Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Specificity of Carbohydrate‐Lectin Recognition

A galactose-specific protein (RC1) isolated from Ricinus communis beans was found to give a precipitin reaction with concanavalin A. Its carbohydrate content amounted to 8–9% of the total protein and was found to be rich in mannose. The interaction of RC1 with galactose and lactose was measured in 0.05 M phosphate buffer containing 0.2 M NaCl (pH 6.8) by the method of conventional equilibrium dialysis. From the analysis of the binding data according to Scatchard method the association constant (Ka) at 5°C was calculated as 3.8 mM−1 and 1.2 mM−1 for lactose and galactose, respectively. In both cases the number of binding sites per molecule of RC1 with molecular weight of 120000 was found to be 2. From the temperature-dependent Ka values for the binding of lactose, the values of –5.7 kcal/mol and –4.3 cal × mol−1× K−1 were calculated for ΔH and ΔS, respectively. The addition of concanavalin A to RC1 or vice versa led to the formation of the insoluble complex RC1· ConA4 containing one molecule of RC1 and one molecule of tetrameric concanavalin A (ConA4) which could be dissociated upon addition of concanavalin A-specific sugars. The complex formation results in a time-dependent appearance of turbidity in the time range from 10s to 10 min. From the measurement of the time-dependent appearance and disappearance of the turbidity the formation (kf) and dissociation (kd) rate constants were calculated as 3 mM−1× s−1 and 0.07 ks−1 respectively. The ratio kf/kd (43μM −1), that corresponds to the association constant of complex RC1· ConA4, is higher than that of mannoside · ConA4 and thereby suggests that protein-protein interaction contributes significantly in stabilising glycoprotein · lectin complexes. The relevance of this finding to the understanding of the chemical specificities that are involved in a model cell-lectin interaction is discussed.
Preservation of avian blood and tissue samples for DNA analyses

A problem frequently faced by researchers involved in collecting tissues for DNA isolation is the preservation of samples in the field prior to and during their transportation to the laboratory. Prevention of DNA degradation is usually achieved through freezing. As this is not always practical, we have tested the efficiency of chemical solutions containing high concentrations of salts (e.g., NaCl, EDTA, and diaminocyclohexanetetraacetate) and detergent at preserving DNA in bird tissue and blood samples stored at ambient temperature for extended periods of time. For blood samples, we recommend the use of a buffer that lyses the cells and nuclei and contains 0.01 M Tris, 0.01 M NaCl, 0.01 M EDTA, and 1% n-lauroylsarcosine, Ph 7.5. Tissue samples are best preserved as small pieces in a saline solution made of 20% dimethyl sulfoxyde, 0.25 M EDTA, saturated with NaCl, pH 8.0. DNA extracted from samples preserved in these solutions for up to 24 weeks was compared with DNA recovered from tissue samples stored at.
Dynamic transcriptome profiling of bovine endometrium during the oestrous cycle

Fertility problems are the main reason for slaughter of high-performance milk cows, because prolonged calving intervals result in financial losses for the farmer and retard genetic progress. Genetic improvement of fertility would be of great benefit, but functional traits for effective selection are missing. Recent advances in functional genomics tools like DNA microarrays could be the key to identify gene expression patterns in the endometrium that correlate with maternal fertility. Therefore, a bovine oviduct and endometrium cDNA array was established that contains a set of 1,440 cDNA clones and long oligonucleotides representing 950 different genes. The major part of these genes results from a series of differential gene expression studies in endometrium (different stages of the oestrous cycle, day 18 and day 15 pregnant vs. nonpregnant) and oviduct epithelial cells (different stages of the oestrous cycle). Using this custom-made cDNA array the response of the endometrium was studied to the changing hormonal environment during the bovine oestrous cycle. Endometrium samples were recovered from Simmental heifers slaughtered on day 0 (oestrus), 3.5 (metoestrus), 12 (dioestrus) and 18. The latter group was divided into animals with high (late dioestrus) and low progesterone levels (preoestrus). Statistical analysis with the Significance Analysis of Microarrays (SAM) method revealed 269 genes exhibiting significant changes in their transcript levels during the oestrous cycle in distinct temporal patterns. Two major types of expression profiles were observed, which showed the highest mRNA levels during the oestrus phase or the highest levels during the luteal phase, respectively. A minor group of genes exhibited the highest mRNA levels on day 3.5. Gene ontology (GO) analyses revealed GO categories related to extracellular matrix remodelling, transport, and cell growth and morphogenesis enriched at oestrus, whereas immune response and particular metabolic pathways were overrepresented at dioestrus. Generation of gene interaction networks uncovered genes possibly involved in biological processes important for establishment of early pregnancy, such as endometrial remodelling (e.g. collagen genes, MMP2, TIMP1), regulation of angiogenesis (e.g. ANGPTL2, TEK), regulation of invasive growth (e.g. PCSK5, tight junction proteins, ITGB4), cell adhesion (e.g. MUC16, LGALS3BP) and embryo feeding (e.g. SLC1A1, ENPP1). Localisation of mRNA expression in the endometrium was analysed for CLDN4, CLDN10, TJP1, PCSK5, MAGED1, and LGALS1. Future application of the BOE array, based on the knowledge from the cycle study, could be the use in systematic studies of interactions between the metabolic status and functionality of the endometrium to identify genes that could be used for differential diagnosis of fertility problems.
Observations on the Topography of the Reproductive Tract of the Arabian Female Camel

