Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the long‐term impact of Ranavirus infection in wild common frog populations

Amphibians are declining worldwide, and one cause of this is infectious disease emergence. Mass mortalities caused by a virus or a group of viruses belonging to the genus Ranavirus have occurred in wild common frogs Rana temporaria in England since the 1980s, and ranaviral disease is widespread in amphibians in North America and Canada, where it can also cause mass die‐offs. Although there have been numerous reports of Ranavirus‐associated mass mortality events, no study has yet evaluated the long‐term impacts of this disease. This study follows up archived records of English common frog mortalities likely caused by Ranavirus. There is a preliminary indication that common frog populations can respond differently to the emergence of disease: emergence may be transient, catastrophic, or persistent with recurrent mortality events. We subsequently focused on populations that had recurring mortality events (n=18), and we report median declines of 81% in the number of adult frogs in these populations from 1996 to 2008. Comparable uninfected populations (n=16) showed no change in population size over the same time period. Regressions show that larger frog populations may be more likely to experience larger declines than smaller populations, and linear models show that percentage population size change is significantly correlated with disease status, but that habitat age (a possible proxy for environmental quality) has no significant effect on population size change. Our results provide the first evidence of long‐term localized population declines of an amphibian species which appear to be best explained by the presence of Ranavirus infection.
Management of Glyphosate-Tolerant Common Lambsquarters (Chenopodium album) in Glyphosate-Resistant Soybean

Abstract Field studies were conducted in 2006 and 2007 to evaluate strategies for management of four glyphosate-tolerant common lambsquarters populations in glyphosate-resistant soybeans. Treatments consisted of several different preplant herbicide combinations followed by one or two postemergence applications of 0.84 to 3.36 kg ae/ha of glyphosate. Preplant application of a combination of glyphosate, 2,4-D ester and residual herbicides resulted in the most effective control of all populations, and allowed use of a single postemergence glyphosate application at the lowest rate. Late-season control of common lambsquarters ranged from 66 to 95% where no preplant herbicides were applied, 72 to 97% for preplant application of glyphosate and 2,4-D, and 96 to 100% for the combination of glyphosate, 2,4-D, flumioxazin, and cloransulam-methyl. Individual plants survived and produced seed following single postemergence glyphosate applications of 3.36 kg ae/ha, and multiple glyphosate applications totaling 2.5 kg ae/ha. Multiple postemergence treatments were more effective than single postemergence treatments for reduction of common lambsquarters population density and seed production. The progeny of plants that survived high rates of glyphosate in the field were screened for their response to glyphosate in the greenhouse. Progeny from one of three populations exhibited increased glyphosate tolerance from 1 yr of selection pressure. Nomenclature: Glyphosate; common lambsquarters, Chenopodium album L;soybean, Glycine max (L.) Merr
Feasibility analysis of leaf disc samples produced via agroinfiltration for promoter trapping studies

Promoter trapping is a method used to isolate and characterize regulatory regions from genomes by elucidating the expression of a promoterless reporter gene flanked by two transposable elements. The conventional method of promoter trapping requires the generation of stable transformed tissue culture derived plant lines. Nevertheless,this method can be laborious, time consuming and expensive. As an alternative method, leaf disc samples produced via leaf agroinfiltration was employed in this work. A promoter trapping construct named pCAMDIN was created which contains a promoterless GUS (β-glucuronidase) gene flanked by the left and right T-DNA border using pCAMBIA 1301 and pBI 121. Following that,the protocol for agroinfiltration of tomato plants using both direct agroinfiltration and vacuum agroinfiltration was optimized. Non-destructive protocols for detection of GUS genes were tested and optimised. Following that, GUS gene expression was studied and areas which showed expression were isolated by making leaf punches. Analysis was carried out by Southern blotting and T-DNA fingerprinting to determine the gene copy number.
The development of ideas on the role of glucose in regulating milk secretion

