Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Adaptations that Promote Softwood Utilization by the White-rot Basidiomycete Fungus, Phanerochaete carnosa

Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus Phanerochaete carnosa has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by P. carnosa, its genome was sequenced and transcriptomes were evaluated after growth on wood compared to liquid medium. Results indicate that P. carnosa differs from P. chrysosporium in the number and expression levels of genes that encode lignin peroxidase (LiP) and manganese peroxidase (MnP), two enzymes that modify lignin present in wood. P. carnosa has more genes for MnP with higher expression levels than LiP, while the reverse has been observed for P. chrysosporium. The abundances of transcripts predicted to encode lignocellulose-modifying enzymes were then measured over the course of P. carnosa cultivation on four wood species. Profiles iii were consistent with decay of lignin before carbohydrates. Transcripts encoding MnP were highly abundant, and those encoding MnP and LiP featured significant substrate-dependent
Cápsidas vacías del virus de la enfermedad hemorrágica del conejo como plataforma para la inducción de respuesta humoral neutralizante y protectora frente a epítopos B heterólogos

Las VLPs (virus-like particles) son ensamblados macromoleculares constituidos por proteinas estructurales virales, que carecen de material genetico y pueden someterse a modificacion quimica o mediante ingenieria genetica, para ser utilizadas como plataformas de presentacion multimerica de antigenos foraneos. En esta tesis se describe la generacion y caracterizacion de VLPs quimericas derivadas del virus de la enfermedad hemorragica del conejo (RHDV) incorporando epitopos B heterologos. El virus RHDV es el prototipo del genero Lagovirus, perteneciente a la familia Caliciviridae. Posee una capsida formada por 180 copias de la proteina estructural (VP60). Con el fin de evaluar la capacidad de las VLPs quimericas de RHDV para inducir respuesta humoral especifica y protectora frente a antigenos foraneos, seleccionamos dos epitopos B diferentes: un epitopo neutralizante, derivado de la capsida del calicivirus felino (FCV), recientemente identificado por nuestro grupo, y un epitopo muy bien caracterizado correspondiente al dominio extracelular de la proteina M2 del virus de la gripe (M2e). Se obtuvieron VLPs quimericas de RHDV con epitopos heterologos insertados en tres localizaciones distintas de la proteinaVP60 y en diferente numero de copias por sitio de insercion. La inmunogenicidad de las VLPs quimericas se evaluo en el modelo murino. Los resultados obtenidos indicaron que las VLPs quimericas de RHDV son capaces de inducir respuesta humoral especifica y protectora frente a los epitopos B foraneos, demostrada tanto por la neutralizacion in vitro, como por la proteccion in vivo inducida frente a un desafio viral letal. Ademas, mediante la realizacion de ensayos de PEPSCAN, en esta tesis se han identificado tres regiones lineales inmunodominantes en el subdominio P2 de la proteina VP60. Una de dichas regiones presenta propiedades estructurales potencialmente adecuadas para constituir un nuevo sitio de insercion de epitopos B heterologos. Los resultados presentados demuestran: (i) que se pueden insertar epitopos B foraneos en al menos tres localizaciones diferentes, incluso simultaneamente, sin afectar la capacidad de la proteina VP60 de autoensamblarse en VLPs, (ii) que las VLPs de RHDV toleran la insercion de al menos tres copias en tandem de un epitopo foraneo (62 aa) en el bucle expuesto L1, dos copias (42 aa) en el extremo N-terminal o una copia (22 aa) en el extremo C-terminal, (iii) que el subdominio P2 contiene tres sitios lineales inmunodominantes conservados. En conjunto, los resultados obtenidos en esta tesis amplian el potencial de las VLPs de RHDV como plataforma para el desarrollo de nuevas vacunas, demostrando su capacidad para inducir respuestas humorales potentes y protectoras frente a epitopos B heterologos insertos en ellas.
Ursolic acid and oleanolic acid as novel therapeutic agents in breast cancer

