Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin Structure and Control of β-Like Globin Gene Switching

The human β-globin locus is a complex genetic system widely used for analysis of eukaryotic gene expression. The locus consists of five functional β-like globin genes, ε, Gγ, Aγ, δ, and β, arrayed on the chromosome in the order that they are expressed during ontogeny. Globin gene expression is regulated, in part, by the locus control region, which physically consists of five DNasel-hypersensitive sites located 6-22 Kb upstream of the ε-globin gene. During ontogeny two switches occur in β-globin gene expression that reflect the changing oxygen requirements of the fetus. The first switch from embryonic ε- to fetal γ-globin occurs at six weeks of gestation. The second switch from γ- to adult δ- and β-globin occurs shortly after birth. Throughout the locus, cis-acting elements exist that are dynamically bound by trans-acting proteins, including transcription factors, co-activators, repressors, and chromatin modifiers. Discovery of novel erythroid-specific transcription factors and a role for chromatin structure in gene expression have enhanced our understanding of the mechanism of globin gene switching. However, the hierarchy of events regulating gene expression during development, from extracellular signaling to transcriptional activation or repression, is complex. In this review we attempt to unify the current knowledge regarding the interplay of cis-acting elements, transcription factors, and chromatin modifiers into a comprehensive overview of globin gene switching.
Do fragmented coastal heathlands have habitat value to birds in eastern Australia

This study investigated the effects of habitat clearance and fragmentation on birds of coastal heathlands in subtropical eastern Australia. Abundance and species composition were compared among two types of cleared habitat (residential suburbs and sugar cane cropland) and four sizes of heathland remnant (1–2 ha, 5–10 ha, 20–50 ha and >500 ha) in summer and winter. Cleared land contained a distinctly different bird species assemblage from heathland remnants. Residential sites contained a distinct suite of species consistent with that described for ‘open/developed land’ habitat elsewhere in the region. In contrast, cane cropland supported very few species. Heathland remnants >500 ha contained high densities of ‘natural-vegetation-dependent’ species, whereas species of open/developed land were absent. Remnants of 1–2 ha had lowered densities of many natural-vegetation-dependent species, and a relatively high abundance of open/developed land species. Some of the avifaunal differences in the >500-ha remnants and 5–50-ha range are probably due to confounding of remnant size with habitat, resulting from selective clearing of the landscape. Most of the heathland birds were intolerant of the matrix habitat (residential and cane cropland), but tolerant of decreased remnant area, down to a threshold of about 5 ha. However, the distinctive floristic associations of heathland vegetation are dependent on an environmental regime (low nutrient, low pH, fire, in some cases inundation) that is unlikely to persist in remnants tens of hectares in size, and longer-term declines in heathland birds, are predicted.
The Role of Work Experience and Self-Efficacy in STEM Student Selection

The authors report the results of a three-year longitudinal study of retention among undergraduate engineering students enrolled at four major universities. The study demonstrates that self-efficacy can be a critical factor in student persistence and can be broken down into three components: work, career, and academic self-efficacy. The authors explain the relationship between two of these forms of efficacy and retention and also explore the contributing roles of gender, academic support, and work experience along with its accompanying instruction. Of note, both the quantity and quality of co-op placements in addition to efficacy and support were found to sustain collegiate persistence.
The air space and embryonic respiration

Synopsis Covering the whole shell or the shell over the chorio‐allantoic membrane with liquid paraffin resulted in the diffusion of oxygen through the shell over the air space before the onset of pulmonary respiration being reduced to a level insufficient to keep the embryo alive. During the parafoetal period respiratory exchange through the air space becomes progressively more important than that through the allantois with the result that the embryo can survive a blocking of the whole shell or allantoic shell during this period, provided that pulmonary respiration has been developed sufficiently and that the shell is pipped within a certain time limit. After pipping respiratory exchange can be effected by pulmonary respiration alone, without great danger to the embryo. It was found that diffusion through the shell over the air space could be abolished, by a covering of liquid paraffin, for at least 2 days without causing the death of the embryo. On the other hand, increasing the gaseous exchange through .
Atlantic salmon (Salmo salar) neutrophil responses to Aeromonas salmonicida

