Miracle-dz/UniFAR-FTUs huggingface dataset:
Site-directed Spin Labeling Study of Subunit Interactions in the α-Crystallin Domain of Small Heat-shock Proteins

Site-directed spin labeling was used to investigate quaternary interactions along a conserved sequence in the α-crystallin domain of αA-crystallin, heat-shock protein 27 (HSP 27), and Mycobacterium tuberculosis heat-shock protein (HSP 16.3). In previous work, it was demonstrated that this sequence in αA-crystallin and HSP 27 forms a β-strand involved in subunit contacts. In this study, the symmetry and geometry of the resulting interface were investigated. For this purpose, the pattern of spin-spin interactions was analyzed, and the number of interacting spins was determined in αA-crystallin and HSP 27. The results reveal a 2-fold symmetric interface consisting of two β-strands interacting near their N termini in an antiparallel fashion. Remarkably, subunit interactions along this interface persist when the α-crystallin domains are expressed in isolation. Because this domain in αA-crystallin forms dimers and tetramers, it is inferred that interactions along this interface mediate the formation of a basic dimeric unit. In contrast, in HSP 16.3, spin-spin interactions are observed at only one site near the C terminus of the sequence. Furthermore, cysteine substitutions at residues flanking the N terminus resulted in the dissociation of the oligomeric structure. Analysis of the spin-spin interactions and size exclusion chromatography indicates a 3-fold symmetric interface. Taken together, our results demonstrate that subunit interactions in the α-crystallin domain of mammalian small heat-shock proteins assemble a basic building block of the oligomeric structure. Sequence divergence in this domain results in variations in the size and symmetry of the quaternary structure between distant members of the small heat-shock protein family.
Dietary effects on the composition of pig slurry and on the plant utilization of pig slurry nitrogen

The composition of animal manure is influenced by the diet fed. Efforts are made to decrease nitrogen emission from pig production by optimizing diet composition. This normally results in a lower proportion of N excreted in urine relative to faeces, and may also influence the turnover and utilization of manure N after field application. The effects of pig feed composition on the excretion of urinary and faecal N, on the dynamics of manure N in soil and on the potential utilization of manure N in the field was studied. Growing pigs and sows were fed 12 different diets with variable contents of fibre and protein (with or without synthetic amino acids). Slurries consisting of a mixture of faeces and urine were stored according to common agricultural practice in Northern Europe. The plant availability of N in the resultant slurries originating from animals fed known diets was tested in small field plots with barley, under conditions with minimal N losses. Separate plots were fertilized with increasing amounts of mineral N. Nitrogen uptake in barley was determined and the utilization of slurry N was compared with that of mineral fertilizer N. The net release of mineral N and C from the slurries in soil was also measured in a parallel incubation study. The mineral fertilizer equivalent of pig slurry N was 72–100% and significantly influenced by feed fibre composition, but not significantly influenced by the protein content. There was a significant positive correlation between enzyme-digestible organic matter in the pig diet (measurement used for feed evaluation) and the plant availability of pig slurry N (R2=0·90). The ammonium content of stored pig slurry could not be used for prediction of the N availability since the net mineralization of pig slurry N was variable, but there was a significant negative correlation between the pig slurry C/N ratio and the plant availability of slurry N (R2=0·86). Increased dietary concentration of fermentable structural carbohydrates (e.g. by including sugar beet pulp in the diet) reduces the excretion of N in urine without affecting the availability of slurry total N, whereas an increased concentration of dietary fibre with a low fermentability (straw) results in less urinary N, but also a lower plant availability of slurry N.
Systematic revision of the genera Chalinus Konow, 1897 and Mocsarya Konow, 1897 (Hymenoptera: Orussidae)