X List of abbreviation . XII List of Figures . XVI List of Tables . XX 1 Literature Review . 1 1.1 Breast Cancer: An insight into incidence and survival . 1 1.2 Cell cycle . 4 1.2.1 Cyclins . 6 1.3 Control of the cell cycle . 8 1.3.1 Cell cycle progression through phosphorylation/dephosphorylation . 8 1.3.2 Cell cycle checkpoints . 8 1.3.2.1 DNA damage response pathways of G1 phase . 9 1.3.2.2 The P53 response to DNA damage . 9 1.3.2.3 The Cdc25A pathway . 11 1.3. 3 S phase DNA damage checkpoints . 11 1.3. 3.1 The intra-S phase checkpoint . 11 1.3. 3.2 The DNA replication (S/M) checkpoint . 12 1.3. 4 G2 (G2/M) checkpoint . 12 1.3. 5 The spindle assembly checkpoint . 13 1.4 Cell death . 15
Syntax in C. elegans locomotion

Visible phenotypes have played a critical role in understanding the molecular basis of behaviour in model organisms. In previous work, we have shown that automated tracking and quantitative measurement of posture and motion parameters can sensitively identify new phenotypes in mutants of the nematode worm C. elegans [1]. However, it is not clear whether these parameters are in any way optimal nor whether they are useful for discovering new behaviours that we did not think to measure. As an alternative, we have also used unsupervised methods to automatically detect repeated behaviours in an unbiased way. A dictionary of such ‘behavioural motifs’ can be used to construct a phenotypic fingerprint for mutant strains and seems to be a promising way of predicting possible genetic associations [2].
Seasonal Variations in Food Supply for Wild Primates

During my different field studies on wild primates, I have been particularly impressed by the importance of seasonal variations, even for species living in a supposed 'stable' environment such as t he tropical rain forest. This might reflect that the annual variation in food supply, and the subsequent seasonal variations in the diet of the different species, is the common basis of primate feeding behaviour. Facing such variations has certainly been an important motor of evolution, and the measure of these variations among the extant species provides a basis to understand past and present selective pressures.
Coffee But Not Anticipation of Coffee Alters the Outcome of Explosive Bench Pressing

When administering a drug, the degree of anticipation influences perceptual outcomes in migraine research (Slavenka Kam‐Hansen, 2014). Specifically, pain scores vary depending on the information given (percent anticipation). Little is known, however, to what extent anticipation affects physical performance. Often, coffee and caffeine research include a 50% anticipation in the form of experimental beverage or placebo. Few coffee studies, though, also include a true control such as water. The purpose of this study was to compare a highly‐caffeinated instant coffee (VIA) to both an identical decaffeinated placebo (DCF) and to water (WTR). This provides the typical 50% anticipation comparison and a 0% anticipation true control. We hypothesized that VIA would increase explosive performance compared to both DCF (50% anticipation) and to WTR (0% anticipation). Further, we hypothesized that DCF (50% anticipation) would increase performance and psychostimulant variables compared to WTR (0% anticipation). Ten resistance‐trained participants with varied levels of coffee habituation were tested at 50% of one‐repetition maximum (1RM) in the Smith bench press 60 minutes after ingesting 20 oz. (2 packets) VIA, DCF, or WTR. Force, bar velocity (VEL), power (POW), rate of force development (RFD) and time to peak power (TPP) were measured using the Smith bench press and a Ballistic Measurement System (BMS, Innervations, Inc., South Australia). Psychostimulant testing included Likert‐type (1–5 scale) ratings of alertness, focus and energy. After repeated measures analysis of variance and Newman‐Keuls post hoc testing, VEL and POW increased after consuming VIA versus DCF or WTR (mean ± SE: 1.15 ± 0.05 m/s vs. 0.99 ± 0.05 m/s and 1.01 ± 0.05 m/s; p=0.004 and p=0.005, respectively and 561.1 ± 109.4 W vs. 482.2 ± 92.4 W and 465.4 ± 84.7 W; p=0.009 and p=0.007 respectively). No performance differences were noted between DCF and WTR. Upon psychostimulant analysis, VIA increased alertness compared to DCF and WTR (4.22 ± 0.22 vs. 3.44 ± 0.29 and 2.94 ± 0.34; p=0.006 and p=0.0004 respectively). There was a trend for DCF to increase alertness versus WTR (3.44 ± 0.29 vs. 2.94 ± 0.34; p=0.06). Within the limitations of this design, we conclude that our hypothesis regarding VIA and physical performance was supported but the hypothesis involving anticipation of DCF largely was not. DCF had no effect on explosive physical performance but did tend to affect perception of alertness.
Habitat Use and Arrival Timing of Hatchery and Naturalized Chinook Salmon Spawning in a Great Lakes Tributary

