Miracle-dz/UniFAR-FTUs huggingface dataset:
Specific and non-specific interactions in bacterial adhesion to solid substrata

Based on a literature review, a hypothesis is forwarded on the mechanism of initial bacterial adhesion to solid substrata, which accounts both for the role of specific microscopic surface components as well as for the role of non-specific macroscopic surface properties (surface free energy, zeta potential or hydrophobicity). Three distinct regions in the adhesion process are suggested in which at large and intermediate separation distances adhesion is mediated by the macroscopic surface properties as surface free energy and surface charge, respectively. At small separation distances specific short-range interactions can occur, leading to a strong and irreversible bonding, provided the water film present in between the interaction surfaces can be removed. A major role of hydrophobic groups, supposed to be associated with bacterial surface appendages is suggested to be its dehydrating capacity, enabling the removal of the vicinal water film yielding small areas of direct contact between protruberant parts of the cell surface and the substratum.
Biochemical and Biophysical Properties of the Core-binding Factor α2 (AML1) DNA-binding Domain*

The Runt domain is the DNA-binding domain defining a small family of transcription factors that are involved in important developmental processes. Developmental pathways controlled by Runt domain proteins include sex determination, neurogenesis, segmentation, and eye development in Drosophila and hematopoiesis in mammals. In addition to binding DNA, the Runt domain also mediates heterodimerization with another subunit called the core-binding factor β (CBFβ) subunit. In this study we overexpress the Runt domain from the mouse CBFα2 (AML1) protein in Escherichia coli, and purify it from the insoluble fraction. We determine the equilibrium constants for Runt domain binding to two different DNA sequences by surface plasmon resonance technology. Circular dichroism spectroscopy demonstrates that the Runt domain is a folded β-domain with essentially no α-helical content. The single tryptophan residue in the CBFα2 Runt domain at amino acid 79 is shown by tryptophan fluorescence spectroscopy to reside in a polar environment. Finally, we demonstrate that ATP can be UV cross-linked to the Runt domain and that ATP binding is sensitive to an amino acid substitution in the putative Kinase-1a motif (P-loop).
Proteolytic activity of alkaliphilic, salt-tolerant actinomycetes from various regions in Saudi Arabia

Actinomycetes were isolated from various desert soil samples of Saudi Arabia using alkaline and normal pH media. A total of 42 akaliphilic actinomycetes isolated from yeast extract-soluble starch (YS) agar media (pH 11.0 ± 1) and 102 actinomycetes were isolated from tap water agar media (pH 7.0 ± 1) for comparison. Aerial mycelium colours of actinomycetes were observed for the detection of strain varieties in the different soil samples from different areas. Colour types were more abundant in isolates grown tap water agar (TWA) than in isolates grown on YS agar medium (pH 11.0). On the TWA medium, there were 18 colour types of actinomycetes and on YS agar medium (pH 11.0) there were 10 colour types. The number of neutrophilic actinomycetes isolated in this study is higher than the alkaliphilic actinomycetes. Among the 42 alkaliphilic actinomycetes isolates, 30 isolates were salt tolerant alkaliphilic. Later about 16 alkaliphilic actinomycetes were screened on skim milk agar for preliminary proteolytic activity. A total of 10 isolates showed proteolytic activity. Of the 10 isolates, three isolates were alkaliphilic and seven isolates were salt-tolerant alkaliphilic. All the isolates need to be further studied for the ability of their potential protease enzyme production.
Variable sensitivity of plant communities in Iceland to experimental warming

Facing an increased threat of rapid climate change in cold‐climate regions, it is important to understand the sensitivity of plant communities both in terms of degree and direction of community change. We studied responses to 3–5 years of moderate experimental warming by open‐top chambers in two widespread but contrasting tundra communities in Iceland. In a species‐poor and nutrient‐deficient moss heath, dominated by Racomitrium lanuginosum, mean daily air temperatures at surface were 1–2°C higher in the warmed plots than the controls whereas soil temperatures tended to be lower in the warmed plots throughout the season. In a species‐rich dwarf shrub heath on relatively rich soils at a cooler site, dominated by Betula nana and R. lanuginosum, temperature changes were in the same direction although more moderate. In the moss heath, there were no detectable community changes while significant changes were detected in the dwarf shrub heath: the abundance of deciduous and evergreen dwarf shrubs significantly increased (>50%), bryophytes decreased (18%) and canopy height increased (100%). Contrary to some other studies of tundra communities, we detected no changes in species richness or other diversity measures in either community and the abundance of lichens did not change. It is concluded that the sensitivity of Icelandic tundra communities to climate warming varies greatly depending on initial conditions in terms of species diversity, dominant species, soil and climatic conditions as well as land‐use history.
Dilated Blood and Lymphatic Microvessels, Angiogenesis, Increased Macrophages, and Adipocyte Hypertrophy in Lipedema Thigh Skin and Fat Tissue

