Miracle-dz/UniFAR-FTUs huggingface dataset:
Dopamine-induced exocytosis of Na,K-ATPase is dependent on activation of protein kinase C-ε and -δ

The purpose of this study was to define mechanisms by which dopamine (DA) regulates the Na,K-ATPase in alveolar epithelial type 2 (AT2) cells. The Na,K-ATPase activity increased by twofold in cells incubated with either 1 microM DA or a dopaminergic D(1) agonist, fenoldopam, but not with the dopaminergic D(2) agonist quinpirole. The increase in activity paralleled an increase in Na,K-ATPase alpha1 and beta1 protein abundance in the basolateral membrane (BLM) of AT2 cells. This increase in protein abundance was mediated by the exocytosis of Na,K-pumps from late endosomal compartments into the BLM. Down-regulation of diacylglycerol-sensitive types of protein kinase C (PKC) by pretreatment with phorbol 12-myristate 13-acetate or inhibition with bisindolylmaleimide prevented the DA-mediated increase in Na,K-ATPase activity and exocytosis of Na,K-pumps to the BLM. Preincubation of AT2 cells with either 2-[1-(3-dimethylaminopropyl)-5-methoxyindol-3-yl]-3-(1H-indol-3-yl)maleimide (Go6983), a selective inhibitor of PKC-delta, or isozyme-specific inhibitor peptides for PKC-delta or PKC-epsilon inhibited the DA-mediated increase in Na,K-ATPase. PKC-delta and PKC-epsilon, but not PKC-alpha or -beta, translocated from the cytosol to the membrane fraction after exposure to DA. PKC-delta- and PKC-epsilon-specific peptide agonists increased Na,K-ATPase protein abundance in the BLM. Accordingly, dopamine increased Na,K-ATPase activity in alveolar epithelial cells through the exocytosis of Na,K-pumps from late endosomes into the basolateral membrane in a mechanism-dependent activation of the novel protein kinase C isozymes PKC-delta and PKC-epsilon.
Intracellular peptide library screening to derive inhibitors of Parkinson's disease associated α-synuclein aggregation

Aggregation of α-synuclein (α-syn) into toxic fibrils is a pathogenic hallmark of Parkinson’s disease (PD). This research aimed to develop peptides capable of inhibiting α-syn aggregation using a semi-rational design combined with a multiplexed intracellular Protein-fragment Complementation Assay (PCA) library screening system. Successfully selected peptides must bind to full length α-syn and lower its toxicity to confer bacterial growth. PCA selected peptides were characterized using several biophysical assays and a cell viability assay. The peptides were screened using library templates based on α-syn71-82 initially and later on the α-syn45-54 region in which many key mutations associated with early onset PD are found. In both cases we targeted the peptide libraries at the wild type protein or again by using mutated versions of α-syn. Results demonstrate that some of those selected peptides had the effect of delaying or even preventing the aggregation process, with others providing more subtle effects in reversing the fully formed amyloid fibrils. PCA peptides selected against 71-82 region of wild type α-syn showed a moderate level of efficacy whereas against mutants, it showed a low level of efficacy in inhibiting amyloid fibril formation. In the final part of the study, the peptide selected against 45-54 region of wild type α-syn was capable of preventing the aggregation and reducing the amyloid cytotoxicity at an equimolar ratio. We have thus demonstrated that the PCA strategy can be used as a generalised method for deriving peptide antagonists of α-syn aggregation, together with a new region; α-syn45-54 as an inhibitor target and produced a peptide inhibitor expected to provide a scaffold for future drug candidates to slow or even prevent the onset of PD.
The uncoupling of oxidative phosphorylation in pea shoot mitochondria by 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) and related compounds

SUMMARY The effect of the new herbicide, ioxynil, and several related compounds, on the oxidative phosphorylation of respiring, isolated pea shoot particles has been studied. Ioxynil and its analogues were found to depress the uptake of inorganic phosphate and, to a lesser extent, of oxygen by the particles; the calculated P/O ratio was eventually reduced to zero. The effect of ioxynil was far greater than that of the well-known uncoupling agent 2,4-dinitrophenol and was similar in magnitude to that of the contact herbicide dinitro-ortho-cresol.
Dismissal of Acoelomorpha: Acoela and Nemertodermatida are separate early bilaterian clades

