Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic stability in a population of a plant pathogenic fungus over time

Collections of the plant pathogenic fungus Mycosphaerella graminicola were made from the same field of wheat over a 3‐year period. The field was planted with small plots containing four varieties of wheat grown in pure stand and in all possible two‐, three‐ and four‐way mixtures. In each year, the wheat field was recolonized by a local source of inoculum of unknown origin. Allele frequencies at 10 RFLP loci were compared at two different times within a growing season and over the 3‐year period. No significant differences in allele frequencies were found for any of the RFLP loci over any of the time periods. DNA fingerprints were used to identify clones produced by asexual reproduction. Genotypic diversity based on the frequency of each clone was compared for each collection. No significant changes in genotypic diversity were found within a year or between years. Identical genotypes were found in the field at different times within a season, but no clones were conserved between years. No clone existed in a high frequency in any year, suggesting that selection for particular asexual lineages was weak. The founding population each year probably originated from wind‐borne ascospores of the teleomorph, which may exist as an indigenous population on alternative hosts, such as Poa annua (annual bluegrass).
Fruit eating and seed dispersal by howling monkeys (Alouatta palliata) in the tropical rain forest of Los Tuxtlas, Mexico

The frugivory and ranging habits of howling monkeys living in the rain forest of Los Tuxtlas, Veracruz, Mexico, were studied for 5 consecutive years with the aim of investigating the role of seed dispersal agents played by the howling monkeys. The howling monkeys' consumption of fruit occupied half of their feeding time, and 80% of this time was spent feeding on mature fruit. Observations confirmed use of 19 tree species and a preference for a few species of Moraceae and Lauraceae. Fruit exploitation was very seasonal; only two species provided fruit year‐round. Home range size was about 60 ha, and animals in the troop (N = 16) showed a day range of 10–893 m. Monthly collection of fecal samples during 2 years indicated that 90% of the seeds (N = 7,928) in the samples belonged to eight tree species and to one liana; the rest belonged to 15 unidentified species of vines. Germination success for the seeds in the feces was about 60% and for control seeds was 35%. Howling monkeys created diverse seed shadows in the vicinity of their leaf and fruit sources, and while they dispersed the seeds of some plant species, they also produced a great deal of fruit and seed waste for others.
The Sequence and Function Relationship of Elastin: How Repetitive Sequences can Influence the Physical Properties of Elastin

Elastin is an essential extracellular protein that is a key component of elastic fibres, providing elasticity to cardiac, dermal, and arterial tissues. During the development of the human cardiovascular system, elastin self-assembles before being integrated into fibres, undergoing no significant turnover during the human lifetime. Abnormalities in elastin can adversely affect its self-assembly, and may lead to malformed elastic fibres. Due to the longevity required of these fibres, even minor abnormalities may have a large cumulative effect over the course of a lifetime, leading to late-onset vascular diseases. This thesis project has identified important, over-represented repetitive elements in elastin which are believed to be important for the selfassembly and elastomeric properties of elastin. Initial studies of single nucleotide polymorphisms (SNPs) from the HapMap project and dbSNP resulted in a set of genetic variation sites in the elastin gene. Based on these studies, glycine to serine and lysine to arginine substitutions were introduced in elastin-like polypeptides. The self-assembly properties of the resulting elastin-like polypeptides were observed under microscope and measured using absorbance at 440nm.
Protein Kinase Bα/Akt1 Regulates Placental Development and Fetal Growth*