Abstract Using in vitro assays, a comparison was made of the Atlantic salmon neutrophil responses (production of O 2 - , measured as nitroblue tetrazolium (NBT) reduction, migration and phagocytosis) to two A. salmonicida strains (strain 004, avirulent lacking A-layer, and strain 423, virulent possessing A-layer). The influence of serum, heat-inactivated serum and antibodies on these responses were also analysed. Incubation of neutrophils with bacteria induced an increase in the NBT reduction which was maximum after 60 min incubation. Live bacteria were more stimulatory than killed bacteria. Opsonisation by normal serum or heat-inactivated serum containing antibodies enhanced NBT reduction, suggesting the presence of receptors for both complement and immunoglobulin in salmon neutrophils. Bacteria opsonised with both anti-body and complement induced the highest O 2 - responses. The avirulent strain elicited greater NBT responses in neutrophils than the virulent strain. When the ratio of live bacteria:neutrophil was higher than 100:1 with strain 004 and 50:1 with strain 423, bacteria were toxic to cultured neutrophils. Killed bacteria were not toxic. Bacteria in saline induced neutrophil migration but serum was necessary for maximum migration. In the presence of normal serum, strain 004 was a more potent activator of migration than strain 423. Phagocytosis was also enhanced in the presence of normal serum, and was higher with strain 004 than with strain 423. Strain 004 was markedly more efficient at activating the alternative complement pathway than strain 423. The differences observed in the neutrophil responses to the two strains of bacteria could be related to differences in fixation of complement.
The causes of southern African spatial patterns in species richness: speciation, extinction and dispersal in the Danthonioideae (Poaceae)

Four factors (time, dispersal, extinction and speciation) shape the differences in species richness within a clade between two regions. The southern African summer‐rainfall ‘Highveld’ is less species rich than the adjacent winter‐rainfall ‘Greater Cape Floristic Region’. In many clades, this may be the result of a Cape origin of these temperate clades, with later dispersal to the cool uplands of the Highveld. We explored an alternative scenario of a widespread southern African Miocene temperate flora, which survived in the Cape. We used these four factors to seek the more likely scenario for the Danthonioideae.
Seasonal changes in the abundance and composition of picophytoplankton in relation to the occurrence of 'Kyucho' and bottom intrusion in Uchiumi Bay, Japan

Uchiumi Bay experiences intermittent physical events of 'Kyucho' and bottom intrusion. A Kyucho is an intrusion of warm surface water from the Kuroshio in the Pacific Ocean. Bottom intrusion, which contains a large amount of nitrates, phosphates, and silicates, slips through just above the continental shelf. We investigated seasonal changes in the abundance of Prochlorococcus, Syne- chococcus, and eukaryotic picophytoplankton while monitoring Kyucho and bottom intrusion from March to October 2002. Kyucho and bottom intrusion frequently occurred from June to September. Relatively high concentrations of nitrate + nitrite (>0.8 µmol N l -1 ) and phosphate (>0.1 µmol P l -1 ) were found when bottom intrusion occurred. The cell densities of Prochlorococcus were relatively high (>1 × 10 4 cells ml -1 ) when Kyucho occurred. Those of Synechococcus were high (2 to 30 × 10 4 cells ml -1 ) during the period of thermal stratification except in July, when bottom intrusion occurred. The cell densities of eukaryotic picophytoplankton were high (2 to 8 × 10 4 cells ml -1 ) in May and July. To examine the effects on picophytoplankton growth of the nutrients supplied by bottom intrusion, we conducted nutrient-enrichment experiments. The growth rates of Prochlorococcus and Synechococcus were not stimulated by the addition of any kinds of nutrients. The growth rates of Prochlorococcus were negative in most cases. In July, the growth rate of eukaryotic picophytoplankton was stimulated by nitrate and phosphate additions. Thus, Prochlorococcus detected in Uchiumi Bay might have been transported by Kyucho from the Pacific Ocean and could therefore not grow vigorously. Synechococ- cus may have been flushed out by bottom intrusion, and its growth was not limited by the nutrient con- centrations. Eukaryotic picophytoplankton was abundant in spring, and its growth might have been limited by the nutrient concentrations in some cases. These results suggest that Kyucho and bottom intrusion have different effects on the abundance and growth rate of the 3 picophytoplankton groups.
Parentage analysis of international spring wheat yield nurseries 17 to 27

