Miracle-dz/UniFAR-FTUs huggingface dataset:
The role and epigenetic regulation of the CDX gene family in human cancer

The caudal (Cdx) family of DNA binding proteins was originally identified in Drosophila ; however, homologues with conserved molecular structure and function have been described in several organisms including humans. The three members of the Cdx family in mice and humans, Cdx1 , Cdx2 , and Cdx4 , have been intensively studied for their involvement in axial elongation and early antero-posterior patterning. Cdx1 and Cdx2 regulate cell growth and differentiation, and they are involved in embryonic development of the intestinal tract, intestinal inflammation and tumorigenesis. In colon cancer, CDX1 and CDX2 suppress colon cell proliferation, migration and invasion by inhibiting β-catenin/TCF transcriptional activity. The expression of CDX1 and CDX2 exists in intestinal metaplasia but not in normal gastric and esophageal mucosa. CDX genes are overexpressed in leukemias. The changes in expression levels of Cdx genes correlate with oncogenic transformation. CDX2 serves as a Wnt signaling inhibitor and is frequently methylated in lung cancer. CDX2 methylation is also a feature of human esophageal squamous cancer, and it may serve as a cancer detection marker.
Indigenous chicken genetic resources in Kenya: their unique attributes and conservation options for improved use

The indigenous chicken (Gallus gallus domesticus) genetic resources (IC) comprise more than 80% of the overall poultry population in rural villages despite their low productivity. However, a holistic approach that increases productivity without increasing production costs or leading to loss of biodiversity is presently limited. Conversely, in most developing countries, there is almost no organizational structure for breeding programmes for improving and conserving IC. These locally adapted IC can only be conserved in the most rational and sustainable way by ensuring that they are functional part of different production systems. Their conservation should be through utilisation if they are to be of any benefit to the poor rural households. This discussion focuses on five very relevant questions that need to be answered if the conservation of IC is to be effective and sustainable: What, why and how should we conserve, who are the stakeholders and what are their roles in conservation efforts?
Amino acid composition of degradation-resistant peptides in extracellular rumen fluid of sheep

SUMMARY Rumen fluid was removed from four sheep 6 h after feeding, and the fluid was centrifuged to remove the micro-organisms. Perchloric acid (PCA) was added to the supernatant fluid to precipitate soluble proteins, which were again removed by centrifugation. The PCA extract was neutralized with KOH and the precipitate was removed by centrifugation. The supernatant fluid was hydrolysed with 6 MHC1 at 110 °C for 24 h, then dried by rotary evaporation, and the amino acid composition of each extract was analysed by ion-exchange chromatography. The recovery of amino acids was 98%, except for methionine, cysteine and tryptophan, which were destroyed. The recovery of amino acids from added Trypticase was 92% of the peptide mixture as amino acids. The free amino acid composition of extracellular rumen fluid was low and variable in both amount and composition (0·36, S.D. 0·49, μmol/ml). The concentration of amino acids released by acid hydrolysis of the PCA extract, presumed to be derived from peptides, was larger and its composition was less variable (1 ·02, S.D. 0·30, μmol/ml). Aspartic acid and histidine were enriched in peptides in comparison with the amino acids present in the feed or in rumen particulate material. Glycine and proline contents were higher in peptides that in particulate material. In contrast, the contents of isoleucine, leucine, tyrosine and phenylalanine tended to be lower in peptides than in the other materials. It was concluded that extracellular degradation-resistant peptides had a composition that was different to microbial protein and to the feed. The peptides appeared to be enriched for amino acids which previous studies with pure peptides had shown tend to make peptides more resistant to degradation.
Individual, Population, Community, and Ecosystem Consequences of a Fish Invader in New Zealand Streams

