Miracle-dz/UniFAR-FTUs huggingface dataset:
Specificity in PI3K-PKB/AKT-PTEN Signaling: Subcellular Locus-specific Functions of Pathway Targets

The PI3K-PKB/Akt-PTEN signal transduction pathway orchestrates a variety of fundamental cell processes and its deregulation is implicated in several human diseases, including cancer. While the importance of this pathway to many cellular functions is well established, the mechanisms leading to context-specific physiological outcomes in response to a variety of stimuli remain largely unknown. Spatial restriction of signaling events is one of the means to coordinate specific cellular responses. To investigate the subcellular locus-specific roles of the major PI3K effector PKB/Akt in various cell processes, I have devised a novel experimental system employing cellular compartment-directed PKB/Akt pseudosubstrate inhibitors. The work herein describes the development and characterization of the localized PKB/Akt pseudosubstrate inhibitor system and its application to investigate potential locus-specific functions in established PKB/Akt-regulated cellular processes. Subcellular compartment-restricted PKB/Akt inhibition in the 3T3L1 adipocyte differentiation model revealed that nuclear and plasma membrane, but not cytoplasmic, PKB/Akt activity is required for terminal adipocyte differentiation. Nuclear and plasma membrane pools of PKB/Akt were found to contribute to distinct stages of adipocyte differentiation, revealing that PKB/Akt activity impacts multiple points of this program. The localized PKB/Akt pseudosubstrate inhibitor system was also utilized to investigate the importance of distinct subcellular pools of PKB/Akt in breast epithelial cells. MCF-10A human breast epithelial cells can be grown in three-dimensional culture to form acinar structures that recapitulate in vivo mammary glandular architecture. Expression of the plasma membrane PKB/Akt inhibitor during cell growth in three-dimensional culture severely impaired acinar formation. On the other hand, expression of the nuclear PKB/Akt inhibitor during acinar development resulted in the formation of large, misshapen, multi-acinar structures. Assessment of the migratory capacity of MCF-10A cells upon localized PKB/Akt inhibition revealed that nuclear PKB/Akt inhibition promoted, while plasma membrane PKB/Akt inhibition impaired, MCF-10A cell migration. The development of locus-specific PKB/Akt inhibitors represents the first attempt to prioritize the targets of this kinase based on their subcellular localization. This work and its immediate extensions will further our understanding of the biology of PKB/Akt, a multi-tasking kinase with profound roles in development, cellular and organismal homeostasis and disease. %%%%PhD
Dropping of pea aphids from feeding site: a consequence of parasitism by the wasp, Monoctonus paulensis

We examined the dropping behaviour of the pea aphid, Acyrthosiphon pisum (Harris), feeding on broad‐bean plants in the laboratory. Aphid responses to foraging and oviposition by females of Monoctonus paulensis (Ashmead) were instar‐specific and included kicking with the hind legs, walking away and dropping from the feeding site. Fourth nymphal instars were most likely to drop, followed by second, third, and first instars, in that order. Compared with first instars, the odds that a fourth‐instar aphid will drop were 6‐times higher independent of the stimulus, and 16‐times higher after parasitoid attack. Dropping from the feeding site increases an aphid's mortality risk. If parasitoid offspring are more likely to survive in small pea aphids, it may be adaptive for M. paulensis to choose smaller hosts, regardless of possible fitness gains due to increased body size from development in larger aphids.
PROBLEMS WITH SAMPLING DESERT TORTOISES: A SIMULATION ANALYSIS BASED ON FIELD DATA