The genera Chalinus Konow and Mocsarya Konow are revised. Eight species are recognised in Chalinus: C. berlandi Guiglia, C. braunsi (Enslin), C. haugi du Buysson, C. imperialis (Westwood), C. orientalis Guiglia, C. purpureiventris Cameron, C. somalicus Guiglia, C. timnaensis Kraus. Chalinus balianii Guiglia is proposed as a new synonym of C. berlandi Guiglia, C. schulthessi Guiglia as a new synonym of C. braunsi (Enslin), and the synonymy of C. congoensis Guiglia with C. imperialis (Westwood) is reestablished. Two species are recognised in Mocsarya: M. metallica (Mocsary); M. syriaca Benson. Two nominal species, Oryssus oberthueri Saussure and Oryssus plumicornis Guerin-Menneville are treated as species inquirendae in Chalinus. Keys, redescriptions and distribution maps are provided for all recognised species.
A Phylogeny for the African Restionaceae and New Perspectives on Morphology’s Role in Generating Complete Species Phylogenies for Large Clades

Difficulties with obtaining complete species‐level phylogenies include (1) the accurate identification and sampling of species, (2) obtaining a complete species sampling, and (3) resolving relationships among closely related species. We addressed these in a study of 317 species and subspecies of the African Restionaceae. Accurate species identification and collection in the field was facilitated by a morphology‐based interactive key to all species. Despite intensive fieldwork, however, material for DNA extraction could not be obtained for 20 of the 292 species of the focal Restio subclade. Furthermore, the 6831 aligned nucleotides and 1685 parsimony‐informative sequence characters were insufficient to resolve relationships fully within the clade. A simulation indicated that an additional 5000–7000 bases may have been needed to achieve supported resolution in the neighborhood of 95%–100%. Instead of further sequencing, we investigated the phylogenetic utility of the large set of characters contained within the interactive key data set, exploiting recent advances in parsimony and Bayesian programs that allow multistate and supermultistate (including continuous for parsimony) morphological characters. On doing so, parsimony resolution increased 17% to nearly 100%, and overall support increased in both parsimony (bootstrap) and Bayesian (posterior probability) frameworks. Taxa for which DNA data were lacking could be placed in fully resolved positions. Experiments using the parsimony ratchet indicated that placement of these morphology‐only taxa may have been completely accurate 30% of the time, to within three nodes of accuracy 60% of time, and accurate to genus 96% of the time. Accurate placement of morphology‐only taxa through Bayesian analysis may require extensive effort devoted toward exploring tree and parameter space. We conclude that the increasingly available large morphological data sets associated with interactive keys or informatics initiatives represent convenient yet potentially powerful tools in overcoming many of the commonly encountered obstacles in molecular‐based species‐level phylogenetics.
Foraging Habits and Habitat Use by Edible-nest and Glossy Swiftlets in the Andaman Islands, India

Abstract Foraging habits and habitats of exclusive aerial insectivores, the Edible-nest Swiftlet (Aerodramus fuciphagus inexpectatus) and Glossy Swiftlet (Collocalia esculenta affinis), were studied in Andaman Islands, India. Observations were made during January to June 2004 between 0500 and 1800 hrs at four locations in the forest and on open paddy land. Edible-nest and Glossy swiftlets, respectively, spent (x¯ ± SD) 17.2 ± 11.4% and 25.8 ± 15.6% of their time foraging with significant temporal variations. Glossy Swiftlets had spatial variations in twist, flutter, and tail-wing-open foraging maneuvers. This species also had diurnal variations in flock size, which were positively correlated with feeding attempts. Both swiftlets shared all microhabitats except Inside Forest Canopy and Inside Stream Bank Canopy. Microhabitat use did not vary significantly in Below Stream Bank Canopy, >10 m Above Forest Canopy, >30 m Above Ground, and Above Forest Canopy for Edible-nest Swiftlets. Inside Forest Canopy and Inside Stream Bank Canopy categories for Glossy Swiftlets were relatively important in descending order. Deforestation near and distant from caves used by swiftlets for breeding in the islands can severely affect the wild population of both species.
Parasite–host elemental content and the effects of a parasite on host-consumer-driven nutrient recycling