This study was conducted to investigate the topography of normal and diseased reproductive tract of the Arabian female camels and to assess the type and prevalence of abnormalities occurring in the genital tract. The genital tracts of slaughtered camels (n=124) were examined in hanged carcass before eviscerating the abdominal contents. Position, mobility and relationship of the genital tract to the surrounding organs and structures were determined. Relationship between the pregnant horn and corpus luteum was studied. The results showed that the reproductive tract was located cranial to the pelvic cavity in all examined females. The left uterine horn was always larger than the right horn. Pregnancy was found exclusively in the left horn. Hydro-bursitis (encapsulation of the ovarian bursa, 4.8%) was observed as a fluctuated enlargement lateral and cranial to the uterine horn pulling the genital tract into the abdominal cavity. Adhesion of the genital tract was observed in 2.4% of the examined cases. The left ovary was found lateral or hanged underneath the left horn in frequencies of 28.2% and 71.8%, respectively. The frequencies for the right ovary were 36.3% and 63.7%, respectively. Single and double corpora lutea were detected in 55.6% and 44.4% of the pregnant cases, respectively. Double corpora lutea in case of pregnancy were almost found on the same ovary and were unequal in diameter, P=0.03. Paired ovaries with overgrown follicles (> 20 mm) had at the same time growing or mature follicles (56.3%), corpus luteum (6.2%), or no structures (37.5%). Hydrometra and pyometra were observed in 0.9% and 4.7% of the examined cases, respectively. In conclusion, these results help the interpretation of ultrasound images in diagnosis some difficult clinical cases like adhesions and hydro-bursitis in female camels.
In situ interactions between the effects of season, current velocity and pollution on a river biofilm

SUMMARY 1. The development of periphytic algae and bacteria is controlled by a combination of interacting biotic processes and abiotic factors. Distinguishing between the selection pressure resulting from pollution and that of natural environmental factors is therefore one of the most critical aspects of assessing the impact of pollutants on the diversity and function of benthic microbial communities in natural ecosystems. 2. We studied how current velocity and season affect the ability of river biofilms to cope with complex chemical pollution. We compared the diversity, structure and production of periphytic algae and bacteria from four sampling zones with differing chemical water quality levels and different flow velocities over the course of two seasons (summer and winter). 3. The three factors tested all influenced biofilm development, but this depended on the biological variable being measured. Bacterial and algal densities were highly dependent on season and chemical water quality. Algal density was lower in summer than in winter, but bacterial density and production increased from upstream (reference) to downstream (polluted), and this increase was more marked in winter. The impact of chemical water quality was also dependent on the season. 4. An interaction between current velocity and pollution was also detected. During the summer, there was no difference in bacterial density or production between the upstream and downstream segments in the fast current zones, whereas both variables were higher downstream in the slow current zones. Such interactions between environmental factors and the impact of water quality on biofilms must be taken into account in assessments of the effects of chemicals on biofilm community structure and functioning in rivers.
Allozyme variation in natural populations of the Italian range of Pinus sylvestris L.