AbstractLarge-scale stocking programs have been used to introduce and maintain Chinook Salmon Oncorhynchus tshawytscha fisheries in the Laurentian Great Lakes since the late 1960s, with discoveries of naturalized populations in tributaries soon after the initial introduction. Characterizing ecological differences between hatchery and naturalized Chinook Salmon is becoming increasingly important for sustainable management of this species. We hypothesized that nonheritable traits (i.e., homing) and artificial selection might result in different habitat use and arrival timing between rearing origins occupying the same river, with the potential for reproductive isolation and divergence of naturalized and hatchery strains. In 2010 and 2011, using visual observations and PIT tags, we tracked individual hatchery and naturalized Chinook Salmon that spawned in the Sydenham River (Owen Sound, Ontario), one of the first tributaries in Lake Huron to be colonized by hatchery strays and establish a naturalized populati.
Identification of novel Ebola virus (EBOV) VP24 inhibitor from Indonesian natural products through in silico drug design approach

Ebola remains as one of the deadliest diseases in the world, with almost 29,000 cases were reported and kill 11,000 of them, and yet neither treatment nor vaccine that can combat this disease effectively. This disease is caused by ebolavirus (EBOV), a primary member of Filoviridae family. The life cycle of this virus has been operated by several key proteins, one of them is VP24 protein, which has been known for its crucial role in the transcription and replication of EBOV. Therefore, targeting VP24 protein can be a solution for treating this pathogenic disease. In this study, virtual screening of Indonesian natural products as EBOV VP24 inhibitor was performed. About 2,020 ligands from many sources, including HerbalDB database, were obtained and screened by using DataWarrior software to measure its molecular and pharmacological properties, resulting 301 ligands in the process. Then, the molecular docking simulation was performed to check the ligand’s binding interaction and affinity with EBOV VP24 protein; this simulation was done by using MOE 2014.09 software. This study resulted that cycloartocarpin was the best ligand to inhibit the EBOV VP24 protein. Therefore, this ligand should be checked its stability through molecular dynamics simulation and performed in vitro test to verify its bioactivity against the EBOV VP24 protein.Ebola remains as one of the deadliest diseases in the world, with almost 29,000 cases were reported and kill 11,000 of them, and yet neither treatment nor vaccine that can combat this disease effectively. This disease is caused by ebolavirus (EBOV), a primary member of Filoviridae family. The life cycle of this virus has been operated by several key proteins, one of them is VP24 protein, which has been known for its crucial role in the transcription and replication of EBOV. Therefore, targeting VP24 protein can be a solution for treating this pathogenic disease. In this study, virtual screening of Indonesian natural products as EBOV VP24 inhibitor was performed. About 2,020 ligands from many sources, including HerbalDB database, were obtained and screened by using DataWarrior software to measure its molecular and pharmacological properties, resulting 301 ligands in the process. Then, the molecular docking simulation was performed to check the ligand’s binding interaction and affinity with EBOV VP24 protei.
Interfascicular Interfaces for Peripheral Nerve Stimulation: Directed Stimulation within the Epineurial Space

Understanding the biomechanical properties of the nerve membranes is important for effective interfacing in various functional electrical stimulation (FES) applications. Peripheral nerve interfaces interact with one or more of the three connective tissue layers surrounding axons: epineurium, perineurium, and endoneurium. Trauma resulting from insertion and chronic implantation of a penetrating nerve interface can be reduced by choosing materials and insertion techniques that are based on the biomechanical properties of the nerve. Previous work has reported the forces needed to penetrate the whole nerve, but the mechanical differences between epineurium and perineurium were not reported. This study quantified the Young’s moduli and ultimate strains of the perineurium and the epineurium separately and forces necessary to penetrate each individually. A custom-built microtensile tester was used to measure the Young’s modulus values. The Young’s moduli of the epineurium and the perineurium were 0.4 ± 0.1 MPa and 3.0 ± 0.3 MPa respectively. A custom setup was used to measure the force required for wire-based probes to be inserted into isolated epineurial tissue and perineurial tissue. These data provide design guidelines that can be used to engineer materials for insertion into and mechanical matching of the two main tissue layers of the peripheral nerve.
The Influence of Probiotic Supplements on Microbial Diversity in the Gastrointestinal Microbiome of Healthy Horses