We used new 18S and 28S rRNA sequences analysed with parsimony, maximum likelihood and Bayesian methods of phylogenetic reconstruction to show that Nemertodermatida, generally classified as the sister group of Acoela within the recently proposed Phylum Acoelomorpha, are a separate basal bilaterian lineage. We used several analytical approaches to control for possible long branch attraction (LBA) artefacts in our results. Parsimony and the model based phylogenetic reconstruction methods that incorporate ‘corrections’ for substitution rate heterogenities yielded concordant results. When putative long branch taxa were experimentally removed the resulting topologies were consistent with our total evidence analysis. Deletion of fast‐evolving nucleotide sites decreased resolution and clade support, but did not support a topology conflicting with the total evidence analysis. Establishment of Acoela and Nemertodermatida as two early lineages facilitates reconstruction of ancestral bilaterian features. The ancestor of extant Bilateria was a small, benthic direct developer without coelom or a planktonic larval stage. The previously proposed Phylum Acoelomorpha is dismissed as paraphyletic.
Diet of Crotalus lepidus klauberi (Banded Rock Rattlesnake)

Abstract We describe the diet of Crotalus lepidus klauberi (Banded Rock Rattlesnake) using samples collected in the field and from museum specimens, as well as several records from unpublished reports. Most records (approximately 91%) were from the northern Sierra Madrean Archipelago. Diet consisted of 55.4% lizards, 28.3% scolopendromorph centipedes, 13.8% mammals, 1.9% birds, and 0.6% snakes. Sceloporus spp. comprised 92.4% of lizards. Extrapolation suggests that Sceloporus jarrovii represents 82.3% of lizard records. Diet was independent of geographic distribution (mountain range), sex, source of sample (stomach vs. intestine/feces), and age class. However, predator snout–vent length differed significantly among prey types; snakes that ate birds were longest, followed in turn by those that ate mammals, lizards, and centipedes. Collection date also differed significantly among prey classes; the mean date for centipede records was later than the mean date for squamate, bird, or mammal records. We found no difference in the elevation of collection sites among prey classes.
Molecular Pathogenesis of Genetic and Inherited Diseases Transgenic Expression of 7 1 Integrin Maintains Muscle Integrity, Increases Regenerative Capacity, Promotes Hypertrophy, and Reduces Cardiomyopathy in Dystrophic Mice

We previously reported that enhanced expression of the 7 1 integrin ameliorates the development of muscular dystrophy and extends longevity in 7BX2mdx/utr / transgenic mice (Burkin DJ, Wallace GQ, Nicol KJ, Kaufman DJ, Kaufman SJ: Enhanced expression of the 7 1 integrin reduces muscular dystrophy and restores viability in dystrophic mice. J Cell Biol 2001, 152:1207–1218). We now report on the mechanism by which these mice were rescued by the integrin. As a result of increased integrin in 7BX2-mdx/ utr / mice the structural integrity of the myotendinous and neuromuscular junctions are maintained. A twofold increase in satellite cells in 7BX2-mdx/utr / skeletal muscle was detected by immunofluorescence using the satellite cell marker c-met. These cells enhanced the regenerative capacity of muscle in the transgenic animals as determined by fusion of BrdUrd-labeled cells into muscle fibers. Increased integrin also leads to hypertrophy. Finally, transgenic expression of 7BX2 integrin chain in skeletal muscle secondarily reduces the development of cardiomyopathy, the ultimate cause of death in these animals. We believe this multiplicity of responses to increased 7 1 integrin collectively inhibits the development of muscle disease and increases longevity in these mice. (Am J Pathol 2005, 166:253–263)
Diet selection and density estimates of forest buffalo in Campo-Ma'an National Park, Cameroon

