Miracle-dz/UniFAR-FTUs huggingface dataset:
The endogenous protein content of ruminant proximal duodenal digesta

Protein arriving at the ruminant proximal duodenum consists of microbial protein, undegraded feed protein and endogenous protein. In this study, endogenous protein is defined as that fraction of the digesta derived from the animal itself (e.g. enzymes, plasma proteins, sloughed cells and mucus), not including any endogenous protein which may have been incorporated into the microorganisms. Recent feeding schemes (e.g. ARC 1980, 1984) require an accurate value of the degradability of feed in the rumen. When degradability is determined in vivo failure to account for a quantity of endogenous protein in the proximal duodenal digesta results in an underestimate of the degradability of a ration. Direct estimates of the endogenous protein content of proximal duodenal digesta are therefore required. This thesis describes the development of a method to do this and its application to sheep and cattle. The approach adopted, based on the concept of isotope dilution, involved a continuous intravenous infusion of L-[4,5-3H]-leucine. This resulted in all body protein becoming labelled. Any label detected in the duodenal digesta must therefore be derived from the animal itself. A comparison of the specific activity of duodenal digesta with that of suitable precursor proteins provided an estimate of the proportion of duodenal digesta of endogenous origin. Interestingly, the bacterial fraction of duodenal digesta was also labelled. This indicated that bacteria were utilising an endogenous source of leucine and circumstantial evidence suggested that this was derived largely from the rumen epithelium. The validity of the L-[4,5-3H]-leucine technique was investigated using three sheep fed an essentially protein free diet. Values of endogenous protein flow derived via the proposed technique (2.6 + 1.00 g N/day) were compared with those calculated by difference (2.1 + 0.92 g N/day). A possible dietary influence on the endogenous protein content of ruminant proximal duodenal digesta was examined. An estimate of 2.6 + 0.58 g N/day was derived for three sheep fed a concentrate diet and 2.1 + 0.22 g N/day for three sheep fed long hay. Thus, contrary to previous suggestions, no significant dietary effect was observed. Possible reasons for this are discussed. The proposed technique was also applied to derive estimates in cattle. A value of 11.3 + 1.73 g N/day was obtained for four steers (170 kg) fed silage supplemented with fishmeal. The continuous intravenous infusion of L-[4,5-3H]-leucine method is the first technique to provide a direct determination of the endogenous protein component of ruminant proximal duodenal digesta which can be applied to any dietary regime and used in sheep and cattle.
Metapneumovirus: determinants of host range and replication

textabstractThe general composition of the metapneumovirus genome is similar to that of pneumoviruses but differs in the number of genes and their order in the genome (Figure 2) (237). Metapneumoviruses do not encode the nonstructural proteins NS1 and NS2, and the small hydrophobic (SH) and attachment (G) protein genes follow the fusion (F), M2.1 and M2.2 protein genes, whereas for pneumoviruses this is the other way around. In evolutionary terms, this difference is very striking since recombination for members of the subfamily Pneumovirinae has been observed in a laboratory setting only (218). The 3’ and 5’ ends of the genome consist of short extragenic regions, referred to as the leader and trailer regions, and approximately the terminal 12 nt of the leader and the terminal 12 nt of the trailer are complementary, most likely due to the fact that each contains the basic elements of the viral promoter (21, 57, 163). The 3’ end of the viral RNA (vRNA) directs both replication and transcription, while the 5’ end of the genome contains signals that direct the replication of the antigenome. Each gene is preceded by a gene start (GS) signal at which the synthesis of mRNA initiates. Subsequently, each gene terminates with a semiconserved gene end (GE) signal that directs polyadenylation and termination of the completed mRNA. The genomes of metapneumoviruses consist of non-segmented negative stranded RNA and are smaller (~13.000 kb) than those of pneumoviruses (~15.000 kb) (70). For members of the subfamily Paramyxovirinae, the nucleotide length of each genome is a multiplicity of six (“rule of six”), reflecting a requirement of the nucleocapsid for RNA binding (e.g., binding units of six nucleotides) (34). This rule does not apply for the subfamily Pneumovirinae (201), although the reasons underlying this discrepancy have not been determined.
Use of quantitative trait loci (QTL) affecting muscling in sheep for breeding