The genetic structure of eight populations of Scots pine (Pinus sylvestris L.) - seven Alpine and one Apennine, representative of the Italian range of this species - has been studied by means of electrophoretic analysis of six enzyme systems (LAP, GOT, PGM, MDH, GDH, SKDH), for a total of 12 allozyme loci. On the whole, genetic diversity parameters show rather high values; the average value of expected heterozygosity according to HardyWeinberg (0.283) is higher than the average value estimated for gymnosperms. Differentiation between populations is low, as revealed by parameters G,,(2.6 70) and 6 (4.7 %), as well as by the mean values of genetic distance by Nei and Gregorius (0.01 3 and 0.075, respectively), as observed in most conifers. Nevertheless, the obtained results reveal a sharp differentiation of the Apennine population. This is one of the few relict indigenous populations of this species in the Ligurian-Emilian Apennine, remnants from glacial migrations. Because of its peculiarity, this relict population, whose intrapopulation genetic variation is almost as high as in the Alpine populations, is an important genetic resource that requires specific protection measures.
Senescence or ageing in wallflower petals

Senescence is the final event in the life of many plant tissues. It is concerned with remobilisation of metabolites from the senescing organ and is distinct from other forms of cell death. It is a highly regulated process involving structural, biochemical and molecular changes. Gene expression is tightly regulated, with many genes down regulated and others induced. Conversely, ageing is a passive degradation. Petals and leaves are good model organs for developmental studies, as petal development is irreversible and tightly controlled, and leaves are an extensively studied senescent system. Similarities between these organs allow direct comparison of late developmental events to establish whether petals senesce, as leaves do, or age however, important differences in function lead to the hypothesis that petal deterioration and leaf senescence are distinct. Wallflowers were chosen as they are closely related to Arabidopsis and Brassica spp. , have large petals, and are commercially relevant ornamental plants. Changes in wallflower morphology and physiology were examined over development. A high degree of gene homology was shown between wallflowers and Arabidopsis by northern blotting. 1632 genes upregulated in old wallflower tissues were cloned using subtractive selective hybridisation and a microarray of these genes, along with 91 Arabidopsis senescence associated genes, was constructed. Probing the microarray with RNA from different leaf and petal developmental stages identified 298 common genes significantly upregulated during both leaf senescence and late petal development, and expression patterns were compared between the two tissues. The expression patterns of selected genes were confirmed by RT-PCR. Late development in petals was shown to be an active process, and was tentatively concluded to be senescence due to upregulation of genes involved with nutrient remobilisation and the strong upregulation of the SAG 12 gene---a molecular marker for leaf senescence that is not upregulated during other forms of death in leaves.
Carbon Monoxide and Clocks

Several gaseous molecules, including nitric oxide and carbon monoxide (CO), are important neurotransmitters. In their Perspective, [Boehning and Snyder][1] comment on new work ([Dioum][2] et al .) that reveals another important activity for CO, that of modulator of the transcription factor NPAS2, a crucial component of the circadian clock. [1]: http://www.sciencemag. org/cgi/content/full/298/5602/2339 [2]: http://www.sciencemag. org/cgi/content/short/298/5602/2385
Discordant patterns of geographic variation between mitochondrial and microsatellite markers in the Mexican black iguana (Ctenosaura pectinata) in a contact zone

Aim To delimit the distribution of matrilines of the black iguana (Ctenosaura pectinata), detect potential contact zones between them, and test the hypothesis of geographic concordance in the structuring of matrilines with respect to genetic structuring across the nuclear genome.
Phylogenetic analysis of algicidal bacteria (family Flavobacteriaceae) and selective detection by PCR using a specific primer set

