Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative metabolomics of erythroid lineage and Plasmodium life stages reveal novel host and parasite metabolism

Malaria, caused by the Apicomplexan parasite Plasmodium is a deadly disease which poses a huge health and economic burden over many populations in the world, mostly in sub-Saharan Africa and Asia. To design new intervention strategies and to improve upon existing drugs against malaria, it is important to understand the biochemistry of the Plasmodium parasite and its interaction with the host. We used metabolomics to dissect the biology of the reticulocyte preferring rodent malaria parasite Plasmodium berghei and showed that metabolic reserves in the reticulocytes can aid in survival of malaria parasites when their metabolism is genetically or chemically disrupted, pointing towards a direct role of host cell metabolism in parasite survival. These results have implications for currently used ways of intermediation in malaria infections which target only parasite metabolism against the human malaria parasites, Plasmodium vivax which prefers to infect reticulocytes and Plasmodium falciparum which is capable of infecting all erythrocytes. We also used metabolomics to show the biochemical differences between the asexual and sexual stages of P. berghei parasites and our data gave additional insights into the preparatory phase of the gametocyte stage at the metabolic level with the discovery of a phosphagen system which plays a role in gametogenesis. Targeted metabolomics of P. berghei life stages using isotopic labelling showed that TCA cycle metabolism is predominant in the mosquito stages. Discovery of a reductive arm of TCA metabolism in reticulocytes pointed towards the existence of rudimentary mitochondria in young erythrocytes. Another surprising discovery was the presence of up regulated γ-Aminobutyric acid (GABA) metabolism in the ookinete stage in P. berghei which may act as an energy source during the ookinete to oocyst transition in the mosquito. This pathway presented novel candidates for transmission blocking.
Phthalate biodegradation: gene organization, regulation and detection

The three phthalate isomers are widely found in the environment due to their extensive use in the manufacture of plastics. Many microorganisms have been isolated for their ability to degrade phthalate isomers. In this study, we focused on nine different phthalate degrading bacterial strains (YZW-A, -B, -C, -D, -E, -F, -G, -H, and -I) which were isolated from Passaic River sediment and belong to different genera (Comamonas, Pseudomonas, Acinetobacter, and Arthrobacter). Our work aims to identify the presence and divergence of the phthalate, isophthalate and terephthalate degradative genes in the nine strains isolated from the same sediment sample. The oph, iph, and/or tph genes in Comamonas testosteroni strains (YZW-B, -E, and -F) and Pseudomonas strains (YZW-A and -G) were determined by PCR and inverse PCR. Sequence analyses indicate that phthalate, isophthalate and terephthalate degrading bacterial isolates at the same location are not simply clones of each other and that the genes identified are linked specifically to these bacterial strains. In order to investigate whether each phthalate isomer would specifically induce the corresponding degradative gene cluster and how regulatory genes control phthalate isomers degradation, we used quantitative real time PCR to measure the expression of genes encoding phthalate (ophA2), isophthalate (iphA2), terephthalate (tphA2) dioxygenase in YZW-B. qPCR data showed that the ophA2, iphA2, and tphA2 genes were specifically induced by phthalate, isophthalate, and terephthalate, respectively. The tphA2 gene was slightly upregulated by isophthalate. Furthermore, we knocked out phthalate regulatory gene ophR and isophthalate regulatory gene iphR in YZW-B and analyzed the ophA2, iphA2, and tphA2 gene expression patterns in the ophR or iphR knock out mutant using qPCR. Gene knockout and qPCR showed that the ophR gene and the iphR gene encoded repressors that negatively controlled the phthalate and the isophthalate gene expression, respectively. %%%%
The ecological differentiation of asexual lineages of cotton aphids: alate behaviour, sensory physiology, and differential host associations