Protein kinase Bα (PKBα/Akt1) is implicated in the regulation of metabolism, transcription, cell survival, angiogenesis, cell migration, growth, and tumorigenesis. Previously, it was reported that PKBα-deficient mice are small with increased neonatal mortality (Cho, H., Thorvaldsen, J. L., Chu, Q., Feng, F., and Birnbaum, M. J. (2001) J. Biol. Chem. 276, 38349–38352 and Chen, W. S. , Xu, P. Z. , Gottlob, K. , Chen, M. L. , Sokol, K. , Shiyanova, T. , Roninson, I. , Wenig, W. , Suzuki, R. , Tobe, K. , Kadowaki, T. , and Hay, N. (2001) Genes Dev. 15, 2203–2208). Here we show that PKBα is widely expressed in placenta including all types of trophoblast and vascular endothelial cells. Pkbα–/– placentae display significant hypotrophy, with marked reduction of the decidual basalis and nearly complete loss of glycogen-containing cells in the spongiotrophoblast, and exhibit decreased vascularization. Pkbα–/– placentae also show significant reduction of phosphorylation of PKB and endothelial nitric-oxide synthase. These defects may cause placental insufficiency, fetal growth impairment, and neonatal mortality. These data represent the first evidence for the role of PKBα and endothelial nitricoxide synthase in regulating placental development and provide an animal model for intrauterine growth retardation.
Emerging clinical applications of nucleic acids

Attempts to employ nucleic acids in gene therapy have become commonplace in recent years, but efficient gene transfer methods have proved unexpectedly difficult to devise, and safety concerns linger. At the same time, however, the study of nucleic acids has revealed remarkable properties of DNA and RNA molecules that could make them attractive therapeutic agents, independent of their well-known ability to encode biologically active proteins. Now would seem to be a good time to consider alternative uses of nucleic acids that do not rely on virus-based vectors or even on gene transfer. Accordingly, the strategies explored in this Perspective series exploit a number of different facets of RNA and DNA biochemistry. Certain nucleic acid molecules can bind to and inhibit the function of target proteins, while others provide a source of tumor antigens, and still others can perform catalysis. Recently, therapies that employ nucleic acids in some of these novel ways have passed the stage of in vitro and animal tests and have begun to be evaluated in clinical trials for treating a variety of disorders. This Perspective series offers an update on the progress in this field.
Functional expression of indoleamine 2,3-dioxygenase by murine CD8α+ dendritic cells

Immunoregulatory antigen-presenting cells (APC) play an important role in maintaining T cell homeostasis and self-tolerance. In particular, recent evidence demonstrates a role for inhibition of T cell proliferation by macrophage tryptophan catabolism involving the activity of the enzyme indoleamine 2,3-dioxygenase (IDO). Dendritic cells (DC) have also been shown to exert immunoregulatory effects mediated by tryptophan catabolism and to cause T cell apoptosis. In the present study, we have comparatively analyzed the expression of IDO activity by murine macrophages and splenic DC. By means of PCR, Western blotting and measurements of enzyme functional activity, we obtained evidence that, different from macrophages, DC constitutively express IDO. Following activation by IFN-gamma, the latter cells, in particular the CD8 alpha(+) subset, exhibit high functional activity and, unlike macrophages, mediate apoptosis of T(h) cells in vitro. Therefore, in the mouse, CD8 alpha(+) DC may be unique APC capable of fully expressing the IDO mechanism functionally.
Conifer stem growth at the altitudinal treeline in response to four years of CO2 enrichment

Northern latitude and upper altitude climatic treelines have received increasing attention given their potential sensitivity to atmospheric and climate change. While greater radial stem growth at treeline sites in recent decades has been attributed largely to increasing temperature, rising atmospheric CO2 concentration may also be contributing to this growth stimulation. Tree ring increments of mature Larix decidua and Pinus uncinata were measured over 4 years in a free air CO2 enrichment experiment at treeline in the Swiss Central Alps (2180 m a.s.l.). In addition, a one‐time defoliation treatment in the second year (2002) of the experiment was used to simulate one of the common natural insect outbreak events. In response to elevated atmospheric CO2, Larix showed a cumulative 4‐year growth response of+41%, with particularly strong responses in the third and fourth year. This increase in radial stem wood growth was the result of more latewood production, in particular, the formation of larger tracheids, rather than a greater number of cells. In contrast, Pinus showed no change in ring width to elevated [CO2], neither in each of the treatment years, nor in the cumulative response over 4 years, although an increase in tracheid size was observed in the third year. Defoliation led to a pronounced decrease in annual ring width of both species, marked in particular by less latewood production, in the treatment, as well as subsequent years. There was no significant interaction between defoliation and CO2 enrichment. Although Pinus showed no growth response to CO2, the positive growth response observed in Larix after 4 years of CO2 enrichment implies that the sensitivity of treeline trees to global change may not be purely temperature driven. We conclude that the open sparse canopy in the treeline ecotone favours the indeterminate growth strategy of the early successional Larix when neither weather nor carbon are limiting, whereas the later successional Pinus does not show any indication of more vigorous growth under future higher atmospheric CO2 concentrations.
Implication of persimmon fruit hemicellulose metabolism in the softening process. Importance of xyloglucan endotransglycosylase