ii Dedication.v Acknowledgments.vi Vita.viii List of Tables.xii List of Figures.xiii Chapter 1: Literature Review. 1 Gastrointestinal Microbiome. 2 Factors Influencing the Gastrointestinal Microbiome. 7 Probiotics. 12 Chapter 2: The Influence of Probiotic Supplementation on the Microbial Diversity in the Gastrointestinal Microbiome of Quarter Horse Mares. 18 Abstract.19 Introduction. 21 Materials and Methods. 24 Results. 27 Discussion. 29 Chapter 3: The Influence of Probiotic Supplementation on the Microbial Diversity in the Gastrointestinal Microbiome of Young Quarter Horses. 31
An investigation into specific therapeutic targeting of the HIV-1 translational frameshift element

HIV-1 is a pathogenic retrovirus, which often develops into acquired immune deficiency syndrome (AIDS) and inevitably leads to death. The virus has directly caused an estimated 36 million deaths worldwide, and is the second highest attributed contributor to deaths caused by communicable diseases. This high mortality rate is due to the virus’ ability to evade treatment regimes by having an incredibly high rate of genomic mutation. However a highly conserved mechanism has been discovered that exhibits a novel control of protein expression. The -1 programmed ribosomal frameshifting region (-1PRF) is located between the gag and pol coding regions of the HIV-1 genome. By developing a mechanism that allows shifting between frames, HIV-1 has been able to condense its genome and tightly control expression of the Gag-Pol protein products. The PRF element is made up of three sub-elements, known as the slippery sequence, intercodon and secondary structural element (SSE). Although previous studies have hypothesised the importance of each sub-element, the interaction and causative effect was unknown. Substitution of the SSEs of HIV-1 and Paternally Expressed Gene 10 (PEG10) showed that the much larger PEG10 pseudoknot increased the efficiency of frameshifting in HIV-1 by 60%, whereas the contrasting substitution dropped PEG10 efficiency down 95%. This indicates that PEG10 relies heavily on the SSE to produce its high native frameshift efficiency. Substitution of the intercodon revealed a degree of ribosomal sampling in HIV-1 as a small increase was observed, however no variation in the PEG10 construct implied that no such sampling occurs in this mechanism. Due to the mechanism’s highly conserved nature, it is the ideal candidate for RNA targeting molecules. The Tate laboratory previously discovered three small molecule modulatory compounds, which were shown to affect HIV-1 frameshifting efficiency. However as there are several known retrotransposonderived elements within mammals, there was a possibility of interaction between the compound and human -1PRF mechanisms. When exposed to a range of concentrations up to 20μM of compound A3, CCR5 exhibited minimal increases, similar to those seen in PEG10 and far below the interaction seen in HIV-1. Binding of the compounds were shown to be in the SSE of HIV-1, which due to the differing nature of -1PRF SSEs may provide insight into the specificity observed. Thus, small molecule compounds developed for the targeting of the HIV-1 -1PRF region are unlikely to negatively affect the efficacy of known human orthologues, due to the differences in secondary structure and the underlying mechanism of action.
Wild bee and floral diversity co‐vary in response to the direct and indirect impacts of land use