The cotton aphid (Aphis gossypii Glover) is a cosmopolitan pest species consisting of various host plant-associated lineages that appear to have different patterns of insecticide resistance, electrophoretic banding, and reproductive output across alternative host species. Debate continues as to whether these differences represent intraspecific variation or indicate a complex of cryptic or sibling species. We studied the host plant-related ecology of two asexual lineages of A. gossypii associated with the families Malvaceae and Cucurbitaceae, respectively, in particular the host plant finding and acceptance processes of the alate forms. The two lineages proved to be differentiated across host plants in terms of: (1) their landing and settling behaviour, nymphal production rate, and subsequent colony establishment (i.e. nymphal survival and development) and (2) their sensory abilities in relation to host plant-derived odours. Furthermore, genetic structuring according to host plant type was detected using the gene for elongation factor 1-α. The magnitude of the genetic differentiation across lineages was low, perhaps indicating a relatively recent divergence. The results demonstrate: (1) the presence of (at least) two cryptic species within the current definition of A. gossypii, as anticipated in previous studies, and (2) the practicalities of using a multidisciplinary approach to understanding the 'limits' of asexual species. If sexuals can be generated from each of these lineages, this conclusion will be open to further testing.
Studies on varagu starch.

Starch was isolated from varagu millet in 63% yield. Study of the physical properties revealed moderate swelling (about 15 at 95 degree C) and low solubility in water (55% at 95 degree C), extensive solubility in dimethyl sulphoxide ( greater than 95% in 30 h), probably indicative of easy solvent penetration due to labile and heterogeneous bonding forces within the granule. Brabender amylograms indicated little retrogradation on cooling, owing to strong bonding between the linear and branched molecules. The amylose content determined by paper chromatographic fractionation and 'blue value' was 24%.
Reserve Utilization in Seeds of Arabidopsis thaliana Germinating in Microgravity

Seed reserve lipid utilization in Arabidopsis thaliana (L.) Heynh. , ecotype Landsberg erecta, is delayed when germination takes place in microgravity; the cotyledon symplast lipid volume fraction is less than 7% in controls, whereas in microgravity samples over 15% of the symplast volume is lipid. Growth rate in the root is reduced in microgravity. These effects are interpreted as probably being the result of localized anoxia in the absence of atmospheric convection and mixing in the sealed growth chambers used.
Methods for early nutrition and their potential

Several factors may limit the development and viability of late-term embryos and hatchlings: 1) The nutrient content of the egg needed for the development of tissues and nutrient reserves (glycogen, muscle, yolk) of the embryo through to hatch; 2 The ability of the gastrointestinal tract to digest utilize nutrients from an external carbohydrate and protein-rich diet; and 3) The ability of chicks and poults to rely on the residual nutrients in the yolk sac during the first few days post-hatch. These limitations are manifested by in the “chick or poult quality” phenomena. Approximately 2% to 5% of hatchlings do not survive the critical post-hatch “adjustment” period and many survivors exhibit stunted growth, inefficient feed utilization, reduced disease resistance, or poor meat yield. These limitations can be alleviated by the administration of food in the hatchery immediately post-hatch, a technology termed “Early Feeding”, or by administration of food into the amnion of late term embryo, what we define as “In Ovo Feeding”. A great potential exists in “combining” the early feeding and the in ovo feeding methods. Since the modern broiler increases its body weight by 50-fold from hatch until market age at 42 days, the first few critical days of “adjustment” represent a much greater proportion of the bird's life span than in the past. Consequently, early feeding methods will have a great impact on overall growth and well-being of the bird, particularly as genetic selection for increased growth performance continues in the future.
The Use of a Random Regression Model on the Estimation of Genetic Parameters for Weight at Performance Test in Appenninica Sheep Breed