Breeders can increase genetic diversity by selecting lines with novel parentage from international nurseries. A database program, WCOP, an application of the International Center for Maize and Wheat Improvement (CIMMYT) Wheat Pedigree Management System (WPMS), calculated the coefficient of parentage (COP) among cultivars and was used to study 169 wheats from the International Spring Wheat Yield Nurseries (ISWYN) No.17 to 27, and a set of 27 reference cultivars. The average COP (excluding similarity values of cultivars with themselves) among the 196 lines was 0.14. The similarity between the ISWYN cultivar group and the reference cultivar group was 0.08. Average internal COP values for U.S.-Canadian, Australian, and ISWYN sets were 0.18, 0.30, and 0.14, respectively. The ISWYN cultivars were clustered by means of COP values into genealogically similar groups. The largest ISWYN clusters were divergent from U.S., Canadian, and Australian standard spring cultivars. The clusters highlight divergent germplasm that may broaden the genetic base of breeding programs in temperate zones.
Green leaf volatiles disrupt and enhance response by the ambrosia beetle, Gnathotrichus retusus (Coleoptera: Scolytidae) to pheromone-baited traps

Experiments were conducted to test the null hypothesis that green leaf volatiles, abundant in herbaceous plants and angiosperm trees, have no effect on the response by the conifer-infesting ambrosia beetle, Gnathotrichus retusus (LeConte), to pheromonebaited traps. A blend of four green leaf alcohols, 1-hexanol, (E)-2-hexen-1-ol, (Z)-2-hexen-1-ol, and (Z)-3-hexen-1-ol, each released at ca. 4 mg per 24 h, combined with a blend of two green leaf aldehydes, hexanal and (E)-2-hexenal, each released at ca. 13.0 mg per 24 h, reduced catches of females to levels not significantly different from those in unbaited control traps. Any of the four green leaf alcohols released alone disrupted responses of females, while 1-hexanol and (E)-2-hexen-1-ol strongly reduced catches of males. The two green leaf aldehydes released together, and (E)-2-hexenal released alone, weakly enhanced trap catches. These results lead to rejection of the null hypothesis on the basis of both positive and negative effects. Disruptive green leaf volatiles may have promise as forest product protectants against ambrosia beetles, by disguising hosts as non-hosts.
Determination of the presence of Babesia species in blood samples of cattle, camel and sheep in Iran by PCR

Babesia species are protozoan parasites that parasitize the erythrocytes of domestic animals and humans, causing anemia in the host. The parasites cause a zoonotic disease known as babesiosis. Polymerase chain reaction (PCR) has proven to be very sensitive for detecting Babesia in blood samples of affected animals, particular in ruminants. The purpose of the current study was to determine the presence of Babesia spp. in blood samples obtained from 2 cattle, camel and sheep in Iran. In addition, the study aimed at establishing a rapid, reliable, specific and sensitive molecular tool, the polymerase chain reaction (PCR), for the detection of Babesia spp. in ruminants. Blood samples were collected from 372 ruminants (155 cattle, 95 sheep and 122 camel) kept at the Livestock Experimental Station. The animals came from randomly selected herds located in the important livestock-production regions of Iran of Isfahan and Chaharmahal va Bakhtiary during December 2012 to March 2013. PCR was used to detect Babesia spp. in the blood samples whereby an amplified band size of 428 bp was considered positive for Babesia spp. The results show that 7.10% (n= 155), 6.56% (n= 122) and 0.00% (n= 95) of the blood samples from cattle, camel and sheep, respectively, were positive for Babesia spp. The findings from this study revealed that there were Babesia spp. in blood taken from cattle and camel. To our knowledge, this is the first report to show the presence of Babesia spp. in blood samples of Iranian ruminants in Chaharmahal Va Bakhtiari and Isfahan provinces by PCR. These findings justify the importance of control of and eradication plans for Babesia spp. infection in cattle and camel in Iran. As diagnosis of low-level infections by the parasite is important for epidemiological studies, our findings support the power of PCR test for Babesia spp. detection in blood samples and could be easily used for routine diagnosis.
Chlorobenzene, Addendum [BAT Value Documentation, 2010]

