Miracle-dz/UniFAR-FTUs huggingface dataset:
Arginine Synthesis in Humans

Arginine synthesis is a complex, age-dependant process involving multiple precursors and enzymes, and the interorgan transfer of substrates. The objectives of this thesis were to elucidate arginine synthesis from enteral precursors in newborn infants and in healthy adults using stable isotope methodology. In the first, of four studies, I validated the use of a non-invasive methodology using urinary amino acids for stable isotope studies of arginine synthesis and demonstrated a known, but under-recognised, problem with D-amino acid contamination of tracers. Implementing chiral chromatography, this issue was further investigated using samples from previous studies in our laboratory with several different isotopes. I demonstrated the novel finding that the impact of Damino acids is dependent on the tracer used, and also on the age of the subject. In the second study, I used a multi-tracer design to assess arginine synthesis from enteral proline or glutamate in healthy preterm infants. Labeled arginine (M+2), proline (M+1) and glutamate (M+3) were given enterally to fifteen stable, growing preterm infants (gestational age at birth 30-35 weeks) at 1-3 weeks’ postnatal age. I found only arginine synthesis from proline,
Imaging the effects of ADHD risk genes.

Het proefschrift bestaat uit twee delen. Eerst worden de associaties tussen kandidaat-genen en enkele endofenotypen van ADHD bestudeerd (hoofdstuk 3, 4 en 5) en daarna (hoofdstuk 6) komt de associatie tussen endofenotypen en het klinische fenotype aan de orde. Dit alles bij volwassenen omdat de genetische heterogeniteit in die groep minder groot is dan bij kinderen. Structurele en functionele MRI-gegevens werden verzameld, een psychiatrisch interview werd afgenomen en natuurlijk werd het DNA onderzocht. Bij ADHD-ers werd het 6-9-haplotype van het DAT-gen vaker gevonden. Dat zou iets kunnen betekenen voor het functioneren van het striatum wanneer het gaat over de verwerking van beloning, maar in een functionele studie werden geen verschillen gevonden tussen mensen met en zonder dit haplotype en ook niet tussen ADHD en controles. Wel werd daarbij een effect gevonden van het NOS1-gen, dat verbonden lijkt te zijn met impulsiviteit. Ook is het effect van aan/afwezigheid van het DRD4-gen op het werkgeheugen geanalyseerd: aanwezigheid leidde in de ADHD-groep tot een betere prestatie en hogere frontale activiteit, bij controles was dit omgekeerd. Zelfgerapporteerde ADHD-verschijnselen blijken samen te hangen met hersenvolume. We hebben te maken met een dimensionele variabele en met een globale maat: een staartje van een normaalverdeling.
Studies of alternaria black spot disease of pomegranate caused by Alternaria alternata in Punjab

Alternaria black spot of pomegranate caused by Alternaria alternata pose significant economic losses in India as it reduce the crop yield. Farm survey was undertaken at Punjab Agricultural University, Pomegranate Research Block, Fruit Research Station, Jallowal- Lesriwal Jalandhar during 2015. Among all the five cultivars highest disease incidence (70%) and severity (30%) was registered in cultivar Bhagwa. Twenty two isolates of A. alternata were recovered from infected fruits and clustered using UPGMA (unweighted pair group method with arithmetic averages) on the basis of disease score produced in five cultivars (Ganesh, Ruby, Bhagwa, Jyoti and Mridula). It was revealed that five isolates namely AL14, AL15, AL20, AL21 and AL22 were highly virulent on almost all the pomegranate cultivars. Two cultivars viz. Bhagwa and Mridula were found to be most susceptible as 45.45 % isolates were found to be highly virulent on them.Thein vitro antifungal effects of the six fungicides on mycelial growth were investigated. Based on the inhibition of mycelial growth, all the fungicides showed most toxic reaction with 50% effective concentrations (EC50) of 20 ppm. However, two fungicides namely Dithane Z-78 and Bavistin showed less toxicity against Alternaria alternata as compared to other with EC90 value at concentrations 25 ppm. Azole group fungicides (Tilt and Folicur) were found most effective to inhibit the pathogen growth.
Obesity and adipose tissue biology in fish. Influence of nitritional, genetic and environmental factors