Background and Aim Lipedema is a common painful SAT disorder characterized by enlargement of fat primarily in the legs of women. Case reports of lipedema tissue samples demonstrate fluid and fibrosis in the interstitial matrix, increased macrophages, and adipocyte hypertrophy. The aims of this project are to investigate blood vasculature, immune cells, and structure of lipedema tissue in a cohort of women. Methods Forty-nine participants, 19 controls and 30 with lipedema, were divided into groups based on body mass index (BMI): Non-Obese (BMI 20 to <30 kg/m2) and Obese (BMI 30 to <40 kg/m2). Histological sections from thigh skin and fat were stained with H&E. Adipocyte area and blood vessel size and number were quantified using ImageJ software. Markers for macrophages (CD68), mast cells (CD117), T cells (CD3), endothelial cells (CD31), blood (SMA), and lymphatic (D2-40 and Lyve-1) vessels were investigated by IHC and IF. Results Non-Obese Lipedema adipocyte area was larger than Non-Obese Controls (p=0.005) and similar to Obese Lipedema and Obese Controls. Macrophage numbers were significantly increased in Non-Obese (p < 0.005) and Obese (p < 0.05) Lipedema skin and fat compared to Control groups. No differences in T lymphocytes or mast cells were observed when comparing Lipedema to Control in both groups. SMA staining revealed increased dermal vessels in Non-Obese Lipedema patients (p < 0.001) compared to Non-Obese Controls. Lyve-1 and D2-40 staining showed a significant increase in lymphatic vessel area but not in number or perimeter in Obese Lipedema participants (p < 0.05) compared to Controls (Obese and Non-Obese). Areas of angiogenesis were found in the fat in 30% of lipedema participants but not controls. Conclusion Hypertrophic adipocytes, increased numbers of macrophages and blood vessels, and dilation of capillaries in thigh tissue of non-obese women with lipedema suggest inflammation, and angiogenesis occurs independent of obesity and demonstrates a role of altered vasculature in the manifestation of the disease.
Seasonal changes in leaf water relations and cell membrane stability in orchardgrass (Dactylis glomerata)

SUMMARY Fifteen cultivars of orchardgrass (Dactylis glomerata L.) were grown in the field at Hiroshima University, Japan, to investigate seasonal changes in leaf water relations and cell membrane stability (CMS) measured by the polyethylene glycol (PEG) test. Leaf water potential and osmotic potential were measured from August 1988 to August 1989. Solute concentration in leaf cell sap was also estimated. Cell membrane stability increased, leaf water potential and osmotic potential decreased and turgor potential increased with decreasing environmental temperatures during autumn and winter. The significant increases observed in CMS may enable plants to tolerate freezing temperatures during winter. Decrease in leaf water potential may be a result of water-deficit effects due to soil freezing at low temperatures and the decrease in osmotic potential may help plants to maintain turgor and tolerate freezing conditions. Plants maintained higher turgor as the osmotic potential decreased to values as low as – 3·98 MPa during winter; the maintenance of turgor helps to maintain water uptake under water deficit conditions at low temperatures. Sugar and K were the major osmotic contributors in orchardgrass leaves. Sugar and Ca concentrations increased and Mg and P concentrations decreased at cold temperatures. K concentration increased in six cultivars and decreased in nine others at cold temperatures. Sugar concentration in cell sap was negatively correlated with osmotic potential. It was concluded that seasonal changes in CMS may be mainly associated with the osmotic potential of the leaf tissues.
Characterization of Two New Isolates of Mushroom-Shaped Budding Bacteria