The Appenninica breed is an Italian meat sheep; the rams are approved according to a phenotypic index that is based on an average daily gain at performance test. The 8546 live weights of 1930 Appenninica male lambs tested in the performance station of the ASSONAPA (National Sheep Breeders Association, Italy) from 1986 to 2010 showed a great variability in age at weighing and in number of records by year. The goal of the study is to verify the feasibility of the estimation of a genetic index for weight in the Appenninica sheep by a mixed model, and to explore the use of random regression to avoid the corrections for weighing at different ages. The heritability and repeatability (mean±SE) of the average live weight were 0.27±0.04 and 0.54±0.08 respectively; the heritabilities of weights recorded at different weighing days ranged from 0.27 to 0.58, while the heritabilities of weights at different ages showed a narrower variability (0.29÷0.41). The estimates of live weight heritability by random regressions ranged between 0.34 at 123 d of age and 0.52 at 411 d. The results proved that the random regression model is the most adequate to analyse the data of Appenninica breed.
Growth performance of juvenile kuruma shrimp, Marsupenaeus japonicus (Bate) fed diets replacing fishmeal with soybean meal

A feeding trail was conducted to evaluate the effect of lowering dietary fishmeal (FM) levels while increasing levels of dehulled soybean meal (SBM) on growth, nutrient utilization and body composition of juvenile kuruma shrimp, Marsupenaeus japonicas. Five experimental diets were formulated to be isoenergetic, isolipidic and isonitrogenous with decreasing FM levels from 40 to 16% while increasing SBM from 0 to 33% respectively. Quadruplicate groups of shrimp (initial wt = 1.5 g) were fed the test diets for 56 days under the flow-through system. There were no significant differences in final weight (g) and specific growth rate (SGR, % day) among shrimp fed FM40, FM34, FM28 and FM22 diets respectively. Growth parameters significantly decreased in shrimp when fed FM16 diet, which was the lowest level of FM. Feed intake was positively correlated with the SGR of shrimp, and the lowest one was found in shrimp fed FM16 diet. Protein gain and retention, whole body lipid, arginine and methionine significantly decreased in FM16 fed group. Thus, it is concluded that dietary FM could be reduced down to 22% with SBM without compromising growth, nutrient utilization and retention, and whole body composition of kuruma shrimp.
Occurrence of Senecio aquaticus in relation to grassland management

ABSTRACT Background: Senecio aquaticus is an esteemed wetland species, but it is also a poisonous species in grasslands for forage production of various countries (e.g. Great Britain and Central European states), and its further spread onto farmland must be prevented. To reveal links between management practice and the occurrence of S. aquaticus, a survey was carried out on agricultural grassland in the summer of 2005. Location: The mountain region in the northern and central part of Switzerland. Methods: Botanical assessments were carried out on management units (parcels) where S. aquaticus occurred and on neighbouring parcels without occurrence. For all parcels, we analysed the soil nutrients and the details of management such as intensity of fertilisation and defoliation frequency. Results: There was a high risk of S. aquaticus occurrence in parcels with low nitrogen fertilisation, a change of management intensity in the preceding 15 years, high inclination, and gaps in the sward. The change in the vegetation composition caused by altering the management intensity most probably provided gaps in the sward, which were then colonised by S. aquaticus. A novel finding is that, despite its preference for low-nutrient sites, the species was also persistent at sites with a moderate to high management intensity. Conclusion: A long-term control of S. aquaticus on agricultural grasslands can best be achieved by avoiding sward damage and by promoting dense and stable swards. The management should be adjusted to the local environmental conditions and the requirements of the favourable plant species. This could prevent the spread of S. aquaticus from the protected wetlands onto agricultural grasslands, where the species would threaten animal health. Nomenclature: Lauber & Wagner (2007).
Sand shinnery oak as forage for Angora and Spanish goats.

