinidad

In 2005, Alex De Verteuil, Reginald Potter, Stephen Broadbridge and myself were filming frogs along the Exchange Road between Waterloo and Couva (grid ref: 667800E- 1158300N) when we observed a frog, Rhinella beebei , Beebe’s toad, being preyed upon by a spider, Ancylometes bogotensis.
Development of a Bioinformatic approach to Identify Candidate Pathogenic Variants in Canine Pharmacogenomic Genes

Genetic variations in pharmacogenomic genes result in diverse response of individuals to different drugs. Understanding the functional implications of these variations has gathered a significant research interest over the past decades providing a prime example for personalized medicine. Personalized medicine is a rapidly evolving field of pharmacogenetics that involves individual design of drug composition and dosage based on the genetic profile. The annotation of the genomes of domestic animals such as dog followed by an increasing amount of available whole genome sequencing data opens new opportunities for pharmacogenomics (PGx) in animal models. Despite some highlighted examples of canine PGx, e.g. MDR1 susceptibility, canine PGx is still poorly characterized. The major aim of this thesis was to utilize the growing number of WGS (Whole Genome Sequence) data for PGx profiling by developing a bioinformatic analysis pipeline that can identify potential candidate pathogenic variants. Canine orthologs for 540 Human PGx genes were retrieved resulting in 495 canine PGx genes. Ensembl’s phylogenetic trees were used to identify the orthologs. The pipeline analysis was piloted in 24 dogs in Border collie. A pipeline was developed to analyze the WGS of these dogs and to identify the pathogenic variants. The analysis altogether revealed 2964 variants in the coding regions of these 495 Canine pharmacogenomic genes. Out of these, 56 variants (1.8%) were predicted to be pathogenic and could be prioritized for further validation to determine their prevalence and functional significance. A pharmacogenomic annotation of these genes was also established, using available human data as a reference model. This annotation categorizes them based on their ortholog relationship, role in drug processing and importance in pharmacogenomics.
Novel insights into the elm yellows phytoplasma genome and into the metagenome of elm yellows-infected elms

In North America, American elms were historically present throughout the northeastern United States and southeastern Canada. The longevity of these trees, their resistance to the harsh urban environment, and their aesthetics led to their wide use in landscaping and streetscaping over several decades. American elms were one of most cultivated plants in the United States until the arrival of Dutch elm disease (DED) and elm yellows disease (EY). EY epidemics have killed large numbers of elm trees in the northeastern United States beginning in the 1940s. Since then, the disease has gradually been spreading to the southern and western regions of the United States while remaining endemic in the Northeast. Today EY, together with DED, is responsible for the death of most of the American species of elm trees, including (Ulmus americana (L.), U. rubra (Muh.), U. alata (Michx.), U. crassifolia (Nutt.) U. serotina (Sarg)) and of some of their natural hybrids (i.e. U. pumila × rubra). We performed next-generation sequencing on EY-infected elm trees to discover EY effector genes involved in plant-phytoplasma interactions and to survey the metagenome of the infected elms. This research is a basic step to understand how EY infection shapes the elm microbial communities and, in the long term, will lead to a better understanding of the pathogenesis of EY infection in elm and the interactions between EY and its leafhopper vectors.
Evolutionary trade-offs in a small mammal : a quantitative genetics approach

Schroderus, Eero Evolutionary trade-offs in a small mammal a quantitative genetics approach Jyväskylä: University of Jyväskylä, 2017, 48 p. (Jyväskylä Studies in Biological and Environmental Science ISSN 1456-9701; 333) ISBN 978-951-39-7112-0 (nid.) ISBN 978-951-39-7113-7 (PDF) Yhteenveto: Pikkunisäkkäään evolutiiviset valinnat tarkasteltuna kvantitatiivisen genetiikan menetelmin Diss. Limited resources force individuals to trade-off between life-history traits. A vast diversity of life-history strategies, which optimally combine life history traits, can be found. Knowledge of the genetic basis of this phenotypic variation is key to understanding evolutionary processes. I approached life-history evolution by estimating quantitative genetic parameters for a set of life-history traits in the bank vole (Myodes glareolus). The work is based on a laboratory-kept colony subjected to two-way selection for litter size (High(H) and Low(L) lines). Costs of the created reproductive strategies were observed in natural conditions. Selection increased the difference in litter size between lines, even though the response was asymmetric. The difference persisted in outdoor enclosures. A life-history trade-off between offspring number and offspring size was explained by environmental correlations as associated genetic correlations were even positive. Lines did not diverge in offspring size. In the enclosures maternal body mass had greater effect on pup survival in the L-line. Litter and maternal environment explained most of the phenotypic variation in pup body mass during the nursing period, while direct genetic variation emerged later, implicating selection on early size in the bank vole. Male and female metabolic rate did not seem to share genetic background; the first lacking additive genetic variation and the latter being bound to fecundity by genetic correlation close to one. Testosterone, a principle determinant of male reproductive success in the bank vole, was contrasted with humoral immune system in the both sexes. In general, with the exception of metabolism, the estimated genetic parameters did not set absolute constraints for life-history evolution. However, dimensionality of the additive genetic co(variance) matrix constrains evolution to act along certain trait combinations. In the future, research should strive to find genetic mechanisms, which, through the endocrine system, produces phenotypic co(variation) in different life-history traits.
The influence of the evolution of anatomical characters on leaf hydraulic capacity