Sequencing the 16S rDNA and phylogenetic analysis were performed on algicidal bacteria belong ing to the family Flavobacteriaceae, Chattonella-killing Cytophaga sp. strain J18/MOI, Heterocapsa killing Cytophaga sp. strains AA8-2 and AA8-3, and Gymnodinium growth-inhibiting Flavobacterium sp. strain 5N-3. These algicidal strains were clustered phylogenetically within the marine Cytophaga/Flavobacter/Bacteroides (CFB) group. Flavobacterium sp. 5N-3 was phylogenetically clustered with Psychroserpens burtonensis but not with the algicidal gliding bacteria. The sequence simi larity between strain 5N-3 and P. burtonensis was only 92%. The strains J18/M01 and AA8-2 (AA8-3) exhibited the high level of sequence similarity of 98.5%. Despite the differences of host algae and of lo cality and year of isolation, these algicidal bacteria were phylogenetically located on the same terminal branch. The PCR amplification of the 16S rDNA of the CFB strains using a single set of J18/MO1-specific primers resulted in specific detection of the J18/M01, indicating that the J18/M01-specific sequence in the 16S rDNA is useful for selective detection of the strain J18/M01.
The Biology of Canadian Weeds. 149. Rumex acetosella L.

Stopps, G. J., White, S. N. , Clements, D. R. and Upadhyaya, M. K. 2011. The Biology of Canadian weeds. 149. Rumex acetosella L. Can. J. Plant Sci. 91: 1037–1052. Rumex acetosella L. , sheep sorrel, is a perennial herb originating from Europe and southwestern Asia, now found in at least 70 countries worldwide. A common weed, it appears in grasslands, pastures, rangelands, waste areas, and along roadsides across North America. It frequently occurs as a weed in lowbush blueberry fields in Atlantic Canada, particularly in Nova Scotia. Rumex acetosella thrives on poor, acidic, and disturbed soils across a broad range of climatic conditions. A persistent seed bank and vegetative reproduction from creeping roots contribute to the ability of R. acetosella to tolerate various methods of control including certain herbicides, fire, and tillage. Tart-tasting leaves, rich in vitamin C have led to the use of R. acetosella in European and North American cultures as both a source of food and a component of herbal medicine.
Production of antibodies to pseudomonas solanacearum the causative agent of bacterial wilt

Both polyclonal and monoclonal antibodies have been developed to Pseudomonas solanacearum, the causative agent of bacterial wilt. When used in an indirect enzyme‐linked immunosorbent assay, the polyclonal antibodies detected as few as 1 X 104 bacterial cells ml‐1 in infected plant or soil samples, but they could not distinguish between P. solanacearum, P. celebensis, P. syzygii and P. picketti. The monoclonal antibodies developed had differing specificities, but, using selective immunization schedules, several were obtained which no longer cross‐reacted with closely related bacteria. These monoclonal antibodies were not as sensitive as the polyclonal antibodies and were only able to detect down to 1 X 106 cells ml‐1.
Phenotypic variation for in sacco dry matter and fibre degradation kinetics in lucerne

Energy content is an important criterion for evaluation in lucerne breeding. The in sacco method was used to investigate the phenotypic variation in the kinetics of degradation of dry matter and fibre for 15 lucerne cultivars grown in one location, and to compare these kinetic parameters with laboratory analyses of dry matter solubility, fibre content (NDF, neutral detergent fibre), and fibre solubility. Bags containing forage samples were incubated for 2, 4, 8, 12, 24, 48, and 72 h in 3 fistulated Holstein cows. Dry matter and NDF degradation curves were modelled with a sigmoid curve with 3 parameters. Phenotypic variations were observed for dry matter and NDF disappearance at each time interval, and for the parameters of the degradation kinetics. For both dry matter and NDF, the totally degraded fraction was correlated with the solubility measured by wet chemistry, but the rate of degradation of the slowly degraded fraction was not correlated with chemical analyses. The effect of the variations in the parameters of dry matter and fibre degradation on ruminant performance needs to be studied further.
A method for experimental heating of intact soil profiles for application to climate change experiments