Some natural products, known sources of bioactive compounds with a wide range of properties, may have therapeutic values in human health and diseases, as well as agronomic applications. The effect of three compounds of plant origin with well-known dietary antioxidant properties, astaxanthin (ATX), caffeic acid (CA) and hydroxytyrosol (HT), on zebrafish (Danio rerio) larval adiposity and rainbow trout (Onchorynchus mykiss) adipocytes was assessed. The zebrafish obesogenic test (ZOT) demonstrated the anti-obesogenic activity of CA and HT. These compounds were able to counteract the obesogenic effect produced by the peroxisome proliferator-activated receptor gamma (PPARγ) agonist, rosiglitazone (RGZ). CA and HT suppressed RGZ-increased PPARγ protein expression and lipid accumulation in primary-cultured rainbow trout adipocytes. HT also significantly reduced plasma triacylglycerol concentrations, as well as mRNA levels of the fasn adipogenic gene in the adipose tissue of HT-injected rainbow trout. In conclusion, in vitro and in vivo approaches demonstrated the anti-obesogenic potential of CA and HT on teleost fish models that may be relevant for studying their molecular mode of action. Further studies are required to evaluate the effect of these bioactive components as food supplements for modulating adiposity in farmed fish. Introduction Obesity has become a worldwide epidemic and is considered one of the most serious public health problems of our time [1,2]. Overweight and obesity occur when energy intake exceeds energy expenditure, leading to increased storage of triacylglycerols (TAG), mainly in white adipose tissue (WAT). In addition to TAG storage in adipocyte lipid droplets, WAT has been recognized as a multi-functional endocrine organ that plays a critical role in modulating several physiological processes, such as appetite, whole-body energy metabolism and homeostasis, as well as tissue inflammation responses [3]. Consequently, concomitant with enlarged fat PLOS ONE | https://doi.org/10.1371/journal.pone. 0178833 June 1, 2017 1 / 21 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111
Morphological and molecular characterization of Hapalospongidion gelatinosum, Hapalospongidiaceae fam. nov. (Ralfsiales, Phaeophyceae) from Mexico

Abstract The morphology of the crustose brown alga Hapalospongidion gelatinosum is described in detail based on specimens collected on the Mexican tropical Pacific coast. Molecular phylogenetic analysis of DNA sequences of chloroplast-encoded RuBisCo large subunit (rbcL) and mitochondrial-encoded cytochrome c oxidase subunit 1 (Cox-1) genes, reveals that our samples form a newly recognized clade distinct and distant from the clades of other families in Ralfsiales. Contrary to the previously proposed synonymy between Hapalospongidion and Mesospora, we conclude that both are distinct genera. We also provide a different interpretation of a diagnostic character that allows a distinction of Basispora from the latter two genera. We propose the erection of the new family Hapalospongidiaceae to accommodate the sole genus Hapalospongidion. A Lectotype and an Epitype for H. gelatinosum are designated.
Structural and Functional Analysis of the Natural JNK1 Inhibitor Quercetagetin. Structure of the Stapled p53 Peptide Bound to HDM2

C-Jun NH2-terminal kinases (JNK) and PI3-kinases play an important role in different diseases. The inhibitory potential of Quercetagetin was assessed with various methods for JNK1 and PI3-K. The inactivation of p53 is one of the most common defects in human cancer. The first crystal structure of a stapled peptide in complex with HDM2 shows a new mechanism to reconstitute the functionality of p53.
Precipitation during anthesis reduces seed set in perennial ryegrass

In perennial ryegrass seed production, the establishment of seed yield potential occurs until the point of anthesis. However, utilizing potential seed yield is predominately focused on processes after anthesis, namely seed set (%) and seed filling. In practice, seed yield is the product of the number of harvested seeds remaining after cleaning and average seed weight. For this study, the anthesis patterns and seed set were recorded in a diploid variety grown in seed production fields in three different Danish regions with contrasting weather conditions and investigated in 2013 and 2014. Increases in the total precipitation during anthesis reduced the anthesis synchrony and the seed set, which ranged from 50% to 66%. Under semi-controlled environmental conditions in which the influence of precipitation was excluded, the seed set was found to be influenced by the floret position in the spikelet and ranged from 73% in the florets in basal positions to 25% in the distal florets. It is suggested that a lower number of florets per spikelet will reduce the anthesis period. These results may provide insights for breeding programmes focused on increasing seed yield.
Inhibitory activities of kaempferol, galangin, carnosic acid and polydatin against glycation and &agr;‐amylase and &agr;‐glucosidase enzymes