We studied diet selection and density of forest buffalo in the Campo Ma’an National Park of southern Cameroon. The buffalo’s diet in this rainforest comprised 43% grass, including 15% Leptochloa caerulecens. Other species eaten were non-graminoid monocots (21.3%), mainly Commelinaceae (18.2%), including Palisota spp. and dicotyledons (32.7%), mainly leaves (26.5%). This diet revealed that buffalo collect their food on road verges, logging tracks and along large rivers. This agrees well with the distribution of buffalo tracks in the study area. Mean buffalo density in the forest was only 0.01 buffalo km )2 , whereas the density on the road together with its direct surroundings was 0.4 buffalo per km of road. We estimated the total number of buffalo in the 650 km 2 southern part of National Park Campo-Ma’an of only twenty individuals. We suggest that the buffalo’s ancestral niche was not a primeval type of rainforest, as suggested by Kingdon, but an interface between savanna and rainforest. The Campo-Ma’an buffalo most likely depend to a very large extent on anthropogenic vegetation types. Maintaining some grass cover by annual clear-cutting along roads and on logging tracks might be necessary for the survival of the buffalo population within the National Park.
Comparison of scales used for categorising the development of wheat, barley, rye and oats

Summary A review of the scales used to assess the development of cereals is presented. Twenty-three scales are identified and they are separated into those that codify the external development of plants and those that describe events at the apical meristem. Comparison of the scales is made for wheat, barley, rye and oats, where this is possible. Attention is drawn to the divergence in the descriptions of similar plants on different scales. Theoretical aspects of the general usage of developmental scales are also discussed.
The economics of fertility in the dairy herd

A method to establish the economic optimum (minimum) cost of fertility in the dairy herd is described and demonstrated. A Markov chain model is used iteratively to establish the gross margin of the herd in the long term at various levels of oestrous detection rate and under two different rebreeding strategies. These gross margins are required by the optimization methodology. Under the initial assumptions reflecting current commercial practice in the United Kingdom, gross margin was £806 per cow. This figure varied by proportionately 0·15 over the range of oestrous detection rates assumed (0·4 to 0·7) while delaying rebreeding by 20 days caused gross margin to drop by approximately 0·04. It was concluded that it is important to optimize fertility control as well as rebreeding strategy in order to establish the economic impact of fertility in the dairy herd. The economic value of fertility was also expressed per unit of calving interval and adjusted calving interval (ACI). ACI was calculated by dividing calving interval by the proportion of cows not culled for reproductive failure. Under the assumptions made, the marginal value of calving interval at the optimum oestrous detection rate was £6·22 per day, rising to £7·44 per day if rebreeding was delayed. The corresponding figures for ACI were £1·57 per day and £1·24 per day. The range in marginal values at sub-optimal oestrous detection rates were £4·38 for calving interval and £0·61 for ACI. It was concluded that the lower variation in ACI at different levels of fertility may make it a more representative trait for inclusion in a selection index provided the necessary genetic parameters can be reliably estimated.
RESTITUTION OF MASS–SIZE RESIDUALS: VALIDATING BODY CONDITION INDICES

Body condition can have important fitness consequences, but measuring body condition of live animals from wild populations has been the subject of much recent debate. Using the residuals from a regression of body mass on a linear measure of body size is one of the most common methods of measuring condition and has been used in many vertebrate taxa. Recently, the use of this method has been criticized because assumptions are likely violated. We tested several assumptions regarding the use of this method with body composition and morphometric data from five species of small mammals and with statistical simulations. We tested the assumptions that the relationship between body mass and body size is linear, and that the proportion of mass associated with energy reserves is independent of body size. In addition, we tested whether the residuals from reduced major axis (RMA) regression or major axis (MA) regression performed better than the residuals from ordinary least squares (OLS) regression as indices of body condition. We found no evidence of nonlinear relationships between body mass and body size. Relative energy reserves (fat and lean dry mass) were generally independent or weakly dependent on body size. Residuals from MA and RMA regression consistently explained less variation in body composition than OLS regression. Using statistical simulations, we compared the effects of violations of the assumption that true condition and residual indices are independent of body size on the OLS, MA, and RMA procedures and found that OLS performed better than the RMA and MA procedures. Despite recent criticisms of residuals from mass-size OLS regressions, these indices of body condition appear to satisfy critical assumptions. Although some caution is warranted when using residuals, especially when both inter- individual variation in body size and measurement error are high, we found no reason to reject OLS residuals as legitimate indices of body condition.
Investigation of the influence of prescribed burning on ITS profiles of ectomycorrhizal and other soil fungi at three Australian sclerophyll forest sites