Two new strains of mushroom-shaped budding bacteria were isolated from a pulp mill oxidation lagoon. These isolates were morphologically similar to previous isolates from England and Russia. However, the carbon source utilization patterns and phage typing by newly isolated phages indicated that the four strains were not identical to one another. This was confirmed by deoxyribonucleic acid (DNA)/DNA homology studies in which reference DNA from a lagoon strain exhibited 39, 41, and 85% homologies with the other strains. Homology studies indicated that the mushroom-shaped budding bacteria are different from the members of the presently recognized genera of budding bacteria.
The digestion of wheat starch in broiler chickens

Apparent metabolizable energy (AME) of wheat for 6-week-old male broiler chickens was highly correlated with starch digestibility when pelleted diets containing 820 g wheat per kg were fed. Starch isolated from low-AME wheats was hydrolysed in vitro by chicken pancreatic amylase as rapidly as starch from high-AME wheats. When included in semi-purified diets the isolated starches were completely digestible. Digestibility of starch was poor and highly variable when 3-week-old chickens were fed unpelleted wheat diets, but improved with age. Oat hulls improved the digestibility of starch in young chickens fed unpelleted diets.
Redução do nível de proteína bruta em rações para frangos de corte em ambiente de termoneutralidade

The objective of this experiment was to evaluate the effects of dietary crude protein (CP) level reduction of ration formulated according to ideal protein concept and with supplementation of industrial amino acids on the performance and yield of noble cuts of broilers from 22 to 42 days of age kept under thermoneutral conditions. It was used 280 "Cobb" male broilers with initial weight of 856 ± 6.48 g, distributed in a completely randomized experimental design, with five treatments (21.6; 20.6; 19.6; 18.6 and 17.6% CP) and eight replications with seven birds per experimental unit. Temperatures inside the rooms were maintained at 21.6 ± 0.7°C, relative humidity at 74.4. 0% and black globe temperature of 22.5 ± 0.7°C. Black globe temperature and humidity index (BGHTI) calculated for a period of 70 ± 0.9. There was no effect of the reduction of the levels of CP on weight gain and on feed intake but feed conversion was influenced by the reduction of the CP levels, and the birds fed diet with 22.0% of CP presented a better result. The reduction of the levels of CP did not influence absolute carcass weight and absolute and relative weights of breast, thigh and drumstick. Reduction of the level of dietary CP from 21.6 to 17.6% and formulated according to ideal protein concept worsens feed conversion of broilers kept in thermoneutral environment, not influencing the other studied variables.
Mechanisms of Weed Suppression in Cover Crop-based Production Systems

Field and laboratory studies were conducted to investigate the mechanisms of weed suppression by cover crops. High-performance liquid chromatograph analysis and a seed germination bioassay demonstrated that rye (Secale cereale L.) can be leached of its allelochemicals, redried, and used as an inert control for separating physical suppression from other types of interference. In a field study, rye, crimson clover (Trifolium incarnatum L.), hairy vetch (Vicia villosa Roth.), barley (Hordeum vulgare L.), and a mixture of the four species suppressed the emergence of eastern black nightshade (Solanum ptycanthum Dun.). Crimson clover inhibited the emergence of eastern black nightshade beyond what could be attributed to physical suppression alone. The emergence of yellow foxtail [Setaria glauca (L.) Beauv. ] was inhibited by rye and barley but not by the other cover crops or the cover crop mixture.
Reproductive abnormalities in glyphosate-resistant cotton caused by lower CP4-EPSPS levels in the male reproductive tissue