Abstract The desert tortoise (Gopherus agassizii) was listed as a U.S. threatened species in 1990 based largely on population declines inferred from mark–recapture surveys of 2.59-km2 (1-mi2) plots. Since then, several census methods have been proposed and tested, but all methods still pose logistical or statistical difficulties. We conducted computer simulations using actual tortoise location data from 21-mi2 plot surveys in southern California, USA, to identify strengths and weaknesses of current sampling strategies. We considered tortoise population estimates based on these plots as “truth” and then tested various sampling methods based on sampling smaller plots or transect lines passing through the mile squares. Data were analyzed using Schnabel's mark–recapture estimate and program CAPTURE. Experimental subsampling with replacement of the 1-mi2 data using 1-km2 and 0.25-km2 plot boundaries produced data sets of smaller plot sizes, which we compared to estimates from the 1-mi2 plots. We also tested distance sampling by saturating a 1-mi2 site with computer simulated transect lines, once again evaluating bias in density estimates. Subsampling estimates from 1-km2 plots did not differ significantly from the estimates derived at 1-mi2. The 0.25-km2 subsamples significantly overestimated population sizes, chiefly because too few recaptures were made. Distance sampling simulations were biased 80% of the time and had high coefficient of variation to density ratios. Furthermore, a prospective power analysis suggested limited ability to detect population declines as high as 50%. We concluded that poor performance and bias of both sampling procedures was driven by insufficient sample size, suggesting that all efforts must be directed to increasing numbers found in order to produce reliable results. Our results suggest that present methods may not be capable of accurately estimating desert tortoise populations.
A Modern Landscape Ecology of Black-Tailed Godwits: Habitat Selection in Southwest Friesland, The Netherlands

For a long time, agricultural areas had considerable ornithological value, an ecological richness which in The Netherlands was epitomised by the term ‘meadow birds’. However, over the last half century, agricultural intensification has negatively affected the quality of meadow bird habitats. Here we provide a quantitative characterization of agricultural habitats and their use by Blacktailed Godwits Limosa I. limosa in the south-western part of the province of Friesland, The Netherlands, in 2009, to provide a yardstick to evaluate further change. We used groundwater level, vegetation typology, relief in the landscape, the occurrence of foot drains, land use and soil characteristics such as textures and peat to describe the landscape that comprised 43 polders covering 8480 ha. We used a Principal Component Analysis to summarize landscape characteristics and find that much of the habitat variation is explained by a combination of herb richness of the vegetation, the presence or absence of foot drains and groundwater level. The modern agricultural landscape of southwest Friesland consists of 80% of uniform, intensively managed landscape with herb-poor meadows and low groundwater levels, the remaining 20% being taken by remnants of the former herb-rich meadows. The whole study area was searched weekly and Black-tailed Godwits were mapped between arrival and egg-laying. The positive relationship between godwit density and the first PC axis indicates that Black-tailed Godwits preferred herb-rich polders with high groundwater levels and the presence of foot drains. Soil texture was poorly correlated with godwit breeding densities for intensively managed (herb-poor) parcels, but for herb-rich meadows, soils of sandy clay loam and sandy clay harboured the highest densities of godwits. To protect Black-tailed Godwits, areas should have a herb-rich vegetation, contain foot drains and high groundwater tables should be re-established.
Modeling Demographic Response to Constant Temperature in Bryobia rubrioculus (Acari: Tetranychidae)

The demographic parameters of brown mite, Bryobia rubrioculus Scheuten were carried out in order to characterize the population growth potential at five constant temperatures: 20, 22.5, 25, 27.5 and 30 o C, 60 ± 5 % RH and 16: 8 (L: D) h. The highest intrinsic rate of natural increase ( r m = 0.0243/day), net reproductive rate ( R 0 = 2.4 ♀/♀/T) and finite rate of increase (λ = 1.0245 day -1 ) values were determined at 22.5°C. The mean generation time (T) of the population ranged from 22.7 days at 30°C to 45.8 days at 20°C. The maximum and minimum survival rates ( l x ) were recorded at 22.5oC and 30oC. Survivorship data ( lx ) of adult females were summarized and compared using the shape and scale parameters of the Weibull frequency distribution model across. The age specific fecundity data ( m x ) was modeled as a function of time by using Polynomial model. The lower temperature threshold ( t ) and thermal constant ( k ) of the immature stages were estimated using Ikemoto and Takai linear model to be 12.85 o C and 279.7 degree days (DD), respectively. Of the non-linear models, the Analitis-1, Analitis-2, Analitis-3 and Analitis/Allahyari models were found to be the best for the modeling development rate of immature stages of B. rubrioculus . The optimal temperature for population growth of brown mite on apple was found at 22.5°C.
Yield of willow (Salix spp.) grown in short rotation coppice mixtures in a long‐term trial