Abstract: Knowledge of the population biology of invading species will often be necessary to develop effective management procedures and policies. But because invaders can have unexpected indirect effects in food webs, invasion ecologists need to integrate processes at the population level and other ecological levels. I describe a series of coordinated studies in New Zealand streams that address the effect of an exotic fish on individual behavior, population, community, and ecosystem patterns. Such case studies are important as an aid to the formulation of policy about invasions that are especially likely to become problematic. At the individual level, grazing invertebrates showed changes in behavior as a result of the introduction of brown trout ( Salmo trutta), a predator that exerts a very different selection pressure than do native fish. At the population level, trout have replaced nonmigratory galaxiid fish in some streams but not others, and have affected the distributions of crayfish and other large invertebrates. At the community level, trout have suppressed grazing pressure from invertebrates and are thus responsible for enhancing algal biomass and changing algal species composition. Finally, at the ecosystem level, essentially all annual production of invertebrates is consumed by trout ( but not by galaxiids), and algal primary productivity is six times higher in a trout stream. This leads, in turn, to an increased flux of nutrients from the water to the benthic community. The trout invasion has led to strong top‐down control of community structure and ecosystem functioning via its effects on individual behavior and population distribution and abundance. Particular physiological, behavioral, and demographic traits of invaders can lead to profound ecosystem consequences that managers need to take into account.
Characterization of the adhesion genes of probiotic lactic acid bacteria

Expression of the mucus adhesion genes mub and mapA, adhesion-like factor EF-Tu and bacteriocin gene plaA by Lactobacillus plantarum 423, and expression of mub, slp and EF-Tu by Lactobacillus acidophilus ATCC 4356, grown in the presence of mucin, bile, pancreatin and at low pH, was studied by real time PCR. mub, mapA and EF-Tu of strain 423 were up-regulated in the presence of mucus, proportional to increasing concentrations. Expression of mapA by strain 423 was up-regulated in the presence of 0.3% (w/v) bile and 0.3% (w/v) pancreatin at pH 6.5. Similar results were recorded in the presence of 1.0% (w/v) bile and 1.0% (w/v) pancreatin at pH 6.5. Expression of mub, on the other hand, was downregulated in the presence of bile and pancreatin at pH 6.5, whilst the expression of EF-Tu and plaA remained unchanged under these conditions at pH 6.5. Expression of mapA and mub by strain 423 remained unchanged at pH 4.0, whilst expression of EF-Tu and plaA were up-regulated. Expression of mapA was downregulated in the presence of 0.1% (w/v) cysteine, suggesting that the gene is regulated by a mechanism of transcription attenuation that involves cysteine. In the case of strain ATCC 4356, none of the genes were up-regulated under increasing concentrations of mucin, whilst slp and EF-Tu were up-regulated under normal and stress conditions. Expression of mub was not affected under normal conditions but was down-regulated under stress conditions. Stellenbosch University http://scholar.sun.ac.za
Perspectives on photoinhibition and photorespiration in the field: quintessential inefficiencies of the light and dark reactions of photosynthesis?

Taking the long-held view that photoinhibition embraces several processes leading to a reduction in the efficiency of light utilization in photosynthesis, and that photorespiration embraces several processes associated with 02 uptake in the light, photoinhibition and photorespiration now can be considered as inevit able, but essential inefficiencies of photosynthesis which help preserve photosynthetic competence in bright light. Photorespiratory 02 uptake via Rubisco, and 02 uptake via the Mehler reaction, both promote non-assimilatory electron transport, and stimulate photon utilization during C02-Iimited photosynthesis in bright light. Although fluorescence studies show that the proportion of total photon use via oxygenase photorespiration in air may decline to only about 10% in full sunlight, mass spectrometer studies show that 02 uptake in Mehler reaction photorespiration in C3 and CAM plants can still account for up to 50% of electron flow in saturating C02 and light. The Mehler ascorbate peroxidase reaction has an additional role in sustaining membrane energization which promotes dynamic photoinhibition and photon protection (rapidly reversible decrease in PSII efficiency involving dissipa tion of the energy of excess photons in the antennae). Net C02 and 02 exchange studies evidently underesti mate the extent of total electron transport, and hence overestimate the extent of photon excess in bright light, leading to overestimates of the role of energy dependent photon dissipation through dynamic photo inhibition. Nevertheless, in C3 plants in air all of these processes help to mitigate chronic photoinhibition and photon damage (slowly reversible decrease in PSII effi ciency involving loss of reaction centre function). The possibility remains that residual electron transport to 02 from intermediates in the vicinity of PSII may also lead to reactive 02 species that potentiate this photon
Observations on the biology of pandalus montagui [Crustacea: Decapoda]