Abstract Glyphosate treatments to glyphosate-resistant (GR) cotton have been associated with poor pollination and increased boll abortion. Anatomical studies were conducted to characterize the effect of glyphosate treatments on the development of male and female reproductive organs of cotton flowers at anthesis. In comparison with nontreated plants, glyphosate applied at both the four-leaf stage postemergence (POST) and at the eight-leaf stage POST directed inhibited the elongation of the staminal column and filament, which increased the distance from the anthers to the receptive stigma tip by 4.9 to 5.7 mm during the first week of flowering. The increased distance from the anthers to the stigma resulted in 42% less pollen deposited on stigmas of glyphosate-treated plants than in nontreated plants. Moreover, pollen from glyphosate-treated plants showed numerous morphological abnormalities. Transmission electron microscopy showed the presence of large vacuoles, numerous starch grains, and less organized pockets of the endoplasmic reticulum containing fewer ribosomes in pollen from glyphosate-treated plants than from nontreated plants. Pollen development in glyphosate-treated plants is likely inhibited or aborted at the vacuolate microspore and vacuolate microgamete stages of microgametogenesis, resulting in immature pollen at anthesis. Although stigmas from glyphosate-treated plants were 1.2 to 1.4 mm longer than those from nontreated plants, no other anatomical differences in stigmas were visibly evident. The presence of the GR 5-enolpyruvylshikimate-3-phosphate synthase (CP4-EPSPS) enzyme from Agrobacterium sp. strain CP4 was quantified in reproductive and vegetative tissues using enzyme-linked immunosorbent assay. The content of CP4-EPSPS in the stigma, anther, preanthesis floral bud (square), and flower petals was significantly less than that in the vegetative leaf tissue. Glyphosate effects on the male reproductive development resulting in poor pollen deposition on the stigma, as well as production of aborted pollen with reduced viability, provide a likely explanation for reports of increased boll abortion and pollination problems in glyphosate-treated GR cotton. Nomenclature: Glyphosate; cotton, Gossypium hirsutum L. ‘Delta Pine & Land 5415RR’, ‘Delta Pine & Land 50’, ‘Delta Pine & Land 90’, ‘SureGrow 125RR’.
The Alcoholic Ferment of Yeast-Juice. Part II.--The Conferment of Yeast-Juice

In a previous communication it was shown that the fermentation of glucose by yeast-juice is dependent upon the presence of a dialysable substance which is not destroyed by heat. This substance is contained in the active yeast-juice prepared by disintegrating living yeast, and, therefore, most probably exists in the yeast cell side by side with the zymase. The occurrence of an analogous activating substance has been described by Magnus in the case of the lipase of the liver. He observed that the active juice of this organ became inactive when dialysed into water, but regained its activity when the dialysate or boiled liver juice was added. The term coferment was suggested by Bertrand to denote substances of this kind, and he applied it in two instances—to the calcium salt, which he considered was necessary for the action of pectase on pecten substances, and to the manganese of laccase, which he supposed to be essential for the activity of this enzyme. Although not entirely satisfactory, this term may be provisionally applied to activating substances such as those present in liver lipase and yeast-juice, until further knowledge of their nature and function permits of a more rational terminology.
Management of root rot disease of groundnut (Arachis hypogeae L.) by plant extracts

A field experiment was conducted during 2009 to 2010 crop season in district Chakwal to evaluate the efficiency of aqueous extracts of five plant species, namely Allium cepa L. (onion), Allium sativum L. (garlic), Boerhaavia diffusa auct. Plur. , Calotropis procera (Aiton) W.T. Aiton. , Cannabis sativa L. , and two fungicide antracol and ridomil and both fungicides in mixture form, to manage the root rot disease of groundnut ( Arachis hypogeae L.) caused by a fungal pathogen Fusarium solani (Mart) Sacc. Fusarium inoculation showed 98% disease incidence with 22% mortality. Recommended dose of the chemical fungicides antracol and ridomil significantly reduced the disease incidence to 17 and 18%, respectively and mortality to 10% each separately. Fungicides in mixture form reduced the disease and mortality to 10 and 7%, respectively. Plant extract treatments exhibited variable effects on the incidence of the disease and mortality of plants. In general, all the test plant extracts managed the root rot disease to varying degrees. Aqueous bulb extracts of A. sativum and A. cepa and the leaf extract of C. procera showed better disease management potential than that of the recommended doses of antracol and ridomil. Fusarium inoculation significantly declined plant growth. In general, antracol and ridomil, as well as aqueous extracts, enhanced plant growth to variable degrees as compared to the Fusarium control.
Estimation of sustained peak yield interval of dairy cattle lactation curves using a broken-line regression approach