The author has reviewed the development of theories, over the last century, on the role of glucose in mammary metabolism, focusing on three overlapping issues, via. the extent of glucose utilization by mammary tissue, the synthesis of lactose, and the way in which glucose supply controls secretion of the aqueous phase of milk. In the first half of the century, deficiencies in technique produced several misleading results, and later progress resulted largely from methodological advances. Methodology has also been important in shaping research programmes, as is evident in the current emphasis on techniques of molecular biology. However, the review indicates the importance of employing a combination of experimental approaches, including whole-animal studies. Through the adoption of such approaches, it is now appreciated that glucose plays a key role in regulating lactation. It is suggested that developments over the last 30 years, which have led to formulation of an apparently resilient theory of milk secretion, conform to the notion of a 'progressive research programme' built on a 'positive heuristic', as proposed by the philosopher of science, I. Lakatos.
Investigations on Heterobasidion annosum s.lat. in central and eastern Asia with the aid of mating tests and DNA fingerprinting

To investigate the taxonomy of Heterobasidion in Eurasia, 49 specimens belonging to H. annosum sensu lato from Asia were identified with the aid of mating tests. Most of the specimens originated from north-eastern and south-western China and from the Altai region in southern Siberia, but a few isolates from Kirghizia, Japan and India were also tested. In addition to mating tests, the material from China was investigated with DNA fingerprinting. Heterobasidion annosum sensu stricto was identified only from the Altai region. Homokaryotic isolates from other specimens, except the Indian ones, were sexually compatible with H. parviporum, but they also showed a high degree of compatibility with H. abietinum and with the North American S group. The isolates from SW China (eastern Himalayas) mated with about equal frequency with the European strains of H. parviporum and H. abietinum. However, the DNA fingerprinting showed that these isolates were more closely related to H. parviporum, and hence they were tentatively included in this species. The North American S group was more distant from these Eurasian taxa. Four old isolates from India mated only weakly with the members of the H. annosum s.lat. According to the species concept presented, the distribution of H. parviporum extends from western Europe through southern Siberia to northern China, Japan and the eastern Himalayas. H. annosum s.str. is so far identified only from the Altai region outside Europe, and H. abietinum only from Europe.
oxidant release by adherent human neutrophils

The signal transduction pathways that are activated by cytokines and growth factors binding to their receptors on human neutrophils (PMN) are poorly understood. When PMN in suspension encounter many of these agonists they are not activated, but rather are primed for subsequent activation. We and others re- ported that when PMN are plated onto librinogen and stimulated with cytokines or with the chemotactic pep- tide N-formyl-methionyl-leucyl-phenylalanine (fMLP) they respond by releasing hydrogen peroxide (H202) and the specific granule component lactoferrin. Trans. forming growth factor43i (1�F431) is released by many cells including PMN. It has been reported that 'RF- 1� i stimulates chemotaxis but not exocytosis or super- oxide production by cells in suspension. We hypothe- sized that UF-�31 would activate PMN to release H202 when they were adherent to fibrinogen, a response mediated by 132 integrm receptors. In this study, we determined whether 'JXF-�31 stimulated H202 and lac- toferrin release by PMN adherent to fibrinogen. IXW- Ii stimulated H202 and lactoferrin release from ad- herent PMN in a concentration-dependent manner, with effects seen in the range of O.i to 100 pg/mL. Both H202 and lactoferrin release were detected by 60 min ant� '�ontinued for at least 180 min. Adhesion and spreading of PMN paralleled H202 and lactofer- rin release. Ethanol (200 mM) blocked both H202 and lactoferrin release, suggesting the involvement of the phospholipase D pathway. In PMN labeled with lyso- �3H)phosphatidylcholine, we observed that 1XF-�31 treatment caused an increase in I3Hlphosphatidate. Propranolol (150 �.tM), an inhibitor of phosphatidate phosphohydrolase, blocked both H202 and lactofer- rin release, suggesting that the conversion of phos- phatidic acid to cliradylglycerol is an important step in PMN activation by 1XF-�31. Overall, these results are similar to those reported for fMLP activation of adherent PMN and suggest that a common pathway is involved in both chemoattractant and cytokine ac- tivation. J. Leukoc. Riot. 60: 772-777; 1996.
A STUDY OF THE RESPIRATION OF BANANAS