Little information is available on goat nutrition and diet selection on shrub-dominated ranges. This study examined the botanical and nutritive composition of Angora and Spanish goat diets, and forage intake when grazing on sand shinnery oak (Quercus havardii Rydb.) range in west Texas during June, July, and August, 1986. A digestion trial evaluated the nutritive value of shinnery oak diets for goats. Angora and Spanish goats consumed similar amounts of shinnery oak, grass, and forbs. Their diets had similar levels of crude protein (CP), fiber, and in vitro digestibility. Consumption of oak by goats increased from 31% of diets in June to 55% in August. Dietary CP levels averaged 8.1 to 9.4% during the summer. In vitro digestibility of diets varied from 44 to 53% during the summer, with lower values during July and August. Spanish goats had higher forage intakes during July and August compared to Angora goats. Digestible energy (DE) intake (Mcal/-day) did not differ between breeds, but increased during the summer. The digestion trial was conducted using 0, 25, and 50% shinnery oak with alfalfa hay. Apparent organic matter digestibility (OMD) declined linearly with increasing levels of oak; the same decline was noted for apparent CP and neutral detergent, but not acid detergent, fiber digestibility. Extrapolated OM and CP digestibilities for 100% oak were 38% and 17%, respectively. Voluntary OM intake did not differ among diets. CP and DE intakes declined linearly as dietary oak levels increased. Fecal N increased and urinary N decreased linearly with increasing levels of oak in diets. We found no evidence of intoxication from shinnery oak in grazing or pen-fed goats. Shinnery oak can contribute substantially to the nutrition of goats foraging on these ranges, but some supplemental feeding may be necessary.
Amphibian Ecology and Conservation: A Handbook of Techniques

PART 1. INTRODUCTION PART 2. LARVAE PART 3. JUVENILES AND ADULTS PART 4. AMPHIBIAN POPULATIONS PART 5. AMPHIBIAN COMMUNITIES PART 6. PHYSIOLOGICAL ECOLOGY AND GENETICS PART 7. MONITORING, STATUS AND TRENDS
Levansucrase of Bacillus subtilis

A covalently linked fructosyl-enzyme complex was isolated from a reaction mixture of enzyme and sucrose submitted to the quenching effect of a large decrease of the pH. The fructosyl-enzyme bond was shown to be stable under acidic and neutral conditions in the presence of high concentration of urea and of sodium dodecyl sulfate. This intermediate did not transfer at a measurable rate its fructosyl group to the usual fructosyl acceptors of the enzyme reaction under the usual conditions of enzyme activity. However stability measurements of the fructosyl-enzyme bond indicated a marked lability at pH values above 8.5. The apparent rate constant of the hydrolytic reaction of this bond evaluated under the standard state of molar concentration of hydroxide ion was of the same order of magnitude as the apparent rate constant of the hydrolytic reaction of the transient fructosyl-enzyme postulated from the kinetic analysis of levansucrase. Furthermore, nucleophilic agents like imidazole enhanced the hydrolytic reaction of the fructosyl-enzyme bond. Identification of the fructosyl binding site on the enzyme was accomplished by proteolytic hydrolysis of the trapped complex. Peptic digestion followed by pronase digestion released a fructosyl-aspartate compound that we have isolated in a high state of purity. The lability of the fructosyl-aspartate bond under mild alkaline conditions suggested that the fructosyl was linked through an ester bond involving the β-carboxyl of the aspartate residue. Treatment of the trapped complex with cyanogen bromide released only one fructosylated peptide. The apparent molecular weight of this peptide was estimated to be lower than 10000.
Factors Influencing Total Bacterial Count in Tanks: An Application of Linear Mixed-Effect Models

The objective of this research was to evaluate the influence of procedures for hygienic milking and cleaning of dairy equipment and milk cooling tanks on the levels of total bacterial count (TBC). Mixed-effect models were used in order to model the structure of dependence between and within dairy farms. To this end, four bulk samples of milk were collected from each tank in eight properties for TBC analysis, employing the flow cytometry method. A questionnaire was applied in each property to assess the current situation of milking procedures on each production system that took part on this research, followed by training of employees in good agricultural practices in the production of milk and monitoring of the TBC measurements. Analysis of longitudinal data was the method employed, which focused on random effects models. The results showed that the handling procedures for milking and the cleanliness of the cooling tanks contributed to a further reduction in the levels of total bacterial count in raw milk cooling tanks.
Predicting Long Non-coding RNAs Based on Genomic Sequence Information