Abstract. Parasites are ubiquitous members of ecological communities but have only recently been recognized as key players in broader interactions and ecosystem dynamics, such as foodweb structure and energy flow. Ecological stoichiometry provides a framework for placing parasites in an ecosystem perspective by considering elemental imbalances and their consequences. I measured the elemental content of trematodes and their gastropod hosts and then estimated the nutrient-recycling effects of parasitism. N∶P of all tissue types in trematodes of the freshwater pulmonate snail, Physa acuta, was similar to N∶P of gastropod gonadal tissue. However, N∶P of trematodes and gastropod gonads was lower than N∶P of other gastropod tissues, a result suggesting an elemental imbalance between parasite and host. N∶P of excreta of P. acuta increased with the N∶P content of their algal food, consistent with consumer-driven nutrient recycling theory. However, gastropods with patent infections of Trichobilharzia physellae excreted greater N∶P than did uninfected snails, a result indicating that infected and uninfected gastropods were functionally different. Overall, these results suggest a significant role for parasites in nutrient recycling.
Reproductive effort and blood parasites of breeding pied flycatchers: the need to control for interannual variation and initial health state

The association between reproductive effort, as assessed by experimentally altered clutch size, and prevalence of blood parasite infections was studied during two breeding seasons in the pied flycatcher (Ficedula hypoleuca). Only in the first study year (1998), enlarged clutches resulted in more fledged young and birds presumably responded to the intended experimental increase in reproductive effort by increasing their provisioning rates. Only on this study year, female body mass was negatively affected by the clutch size manipulation. For both sexes, no significant effect of experimental treatment on the prevalence of blood parasite infections (Trypano soma spp., Haemoproteus balmorali) on day 13 after chick hatching was found in both study years. However, only in the first study year, when the intended increase in parental reproductive effort was achieved, we found a higher within female seasonal increase in Trypanosoma spp. prevalence for birds with enlarged clutches compared to those with control and reduced clutches. In this year, the Trypanosoma spp. prevalence was significantly higher than in the second study year. These results suggest that more than one year has to be covered, and that the knowledge of the premanipulative health status of parents can facilitate detection of the proposed trade-off between reproductive effort and immunocompetence.
The potato leafhopper (Homoptera: Cicadellidae) exhibits different settling distributions on alfalfa and broad bean.

The settling behavior of the potato leafhopper, Empoasca fabae (Harris), was studied on broad bean, Vicia faba L. , and on alfalfa, Medicago sativa L. When caged on broad bean, potato leafhoppers were evenly distributed between stems and abaxial surfaces of leaves. Use of abaxial leaf surfaces was very similar to what was expected based upon the relative availability of leaf surface area. In contrast, use of stems was much greater than their relative availability, suggesting a preference for settling on this site. Leafhoppers caged on alfalfa also preferred stems, but avoided abaxial leaves. However, we could not relate severity of damage symptoms to the proportion of time spent settled on alfalfa stems or leaves. These results show that the leafhoppers exhibited different settling behavior on the two hosts, and thus, the variability in feeding behavior reported in other studies extends also to settling behavior.
Leaf Essential Oils of the Queensland Species of Phebalium (Rutaceae: Boronieae)

Abstract The leaf oils of the eight Queensland specific and subspecific taxa of Phebalium have been examined. Phebalium distans produced a variable oil, with α-pinene (0.8–42%) being the most abundant prominent monoterpene and bicyclogermacrene (12–22%) as the most significant sesquiterpene. In P. glandulosum subsp. glandulosum by far the major component is dihydrotagetone (75–95%). β-Caryophyllene (9–20%) and bicyclogermacrene (7–23%) were the major components of P. longifolium. In P. nottii the principal monoterpene detected was α-pinene (25–42%), while the principal sesquiterpenes detected were guaiol (t-28%) and bulnesol (nil to 34%). The two monoterpene hydrocarbons, α-phellandrene (12–25%) and β-phellandrene (14–15%), together with bicyclogermacrene (2–12%), elemol/hedycaryol (12–36%) were major components in the leaf oil of P. squamulosum subsp. squamulosum, while in P. squamulosum subsp. gracile, geijerene (4–8%) was present together with α-pinene (44–50%) and guaiol (9–11%). The leaf oil of P. whitei contained α-pinene (22–42%), limonene (1–12%) and bicyclogermacrene (11–20%) as major components. In P. woombye the main components were α-pinene (10–21%), β-phellandrene (12–20%), bicyclogermacrene (11–20%) and germacrene D (5–10%).
Prymnesium parvum Population Dynamics During Bloom Development: A Role Assessment of Grazers and Virus 1