The BAT values for chlorobenzene were established in 1992. They were 300 mg total 4-chlorocatechol/g creatinine in the post-shift urine, and 70 mg total 4-chlorocatechol/g creatinine in the urine at the beginning of the next shift. As a result of the limited database, these values were to be regarded as provisional at that point. In the context of more recent findings, a reduction of the MAK value from 50 ppm to 10 ppm (Greim 1995) was made in 1995. A re-evaluation of the BAT value has become necessary as a result of this reduction in the MAK value. At the same time, more recent studies are to be taken into account (Kusters and Lauwerys 1990; Yoshida et al. 1986; Kumagai and Matsunaga 1995; Knecht and Woitowitz 2000). The data on metabolism and kinetics as well as on critical toxicity are to be taken from the earlier BAT documentation.
Back to Front Coach Learning - Reflections on the final study:Epistemological Chaining across the Talent Pathway

This study explored the existence, application, and coherence of the epistemological chain (EC) construct across a British sport’s talent pathway. The high performance director, six National coaches, and 12 players from the pathway were recruited. We employed qualitative methodology to gain understanding of participants’ perceptions and application of the pathway elements. We analysed behavioural differences between coaching levels with reference to an inter coach EC of decision making. Results suggest an inter coach EC present within the talent pathway. Interesting issues arise regarding the ‘3 C’s’ of consistency, clarity, and coherence which appear to be related to the efficacy of the pathway.
Diversity and Complexity

This book provides an introduction to the role of diversity in complex adaptive systems. A complex system--such as an economy or a tropical ecosystem--consists of interacting adaptive entities that produce dynamic patterns and structures. Diversity plays a different role in a complex system than it does in an equilibrium system, where it often merely produces variation around the mean for performance measures. In complex adaptive systems, diversity makes fundamental contributions to system performance. Scott Page gives a concise primer on how diversity happens, how it is maintained, and how it affects complex systems. He explains how diversity underpins system level robustness, allowing for multiple responses to external shocks and internal adaptations; how it provides the seeds for large events by creating outliers that fuel tipping points; and how it drives novelty and innovation. Page looks at the different kinds of diversity--variations within and across types, and distinct community compositions and interaction structures--and covers the evolution of diversity within complex systems and the factors that determine the amount of maintained diversity within a system.Provides a concise and accessible introduction Shows how diversity underpins robustness and fuels tipping points Covers all types of diversity The essential primer on diversity in complex adaptive systems
RETENTION AND TRANSPORT OF NUTRIENTS IN A THIRD-ORDER STREAM IN NORTHWESTERN CALIFORNIA: HYPORHEIC PROCESSES'

Chloride and nitrate were coinjected into the surface waters of a third—order stream for 20 d to examine solute retention, and the fate of nitrate during subsurface transport. A series of wells (shallow pits) 0.5—10 m from the adjacent channel were sampled to estimate the lateral interflow of water. Two subsurface return flows beneath the wetted channel were also examined. The conservative tracer (chloride) was hydrologically transported to all wells. Stream water was >88% of flow in wells <4 m from the wetted channel. The lowest percentage of stream water was 47% at a well 10 m perpendicular to the stream. Retention of solutes was greater in the hyporheic zone than in the channel under summer low—flow conditions. Nominal travel time (the interval required for chloride concentration to reach 50% of the plateau concentration) was variable by well location, indicating different flow paths and presumably permeability differences in subsurface gravels. Nominal travel time was M 24 h for wells <5 m from the we.
MONITORING CHANGES IN GERMINATION AND PERMEABILITY OF BACILLUS CEREUS ENDOSPORES FOLLOWING CHEMICAL, HEAT AND ENZYMATIC TREATMENTS USING FLOW CYTOMETRY