Salix spp. genotypes were grown in random intimate mixtures comprising 5, 10, 15 and 20 components at 3 planting densities (10 000, 15 000 and 20 000 cuttings ha−1). Planted in 1994/95, plots were harvested every 3 years in 1998/99 (previously reported), 2001/02, 2004/05 and 2007/08. Each individual stool in both mono- and mixture plots was weighed. The total yield from mixture plots was consistently higher than the mean of the components in mono-plots and with only limited exceptions higher than the yield of any of the individual components grown in mono-plots. This occurred despite the loss of a number of disease-susceptible genotypes. When a stool died the remaining plants were able to colonise the vacant space and compensate for the loss. There was no clear benefit in increasing the number of components from 10 to 15 or 20 although host diversity is considered to be an important contributor to the effectiveness of a mixture both in disease reduction and yield enhancement. It is argued that the use of Salix spp. mixtures is highly advantageous, even in the absence of any disease pressure, and that mixtures increase the sustainability of a willow plantation.
An eight-year retrospective analysis of laparoscopic surgery for endometriosis, outcomes and complications in a large multicenter unit

Endometriosis is a chronic, inflammatory condition caused by deposits of endometrium-like tissue outside the uterus. Estimates of prevalence are between 2-10% of the female population and in up to 50% of women with fertility issues [1]. The most commonly reported symptom of endometriosis is pain, be it dysmenorrhea, pelvic pain unrelated to menstruation or dyspareunia and while deep infiltrating endometriosis can be diagnosed on ultrasound or magnetic resonance imaging, superficial or peritoneal endometriosis cannot [2]. The most recent European Society of Human Reproduction and Embryology (ESHRE) guidelines, published in 2014, outlining the recommended management of endometriosis, advise that when diagnosed on laparoscopy, clinicians should treat endometriosis and that excision of the lesions is preferred [1]. A review published in 2012, suggests that in women with deep infiltrating endometriosis who have undergone rectovaginal surgery, more than 85% of women have complete resolution of their pain symptoms, and the rate of spontaneous conception is up to 60% [3, 4]. Surgery for deep lesions is effective for treatment of pain but has a higher complication rate [1]. A study by Kondo et al. [5] reported that the intraoperative complication rate for excision of deep infiltrating endometriosis was as high as 2.1%, with a 2.3% rate of conversion to laparotomy. The aim of this study was to evaluate the surgical outcomes and complications rates of endometriosis related laparoscopic surgery in a multicenter tertiary referral health service over a period of eight years. The authors wanted to observe the differences in characteristics, complications, and outcomes for different stages of endometriosis, comparing American Society for Reproductive Medicine (ASRM) stage 1-2 and ASRM stage 3-4.
IκB Kinase Is a Critical Regulator of Chemokine Expression and Lung Inflammation in Respiratory Syncytial Virus Infection

ABSTRACT Respiratory syncytial virus (RSV) is the major etiologic agent of severe epidemic lower respiratory tract infections in infancy. Airway mucosal inflammation plays a critical role in the pathogenesis of RSV disease in both natural and experimental infections. RSV is among the most potent biological stimuli that induce the expression of inflammatory genes, including those encoding chemokines, but the mechanism(s) that controls virus-mediated airway inflammation in vivo has not been fully elucidated. Herein we show that the inoculation of BALB/c mice with RSV results in rapid activation of the multisubunit IκB kinase (IKK) in lung tissue. IKK transduces upstream activating signals into the rate-limiting phosphorylation (and proteolytic degradation) of IκBα, the inhibitory subunit that under normal conditions binds to the nuclear factor (NF)-κB complex and keeps it in an inactive cytoplasmic form. Mice treated intranasally with interleukin-10 or with a specific cell-permeable peptide that blocks the association of the catalytic subunit IKKβ with the regulatory protein NEMO showed a striking reduction of lung NF-κB DNA binding activity, chemokine gene expression, and airway inflammation in response to RSV infection. These findings suggest that IKKβ may be a potential target for the treatment of acute or chronic inflammatory diseases of the lung.
Soay Sheep: Dynamics and Selection in an Island Population