THE rate of production of carbon dioxide by plant tissues is generally easy to measure and not infrequently is a valuable indicator of changes occurring in the tissues, and a graph showing the course of respiration becomes a datum line to which changes in properties of the tissue can be referred. This is especially true of certain fruits and leaves where, in the course of respiration after gathering, there is a well-defined increase in activity, known as the climacteric rise. The occurrence of such a hump has been reported for apples and pears (Kidd & West, 1930), tomatoes (Gustafson, 1929), bananas (Hartshorn, 1931), and leaves (Godwin & Bishop, 1927). Its importance in fruit is due to the fact that this increase in the rate of respiration occurs at the time that the fruit starts to ripen. The respiration of bananas has been measured with fruit of various stages of ripeness under a variety of experimental conditions.
Black yeasts from the slope sediments of Bay of Bengal: phylogenetic and functional characterization

Occurrence of black yeasts in the slope sediments of Bay of Bengal was investigated during FORV Sagar Sampada cruises 236 and 245. The black yeast population was found to be very scanty in the area and the isolates could be obtained from 200m to 1000m depth regions in the slope sediments. The isolates were identified as Hortaea werneckii by Internal Transcribed Spacer (ITS) sequencing. The biodegradation potential of these strains was found to be very high with all the strains exhibiting protease, lipase and amylase production. The optimum growth conditions were pH 8, salinity 30 ppt and temperature 30 o C. The pigment melanin, in these organisms was identified to be of dihydroxynaphthalene type by NMR. The melanin was found to exhibit inhibitory activity against different human and fish pathogens. Melanin degrading enzyme could also be extracted from these organisms.
Nest Boxes Reduce Flying Squirrel Use of Red-Cockaded Woodpecker Cavities

Abstract Reproductive success of red-cockaded woodpeckers (Picoides borealis) appears to be reduced when even a single cavity in a cluster of woodpecker cavities is occupied by a southern flying squirrel (Glaucomys volans). One potential technique for reducing flying squirrel use of woodpecker cavities is the addition of nest boxes to clusters. In this study we evaluated the effects of nest boxes and red-cockaded woodpecker presence (activity) on flying squirrel use of cavities at the Joseph W. Jones Ecological Research Center in Newton, Georgia from 26 September 2002 until 26 June 2003. The interaction between presence of nest boxes and woodpecker activity significantly affected success (proportion of time no flying squirrels occupied any cavities in a cluster; F1,16 = 5.10, P = 0.04). Success was higher in active clusters with nest boxes (95%) than active clusters without nest boxes (83%) but was similar in inactive clusters (success with and without nest boxes = 78%). The proportion of cavities usurped by squirrels cluster−1 month−1 was higher for inactive clusters (0.07) than for active clusters (0.03; F1,16 = 6.59, P = 0.02). The number of usurped nest boxes per cluster was higher for active clusters (5.67) than inactive clusters (2.71; F1,8 = 4.56, P = 0.07). Our results indicate that nest box addition coupled with flying squirrel removal may reduce flying squirrel use of cavities, especially when cavities occur in clusters containing red-cockaded woodpeckers.
Habitat use governs distribution patterns of saprophagous (litter-transforming) macroarthropods - a case study of British woodlice (Isopoda: Oniscidea)

Despite the importance of saprophagous macroarthropods as key facilitators of plant litter decomposition within ecosystems and their likely sensitivity to global climate change and land-use change, a lack of ecological data has precluded attempts to explain their distribution patterns in terms of traits. Using an extensive set of large-scale and long-term biological records, the distribution patterns of 33 woodlice (Crustacea: Oniscidea) species in Britain were characterised by their range size (area of occupancy) and aggregation (degree to which occupied squares are clustered across the range). Body size and seven ecological traits were examined as correlates of range size and fill, while controlling for phylogeny and recording intensity, and comparing fine and broad-scale measures of habitat heterogeneity. Species that used a greater diversity of habitats had larger range sizes. Broad categorisation of habitats (by dominant vegetation) alongside other traits was less accurate in predicting range size than fine-scale habitat (microsites where individuals were discovered) data. The latter explained 25% more variance than broad-scale habitat data, highlighting the value of coupling biological recording of species with data on micro-habitat. Habitat use is an important trait in explaining distribution patterns and we conclude that ensuring land cover heterogeneity will favour conservation of saprophagous macro-arthropod diversity.
Development of New Strains for the Food Industry