Over geological time, changes in climatic factors have contributed to the evolution of plants. CO2 is one environmental factor that affects plants, and changes in CO2 concentration ([CO2]) in the atmosphere across geological time have been thought to have driven evolutionary changes in plant leaf anatomy, enabling plant leaves to adapt to declining atmospheric [CO2] over the last 120 million years. This thesis aimed to study the effect varying anatomical characters had on plant leaf function in different taxa. Atmospheric [CO2] at the crown group age of each species sampled made it possible to link anatomical and physiological variation to the different environmental conditions ([CO2]) each species (or taxa) evolved under. Several leaf gas exchange and hydraulics parameters were measured and leaves were subjected to light step-change and diurnal regimes to ascertain their gas exchange and hydraulic responses over prolonged periods. Results showed significant variation between species in leaf anatomical characteristics (stomatal and vein density). There was also a significant difference between species in their hydraulic responses to changes in light. No significant linear relationship s were found between leaf anatomical characteristics and gas exchange parameters and leaf hydraulics (hydraulic conductance or water flow into the leaf) . However, significant relationships were found among gas exchange parameters with leaf hydraulics, with species exhibiting higher photosynthetic capacities also displaying higher leaf water flow. T he general difference was between angiosperms and other taxa, with angiosperms showing higher values for anatomical and functional characters. Under dynamic light (step-change or diurnal change), angiosperms had more coordination among gas exchange parameters with leaf hydraulic flow. Even though no significant relationships were found between variables measured and [CO2] at the time of taxa divergence, the higher values shown by angiosperms, which evolved under declining atmospheric [CO2], still suggests towards a [CO2] effect on leaf evolution.
Metacaspases and programmed cell death in Skeletonema marinoi in response to silicate limitation

Diatoms comprise up to 40% of annual productivity in the modern ocean, and some stress factors may alter their physiology and survival. Here, we describe the morphological, biochemical and molecular responses that occur during metacaspase-mediated programmed cell death (PCD) in response to silicate limitation in the ubiquitous diatom Skeletonema marinoi. Transmission electron microscopy revealed that vacuolization occurred while the plasma membranes remained intact. Caspase 3-like activity, antioxidant gene expression, phosphatidylserine externalization and activated caspase-like expression were measured using in vivo staining. The results show that each was significantly increased under silicate limitation conditions. Using quantitative reverse transcription-PCR, we identified six distinct putative metacaspase proteins in S. marinoi, and we show that each contains a conserved caspase-like domain and is differentially expressed and that some of their expression profiles were correlated with PCD. Silicate limitation could trigger PCD in S. marinoi as well as an increase of antioxidant genes. PCD could be employed as a strategy to decrease silicate demand of the whole population and probably regulate the fate of S. marinoi.
Isolated from input: Transmodal cortex in the default mode network supports perceptually-decoupled and conceptually-guided cognition

The default mode network supports a variety of mental operations such as semantic processing, episodic memory retrieval, mental time travel and mind-wandering, yet the commonalities between these functions remains unclear. One possibility is that the default mode network supports cognition that is independent of the immediate environment; alternatively or additionally, it might support higher-order conceptual representations that draw together multiple features. We tested these accounts using a novel paradigm that contrasted decisions based on perceptual and conceptual features, while separately manipulating whether these decisions were driven by features in the environment or recovered from memory. Task-based fMRI identified regions that responded when stimulus independence and semantic retrieval were combined: these included left and right angular gyri and left middle temporal gyrus. Although these sites were within the default mode network, they showed a stronger response to demanding memory judgements than to an easier perceptual task, contrary to the view that they support automatic aspects of cognition. In a subsequent analysis, we showed that these regions were located at the extreme end of a macroscale gradient, which describes gradual transitions from sensorimotor to transmodal cortex. This shift in the focus of neural activity towards transmodal default mode regions might reflect isolation from specific sensory inputs, both when decisions are guided by conceptual as opposed to perceptual features and when cognitive states are generated in the absence of input. Highlights Brain regions supporting meaning overlap with stimulus independence. Bilateral angular gyri and left MTG respond strongly to both features of cognition. These patterns reflect a shift in activity towards regions of transmodal cortex. Complex memory representations may emerge in cortical areas distant from input.
Characterisation of cello : an ENU-induced mouse model of early-onset hearing loss