T. Clutton-Brock, J. Pemberton(eds.). 2004. Soay Sheep: Dynamics and Selection in an Island Population. Cambridge University Press, Cambridge University, United Kingdom, 383 pp. ISBN 0-521-82300-5, price (hardcover), $120.00; ISBN 0-521-52990-5, price (paper), $50.00. Twenty-five authors have collaborated remarkably on a 383-page volume with 10 chapters and 3 appendices about once-domestic sheep living freely on an island without human manipulation or predators. St. Kilda lies beyond the Outer Heberides off the northwestern coast of Scotland and consists of an archipelago, including a group of 4 main islands that were once inhabited by humans. In 1930, human occupancy of St. Kilda ended, and domestic sheep from the island of Soay, a 99-ha island where the earliest breeds of sheep were introduced 3,000–4,000 years ago, were brought to another island in the archipelago, Hirta. The sheep were released on Hirta in 1932 to maintain the natural grasslands through grazing, and population expansion was unobstructed until …
Inheritance of resistance to the Papaya ringspot virus-watermelon strain (PRSV-W) from watermelon accession 'PI 595201'

Two watermelon genotypes were used as parental in crosses designed to study the inheritance of resistance to PRSV-W: the cultivar Crimson Sweet (susceptible) and the accession 'PI 595201'(resistant). Plants of the generations P1, P2, F1, F2, BC11 e BC12 were inoculated with a Brazilian isolate of PRSV-W and were evaluated by recording symptoms. Genetic and phenotypic parameters of PRSV-W resistance were estimated and tests based on hypothesis of monogenic inheritance and maximum likelihood methods were performed. The additive component [a] of resistance was higher than the non-additive [d]. The estimates of the broad-sense heritability (0.80) and of narrow-sense heritability (0.67) indicated that the genetic variance was greater than the environmental, allowing higher genetic gains in selecting more resistant plants in segregating populations. The inheritance is more complex than a typical monogenic inheritance. The importance of the additive genetic effects in the expression of resistance to PRSV-W was evidenced.
Spectral fluorometric characterization of Haptophyte dynamics using the FluoroProbe: an application in the eastern English Channel for monitoring Phaeocystis globosa

In this study, we examined the possibility of using the FluoroProbe for monitoring the dynamics of the Haptophyte Phaeocystis globosa in the coastal waters of the eastern English Channel. The FluoroProbe was recalibrated by recording a new fingerprint for P. globosa and the use of this new fingerprint was tested through a series of laboratory and in situ experiments. The annual dynamics of P. globosa estimated using the FluoroProbe and by flow cytometry were similar. A strong relationship was found between the FluoroProbe estimates of P. globosa biomass expressed in terms of chlorophyll a equivalent per litre (eq. m gL 21 ) and flow cytometric cell counts (r ¼ 0.889, P , 0.001, n ¼ 121). The FluoroProbe can be used to detect the flagellated cells as well as the colonial cells of P. globosa but not to distinguish these two cell types in mixed assemblages. The use of the new fingerprint recorded for P. globosa improved the detection of Isochrysis sp . T his suggests the possibility of using the FluoroProbe to monitor Haptophytes other than P. globosa by calibrating the device with species representative of the region of interest. However, it is important to note that the detection of P. globosa at the species level was possible in the eastern English Channel because it was the only Haptophyte species present with a biomass sufficient to be detected by the FluoroProbe. In areas where several Haptophyte species are simultaneously present, their discrimination will be impossible and in such situations the FluoroProbe can be used to monitor the dynamics of the combined Haptophyte group.
Comparison of Escherichia coli Levels Between Bivalve Mollusc Species across Harvesting Sites in England and Wales

ABSTRACT Filter-feeding molluscan shellfish (oysters, mussels, clams, and so forth) are grown in areas classified for sanitary quality under EU Regulation 854/2004 on the basis of Escherichia coli monitoring. Rationalizing monitoring programs through use of a single-indicator shellfish species, rather than monitoring several species, has the benefit of reducing cost. To protect public health, the indicator must show an equivalent or higher level of contamination than the species it represents. This study, using a well-established statistical method (Bland-Altman method comparison) on routine monitoring data, demonstrates that the contamination ratio between species at the same site may change across the range of contamination levels. Nevertheless, an accumulation ordering was established as follows: The common cockle Cerastoderma edule, Tapes philippinarum (Manila clam), and Mytilus spp. (mussels) are broadly equivalent, and each shows a greater level of accumulation than the oysters Crassostrea gigas (Pacific oyster) and Ostrea edulis (native oyster), which both accumulate to a similar extent. Last, Ostrea edulis shows a greater level of accumulation than Mercenaria mercenaria (American hard clam). The data suggest that the use of Mytilus spp. may alone provide an adequate index of fecal pollution impacting the growing areas in England and Wales.
The relationship between sperm morphometry and sperm competition in local goats of Central Java, Indonesia.