Schwierzke, Leslie, Daniel L. Roelke, Bryan W. Brooks, James P. Grover, Theodore W. Valenti, Jr., Mieke Lahousse, Carrie J. Miller, and James L. Pinckney, 2010. Prymnesium parvum Population Dynamics During Bloom Development: A Role Assessment of Grazers and Virus. Journal of the American Water Resources Association (JAWRA) 46(1):63‐75. DOI: 10.1111/j.1752‐1688.2009. 00391.x
Home Range, Habitat Selection, and Movements of California Black Rails at Tidal Marshes at San Francisco Bay, California

Abstract. Little is known about the movements and habitat selection of California Black Rails (Laterallus jamaicensis coturniculus) in coastal California. We captured 130 Black Rails, of which we radio-marked 48, in tidal marshes in San Francisco Bay during 2005 and 2006. Our objective was to examine their home ranges, movements, and habitat selection to improve the species' conservation. The mean fixed-kernel home range was 0.59 ha, the mean core area was 0.14 ha. Home ranges and core areas did not differ by year or site. Males had significantly larger home ranges and core areas than did females. All sites combined, Black Rails used areas with ≥94% total vegetative cover, with perennial pickleweed (Sarcocornia pacifica) the dominant plant. The rails' habitat selection varied by year and site but not by sex. A multivariate analysis of variance indicated that Black Rails selected areas with pickleweed taller and denser than average, greater cover and height of alkali bulrush (Bolboschoenus maritimus) and common saltgrass (Distichlis spicata), more stems between 20 and 30 cm above the ground, maximum vegetation height, and shorter distance to refugia. On average, Black Rails moved 27.6 ±1.8 (SE) m daily and 38.4 ± 5.5 m during extreme high tides. Understanding the California Black Rail's movements, home range, and habitat use is critical for management to benefit the species.
Before Watson and Crick in 1953 Came Friedrich Miescher in 1869

The story of genetics typically omits the original discovery of the molecular nature of DNA: Friedrich Miescher's 1869 discovery of the substance he christened “nuclein”. The article explains how he came. In 1869, the young Swiss biochemist Friedrich Miescher discovered the molecule we now refer to as DNA, developing techniques for its extraction. In this paper we explain why his name is all but forgotten, and his role in the history of genetics is mostly overlooked. We focus on the role of national rivalries and disciplinary turf wars in shaping historical memory, and on how the story we tell shapes our understanding of the science. We highlight that Miescher could just as correctly be portrayed as the person who understood the chemical nature of chromatin (before the term existed), and the first to suggest how stereochemistry might serve as the basis for the transmission of hereditary variation.
Questions

Project Goal: In this process we propose to improve an existing practice: the facility tour. Almost all design projects involve some kind of tour, ranging from seeing comparable facilities across town to multiple national visits. However, current site visits often fall short. While a national tour can cost a design team $50,000 or more in expenses and salaries, participants too often lack the information that allows them to pick the best sites for their purposes, lack support about research and issues as they visit, do not get to hear from clinicians and other stakeholders, lack rigorous information about the performance of the facility they are visiting and do not have structured opportunities to discuss and evaluate what they have seen and to apply the lessons to their own designs.
Topographic Relation Between Iron-Deposition and Cytotoxic Changes in Iron Lactate-Overloaded Rats