A new system for simulating future belowground temperature increases was conceived, simulated, constructed and tested in a temperate deciduous forest in Oak Ridge, TN, USA. The new system uses low‐wattage, 3 m deep heaters installed around the circumference of a defined soil volume. The heaters add the necessary energy to achieve a set soil temperature differential within the treatment area and add exterior energy inputs equal to those, which might be lost from lateral heat conduction. The method, which was designed to work in conjunction with aboveground heated chambers, requires only two control sensor positions one for aboveground air temperatures at 1 m and another for belowground temperatures at 0.8 m. The method is capable of achieving temperature differentials of at least +4.0±0.5 °C for soils to a measured depth of −2 m. These +4 °C differential soil temperatures were sustained in situ throughout 2009, and both diurnal and seasonal cycles at all soil depths were retained using this simple heating approach. Measured mean energy inputs required to sustain the target heating level of +4 °C over the 7.1 m2 target area were substantial for aboveground heating (21.1 kW h day−1 m−2), but 16 times lower for belowground heaters (1.3 kW h day−1 m−2). Observations of soil CO2 efflux from the surface of the target soil volumes showed CO2 losses throughout 2009 that were elevated above the temperature response curve that have been reported in previous near‐surface soil warming studies. Stimulation of biological activity within previously undisturbed deep‐soil carbon stocks is the hypothesized source. Long‐term research programs may be able to apply this new heating method that captures expected future warming and temperature dynamics throughout the soil profile to address uncertainties in process‐level responses of microbial, plant and animal communities in whole, intact ecosystems.
Biodiversity in Soils: Use of Molecular Methods for its Characterization

Extraction of Total Nucleic Acids from Soil Fractionation of Total DNA by mol% G-C Content Analysis of SSU rRNA and Its Encoding Gene (rDNA) Analysis of Functional Genes Microbial Community Fingerprinting Analysis of Microbial Activity at the Functional Level Metagenome Analysis Final Comments Keywords: methodology; molecular methods for soils; nucleic acids extraction from soils; soils
Use of WL Medium to Profile Native Flora Fermentations

Vineyard, winery, barrel, and controlled temperature fermentation samples from a single commercial winery (Luna Vineyards) conducting fermentations with indigenous organisms were plated onto Wallerstein Laboratory Nutrient Agar (WL) to evaluate colony diversity. Seventeen unique colony morphologies were identified. Sequence analysis of the DNA encoding a portion of the large ribosomal 26S rRNA indicated that the colony types defined members of six genera: Hanseniaspora uvarum (Kloeckera apiculata), Saccharomyces cerevisiae, Issatchenkia orientalis, Pichia kluyveri, Candida olephelia, and Metschnikowia. Distinct colony subtypes were identified within the pulcherrimin producers traditionally classified as a single species, Metschnikowia pulcherrima. Sequence analysis of the D1/D2 region of the 26S rDNA of these biotypes showed a high degree of divergence, suggesting that these organisms might define separate species. Analysis of fermentations revealed that colony type as indicated on this medium could be used to monitor the yeast population dynamics.
Polymorphic Microsatellite Loci for Paternity Analysis in the Fiddler Crab Uca mjoebergi

Abstract Microsatellite markers were developed for the fiddler crab Uca mjoebergi for use in paternity assignment. Five highly variable loci were found to amplify reliably in U. mjoebergi, although one locus exhibited evidence for the presence of null alleles, and two loci exhibited evidence of linkage. The number of alleles, expected heterozygosity and probability of paternity exclusion (P > 0.999) suggest that these markers when combined provide sufficient power to determine paternity by exclusion in this species. Three primer pairs were found to also amplify PCR products from three additional fiddler crab species (U. dampieri, U. flammula and U. seismella), and will prove useful for phylogeography and behavioural ecology of fiddler crabs.
Impacto del calentamiento global en la fenología de una variedad de vid cultivada en el Sur de Chile

La tendencia al aumento de las temperaturas provocaria grandes cambios en el ciclo de desarrollo de las plantas y en el estilo de agricultura en una determinada localidad. En el presente trabajo se analizo el efecto de las temperaturas proyectadas por el IPCC sobre la fenologia de Vitis vinifera (L.) variedad Gewurtztraminer, en dos zonas de viticultura de clima frio del sur de Chile. Se ajusto un modelo matematico sobre datos de fenologia y grados–dia recopilados durante dos anos. El modelo obtenido se corrio con datos de temperatura del clima actual y los proyectados con los escenarios A2 y B2 para el periodo 2070–2100. El analisis de los resultados muestra que el clima local presentaria importantes aumentos en las sumas de temperaturas (grados–dia), lo que reduciria hasta 17 d el periodo de brotacion a flotacion y entre 28 a 46 d el periodo de brotacion a cosecha, en el escenario mas extremo. La fenologia es muy sensible a los escenarios de calentamiento global y probable cambio climatico. Caractetizar su posible comportamiento podria servir de rererencia para definir estrategias para la planificacion futura de un vinedo