Summary The activities of four natural phenolics, kaempferol, galangin, carnosic acid and polydatin in scavenging free radicals, inhibiting advanced glycation end-product (AGE) formation, α-amylase and α-glucosidase and trapping methylglyoxal (MGO), were evaluated in this study. Carnosic acid and galangin had the highest activity in scavenging free radicals. Kaempferol and galangin had the greatest activity in preventing bovine serum albumin (BSA) against glycation and reducing glycated proteins. Polydatin had the greatest performance in trapping MGO to reduce glycation reaction. However, there was no significant difference for kaempferol, galangin and carnosic acid in inhibiting AGE formation by BSA-MGO reaction. Kaempferol, galangin and carnosic acid were the competitive inhibitors for α-amylase, while kaempferol and carnosic acid were noncompetitive inhibitors for α-glucosidase. However, polydatin showed as a mixed noncompetitive inhibitor for both α-amylase and α-glucosidase. The results indicated that the four natural phenolics have potential in inhibiting AGE production and the digestive enzymatic activity with different mechanisms.
Transcriptome‐based prediction of hybrid performance with unbalanced data from a maize breeding programme

mRNA transcription profiles are an alternative to DNA markers for predicting hybrid performance. Our objective was to investigate their prediction accuracy in an unbalanced maize data set. We focused on the effectiveness of preselecting a core set of genes for transcription profiling and on the comparison of prediction models. A total of 254 hybrids were evaluated for grain yield and grain dry matter content. The mRNA transcripts of a core set of 2k genes and the genotype of 1k AFLP markers were assessed in the parental lines. Predictions based on transcriptomebased distances determined from the 2k core set of genes resulted in prediction accuracies below 0.5 and could not reach the high accuracies observed with a 46k micro-array in earlier studies. Predictions based on ridge regression resulted in prediction accuracies greater 0.6. Only marginal differences were observed in the prediction accuracies of mRNA transcripts compared with AFLPs. We conclude that mRNA transcription profiles are suitable for hybrid prediction with ridge-regression models in unbalanced designs, even if limited resources allow only transcription profiling of a core set of genes.
Alterations in the relative abundance of Haptoglobin (Hp) transcripts in total milk somatic cells during different stages of lactation cycle in high yielding cross-bred cows

Abstract The expression profile of Haptoglobin (Hp) gene in total milk somatic cells (SCC) of high-yielding cross-bred Karan Fries (KF) was studied during early, mid, and late lactation cycle. Milk samples (200 ml/animals) were collected from 10 high-yielding and 10 low-yielding cows throughout the lactation cycle (from day 7 to day 300) with an interval of one month. Relative mRNA expression profiles of Hp by RT polymerase chain reaction was studied in high-yielding cows, whereas low-yielding cows were taken as control. The folds of induction of Hp was significantly (p < 0.001) downregulated by a mean factor of 0.207 in milk SCC during early lactating cows. Whereas, it was significantly (p < 0.01) upregulated by a mean factor of 20.888 during mid lactation. The expression was unaltered during the late lactation. The study demonstrates that Hp is synthesized within the mammary gland and significantly upregulated during mid-lactation period compared to other stages of lactation cycle.
An Improved Method for Isolation of Genomic DNA from Filamentous Actinomycetes

A simple and efficient method involving the use of liquid nitrogen for rapid isolation of high molecular weight (≥ 50 kb) DNA from actinomycetes is described here. The DNA yields range from 140 to148.3 μg per g (wet weight) of mycelia with purity measured at A 260/280 of 1.78-1.93. The DNA preparation is suitable for PCR protocols.
Novel functions for the CENP-A N-terminus during male meiosis in Drosophila melanogaster