This review examines the desired characteristics and possibilities of genetic manipulation of industrial yeasts. Brewing, wine, and distillers' yeasts are characterized by good utilization of sugar, alcohol tolerance and production, flavor and aroma, flocculation, fermentation rate, cropping ratio, ability to utilize trisaccharides, dextrines and starch, rapid onset of fermentation, nonfoaming fermentation, and low H2S production. The characteristics required for a good bakers' yeast include high potential glycolytic activity, ability to adapt rapidly to changing substrates, high invertase activity, high potential maltose fermentation rate and quality in terms of dough fermentation, storage ability, and osmotic resistance to salts and sugars. In all of these cases, the major desirable factors are under genetic control and hence are potentially subject to improvement by genetic manipulation. However, this control is thought to be governed by several, in most cases, unidentified genes. So, although most genetic techniques developed for laboratory yeasts are potentially applicable to the study and improvement of the properties of industrial yeast strains, traits such as homothallism, aberration in mating behavior, polyploidy, aneuploidy, poor sporulation and poor spore viability, etc., make conventional hybridization and isolation of single spore clones more difficult.
Changes in the volatile flavour components of Jinhua ham during the traditional ageing process

Changes in volatile flavour compounds of Jinhua ham were studied during the traditional ageing process of sun-drying, loft-ageing and post-ageing. About seventy-eight volatile compounds were tentatively identified, including aldehydes (ten to fifteen), carboxylic acids (eight to ten), alcohols (thirteen to fourteen), ketones (eight), esters (eight to ten), aromatic hydrocarbons (five), sulphur-containing compounds (two to three) and pyrazines (zero to four) which were the main components. The percentage content of aldehydes and ketones reduced over time as the temperature rose with each stage of the process, whereas alcohols, carboxylic acids, esters, pyrazines and sulphur-containing compounds increased gradually. Jinhua ham's high-temperature maturating process (40 days at 30-37 °C) made the percentage content of carboxylic acids arising from Maillard reactions markedly increase (from sun-dried ham 8.45% to fully aged ham 19.23%). This was the most obvious difference between Jinhua ham and the Mediterranean dry-cured hams, and was the main factor leading to the unique flavour of Jinhua ham.
Physiological basis for enhanced sucrose accumulation in an engineered sugarcane cell line

Transgenic sugarcane (Saccharum officinarum L. interspecific hybrids) line N3.2 engineered to express a vacuole-targeted sucrose isomerase was found to accumulate sucrose to twice the level of the background genotype Q117 in heterotrophic cell cultures, without adverse effects on cell growth. Isomaltulose levels declined over successive subcultures, but the enhanced sucrose accumulation was stable. Detailed physiological characterisation revealed multiple processes altered in line N3.2 in a direction consistent with enhanced sucrose accumulation. Striking differences from the Q117 control included reduced extracellular invertase activity, slower extracellular sucrose depletion, lower activities of symplastic sucrose-cleavage enzymes (particularly sucrose synthase breakage activity), and enhanced levels of symplastic hexose-6-phosphate and trehalose-6-phosphate (T6P) in advance of enhanced sucrose accumulation. Sucrose biosynthesis by sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) was substantially faster in assays conducted to reflect the elevation in key allosteric metabolite glucose-6-phosphate (G6P). Sucrose-non-fermenting-1-related protein kinase 1 (SnRK1, which typically activates sucrose synthase breakage activity while downregulating SPS in plants) was significantly lower in line N3.2 during the period of fastest sucrose accumulation. For the first time, T6P is also shown to be a negative regulator of SnRK1 activity from sugarcane sink cells, hinting at a control circuitry for parallel activation of key enzymes for enhanced sucrose accumulation in sugarcane.
Responses of the Codominant Grassland Species Andropogon gerardii and Sorghastrum nutans to Long-term Manipulations of Nitrogen and Water