An account is given of the populations of P. montagui occurring off the Northumberland coast at depths ranging from 20 to 50 fm. Sampling, which extended from 1954 to 1961, shows that the population in 20–30 fm is composed predominantly of o-group males and females and smaller numbers of 1-group females while that in 50 fm is composed predominantly of 1 and 2 group males and females. This difference can be explained in terms of sex change and migration. Eggs laid in the period from the last week in November to the first week in January hatch by the end of April. Growth of the new year-group is so rapid that they mature in time for the next breeding season. Egg numbers vary from 200 to 3000. It can be calculated that the number of larvae hatched out inshore exceeds that offshore by 15 times, but many of the larvae produced by the deep-water.
THE EFFECT OF BLUE ALGAE SPIRULINA PLATENSIS ON PIG GROWTH PERFORMANCE AND CARCASS AND MEAT QUALITY

In order to study the effect of fresh blue algae Spirulina platensis biomass on pigs fattening rate and meat quality an experiment was carried out with 85-days-old crossbreds of Landrass and Yorkshire. Two groups - control and experimental - were formed, each containing 16 pigs. Both groups of the pigs were fed standard concentrate forage. 1 kg of forage dry matter contained 13.4 MJ AE and 16 % of crude protein. The pigs of the experimental group were given daily and individually 2 g of 75 % humidity fresh blue algae Spirulina platensis biomass with forage. The pigs were weighed at the beginning and the end of the experiment. Control fattening was considered to be finished when pig weight reached 95 kg. At the end of the experiment, control slaughtering was performed. It was determined that the average daily weight gain of the pigs given 2 g of 75 % humidity fresh biomass of blue algae Spirulina platensis was by 9.26 % higher, 100 kg of weight was reached by 7.37 days faster, and the amount of AE consumed for 1 kg of weight gain was by 1.28 MJ AE lower than in the control group. Carcass output of the experimental pigs was by 2.02 % higher and the amount of intramuscular fat- by 0.33 % lower than in the control group of pigs. Keywords: blue algae Spirulina platensis, pigs, weight gain, carcass, meat quality.
A Ca2+-Dependent Transgenic Model of Cardiac Hypertrophy: A Role for Protein Kinase C&agr;

Background—Calcium imbalances have been implicated as an underlying mechanism of human cardiac dysfunction. The voltage-dependent calcium channel plays a critical role in calcium regulation in the heart. Thus, aberrant calcium signaling arising from this channel could initiate the calcium imbalances observed in heart failure. In the present study, we used a transgenic mouse with an increased number of L-type calcium channels to identify the role of an increased, sustained ingress of calcium as an initiator of hypertrophy. Methods and Results—Whole-heart histology and electrophysiology in isolated cardiomyocytes identified calcium-channel overexpression in the hearts of transgenic mice. Calcium-channel density was increased in 2-, 4-, and 8-month-old transgenic cardiomyocytes. Ventricular fibrosis, damage, and remodeling became more pronounced as the transgenic mice aged. Apoptosis was also present in transgenic hearts at 8 months of age. Increased protein kinase C&agr; activation was elevated before the development of hypertrophy and failure. Conclusions—Transgenic mice developed hypertrophy and severe cardiomyopathy as a function of age, thus confirming that changes in channel density are sufficient to induce disease. The small, sustained increase in the ingress of Ca2+ through the calcium channel elevated protein kinase C&agr; before the development of hypertrophy, suggesting that protein kinase C&agr; plays an important role in triggering hypertrophy.
Neuroprotective effects of Eriobotrya japonica and Salvia miltiorrhiza Bunge in in vitro and in vivo models