VI TABLE OF CONTENTS VIII LIST OF TABLES XIII LIST OF ABBREVIATIONS XVI LIST OF JOURNAL PUBLICATIONS XXV LIST OF PRESENTATIONS AND PUBLICATIONS IN CONFERENCES PROCEEDINGS XXV LIST OF ASSOCIATED AUTHOR PUBLICATIONS XXVI CHAPTER 1 1 GENERAL INTRODUCTION 1 1.1 GENERAL BACKGROUND 2 1.1.1 Sheep industry and lamb consumption 2 1.1.2 Conventional breeding systems 4 1.1.2.1 The UK breeding structure 4 1.1.2.2 Sire Reference Schemes (SRSs) 6 1.2 MOLECULAR-BASED GENETIC ADVANCES 7 1.2.1 The Definition of QTL 8 1.2.2 Genes and QTLs associated with carcass attributes 9 1.2.2.1 The Callipyge gene 9 1.2.2.2 Carwell, REM, LM-QTL, LoinMAXTM 10 1.2.2.3 Texel Muscling QTL (TM-QTL) 12 1.2.2.4 Myostatin 14 1.3 IN-VIVO AND POST-MORTEM TECHNOLOGIES TO ASSESS LAMB CARCASSES 16 1.3. 1 In-vivo technologies 17 1.3. 1.1 Ultrasound scan 17 1.3. 1.2 Computed Tomography 17 1.3. 2 Post-mortem carcass assessment methodologies 20 1.3. 2.1 Meat and livestock classification (MLC) scheme 20 1.3. 2.2 Video Image Analysis (VIA) 21 1.4 PHD OBJECTIVES: 24 1.4. 1 Background 24 1.4. 2 The objectives 25 CHAPTER 2 27 THE EFFECTS OF A LOIN MUSCLING QUANTITATIVE TRAIT LOCUS (LOINMAXTM) ON CARCASS AND VIA-BASED TRAITS IN CROSSBRED LAMBS 27 ABSTRACT 28 2.
The MutS and MutL protein families and their role in the initiation of DNA mismatch repair

In Escherichia coli, MutS initiates mismatch repair (MMR) by binding mispaired DNA. MutL, an intermediary protein, recognizes mispair-activated MutS and activates downstream MMR proteins. In eukaryotes MMR is similarly initiated by a MutS Homologue (MSH) complex called Msh2-Msh6 that binds to a MutL Homologue (MLH) complex, called Mlh1-Pms1, which activates downstream proteins. While the in vitro reconstitution of a MMR reaction using purified Escherichia coli proteins was described nearly twenty years ago (and recently using human proteins), the molecular mechanism of this process is not well understood. Accordingly, several models describe the coordination of MMR events. The studies described in this dissertation use various methods to explore the molecular mechanism of the initiation of MMR. A system was developed for studying MMR protein movement along DNA. This system was characterized using MSH and MLH complexes from Saccharomyces cerevisiae. In addition, an assay was developed to monitor ATP binding in the MSH proteins. These studies revealed that Msh2-Msh6 hydrolyzes ATP to bind mispaired DNA in an ADP-bound form. Mispair binding enables the Msh2-Msh6 to bind ATP in its high-affinity ATP binding site, but inhibits ATP hydrolysis allowing Msh2 to bind an additional ATP, yielding a dual ATP bound form, which is competent for sliding along DNA. Mutant MSH complexes defective for binding ATP in Msh2 failed to slide. The MSH-MLH ternary complex also appeared to slide, but its affinity for DNA ends confounded dissociation analysis. Interestingly, a dominant mutant Msh2-Msh6 complex interacted with Mlh1-Pms1, but failed to slide, suggesting that sliding is important for MMR in vivo. Lastly, small angle x-ray scattering of E. coli MutS and the crystal structure of its C-terminal 34 amino acids containing the tetramer-forming domain provide a model for full length MutS; further analysis revealed that stable dimers, but not tetramers are essential for MMR in vivo. Taken together, these results support a model of MMR initiation where a dimeric MSH complex recognizes the mispair, binds but does not hydrolyze ATP producing a conformational change that enables binding of the MLH complex and sliding along the DNA helix where downstream signaling can be initiated
Negative Regulation of Transactivation Function but Not DNA Binding of NF-κB and AP-1 by IκBβ1 in Breast Cancer Cells*