Hemicellulosic polysaccharides from persimmon fruit (Diospyros kaki L.) pericarp were extracted from depectinated cell walls with 0.5, 1 and 4 M KOH at different stages of development: (I) maximal growth corresponding to the first sigmoidal growth phase; (II) cessation of growth corresponding to the lag between the first and the second sigmoidal phases; (III) maximal growth corresponding to the second sigmoidal phase; and (IV) cessation of growth when the fruit had reached its maximum size and the change in colour (green to red) had taken place. During fruit development the amount of total hemicelluloses per unit dry mass cell wall decreased twofold. Xyloglucan was present in the three hemicellulosic fractions, and also decreased with fruit age, although its amount relative to other hemicelluloses increased. The amount of xyloglucan was especially high in the hemicelluloses extracted with 4 M KOH, representing more than 50% at stages III and IV. The average molecular mass of xyloglucan increased from stage I through stage II (0.5 M hemicellulosic fraction) or through stage III (I and 4 M hemicellulosic fractions) and decreased after that. The xyloglucan endotransglycosylase (XET: EC 2.4.1.-) activity was measured as the incorporation of [3H]XXXGol (reduced xyloglucan heptasaccharide labelled at position 1 of the glucitol moiety) into partially purified persimmon fruit xyloglucan. XET specific activity increased greatly between stages I and II. The importance of this enzyme during fruit ripening is discussed.
Shade Tolerance, a Key Plant Feature of Complex Nature and Consequences

Light gradients are ubiquitous in nature, so all plants are exposed to some degree of shade during their lifetime. The minimum light required for survival, shade tolerance, is a crucial life-history trait that plays a major role in plant community dynamics. There is consensus on the suites of traits that influence shade tolerance, but debate over the relative importance of traits maximizing photosynthetic carbon gain in low light versus those minimizing losses. Shade tolerance is influenced by plant ontogeny and by numerous biotic and abiotic factors. Although phenotypic plasticity tends to be low in shade-tolerant species (e.g., scant elongation in low light), plasticity for certain traits, particularly for morphological features optimizing light capture, can be high. Understanding differential competitive potentials among co-occurring species mediated by shade tolerance is critical to predict ecosystem responses to global change drivers such as elevated CO2, climate change and the spread of invasive spe.
Studies on novel and traditional risk factors of atherosclerosis

The atherosclerotic plaques develop with the adhesion of inflammatory cells and lipids onto the innermost layer of the vessel. They may eventually occlude the vessel impairing blood flow. A severe complication is the rupture of a plaque resulting in the formation of a thrombus that can cause myocardial infarction or stroke. Though a large number of risk factors for atherosclerosis have been identified, the pathogenesis of atherosclerosis is far from unravelled. The aim of the present work was to study both traditional as well as potential novel risk factors of atherosclerosis. The first study examined the relationship between IGF-I concentrations and carotid artery atherosclerosis and its metabolic risk factors. Low IGF-I concentrations were associated with several cardiovascular risk factors. A positive association was observed between IGF-I concentrations and carotid artery intima-media thickness in women. The results suggest that IGFI may be involved in the pathogenesis of atherosclerosis. Interestingly, the effect may manifest differentially in men and women. The second study focused upon the effects of obesity and weight loss on liver gene expression. A global decrease in gene expression was observed. The down-regulated genes included genes involved in the ubiquitin cycle, which may point to a reduction in oxidative stress due to the hypocaloric diet. The down-regulation of peroxisome proliferator-activated receptor gamma cofactor 1 alpha (PGC-1α) may be related to improved insulin sensitivity. Several novel genes not previously linked to obesity and weight loss were also discovered. In the third and fourth studies, the developmental origins of atherosclerosis hypothesis was studied in a rat model of fetal undernutrition. Unfavourable changes in the obesity-related peptide hormones adiponectin and resistin were observed which could predispose to insulin resistance in later life. In addition, total cholesterol levels were elevated in the undernourished offspring. The gene expression changes in the rat pups suggest that the development of pancreas was affected, which might further contribute to disturbances in insulin and glucose metabolism.
Serum ferritin concentration and fat distribution.