Loss of habitat area and diversity poses a threat to communities of wild pollinators and flowering plants in agricultural landscapes. Pollinators, such as wild bees, and insect-pollinated plants are two groups of organisms that closely interact. Nevertheless, it is still not clear how species richness and functional diversity, in terms of pollination-relevant traits, of these two groups influence each other and how they respond to land use change. In the present study, we used data from 24 agricultural landscapes in seven European countries to investigate the effect of landscape composition and habitat richness on species richness and functional diversity of wild bees and insect-pollinated plants. We characterized the relationships between the diversity of bees and flowering plants and identified indirect effects of landscape on bees and plants mediated by these relationships. We found that increasing cover of arable land negatively affected flowering plant species richness, while increasing habitat richness positively affected the species richness and functional diversity of bees. In contrast, the functional diversity of insect-pollinated plants (when corrected for species richness) was unaffected by landscape composition, and habitat richness showed little relation to bee functional diversity. We additionally found that bee species richness positively affected plant species richness and that bee functional diversity was positively affected by both species richness and functional diversity of plants. The relationships between flowering plant and bee diversity were modulated by indirect effects of landscape characteristics on the biotic communities. In conclusion, our findings demonstrate that landscape properties affect plant and bee communities in both direct and indirect ways. The interconnection between the diversities of wild bees and insect-pollinated plants increases the risk for parallel declines, extinctions, and functional depletion. Our study highlights the necessity of considering the interplay between interacting species groups when assessing the response of entire communities to land use changes.
Quality parameters of curd

The aim of this work was measurement of the curd firmness prepared by different volume of rennet solution and comparison of differences of curd firmness between these volumes. Further, it was observed the influence of different volumes of rennet up to thevolume of whey release, curd firmness, dry matter of curd and dry matter of whey. The composition of milk was determined according ISO and Czech state standard. Dry matter content (%) was determined by gravimetry, in drying oven at 102 °C to constant weight (ISO 6731:2010), the protein content (%) by Kjeldahl´s method (EN ISO 8968-1:2002), content of fat (%) by Gerber´s acidobutyrometric method (ISO 2446:2008), content of lactose by polarimetry, titratable acidity by titration Soxhlet-Henkel method, pH and calcium content in milk (g.L -1 ) was determined by complexometric titration with flueroxone as an indicator according to Czech state standart No 57 0530. For coagulation was used microbial rennet CHY-MAX R M 200. There were measured: curd firmness, rennet coagulation time, curd quality, volume of released whey, weight of curd, dry matter of curd and dry matter of whey. Different volumes of rennet solution had influence on curd firmness. Curd firmness (volume of rennet solution) had no significant influence on curd quality (five grade scale). Curd firmness had influence on volume of whey release (mL) out of the curd. With the increasing curd firmness s increased the volume of whey released from the curd. The volume of rennet solution had an influence on weight of curd. Curd dry matter raised with higher volume of rennet solution. Volume of added rennet solution had no statistically significant effect on the change of whey dry matter.
The reproductive seasonality and fecundity of yellowtail clownfish (Amphiprion clarkii) in the Philippines

Understanding the spawning patterns and egg production of clownfish is important for understanding their life history and the factors contributing to population persistence. The egg production and temporal spawning patterns of eight breeding pairs of yellowtail clownfish, Amphiprion clarkii (Bennett, 1830), were observed for a 14-mo period on a coral reef off the Central Visayas, Philippines. Spawning events and egg production revealed a peak breeding season from November through May, which coincides with temperatures below 30 °C. Noticeably fewer spawning events and smaller clutch sizes occurred during the warmer months (30–31.5 °C) of June through October. Within the spawning season, egg production increased weakly leading up to the new moon and decreased after the full moon. The seasonality of spawning events found in our study were comparable to those of clownfish in temperate regions, and surprisingly unlike findings from other tropical latitudes and climates. These findings suggest that recruitment and larval dispersal in this population will be most sensitive to oceanographic conditions during relatively narrow periods of time each year.
AMP accumulation inhibitor in follicular fluid of human origin.

A study of healthy subjects aged 21-40 years with documented evidence of regular ovulatory cycles contributed data which were used in this progress report of an analysis of follicular fluid inhibitor concentration and its correlation to subject endocrine profile (specifically to cyclic adenosine monophosphate accumulation). Results showed that the level of cyclic adenosine 3 5-monophosphate (AMP) in human chorionic gonadotropin-stimulated follicular fluid was lower than expected (P < .025) suggesting that the inhibitor present in follicular fluid in humans both stimulated cyclic AMP degradation and inhibited cyclic AMP formation. The results raise the question whether the cyclic AMP accumulation inhibitor is identical or related to inhibitors of oocyte maturation and luetinization. Since cyclic AMP has an essential role as an intermediate in the processes governing ovarian function the presence in situ of fluctuating levels of cyclic AMP inhibitor may have far-reaching implications in intraovarian regulatory mechanisms.