The transcription factor NF-κB regulates the expression of genes involved in cancer cell invasion, metastasis, angiogenesis, and resistance to chemotherapy. In normal cells NF-κB is maintained in the cytoplasm by protein-protein interaction with inhibitor IκBs. In contrast, in cancer cells a substantial amount of NF-κB is in the nucleus and constitutively activates target genes. To understand the mechanisms of constitutive NF-κB activation, we have analyzed the function of IκBα and IκBβ in breast cancer cells. In most cases, constitutive NF-κB DNA binding correlated with reduced levels of either IκBα or IκBβ isoforms. Overexpression of IκBα but not IκBβ1 resulted in reduced constitutive DNA binding of NF-κB in MDA-MB-231 cells. Unexpectedly, IκBβ1 overexpression moderately increased 12-O-tetradecanoylphorbol-13-acetate- and interleukin-1-inducible NF-κB DNA binding. 12-O-Tetradecanoylphorbol-13-acetate- and interleukin-1-induced transactivation by NF-κB, however, was lower in IκBβ1-overexpressing cells. Mutants of IκBβ1 lacking the C-terminal casein kinase II phosphorylation sites, which form a stable complex with DNA bound NF-κB without inhibiting its transactivation in other cell types, repressed the transactivation by NF-κB in MDA-MB-231 cells. Consistent with the results of transient transfections, the expression of urokinase plasminogen activator, an NF-κB target gene, was reduced in IκBβ1-overexpressing cells. These results suggest that depending on the cell type, IκBβ1 represses the expression of NF-κB-regulated genes by inhibiting either DNA binding or transactivation function of NF-κB.
Population responses to perturbations: Predictions and responses from laboratory mite populations

1. Mathematical models are frequently used to make predictions of the response of a population to management interventions or environmental perturbations, but it is rarely possible to make controlled or replicated tests of the accuracy of these predictions. 2. We report results from replicated laboratory experiments on populations of a soil mite, Sancassania berlesei, living in 'constant' or 'variable' environments. We experimentally perturbed vital rates, via selective harvesting, and examined the population-level responses. The response depends on the stage manipulated and whether there is environmental variability. Increased mortality usually decreased population size and increased population variability. However, egg mortality in a variable environment increased total population size. 3. We used time-series analysis to construct a stage-based population model of this system, incorporating the responses to both density and variation in food supply. 4. The time-series model qualitatively captures the population dynamics, but does not predict well the way the populations will respond to the change in mortality. Elasticity analysis, conducted on the model's output, therefore did not lead to accurate predictions. 5. The presence of indirect positive population effects of a negative perturbation, but only in a variable environment, suggests that predicting the population response will require the incorporation of density dependence and environmental stochasticity. That the considerable biological complexity of our time-series model did not allow accurate predictions suggests that accurate prediction requires modelling processes within a stage class rather than trying to make do with simple functions of total density.
Analysis of optical characteristics of holey photonic crystals with extended coupled-mode formalism

We present a new approach for analysis of optical properties of holey photonic crystal devices. Our approach is based on the Extended coupled-mode formalism, developed for analysis of infinite photonic crystal lattices (arrays of identical coupled waveguides / lasers) and superlattices (periodic sequences of different coupled waveguides / lasers). Our method allows for a fast (tens of seconds) calculation of array modes and photonic band structure of large holey photonic devices. It also allows an analytical prediction of some optical properties of those devices, such as number of photonic bands, their upper and lower limits and bandwidth. Our computations show close agreement between the results, acquired with our new approach on the one hand and the solution of Helmholtz equation (used as a benchmark) on the other hand.
Anopheles (Cellia) nemophilous, a New Species of the Leucosphyrus Group from Peninsular Malaysia and Thailand (Diptera: Culicidae)

Abstract : Anopheles (Cellia) nemophilous, a new species of the Leucosphyrus Group from Peninsular Malaysia and Thailand, is described and illustrated in the adult, pupal and larval stages. The species is contrasted with Anopheles dirus and introlatus, two morphologically similar species. The zoogeography and biology of the species is discussed. The Dirus Complex is characterized in the adult stage.
Ant‐mediated seed dispersal does not facilitate niche expansion

1. Whereas classic niche theory is based on the contraction of the niche via negative interactions, facilitative niche theory suggests that mutualisms can expand the niche via positive interactions. Specifically, animal‐mediated seed dispersal can expand the utilization of physical space by plants and allow greater access to resources and other environmental requirements. Ant‐mediated dispersal of plant propagules (myrmecochory) is a common mutualism throughout the world, particularly in the deciduous forests of the eastern United States where this research is conducted.
Bio-accumulation des métaux lourds et induction des métallo-protéines au niveau de la glande digestive de Mytilus galloprovincialis