In sexually reproducing organisms the germ line is the cellular lineage that gives rise to gametes. All germ cells originate from germline stem cells that divide asymmetrically to generate gonial pre-cursors, which are amplified in number by mitotic divisions, undergo meiosis and eventually differentiate into mature gametes (haploid eggs and sperm). Information transmitted with gametes is inherited by offspring, and potentially by subsequent generations, instructing in organismal development and beyond. Meiosis comprises one round of DNA replication, followed by two rounds of chromosome segregation; homologous chromosomes segregate in the first division (meiosis I) and sister chromatids segregate in the second division (meiosis II). Important mechanistic features of meiosis occur in substages of prophase I and are critical for genetic recombination, including pairing and synapsis of homologous chromosomes (at leptotene and zygotene), crossing-over (at pachytene), and the appearance of chiasmata (at diplotene/diakinesis). Another unique feature of meiosis is the altered centromere/ kinetochore geometry at metaphase I, such that sister kinetochores face the same spindle pole (mono-orientation) and stay together at anaphase I. This chapter reviews centromere dynamics in germ cells, focusing on centromere function and assembly in meiotic cell cycles, as well as centromere inheritance in zygotes. Centromeres are functionally defined by the presence of the histone H3 variant CENP-A, the epigenetic determinant of centromere identity. In most eukaryotes, it is well established that CENP-A function is essential for chromosome segregation in mitosis. CENP-A function in meiosis is less well understood and emerging insights into the differential regulation of meiotic and mitotic CENP-A are discussed. E.M. Dunleavy (&) C.M. Collins Centre for Chromosome Biology, Biomedical Sciences, National University of Ireland, Galway, Ireland e-mail: elaine.dunleavy@nuigalway.ie © Springer International Publishing AG 2017 357 B.E. Black (ed.), Centromeres and Kinetochores, Progress in Molecular and Subcellular Biology 56, DOI 10.1007/978-3-319-58592-5_15
Synchronization Ratio of N-Protein and Energy Supplies as a Basis for Diet Formulation in Ruminant

The experiment was conducted to determine the optimum synchronization ratio of N-protein and fermented organic matter (OM) in the rumen for the purpose of ration formulation for ruminant animals, in order to improve effi ciency of rumen microbial N synthesis and feed effi ciency. Nylon bag technique was adopted to determine ruminal characteristic of protein and OM degradation of feedstuffs (forage and concentrate diet) for which the synchronized index of N-protein and fermented OM in the rumen might be determined. By randomized block design, twelve local cattle were arranged to four groups. Each group was fed three types of diet that was different in synchronization ratio of supplying N-protein and fermented OM in the rumen, namely 20 g N/kg OM (R20); 25 g N /kg OM (R25); and 30 g N /kg MO (R30). The diets had iso-energy and iso-protein contents and had the same synchronization index. The results showed that the type of diet had no effect (P>0.05) on intake and digestibility of nutrients, N retention, average daily gain (ADG), and feed effi ciency. But R20 had better parameter values than those of R25 and R30. It might be concluded that the diet having a synchronization ratio of 20 g N/kg fermented OM in the rumen will generate more effi cient protein synthesis of rumen microbes and feed effi ciency.
Strukturelle und funktionelle Analyse ausgewählter High Mobility Group Gene des Haushundes

Medical advances due to scientific research made remarkable progress in the past decades fighting cancer. Nevertheless according to the United Nation s World Cancer Report 2008 tumour diseases are the leading cause of death with 7.6 million deaths and 12.4 million the new cancer cases a year. According to cancer the dog as an animal model joins the popular rodent model in order to study and understand the molecular genetics of tumour diseases and to develop new therapeutic strategies against cancer. Canine tumour diseases are distinguished by spontaneous development and dogs and humans share striking similarities in the case of oncology. The main part of this thesis comprises the comparative genomics and tumour biology of the human and canine tumour diseases focusing in particular prostate carcinomas by molecular characterisation of the genes and proteins HMGA1, HMGA2, THADA, RAGE, TNFalpha, and IL-alpha/beta. Genomic characterisations of high evolutionary conserved genes are the fundamentals for functional and structural analysis of tumour relevant genes. According to this principle a gene therapeutic approach was developed in order inhibit the HMGA expression of a canine prostate carcinoma cell line with the help of an adeno-associated virus vector. Furthermore and alternative method with gold nanoparticles was established for efficient transfection of eukaryotic cells. In the context of inflammation and angiogenesis during a tumour disease the canine receptor for advanced glycation end products (RAGE) was analysed. The results showed highly conserved molecular similarities (N.B. ligand-receptor domains) between the human and canine RAGE and its isoforms. In both species an aberrant Expression of cytokines e.g. interleukin-1 (IL-1alpha/beta) and the tumour necrosis factor alpha (TNFalpha) plays an important role during the initiation of immune response and inflammation. In particular during the course of the Langerhans cell histiocytosis (LCH) large quantities of cytokines are produced. Interestingly most clinical and pathological features of the canine malignant histiocytosis resemble those of LCH in humans. Finally dogs could be used as an animal model to elucidate the molecular genetics of malignant histiocytosis as well as LCH. In this connection nucleic base pair substitution within evolutionary conserved gene and amino acid sequences of canine and human cytokines were investigated.
Optimization of Keratinase Production by Bacillus olironius Isolated from Poultry Farm Soil