We previously reported that Eriobotrya japonica (EJ) improves the cognitive dysfunction caused by amyloid-β (Aβ) peptide injection. Here, we further examined the possible neuroprotective effects and the combined ameliorating effects of EJ and Salvia miltiorrhiza Bunge (SM) in various in vitro and in vivo models. We confirmed the combined effects of a mixture of 5% ethanol extract from EJ leaves (EJE) and water extract from SM roots (SMW) on Aβ1–42-induced toxicity in an in vitro model. Treatment with the mixture (1:1) of EJ and SM (Mix) produced significantly better protection of cells from Aβ-induced toxicity and more strongly suppressed caspase-3 activity compared to treatment with EJE or SMW alone. Additionally, EJE, SMW, and Mix attenuated CoCl2-induced hypoxic damage and corticosterone-induced impairment in SH-SY5Y cells. To examine the combined effects of EJE and SMW in in vivo models, behavioral performance in the Morris water maze was tested two days after injection of Aβ1–42. Administration of Mix provided significantly more protection of spatial learning and memory against the impairments induced by Aβ1–42 injection than did administration of EJE or SMW alone. Additionally, the behavioral deficits that accompanied Aβ-induced memory impairment were attenuated to a greater extent by the administration of the mixture. Furthermore, acetylcholinesterase (AChE) activity and neuronal apoptosis were significantly more inhibited in rats treated with Aβ and the mixture than in rats treated with Aβ1–42 alone. Thus, the results of this study indicate that the mixture of EJ and SM has combined effects that are neuroprotective against Aβ1–42-induced neuronal toxicity.
DIATOM MINERALIZATION OF SILICIC ACID. V. ENERGETIC AND MACROMOLECULAR REQUIREMENTS FOR Si(OH)4 MINERALIZATION EVENTS DURING THE CELL CYCLE OF NAVICULA PELLICULOSA 1

The reactions and processes which underlie the silicification mechanism (incorporation of soluble pool Si into insoluble material) in the diatom Navicula pelliculosa (Bréb.) Hilse are quite sensitive to low temperature. Furthermore incorporation is completely blocked in 66Ge‐Si(OH)4 preloaded cells treated with an inhibitor of oxidative phosphorylation (2,4‐dinitrophenol) or a sulfhydryl blocking agent (N ‐ethylmaleimide). De novo protein synthesis is not required for incorporation in cells preloaded 3 h, but cycloheximide added to cells preloaded 1 h inhibits incorporation after 2 h. These results are interpreted to indicate that purely chemical reactions, which are uncoupled from cellular metabolism, cannot completely account for Si(OH)4 polycondensation during silica frustule morphogenesis in the diatom. A temperature sensitive cellular process or reaction, postcytokinesis, is also postulated to be required before silicification can occur.
Surface Ozone in China and its Possible Impact on Agricultural Crop Yields

Abstract Emissions of ozone precursors are expected to multiply the next 20 years in China, and the levels of photo-oxidants may increase substantially. Increased surface ozone gives cause for concern regarding the prospects for Chinese agricultural production. We show that crop production may be substantially reduced in the future due to elevated ozone concentrations, and that productivity may already be affected for some crops. However, crop-yield loss estimates obtained by using alternative exposure-response functions vary substantially. Spring wheat, soybean, and corn may be especially vulnerable to future ozone increases, due to a likely concurrence of peak levels of ozone and the growth season of these crops.
Occurrence of Corncrakes Crex crex in mosaic farmland landscapes in south-central Sweden – effects of habitat and landscape structure

Summary Most studies of Corncrakes have been conducted in grasslands used for hay-cutting, and earlier hay-cutting has been suggested as the main cause of population decline in this species. Less is known about habitat preferences in relation to other land-uses and landscape structure. This paper investigated habitat composition and landscape structure in territories and at random sites in arable fields and meadows in south-central Sweden. Calling Corncrakes preferred sites with tall vegetation, moist ground, and locations close to ditches (55% of territories). Suitable conditions occurred on abandoned unmanaged wet meadows (31% of territories), mown wet meadows (14%), leys (30%) and non-rotational set-asides (15% of territories). Corncrakes avoided annual crops and other crops with short vegetation in the spring. Cutting of vegetation before mid-July was recorded in 21% of the territories and resulted in 100% abandonment of these sites. In contrast to many other ground nesting farmland birds, Corncrakes did not avoid forest edges (42% of territories within 100 m of edges). A strategy to conserve Corncrake populations should focus on maintenance of moist natural and sown grasslands (unmanaged or mown late) with tall vegetation and prevention of succession to woodland. Target areas should be in forested landscapes, because many other meadow birds that are more dependent on management (e.g. yearly mowing or grazing) prefer open landscapes.
Phenotypic integration may constrain phenotypic plasticity in plants