L’induction des metalloproteines et l’accumulation du Cuivre, Zinc et Cadmium ont ete etudiees, durant une annee, au niveau de la glande digestive de la moule Mytilus galloprovincialis. Les animaux proviennent soit d’un milieu naturel pollue, situe a proximite des rejets industriels de la region de Jorf Lasfar (Maroc), soit de l’elevage au laboratoire apres traitement par le chlorure de cadmium. Les concentrations du Cu, Zn et Cd presentent des variations qui semblent dependre de la saison et du site de prelevement. Les plus fortes teneurs sont enregistrees au printemps et en automne, preferentiellement chez les animaux des stations avoisinant les rejets. Chez les moules traitees au laboratoire, la concentration du Cd presente une augmentation significative au dela de 48 heures d’exposition, alors que celle du Cu et du Zn reste faible. Le dosage des metalloproteines, chez les animaux preleves dans les differents sites, revele une variation spatio-temporelle. Leur concentration se fait preferentiellement dans les glandes des moules de la station la plus polluee. Concernant les animaux d’elevage, la concentration de ces proteines montre une nette evolution en fonction de la duree d’exposition au chlorure de cadmium.
Intraspecific variability and trait‐based community assembly

1. Trait‐based approaches applied to community ecology have led to a considerable advance in understanding the effect of environmental filters on species assembly. Although plant traits are known to vary both between and within species, little is known about the role of intraspecific trait variability in the non‐random assembly mechanisms controlling the coexistence of species, including habitat filtering and niche differentiation.
Fractal analysis of cell boundary ultrastructure imaged by atomic force microscopy

Fractal analysis has been widely used to determine the complexity of irregular shapes of various natural objects including biological systems. Here we report an investigation into the nature of the cell boundary nanostructure (less than 200 nm in thickness) in an aqueous environment using atomic force microscopy. The box-counting method revealed the fractal nature of detailed contours of cells cultured on a solid substratum. The fractal dimensions (Df) of individual cells of the human epithelial cell line MCF10A converged on a narrow range (Df = 1.352 ± 0.044) despite their morphological diversity. Treatment with cytochalasin D, an inhibitor of actin polymerization, was shown to decrease both the ruggedness and the Df of cell boundaries. These findings suggest that the Df value is a useful parameter for describing the complexity of cellular ultrastructure dependent on the actin cytoskeleton.
ESTIMATIVA DE VOLUME DE MADEIRA EM PLANTIOS DE Eucalyptus spp. UTILIZANDO DADOS HIPERESPECTRAIS E DADOS TOPOGRÁFICOS 1

ABSTRACT – The availability of orbital hyperspectral data has brought new perspectives to both academicand corporative sectors solving demands in forestry science. The main objective of this work was to evaluatethe potential of Hyperion EO-1 hyperspectral data to quantify the biophysical timber volume in Eucalyptus spp stands and the effect of hill shading in that quantification. For this, the correlations between spectraldata and timber volume were performed following the use of Multiple Linear regression models as the descriptorsof the relationships established. The relief effect on the Eucalyptus spp. canopy reflectance was taken intoaccount. The Hyperion EO-1 data were converted to BRF surface values, which were considered the basisof the entire work. The study area was located in the municipality of Capao Bonito (the State of Sao Paulo,Brazil) and included Eucalyptus spp . stands managed by the Votorantim Papel e Celulose company (VCP). Spectral samples were collected in different topographic conditions. In the establishment of the relationshipwith timber volume, the vegetation indices estimated using hyperspectral data resulted in models with higherR2 when considering the topographic illumination effect, showing higher applicability potential of this data.Keywords: Vegetation anisotropy, Biophysical parameters and SRTM.
Desenvolvimento de interface gráfica para o sequenciamento de produção

O trabalho teve como objetivo desenvolver uma interface grafica para o sistema GAMS (General Algebraic Modeling System) de modo a facilitar o acompanhamento de execucao das tarefas planejadas em plantas de polpa de fruta. O uso de interface grafica permite a visualizacao de variaveis de producao, por exemplo, do tempo termino de cada tarefa. Desta forma, foi implementado modelo de sequenciamento de natureza MILP (Mixed Integer Linear Programming) e resolvido pelo sistema GAMS/CPLEX. O GAMS nao possui interface amigavel para a saida dos resultados. Assim, foi desenvolvida interface grafica usando linguagem de programacao JAVA para o sistema GAMS.
The tempo of genetic evolution in birds: body mass and climate effects