In oder to evaluete the chronic toxicity of iron lactate, a food additive, rats consisting of ten male and ten female per group, were fed a powdered commercial diet containing 0%, 0.625%, 1.25%, 2.50% or 5.00% of iron lactate for 3 months. Main histopathologic changes were an accumulation of excess iron in the hepatocytes, renal tubular epithelial cells, macrophages in the reticuloendothelial system of liver, spleen, bone marrow, and lymph nodes. Hemosiderin-laden macrophages aggregated in the mucosal lamina propria of the stomach and the whole length of the intestinal tract, and formed small nodules without any degenerative changes in other mucosal tissue. The number of hemosiderin-laden macrophages also increased in the interstitial tissue of the testes, epididymis, and thyroid glands, but no degenerative changes were detected in cell components of these organs. A slight elevation of AST, ALT, creatinine, and blood urea nitrogen (BUN) levels in the higher dosage group suggested the toxic effect of iron overload on the function of liver and kidneys which accumulated iron deposits in their parenchymal cells. However, apparent histopathologic changes suggesting tissue damage were not clear even in the liver and kidneys, as well as in many organs infiltrated with hemosiderin-laden macrophages in the interstitium. From these results, of damage is not dependent on the amount of iron deposition.
Applicability of ASTER imagery in mapping land use /cover as a basis for biodiversity studies in drylands of northern Ethiopia

We evaluated the applicability of the Visible and Near Infrared bands (15 m spatial resolution) of the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) imagery in mapping land use/cover in the drylands of northern Ethiopia. Ground Control Points were collected from the field using Geographic Positioning System in which half of them were used for classification and the remaining for accuracy assessment. The image was classified into four dominant land use/cover types that represent the major habitats of the study site. Image classification was done using pixel-based supervised classification with the Maximum Likelihood Classification algorithm. The accuracy of classification was evaluated using error matrix and Kappa statistics. Finally, we found an overall classification accuracy of 80% and this implies that ASTER imagery can be used as a good source of data in mapping biodiversity at habitat scale in data scarce drylands of northern Ethiopia.
Design of a Tumor-Homing Cell-Penetrating Peptide

Chemotherapy is often limited by toxicity to normal cells. Therefore, an ideal anticancer drug should discriminate between normal tissue and tumors. This would require a target receptor molecule mostly present in tumors. The cyclic peptide cCPGPEGAGC (PEGA) is a homing peptide that has previously been shown to accumulate in breast tumor tissue in mice. PEGA peptide does not cross the plasma membrane per se; however, when attached to the cell-penetrating peptide pVEC, the conjugate is taken up by different breast cancer cells in vitro. Additionally, the homing capacity of the PEGA-pVEC is conserved in vivo, where the conjugate mainly accumulates in blood vessels in breast tumor tissue and, consequently is taken up. Furthermore, we show that the efficacy of the anticancer drug, chlorambucil, is increased more than 4 times when the drug is conjugated to the PEGA-pVEC chimeric peptide. These data demonstrate that combining a homing sequence with a cell-penetrating sequence yields a peptide that combines the d.
Entry of Rhizobia into Roots of Mimosa scabrella Bentham Occurs between Epidermal Cells

SUMMARY: The nitrogen-fixing symbiosis between Mimosa scabrella and Rhizobium Br 3454 was initiated by an infection sequence consisting of (a) surface colonization of roots; (b) penetration of mucigel and primary layers of radial walls of epidermal cells; (c) further penetration through primary wall layers and intercellular air spaces; (d) occasional intracellular penetration of epidermal and cortical cells, always occurring from a boundary between two neighbouring cells. Root hairs, when present, were never seen to be infected by the well-known infection thread mechanism, nor were infections seen to occur through wounds. This newly described method of infection may be common in legumes.
COMDYN: Software to study the dynamics of animal communities using a capture-recapture approach

COMDYN is a set of programs developed for estimation of parameters associated with community dynamics using count data from two locations or time periods. It is Internet-based, allowing remote users either to input their own data, or to use data from the North American Breeding Bird Survey for analysis. COMDYN allows probability of detection to vary among species and among locations and time periods. The basic estimator for species richness underlying all estimators is the jackknife estimator proposed by Burnham and Overton. Estimators are presented for quantities associated with temporal change in species richness, including rate of change in species richness over time, local extinction probability, local species turnover and number of local colonizing species. Estimators are also presented for quantities associated with spatial variation in species richness, including relative richness at two locations and proportion of species present in one location that are also present at a second location. Applicat.