ABSTRACT The germination inhibition of Bacillus cereus endospores and the removal of various structural components were undertaken using a number of standard treatments. Concomitantly, the changes in the entry and retention of the fluorescent nucleic acid dyes, SYTO 9, propidium iodide (PI) or Hoechst 33342, or hydrolysis of carboxyfluorescein diacetate (CFDA), were analyzed using flow cytometry (FCM) and epifluorescence microscopy. SYTO 9 and PI staining followed by FCM analysis detected six discrete subpopulations of endospores across all treatments, while CFDA/Hoechst 33342 staining allowed the identification of subpopulations of permeabilized endospores possessing intracellular esterase activity. Differential permeability to PI and Hoechst 33342 as revealed using FCM appeared related to the germination stage and the absence of specific structural components. Additionally, endospores halted at specific points during germination had characteristic FCM fluorescence profiles. This study highlighted the potential of FCM as a useful technique for rapidly studying endospore germination and structural alterations following treatment with sporistatic/sporicidal physicochemical treatments. PRACTICAL APPLICATIONS The flow cytometry methods described in this report could be used to differentiate between endospores halted at various stages of germination, e.g., those that have lost dipicolinic acid only versus those that have also begun to degrade their cortex. Furthermore, the methods could simultaneously supply information on the mechanism of action of germination inhibitors and whether or not enzyme activity (nonspecific intracellular esterase) was present in treated endospores. The method also allows the discrimination between endospores with a specific structural component removed, e.g., endospores lacking coat (highly propidium iodide [PI] permeable) versus intact endospores (impermeable to PI). An extension of this methodology would be the quantification of the percentage of endospores exhibiting structural damage, e.g., damage to the exosporium, following treatment with sporistatic/sporicidal physicochemical treatments. Indeed, using these methods, the direct examination of food, environmental or clinical samples to rapidly evaluate the viability/structural integrity of contaminating endospores is possible.
Analysis of drongo, a new Drosophila zinc finger gene expressed during oogenesis and neurogenesis.

This thesis is an investigation into the function of the drongo, a novel gene with a zinc finger motif, orignally isolated via enhancer trapping from its expresssion in the embryonic neuroectoderm. Drongo has previously been shown to be expressed during oogenesis, neurogenesis and eye development. In this project, sequencing of a Drongo cDNA clone, shows homology to human nucleoporin protein hRIP; and a lesser extent to other proteins including the mammalian ARF-l GTPase activating protein (ARF-l GAP), a protein involved in vesicular transport across the cell; and family of yeast zinc finger genes GTSI/GCSI/GL03, members of which have also recently been shown to have GAP activity. Overexpression of drongo during early oogenesis results in egg chambers with supernumary nurse cells, probably as a result of a delay in follicle cell migration; a phenotype similar to that of braniac mutants. Overexpression during late oogenesis causes a mislocalisation of Oskar, producing embryos which lacked denticle belts and which often had posterior defects, suggesting that ectopic expression of the gene at different times in development can have different consequences. A mutagenesis screen carried out generated a number of potential mutant alleles, although none as yet have identified a mutation in the drongo gene. The use of an peptide antibody to the protein on S2 cells and western blots has identified a possible localisation of the Drongo protein to the endoplasmic reticulum, suggesting a role in vesicle transport. Drongo has also been shown to be developmentally expressed and the gene appears to encode two proteins which may or may not be functionally distinct. The role of Drongo as a possible ARF GAP, are discussed.
Behaviour of gray whales (Eschrichtius robustus) summering off the northern California coast, from Patrick's Point to Crescent City

This study quantifies basic dive characteristics and behaviour patterns of undisturbed gray whales (Eschrichtius robustus) observed summering at four northern California locations: the Big Lagoon – Patrick's Point area, Orick, Klamath River mouth, and Crescent City. Observable behaviours were limited to several locomotions (swim slow, swim moderate, swim fast, and floating) seen in different behavioural contexts (milling, circling, pluming, and transit). Sixteen behaviours were observed and they fit naturally into locomotive–context categories (i.e., swim-milling, swim slow – circling, etc.). Each behaviour was described using behavioural observations and dive characteristics. Behaviours that did not appear goal oriented or directed, i.e., milling and floating, had highly variable dive characteristics. More specific behaviours, such as circling and pluming, were less variable. Some specific and less directed behaviours appeared functionally related and usually occurred together. Apparent bottom feeding wa.