Aim Negative relationships between body mass and substitution rates have previously been reported. However, most of these studies have involved contrasted taxa that, due to their highly divergent phylogenetic histories, also differ in many additional characteristics other than mass. In particular, there has been little examination of the potentially confounding effects of climate or population size. Here we test for differences in rates of microevolution among bird species that, although differing in mass, are nonetheless very closely related phylogenetic pairs. We additionally tested for latitudinal/elevational and population size effects across these contrasts.
Antimicrobial effect of aqueous extract of orange peel and its effect on the shelf-life of flavored milk

Background and Objective: The adoption of methods for increasing the shelf life of dairy products by using natural preservatives is necessary. This study was done to determine the antimicrobial activity of aqueous extract of orange peel and its effect on the shelf life of flavored milks. Methods: In this descriptive –analytical studty the antimicrobial activity of aqueous extract of orange peel was investigated by using disk diffusion method and minimum inhibitory concentration (MIC) by successive dilution of culture broth and then its impact on the shelf life of milk. Results: In disk diffusion method and MIC the antimicrobial effect of aqueous extract of orange peel was more effective against Staphylococcus aureus and Candida albicans and less effective on Escherichia coli . The growth diameter of disk diffusion method in aqueous extract of orange peel was 7.11, 29.06 and 50 mm for Staphylococcus aureus , Escherichia coli and Candida albicans , respectively. The inhibitory concentration in the aqueous extract of orange peel was 15, 2 and 2 mg/ml, respectively. Also 0.17 g/ml of aqueous extract of orange peel in milk reduced the growth of microorganisms at the time of 6, 12, 24, 48 and 72 hours. Temperature affected the growth of Candida albicans in the milk, so that the growth of microorganisms reduced with decreasing temperature (P<0.05). The growth inhibitory activity of the aqueous extract of orange peel on Staphylococcus aureus was significantly more than on Escherichia coli (P<0.05). Conclusion: This study showed that the antimicrobial activity of aqueous extract of orange peel on Staphylococcus aureus , Escherichia coli and Candida albicans in vitro and in the milk.
Abstract 15960: Activation of TRAF2-NF-κB Signaling suppresses Mitochondrial Perturbations in Doxorubicin Cardiotoxicity

Doxorubicin (dox) is a highly effective anti-tumour agent, however, its use is limited by its protracted and cardiotoxic effects that manifest as heart failure. The canonical NFκB signaling pathway has been suggested to play a critical survival role in cardiac myocytes. Herein, we demonstrate that, impaired TRAF2 signaling disrupts NFκB activation in hearts of mice treated with dox (20mg/kg) or ventricular myocytes treated with dox (10μM). This was accompanied by severe ultrastructural defects including vacuolization, mitochondrial perturbations including mPTP, loss of [[Unable to Display Character: ∆]]Ψm and ROS production. Further we investigated role of TRAF2 on IKKβ- NFκB signaling in ventricular myocytes. Interestingly, TRAF2 mediated K-63 poly-ubiquitination of Receptor Interacting Protein 1 (RIP1) which recruits Tak-1 complex and activates IKKβ -NF-κB signaling was impaired in cells treated with dox. This coincided with a marked increase in expression and mitochondrial targeting of the Bcl-2 death protein Bnip3. Interestingly, expression of wild type TRAF2 but not the ring finger domain mutant defective for ubiquitination, restored TAK1-IKKβ-NF-κB signaling and suppressed Bnip3 gene activation in cells treated with dox. Concordant with TRAF2’s ability to suppress Bnip3, was accompanied by reduction in dox induced mPTP, ROS and cell death. Hence, our findings reveal a novel signaling pathway that functionally couples TRAF2 mediated NF-κB signaling to mitochondrial function and survival of cardiac myocytes.
Introducing Communicative Function Qualifiers

This paper addresses the annotation and representation of multimodal dialogue behaviour expressing intentions with various possible qualifications, relating to uncertainty, conditionality, partiality or a speaker’s emotional state and attitude towards the information or action is addressed, or towards an addressee. We present a conceptual and empirically-based analysis of this behaviour, propose the introduction of communicative function qualifiers, and describe their use in a dialogue act annotation scheme.