The binary classification of coding and non-coding genes is simplified near to 50 years. Genome-wide transcriptome studies have revealed that there exist tens of thousands of long non-coding RNAs (lncRNAs), while the functions are being uncovered slowly. Accurate identification of lncRNAs is the initial step to the systematic characterization of lncRNAs. The diversity of transcription patterns for lncRNAs challenges the available non-coding RNA prediction algorithms. Until now, prediction of lncRNAs mostly relies on genomic sequence and cross-species alignment information. Here, we introduce the main strategies that can discriminate lncRNA from protein-coding transcripts. Especially, recently available machine learning algorithms are shown efficient to the rapid and accurate identification of lncRNAs from a large number of putative lncRNAs based on transcriptome assembled transcripts, which would provide the basis of understanding of lncRNA biology.
Analysis of the mitochondrial genome of Schistocerca gregaria gregaria (Orthoptera: Acrididae)

In the present study, we present the full sequence of the mitochondrial genome of the African desert locust Schistocerca gregaria gregaria. The size of 15625 bp reported matches very well with mitochondrial genomes of other Orthopteriodea. The mitochondrial genome comprises 13 protein-coding genes, two ribosomal RNAs and 22 t-RNAs with two t-RNA (trnD and trnK) rearrangements that are typical for the taxon Caelifera. We compared the sequence with 12 mitochondrial genes of Schistocerca gregaria flaviventris and Schistocerca americana and used some of these data to construct phylogenetic trees, which confirm the close relationship between the two subspecies S. g. flaviventris and S. g. gregaria. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 296–305. ADDITIONAL KEYWORDS: gene organization – phylogeny – Schistocerca americana – subspecies.
A Comparison of the Binding of the Ligand Trimethoprim to Bacterial and Vertebrate Dihydrofolate Reductases

In this paper, we report on studies of ligand binding to the enzyme dihydrofolate reductase (DHFR). Energy minimizations of four complexes of DHFR with the inhibitor trimethoprim, an antibiotic, and the cofactor NADPH have been carried out in order to investigate the energetics responsible for the 100,000-fold increase in binding affinity of trimethoprim to E. coli DHFR compared with chicken liver DHFR. Several factors suggested to be responsible for the enhanced binding in bacterial DHFR's were investigated in terms of intermolecular and intramolecular energetics. The strain energies of trimethoprim in the four complexes were calculated and found to be about 6 kcal mol−1 in all complexes of the two species. In the binary complex of chicken liver DHFR, where the largest variation was observed, 2 kcal mol−1 higher than in the other complexes, it was found that this increase was compensated for by the slightly more favorable intermolecular interaction of the trimethoxyphenyl moiety with the protein. Comparison of the minimized binary and ternary complexes of E. coli allowed us to investigate the cooperativity in the binding of trimethoprim and NADPH in the bacterial enzyme in terms of the underlying intermolecular forces. This cooperativity was found to be due to a direct trimethoprim - NADPH interaction in the E. coli enzyme rather than enhanced protein-inhibitor interactions induced upon binding of the cofactor. These interactions are not as favorable in the vertebrate enzyme, consistent with the significantly diminished cooperativity observed in this enzyme.
Recent design of glycosyltransferase inhibitors

Carbohydrates are implicated in several biological phenomena and play an important role in fecundation, cancer and bacterial or viral infection. The biosynthesis of oligosaccharides displayed at the surface of the cell through glycoproteins or glycolipids is orchestrated by glycosyltransferases and glycosidases creating and hydrolysing glycosidic bonds, respectively. The present review will provide an overview of the past two decades of glycosyltransferase inhibitors development, and will consider not only the design of bioactive molecules but also fundamental studies of the roles of such proteins. Galactosyltransferases will be discussed since this class of enzymes is amongst the most intensively studied. Inhibitors designed against O‐linked N‐acetylglucosaminyl transferase (OGT) will also be reviewed as this enzyme has been recently identified as an important biological target.