To the Editor: In a recent issue of the Journal, we reported on the results of a study to determine whether the associations that have been found between cardiovascular risk factors and serum ferritin could be explained through confounding by diet (1). During the course of the study, we examined the relationship between serum ferritin and one measure of fat distribution, namely, the waist to hips ratio, a widely used indicator of abdominal fat.
Male greater sac-winged bats gain direct fitness benefits when roosting in multimale colonies

Social groups that are characterized by the presence of male kin are rare in mammals. Theory predicts that males reproducing in such groups need to overcome the costs of local mate competition, which are supposedly severe in polygynous or promiscuous mating systems. Here, we studied in a polygynous mammal with male philopatry whether male group size renders direct fitness benefits for males that could outweigh the costs of competing with related males for access to territories and mates. We used long-term behavioral observations and genetic data of the greater sac-winged bat to investigate the factors affecting lifetime breeding success (LBS) of harem males living in colonies that contain varying numbers of male residents. We show that tenure of harem males increased with the number of male coresidents and that harem male tenure explained a large proportion of variation in their LBS. Thus, our results provide evidence that males gain direct fitness benefits from a social organization in colonies that include additional harem territories and nonharem males. Immigration of males into colonies was significantly lower when nonharem males (young males that are often related to harem males) were permanently present in colonies, suggesting that larger male groups may be better able to maintain a patriline in a colony and thus also ensure future indirect fitness benefits.
Habituation: cultural curiosity or developmental determinant.

The induction and reversal of habituation for auxin or cytokinin have been brought about by exposure of callus tissue to low or high concentrations of the growth substance in question. Since the growth rate of the tissues must be measured in the presence or absence of the growth substance being tested, habituation can be demonstrated only in callus. However some developmental processes in the intact plant seem to imply the possible involvement of habituation-like processes in normal development. Evidence for this, and the implications for the action of growth substances in plant development are considered.
Stem demography of Prosopis glandulosa var. torreyana in vegetation arcs and associated bare areas

Vegetation arcs are characterized by dense patches of up to 100 % plant cover surrounded by bare areas where cover is around 5 %. These patterns of contracted vegetation have been reported mainly in alluvial fans of arid and semiarid zones (known as bajadas) with gentle slopes (0.2 - 2 %), summer rainfall, and heavy showers that run as sheet-flow. It has been suggested that run-off water from bare areas is stopped at the front of the arcs and, depending on the amount of rainfall, may advance superficially into the arc, reaching the downslope limit less often. These dynamics would imply a gradient of water availability inside the arc, higher at the upper edge. We termed this the moisture gradient hypothesis. We indirectly tested this hypothesis by following the demography of a cohort of stems of the honey mesquite Prosopis glandulosa var. torreyana in three vegetation arcs and their corresponding bare areas during a yearly cycle at the Bolson de Mapimi in the Chihuahuan Desert. We selectively removed different plant life-forms (trees, shrubs and herbs) in three positions within the arcs; no manipulation was possible in the bare areas due to low plant cover. The results suggested that removal of other plant life-forms, mainly grasses, affected growth and survival of mesquite low (but not high) stems, making them accessible to medium-sized mammal browsers (jackrabbits and packrats). These results suggest that, at least for the honey mesquite, water availability in vegetation arcs was not the most strongly limiting factor for shoot performance and demography, and that browsing damage, a biotic constraint, took precedence over resource limitation.
A Multivariate Study of Solidago subsect. Junceae and a New Species in South America (Asteraceae: Astereae)