cello is a recessive mouse model of early-onset, sensorineural hearing loss that was identified from a large-scale N-ethyl-N-nitrosourea (ENU) mutagenesis screen undertaken at MRC Harwell. Linkage analysis and whole-genome sequencing identified that cello mice have a non-synonymous point mutation in Ikaros family zinc finger 2 (Ikzf2), which encodes a zinc finger transcription factor called helios. To investigate the role of helios in the auditory system, cello mice underwent comprehensive molecular, phenotypic and functional characterisation. The cello mutation was found to disrupt a highly conserved, zinc-coordinating residue in the final C-terminal zinc finger domain of helios. In vitro analyses demonstrated that mutant helios can still localise to the nucleus, but has an impaired ability to homodimerise – a prerequisite for DNA binding. In both Ikzf2+/+ and Ikzf2cello/cello cochleae, helios is expressed in the nuclei of the outer hair cells (OHCs) from the first postnatal week, coinciding with a critical period of OHC functional maturation. Although Ikzf2cello/cello exhibit severely impaired hearing at postnatal day (P) 16, cochlear morphology appears grossly normal up to one month of age, after which the OHCs and inner hair cells begin to progressively degenerate. Transcriptome profiling was subsequently undertaken to identify potential target genes of helios in the auditory system. Results suggested that loss of helios function leads to dysregulation of over 450 genes in Ikzf2cello/cello cochleae at P8. This included the OHC-specific genes Slc26a5 (which encodes the OHC motor protein, prestin) and Ocm (oncomodulin), both of which were significantly decreased in Ikzf2cello/cello mutants compared to Ikzf2+/+ controls. Electrophysiological studies demonstrated that Ikzf2cello/cello OHCs fail to acquire full electromotility, a property that is fundamental to their function, but otherwise mature normally. Using luciferase reporter assays, wild-type helios was found to induce transactivation of the Slc26a5 promoter, whilst this ability was lost in the mutant protein. Additional in silico network analyses identified helios as a putative direct regulator of 40 genes that are enriched in the OHCs and upregulated during development, which suggests that helios has a key role in regulating the maturing OHC transcriptome. Overall, the work presented in this thesis identifies Ikzf2 as a novel hearing loss-causing gene and establishes that the helios transcription factor is essential for OHC functional maturation in the mammalian auditory system.
Advertisement call and male morphology of the Malagasy treefrog Boophis arcanus from the Ranomafana region, south-eastern Madagascar

JANA C. RIEMANN, SERGE H. NDRIANTSOA, MIGUEL VENCES, MARK-OLIVER RÖDEL & JULIAN GLOS Biocenter Grindel, University of Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany Département de Biologie Animale, Université d’Antananarivo, Antananarivo 101, Madagascar Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Herpetology, Invalidenstr. 43, 10115 Berlin, Germany Corresponding author’s E-mail: Jana.Riemann@uni-hamburg.de
Studies on variability, heritability and genetic advance as per cent of mean in Spanish bunch groundnut genotypes (Arachis hypogaea L.)

Twenty Spanish bunch groundnut genotypes were collected from Agriculture Research Station, Kadiri, Andhra Pradesh, along with the check TMV 2 were used to study their variability, heritability and genetic advance as per cent of mean for nineteen characters viz., days to 50% flowering, SPAD chlorophyll meter reading (SCMR) at 40, 50, 60, 70 DAS and at maturity, days to maturity, number of mature pods per plant, biological yield per plant (g), pod yield per plant (g), biological yield per hectare (q), pod yield per hectare (q), harvest index, 100 kernel weight (g), shelling percentage, kernel yield per plant (g), kernel yield per hectare (q), oil content (%) and oil yield per hectare (q) during summer 2013 at Agricultural College farm, Bapatla. The results revealed that the highest PCV and GCV were observed for number of mature pods per plant. High heritability accompanied with high genetic advance as per cent of mean was recorded for number of mature pods per plant, biological yield per plant (g), pod yield per plant (g), biological yield per hectare (q), pod yield per hectare (q), kernel yield per plant (g), kernel yield per hectare (q), 100 kernel weight (g) and oil yield per hectare (q) indicating the preponderance of additive gene action which might be exploited through simple selection procedures. The study revealed that the genotypes Abhaya and JCG 88 were better for further breeding from yield point of view.
Seasonal foraging strategies of Alaskan gray wolves (Canis lupus) in a salmon subsidized ecosystem

Despite frequent observations of wolves ( Canis lupus L., 1758) using non-ungulate prey, the seasonal and inter-annual variation in the use and relative importance of alternative prey sources to gray wolf diets have not been studied at the individual scale. We used stable isotope analysis (δ 13 C and δ 15 N) of guard hair and blood components (clot and serum) collected over four years to examine the occurrence, extent, and temporal variation of salmon as a food resource by both individual wolves and social groups in Lake Clark National Park and Preserve in southwestern Alaska. Our results demonstrate substantial variability in the use of salmon over time. During summer, diets of five wolves consisted of at least 50% salmon while the diets of 17 wolves consisted of primarily terrestrial prey. Over three years, one group of wolves consistently consumed salmon in summer and switched to terrestrial prey in winter. Prey choices were generally similar within social groups; however, the d.