A broken-line regression model with three straight lines and two breakpoints was used to estimate the sustained peak yield of the lactation curve. A sample of 1548 lactation records of 425 Holstein-Friesian cows was provided by the Research and Application Farm of the Agriculture Faculty of Cukurova University in Adana, Turkey. A total of 13463 test-day milk yields (kg/day), recorded once a month with electronic identification and automatic milking recording systems, between November 1994 and January 2006, were used. The data was classified as first, second, third, fourth, fifth, sixth and seventh parity, and included 4105, 3238, 2495, 1800, 1113, 641 and 71 test-day records, respectively. Times (days) at the beginning and end of sustained peak yield per parity were 73.9 - 160.2, 70.6 - 131.9, 70.8 - 130.7, 71.0 - 130.3, 71.3 - 130.4, 71.2 - 128.2 and 71.1 – 129.8, respectively. The peak yields of lactation curves were 19.1 kg/d, 21.8 kg/d, 23.8 kg/d, 24.2 kg/d, 24.2 kg/d 24.4 kg/d and 21.3 kg/d, and days in milk (DIM) at peak yields of lactation curves per parity were 126, 103, 102, 104, 106, 103 and 104, respectively. Persistency values (days) and total lactation milk yields (kg/lactation) per parity were 86.4, 61.3, 59.9, 59.3, 59.1, 57.0, 58.7 and 4852.2, 5105.7, 5503.5, 5503.7, 5449.3, 5416.3, 4802.4, respectively. Results showed that the first parity had a lactation curve with the lowest milk yield at peak that reached the peak point at the latest time (DIM) after parturition, but the largest interval between the beginning and end of the sustained peak yield among all parities. This means that the cows in the first lactation were more persistent than those in the later lactations.
Estimating tree biomass and changes in root biomass following clear-cutting of Brachystegia-Julbernardia (miombo) woodland in central Zambia

SUMMARY This study aimed at developing allometric models from destructive sample field data for estimating both aboveground and belowground tree biomass and assessing changes in root biomass after old-growth Brachystegia-Julbernardia (miombo) woodland clearing in central Zambia. Logarithmic linear models were selected for estimating tree biomass because they gave the most accurate (low mean error) predictions. On average aboveground and belowground biomass in regrowth woodland represented 29% and 41%, respectively, of the biomass in old-growth woodland. The root:shoot ratios were 0.54 and 0.77 in old-growth and regrowth woodland, respectively. Ten years after clear-cutting old-growth woodland, root biomass loss was about 60% of the original biomass. The main cause of post clearing root biomass loss was fire which at the study sites occurred annually or biannually. Control of fire in cleared sites should be encouraged in forest management for carbon storage and sequestration in miombo woodland of southern Africa.
Complementary impacts of small rodents and semi‐domesticated ungulates limit tall shrub expansion in the tundra

Summary 1. While shrubs appear to be expanding in Arctic tundra due to climatic warming, patches of tall shrubs in riparian habitats are most likely to colonize new areas. Shrub recruits outside established patches represent the forefront of area expansion, but their dynamics may be sensitive to the action of several herbivore species. The empirical evidence for how different-sized herbivores affect recruits of tall shrubs is lacking. Moreover, although management and natural population dynamics of herbivores happens at landscape and regional scales, field research on herbivore impacts on shrubs seldom covers these scales. 2. Reindeer management and different rodent population dynamics result in regional variation in herbivore abundances in arctic Norway. We conducted an herbivore exclusion experiment, covering three low-arctic river catchments with contrasting herbivore abundances. We assessed the impacts of small rodents and reindeer on growth, and survival of willow Salix spp. recruits after 3 years of herbivore exclusion. 3. As expected, the Salix recruits increased in sizes and had lower mortality when released from herbivores. Both types of herbivores had strong impacts on size and survival of Salix recruits. 4. Spatially contrasting results were consistent with regional differences in the abundance of reindeer and rodents; herbivore impacts on shrubs were found when at least one type of herbivore was abundant. However, the impact was not independent of herbivore species. While both browsing from reindeer and rodents pruned the recruits and prevented them from escaping the field layer, the rodents also inflicted substantial mortality and thus thinned the stand of recruits. 5. Synthesis and applications. Sympatric populations of rodents and reindeer have strongly complementary impacts on shrub recruits and may limit the expansion potential of tall shrubs even in the most productive habitats of arctic tundra. The spatial correspondence between shrub recruits performance and herbivore abundances, found after a short time period, suggests that the extent of tall shrub expansion in tundra is contingent on current variation and future trends in herbivore populations. In areas where humans control large herbivore populations, management may opt to counteract climate-driven shrub expansion also in habitats that are most prone to such expansion.