Abstract. A new South American species of Solidago L. (Asteraceae, Astereae) from Argentina, Chile, and Bolivia was identified within the subsection Junceae (Rydb.) G. L. Nesom. Using multivariate analyses on a matrix of 50 characteristics for 79 specimens, the distinctiveness of a South American S. missouriensis-like taxon was tested and determined to be statistically different from four morphologically similar North American species: S. gattingeri Chapm. ex A. Gray, S. juncea Aiton, S. missouriensis Nutt. , and S. pinetorum Small. Therefore, a new South American species is proposed: S. argentinensis Lopez Laph. & Semple.
African papionin phylogenetic history and Plio-Pleistocene biogeography

Stony Brook University Libraries. SBU Graduate School in Anthropology. Lawrence Martin (Dean of Graduate School), John G. Fleagle- Dissertation Advisor Distinguished Professor, Department of Anatomical Sciences, William L. Jungers- Chairperson of Defense Professor and Chair, Department of Anatomical Sciences, Frederick E. Grine Professor, Department of Anthropology, Eric Delson Professor, Department of Anthropology CUNY- Lehman College.
Usage of continuous pressure reader in in vitro gas production technique for evaluation of feedstuffs for ruminants.

This experiment was conducted to determine possibility of usage of automatic system that continuously record pressure and sample gas at certain intervals in in vitro gas production technique. Rumen fluid was collected from 2 ruminally cannulated Holstein heifers weighing an average of 400 kg. Medium was prepared by mixing macromineral (200 ml), micromineral (0.1 ml), buffer (200 ml), reduction (40 ml) and resazurin (1 ml) solutions as well as distilled water (400 ml). The mixtures contained alfalfa hay, maize silage, wheat, maize, cottonseed meal, and soybean meal. Mixtures differing in the roughage:concentrate ratio (20:80, 40:60, 60:40, and 80:20) were formulated to contain rapidly fermentable fraction (B1+B2), insoluble but slowly fermentable fraction (B3,) and 50% of these fractions at three different fermentation characteristics. Gas productions at 6, 12, 24, and 48 h relative to incubation determined using system recording continuously. In automatic system, "dual-pool logistic equation" representing factions either soluble in NDF solution and rapidly fermentable fraction (NDF-F) and fractions or insoluble in NDF solution, but slowly fermentable (NDF-S) were used. The fermentation was completed within 12 h in fully automatic system. While cumulative gas production from NDF-F was positively correlated with gas production within 3 h (r=0.77, P<0.001), cumulative gas production from NDF-S was positively correlated with gas production within 3-20 h (r=0.88, P<0.001). Differences in time to reach maximal fermentation rate from NDF-F and NDF-S increased with increasing NDF (r=0.76, P<0.001) and ADF (r=0.85, P<0.001) levels. These data suggest that fermentation kinetics parameters, such as lag time and time to reach maximal fermentation rate from fractions soluble and insoluble in NDF solution, should be considered in formulation and evaluation of rations.
Root production and turnover and carbon budgets of two contrasting grasslands under ambient and elevated atmospheric carbon dioxide concentrations.

Monoliths of two contrasting vegetation types, a species-rich grassland on a brown earth soil over limestone and species-poor community on a peaty gley, were transferred to solardomes and grown under ambient (350 μ 1-1 ) and elevated (600 μ11-1 ) CO2 for 2 yr. Shoot biomass was unaltered but root biomass increased by 40-50% under elevated CO2 . Root production was increased by elevated CO2 in the peat soil, measured both as instantaneous and cumulative rates, but only the latter measure was increased in the limestone soil. Root growth was stimulated more at 6 cm depth than at 10 cm in the limestone soil. Turnover was faster under elevated CO2 in the peat soil, but there was only a small effect on turnover in the limestone soil. Elevated CO2 reduced nitrogen concentration in roots and might have increased mycorrhizal colonization. Respiration rate was correlated with N concentration, and was therefore lower in roots grown at elevated CO2 . Estimates of the C budget of the two communities, based upon root production and on net C uptake, suggest that C sequestration in the peat soil increases by c. 0.2 kg C m -2 yr-1 (= 2 t ha yr-1 ) under elevated CO2 .