The keratin degrading bacterial strain KRD1 was isolated from poultry farm soil by using enrichment technology. The strain was identified as Bacillus olironius on the basis of biochemical and 16s rRNA sequencing. The keratinase production was maximum in keratin medium under optimum condition (pH 7.5, time 96 h; temperature 37 °C; and 5 % inoculums). The KRD1 keratinase activity decreased by the addition of carbon sources and strain KRD1 produce high keratinase in the presence of 0.1 % yeast extract. Therefore enzymatic hydrolysis of feather wastes could be a safe method for recycling of keratin materials.
Do tissue carbon and nitrogen limit population growth of weevils introduced to control waterhyacinth at a site in the Sacramento-San Joaquin Delta, California?

Waterhyacinth (Eichhornia crassipes(Mart.) Solms), is a serious problem in the Sacramento Delta. Two weevil species (Neochetina bruchi Hustache and N. eichhorniae Warner) have been introduced as biological control agents. The purpose of this study was to test the hypothesis that nitrogen (N) in the tissue of waterhyacinth was not sufficient to support weevil growth and reproduction. Because it grows better on plants with high N content and because it has a greater impact on the growth of high N plants, N. bruchi may be a more effective biological control agent in the Sacramento Delta.
Wetland, Forest, and Open Paddy Land Are the Key Foraging Habitats for Germain’s Swiftlet (Aerodramus inexpectatus germani) in Southern Thailand

Germain’s swiftlets (Aerodramus inexpectatus germani) are farmed regularly in Southeast Asia and produce highly valuable nests for which there is an increasing demand. Some populations of this species are thought to be decreasing, but little is known about the habitat used by swiftlets for foraging. Here, we focused on this swiftlet’s foraging habitat selection and describe their daily and seasonal variations in habitat use. We predict that the prey capture attempts would be highest during twilight periods of each day, but that overall capture rates would vary with season and habitat type. Prey capture attempts at different times of the day and seasons in five different habitats were investigated and compared to flying insect availability (estimate as biomass). For each habitat, insects were trapped immediately 5–10 m above vegetation levels (i.e., tree canopy and open paddies) and 0–5 m above water surfaces in water body habitat. The highest foraging intensity occurred over water bodies, forest, and open paddy land; all of which contained high numbers of major prey insects (Hymenoptera, Diptera, and Hemiptera). Foraging during the wet season was at a greater intensity than during the dry season which was associated with increased insect availability. This suggested that food supply in each habitat type, time of day, and season influenced the bird’s foraging habitat use. To conserve populations of this swiftlet, it is therefore important to protect wetlands, forest areas, and open paddy land to support natural insect prey within the foraging range of local swiftlets.
The impact of ozone on health-promoting, microbiological, and colour properties of Rubus ideaus raspberries

ABSTRACT The purpose of the study was to define the impact of ozonisation duration and concentration on selected chemical, physical, and microbiological properties of Rubus ideaus red-fruited raspberries of the Polka variety. Raspberry fruit was exposed to a stream of ozone in concentration of 0.3 and 0.9 mg/L over a period of 60 and 120 min. The scope of the study covered the measurements of titratable acidity, soluble solids concentration, and such health-promoting indicators as content of phenol compounds, flavonoids, anthocyanins and vitamins C, total antioxidant activity (TAA) on 0, 4th, and 8th day of storage. The ozone treated fruit had higher level of phenol compounds and demonstrated higher TAA compared to untreated raspberries. The use of ozone made it possible to curb the development of yeast and moulds on the surface of raspberries, in which the dosage of 0.9 mg/L and treatment time of 60 min proved most efficient.