Abstract The availability and distribution of essential resources such as water and nitrogen are changing on a global scale and it is important to determine the effects of such alterations on dominant and subdominant species in ecosystems. We examined the effects of long-term additions of water and nitrogen on leaf-level ecophysiological characteristics of the tallgrass prairie codominants Andropogon gerardii (big bluestem) and Sorghastrum nutans (Indian grass). Both species responded to irrigation with increased water potentials and to fertilization with decreased water potentials. Only in S. nutans, however, were net photosynthesis and stomatal conductance greater in response to both water and nitrogen addition. In contrast, A. gerardii, which currently is more abundant than S. nutans, was relatively unresponsive to resource manipulations. If net photosynthesis is positively related to plant productivity, as has been shown for tallgrass prairie species, the differential photosynthetic responses of these two grasses suggests that their patterns of abundance may change in the future if resource availability is altered. These results are also inconsistent with the historical assumption that these two grasses are “ecological equivalents. ”
MOLECULAR PHYLOGENETICS OF THE NEOTOMA ALBIGULA SPECIES GROUP: FURTHER EVIDENCE OF A PARAPHYLETIC ASSEMBLAGE

Abstract Phylogenetic relationships among 8 subspecies of Neotoma albigula and sister species from the United States and Mexico were examined using DNA sequence data from the mitochondrial DNA cytochrome-b gene. Parsimony, likelihood, and neighbor-joining analyses revealed a strong dichotomy between populations of N. albigula from Texas and eastern Mexico (eastern form) and those from New Mexico, Arizona, and northwestern Mexico (western form). These analyses indicate presence of 2 cryptic species within this taxon that are paraphyletic under current taxonomy. A sister-group relationship was found between N. albigula from Texas and eastern Mexico and N. micropus, whereas populations of N. albigula from New Mexico, Arizona, and northwestern Mexico formed a sister-group relationship with N. floridana. That latter group in turn formed a sister-taxon relationship to the Texas–eastern Mexico N. albigula and N. micropus clade. The Rio Grande and Rio Conchos seem to have been the major barriers restricting gene flow between ancestral populations of a N. floridana–like woodrat. Populations of N. floridana were further isolated geographically by reduction of suitable habitat brought about by changing climatic patterns that allowed formation of xeric plant communities soon after the end of the Late Wisconsin.
Microscale investigations of microbial communities in coastal surficial sediments

The upper millimeters of sediments are considered major locations of microbial colonization and activity. The goal of our study was to investigate variations of microbial communities in the uppermost sediment layers of the coastal Baltic Sea with emphasis on the complex interplay between microbiology and physico-chemical sediment properties. We selected a high-resolution methodological approach that combined the cryolanding sampling technique (spatial resolution of 250 μm) with microsensor-, spectrophotometric and microscopic analyses. While the oxygen penetration depths in dark conditions ranged from 1.4 mm to 2.6 mm during the study period, this zone expanded by about 1 mm in light and could be divided into three micro-horizons: (i) an upper zone with a high net O2 production, (ii) an intermediate zone with increased O2 consumption on account of light-stimulated respiration and (iii) a lower zone with lower O2 consumption. Time-series experiments revealed a rapid response of the benthic microbial community to altered light intensities. In May and July, the net O2 budget in the porewater of sediments was positive within 35 and 22 min after illumination, respectively, whereas in June O2 production exceeded O2 consumption after 112 min. The thickness of the O2 production and O2 consumption micro-zones decreased from May to July coinciding with an increase in temperature. In May, sites of enhanced O2 consumption were closely associated with subsurface maxima of microbial numbers and enzymatic activities indicating a tight coupling between photoautotrophic and heterotrophic processes between 1- and 2-mm depth. In June and July, the microbial abundance and enzymatic activity hardly varied with depth. Spatial and temporal microheterogeneity of microbial distribution and activity in O2 gradients was seen as a reflection of the complex interplay between microbiology and physico-chemical sediment properties.