DNA was extracted from soil collected from the upper 15 cm of the profile at three sclerophyll forest sites in New South Wales three days before, and 14 d after prescribed burning events. rDNA internal transcribed spacer (ITS) regions were amplified by PCR using fungus-specific primers, and ITS products cloned. Restriction fragment length polymorphism (RFLP) analysis was conducted on the ITS clones using the endonucleases HaeIII, Hinfl, Mbol and Alul. Cloned ITS products from the three sites were thus separated into 120 RFLP types and the ITS product for each RFLP type was sequenced. Comparison of sequences with those available in the GenBank nucleotide database allowed putative assignment of ITS clones to the following functional groups: ectomycorrhizal (ECM), arbuscular mycorrhizal (AM), ericoid mycorrhizal (ERM), decomposer basidiomycetes (DEC), other soil fungi (OSF). While abundant ECM-like clones were amplified from pre-fire soils at the North Rocks and South Maroota sites, they were largely absent in the post-fire soils at these sites, being replaced mainly by microfungi. In contrast, no decrease in ECM-like ITS clones was observed at the Ridgecrop site following fire. The data indicate that, while the abundance of extraradical ECM fungal propagules in the upper soil profile may be reduced by prescribed burning, the effect is site-specific.
A Literature Review Based on the uses of System Dynamics Model in the Perspective of Supply Chain Management

The use of System Dynamics Modeling in Supply Chain Management has recently re-emerged after a lengthy slack period. Current research on System Dynamics Modeling in supply chain management focuses on inventory decision and policy development, time compression, demand amplification, supply chain design and integration, and international supply chain management. The paper first gives an overview of recent research work in these areas, followed by a discussion of research issues with a vast literature reviews, and it is also an attempt to simulate the behaviors’ of a Supply Chain Management Model using System Dynamics principle. Keywords- Simulation; Supply Chain Management; System Dynamic Model
Warmer more acidic conditions cause decreased productivity and calcification in subtropical coral reef sediment‐dwelling calcifiers

The effects of elevated CO2 and temperature on photosynthesis and calcification in the calcifying algae Halimeda macroloba and Halimeda cylindracea and the symbiont‐bearing benthic foraminifera Marginopora vertebralis were investigated through exposure to a combination of four temperatures (28°C, 30°C, 32°C, and 34°C) and four CO2 levels (39, 61, 101, and 203 Pa; pH 8.1, 7.9, 7.7, and 7.4, respectively). Elevated CO2 caused a profound decline in photosynthetic efficiency (FV : FM), calcification, and growth in all species. After five weeks at 34°C under all CO2 levels, all species died. Chlorophyll (Chl) a and b concentration in Halimeda spp. significantly decreased in 203 Pa, 32°C and 34°C treatments, but Chl a and Chl c2 concentration in M. vertebralis was not affected by temperature alone, with significant declines in the 61, 101, and 203 Pa treatments at 28°C. Significant decreases in FV : FM in all species were found after 5 weeks of exposure to elevated CO2 (203 Pa in all temperature treatments) and temperature (32°C and 34°C in all pH treatments). The rate of oxygen production declined at 61, 101, and 203 Pa in all temperature treatments for all species. The elevated CO2 and temperature treatments greatly reduced calcification (growth and crystal size) in M. vertebralis and, to a lesser extent, in Halimeda spp. These findings indicate that 32°C and 101 Pa CO2, are the upper limits for survival of these species on Heron Island reef, and we conclude that these species will be highly vulnerable to the predicted future climate change scenarios of elevated temperature and ocean acidification.
Biochemical response of mungbean (Vigna radiata L.) under the influence of reduced dose of chemical fertilizer and different time and method of application of biofertilizer.