Phenotypic plasticity is essential for plant adaptation to changing environments but some factors limit its expression, causing plants to fail in producing the best phenotype for a given environment. Phenotypic integration refers to the pattern and magnitude of character correlations and it might play a role as an internal constraint to phenotypic plasticity. We tested the hypothesis that phenotypic integrationestimated as the number of significant phenotypic correlations between traitsconstrains phenotypic plasticity of plants. The rationale is that, for any phenotypic trait, the more linked with other traits it is, the more limited is its range of variation. In the perennial species Convolvulus chilensis (Convolvulaceae) and Lippia alba (Verbenaceae) we determined the relationship between phenotypic plasticity to relevant environmental factorsshading for C. chilensis and drought for L. albaand the magnitude of phenotypic integration of morphological and biomass allocation traits. In C. chilensis plants, plasticity to shading of a given trait decreased with the number of significant correlations that it had with the other traits. Likewise, the characters that showed greater plasticity to experimental drought in L. alba plants had fewer significant phenotypic correlations with other characters. We report a novel limit to phenotypic plasticity of plants by showing that the phenotypic trait architecture may constrain their plastic, functional responses to the environment.
Future climate‐driven shifts in distribution of Calanus finmarchicus

Calanus finmarchicus is a key‐structural species of the North Atlantic polar biome. The species plays an important trophic role in subpolar and polar ecosystems as a grazer of phytoplankton and as a prey for higher trophic levels such as the larval stages of many fish species. Here, we used a recently developed ecological niche model to assess the ecological niche (sensu Hutchinson) of C. finmarchicus and characterize its spatial distribution. This model explained about 65% of the total variance of the observed spatial distribution inferred from an independent dataset (data of the continuous plankton recorder survey). Comparisons with other types of models (structured population and ecophysiological models) revealed a clear similarity between modeled spatial distributions at the scale of the North Atlantic. Contemporary models coupled with future projections indicated a progressive reduction of the spatial habitat of the species at the southern edge and a more pronounced one in the Georges Bank, the Scotian Shelf and the North Sea and a potential increase in abundance at the northern edge of its spatial distribution, especially in the Barents Sea. These major changes will probably lead to a major alteration of the trophodynamics of North Atlantic ecosystems affecting the trophodynamics and the biological carbon pump.
PHOSPHOLIPASE A2INHIBITORS AND LEUKOTRIENE SYNTHESIS INHIBITORS BLOCK TNF-INDUCED NF-κB ACTIVATION

Abstract Tumour necrosis factor (TNF) is a key regulator of inflammation and immunity. The cellular effects exerted by TNF depend, apart from NF-κB-directed gene transcription, largely on its ability to activate phospholipase A2(PLA2), yielding the release of arachidonic acid (AA) and its metabolites. AA metabolites, especially the leukotrienes, act as second messengers in TNF receptor signalling, as different inhibitors of AA metabolism impair a variety of TNF-induced biochemical events. The role, however, of AA and its metabolites in TNF-induced NF-κB activation is still obscure. Here we report that 4-bromophenacyl bromide (4-BPB; an inhibitor of PLA2), nordihydroguaretic acid (NDGA; a 5-lipoxygenase inhibitor), as well as MK-886 [an inhibitor of 5-lipoxygenase-activating protein (FLAP)] interfere with TNF-induced NF-κB-mediated transactivation. However, only 4-BPB inhibited the DNA-binding activity of NF-κB, whereas NDGA and MK-886 did not. Thus, different inhibitors interfere at different points in TNF-induced signalling leading to NF-κB-dependent transcription. Artificial induction of AA metabolism induced neither DNA-binding activity of NF-κB nor NF-κB-dependent transactivation. It was concluded that although TNF-induced signalling to NF-κB-dependent transcription is sensitive to inhibitors of AA metabolism at multiple points during this signalling, AA release is essential but not sufficient for NF-κB-activation.