The objective of this study was to examine the relationship between sperm morphometry and sperm competition in local goats. Forty bucks were used in this study, consisted of 4 breeds namely Ettawa Grade Goat (EGG), Kejobong Goat (KJG), Kacang Goat (KCG), and Jawarandu Goat (JWG), each breeds consisted of 10 bucks. GLM, REG and DISRCRIM procedures of SAS were used to compute all data observed. UPGMA of MEGA 5 was used to illustrate the genetic distance among breeds. The result showed that there were differences in the sperm morphometry among 4 breeds of goats (P<0.05). Sperm length positively related to the level of sperm competition in all local goats (P<0.05) although the value of coefficient of determinant was low (r2= 0.0043). Within breed analysis showed that there was no positive relationship between sperm length and level of sperm competition in EGG and JWG goats. Midpiece area positively related to the principal piece (P<0.05). Sperm morphometry had a significant positive relation to sperm competition in local goats of Central Java.
THE ROLE OF EPIGENETICS IN TRANSCRIPTIONAL REGULATION OF FXR AND SILENCING FXR EXPRESSION IN HUMAN COLON CANCER

iii Acknowledgements. v List of Figures and Legends. xv List of Abbreviations. xvii Chapter 1: Introduction and Background. 1 1.1: Introduction to Farnesoid X Receptor. 1 1.1.1: Role of FXR in the enterohepatic circulation of bile acids. 4 1.1.2: Role of FXR in lipid and glucose metabolism. 9 1.1.3: Targeting FXR for pharmacotherapy. 12 1.2: The Role of Epigenetic Mechanisms in Regulating Nuclear Receptor Function. 15 1.2. 1: Overview of histone modifications associated with active/repressed gene transcription. 16 1.2. 2: Overview of co-factors and pioneer factors that are involved in nuclear receptor-mediated transcriptional regulation. 18 1.3: Introduction to HNF4α in Regulating Liver Homeostasis. 20
Restriction fragment length polymorphism of rDNA in the redfishes Sebastes fasciatus and S. mentella (Scorpaenidae) from the Gulf of St. Lawrence.

A restriction fragment length polymorphism (RFLP) analysis was carried out on nuclear ribosomal DNA (rDNA) of the redfishes Sebastes fasciatus and Sebastes mentella from the Gulf of St. Lawrence in an attempt to describe new molecular markers that would discriminate these two sibling species. The RFLP analysis revealed heterogeneity in the size of the repeat unit within and among individuals that is most likely the result of variation in the length of the intergenic spacer. Double digestion of rDNA with the restriction enzymes EcoRI and ScaI and subsequent hybridization with a 28S probe revealed the presence of three patterns of fragments. Two fragment groups seem to characterize S. mentella and S. fasciatus. Both fragment groups were present in several specimens, suggesting either a restriction-site polymorphism in S. mentella or a hybrid origin for these redfish. Discriminant analysis clearly differentiated all three rDNA patterns. Comparisons of genetic variations at the MDH* locus and of the number of.
Evaluation of Peanut Flour Fermented with Lactic Acid Bacteria as a Probiotic Food

The aim of this study was to evaluate the probiotic value of peanut flour fermented with lactic acid bacteria in vitro and in vivo. Four strains including Lactobacillus delbrueckii LD09, Lactobacillus casei LC35, Lactobacillus acidophilus LA51, and Lactobacillus plantarum P9 were screened for their growth and survival in peanut flour. Among all the strains, L. plantarum P9 grew to the highest cell population (9.48 log cfu/g) in peanut flour after 72 h fermentation at 37°C. After 28 days storage at 4°C, no marked change in the viable count of this strain was observed. Peanut flour fermented with L. plantarum P9 could also increase the content of crude protein and the degree of protein hydrolysis. In an in vitro system, the addition of protein from the fermented peanut flour greatly enhanced the survival of L. plantarum P9 in simulated gastric and bile juices. In vivo studies, supplementation with the fermented peanut flour in the diet of mice increased significantly the number of lactobacilli in the fecal samples compared to the control group. At the same time, the number of enterobacteria decreased significantly. These results indicated that peanut flour fermented with L. plantarum P9 strain could be a novel type of probiotic food.