Fundamental differences between organic and conventional production systems, particularly in soil fertility management, may affect the nutritive composition of plants, including secondary plant metabolites. The availability of inorganic nitrogen in particular has the potential to influence the synthesis of secondary plant metabolites, proteins, and soluble solids. This study was conducted to evaluate the on-farm assessment of biochemical changes in leaves of mungbean by employing different varieties and different treatments such as different reduced doses of N:P:K chemical fertilizer, different method and time of application of biofertilizer. Untreated seeds were used as control. PDM-11 variety showed higher accumulation of chlorophyll, sugar, protein in leaves and PUSHA-9531 reported higher accumulation of amino acid content in leaves. Significant level of variation was observed in the level of plant metabolites and macromolecules in seeds among the six studied mungbean varieties.
New Klebsiella Capsular Antigen, K82, and the Deletion of Five of Those Previously Assigned

A new Klebsiella capsular antigen, K82, is established. K73, K75, K76, K77, and K78 are deleted from the scheme. K73 is a strain of Enterobacter aerogenes, and the others are identical to or in practice serologically indistinguishable from previously established K antigens. The deleted numbers will not be assigned by our laboratories to any new K antigen.
Phytoremediation of heavy metals: Recent techniques

The current remediation technique of heavy metal from contaminated soil-water are expensive, time consuming and environmentally destructive. Unlike organic compounds, metals cannot degrade, and therefore effective cleanup requires their immobilization to reduce or remove toxicity. In recent years, scientists and engineers have started to generate cost effective technologies that include use of microorganisms/biomass or live plants to clean polluted areas. Phytoremediation is an emerging technology for cleaning up contaminated sites, which is cost effective, and has aesthetic advantages and long term applicability. It is best applied at sites with shallow contamination of organic, nutrient or metal pollutants that are amenable to one of the five applications; phytotransformation, rhizosphere bioremediation, phytostabilization, phytoextraction and rhizofiltration. The technology involves efficient use of plants to remove, detoxify or immobilize environmental contaminants in a growth matrix (soil, water or sediments) through the natural, biological, chemical or physical activities or processes of the plants. A brief review on phytoremediation of heavy metals and its effect on plants have been compiled to provide a wide applicability of phytoremediation.
Retrobiosynthetic study of salicylic acid in Catharanthus roseus cell suspension cultures

Salicylic acid (SA) is an important signal compound in systemic acquired resistance in plants. The level of this C6C1 compound in plants increases after a pathogenic attack. There are two biosynthetic pathways of SA, the phenylalanine pathway, which is thought to occur in plants, and the isochorismate pathway, which is found in microorganisms. The biosynthetic pathway of SA in plant is still a matter of debate and some studies showed that the presence of the microbial pathway in plants is also plausible. The present study deals with the production of SA in Catharanthus roseus cell suspension cultures after elicitation with a fungal elicitor (Pythium aphanidermatum extract), the development of a purification method for salicylic acid from plant extract using an ion exchange chromatography, 13C-NMR analysis of purified SA-containing extracts of Catharanthus roseus cells after a labeling experiment with [1-13C]glucose and metabolic profiling of Catharanthus roseus cells elicited with SA. Catharanthus roseus is an important medicinal plant for the production of the anti-tumor agents vincristine and vinblastine, and an excellent model for a retrobiosynthetic study as shown in some studies. We showed by chemistry that in Catharanthus roseus cell suspension cultures, SA is synthesized via the isochorismate pathway.
Organogenesis, Differentiation and Histolocalization of Alkaloids in Cultured Tissues and Organs of Duboisia myoporoides R. Br.

Abstract Duboisia myoporoides R. Br. shoots were regenerated from non-organogenic and organogenic calli induced with nine different cytokinin/auxin combinations. Alkaloid colour reagents localized tropane alkaloids in the vascular regions which had large cells in the secondary xylem of the basal stem sections of the non-rooted shoots. Tropane alkaloids were localized in shoots regenerated from calli induced with two different cytokinin/auxin combinations. No alkaloids were localized in shoots regenerated from calli induced with other cytokinin/auxin combinations. However, only nicotine was detected by GC-MS in the non-rooted shoots regenerated from calli induced with three different cytokinin/auxin combinations. Tropane alkaloids were also localized in xylem cells of roots regenerated from calli induced with two different cytokinin and auxin combinations independently. The presence or absence of nicotine, hyoscyamine and scopolamine in different cultured plant materials was confirmed by GC-MS, indicating that although the root is the main site for alkaloid biosynthesis, with suitable cell differentiation, alkaloid biosynthesis may take place in cultured shoots without root initiation.