Miracle-dz/UniFAR-FTUs huggingface dataset:
Grapevine virus A variants of group II associated with Shiraz disease in South Africa are present in plants affected by Australian Shiraz disease, and have also been detected in the USA

Primers were designed for RT-nested PCR amplification of the highly variable 293-nt fragment from the 5¢ terminal part of the Grapevine virus A (GVA) replicase gene, specific to South African variants of molecular groups I and II. This new technique, along with RT-PCR for simultaneous amplification of variants of groups I, II and III, as well as cloning of amplicons, single-strand conformation polymorphism (SSCP) analysis of clones and sequencing, were used to investigate the populations of variants infecting 16 local Shiraz grapevines with different Shiraz disease (SD) status. The techniques were also used to study variants in GVA-infected grapevines from Australia an dt he USA. The Australian grapevines included seven plants of cvs Shiraz and Merlot affected by Australian Shiraz disease (AuSD), and one plant of cv. Crimson Seedless with unknown AuSD status. Grapevines from the USA included plants of cvs Chardonnay, Thompson Seedless and an unknown cultivar. The results confirmed the association of certain genetic variants of group II with SD and showed the common presence of these variants in AuSD-affected grapevines from Australia. Interestingly, a variant of this group was also detected in grapevine cv. Chardonnay from the USA, although the disease has not yet been reported from that country. The study also supports an earlier observation that members of group II, closely related to variant GTR1-2, are not associated with the disease. The variants were found only in SD-free grapevines. Results show that variants of the most divergent group III, which are common in South Africa, are also present in Australia and the USA. These variants are not associated with SD, but frequently occur in mixed infections with members of group II in plants affected by this disease in South Africa.
Progress in the development of transgenic papaya: transformation of solo papaya using ACC synthase antisense construct

Papaya (cv. Solo) somatic embryos were produced, squashed and used for transient stable transformation. Conditions for transforming somatic embryos were optimized using transient expression of GUS. A total of 11,900 immature zygotic embryos were isolated and 7,730 (65%) produced somatic embryos. All the somatic embryos were squashed, placed in an osmotic medium and bombarded with the antisense ACC synthase construct placed in a co-transformation vector. A total of 160 bombardments were made. The bombarded tissues were subjected to a selection medium containing half-strength MS with 150 mg L-1, then with 300 mg L-1 kanamycin. Embryos surviving kanamycin-selection were regenerated on a full strength De Fossard medium supplemented with 0.25 muM each of BAP and NAA and 10.0 muM GA(3).
Characterisation and identification of olive cultivars from North-eastern Algeria using molecular markers

Summary In the present study, ten microsatellite (simple sequence repeat; SSR) and seven single nucleotide polymorphism (SNP) markers were used to characterise a set of 14 cultivars of olive (Olea europaea L.) from North-eastern Algeria. The genetic profiles of these cultivars were compared with two Tunisian, one Moroccan, and two Algerian cultivars. A total of 77 alleles were amplified for the SSR markers. The mean values of the expected heterozygosity (He), the observed heterozygosity (Ho), and the polymorphic information content (PIC) values were 0.806, 0.851, and 0.752, respectively. A combination of three SSR loci (ssrOeUA-DCA9, ssrOeUA-DCA18, and UDO099-043) permitted the identification of all 14 olive accessions analysed. Although less polymorphic than the SSR markers, the SNP markers used in this study showed relatively high diversity values. The mean He value was 0.374. The same value was obtained for the Ho, and PIC values ranged from 0.373 (Cycl-1) to 0.117 (LS2). Eleven out of all 19 olive cultivars (63%) were identified by means of the SNP markers, confirming the value of the differences from SSR markers in terms of their efficiency for cultivar discrimination and stressing the need to develop more SNP markers. The results obtained in this work highlight the rich genetic diversity available in even a small set of olive germplasm from Algeria and confirm the utility of SSR and SNP markers for genotyping olive cultivars.
Changes in the composition of plasma very low density lipoprotein during pregnancy and lactation in genetic lines of pigs

Plasma very low density lipoproteins (VLDL) of gilts were separated into two sub fractions according to their affinity for heparin. The proportion of VLDL present as subfraction 2 (higher affinity for heparin) varied, according to the genetic line of the pigs, between 0·21 and 0·78 in virgin gilts. The proportions were related to the variation in piglet survival in the same nine genetic lines by a quadratic equation, which predicted that greater than 90% survival to weaning was to be found in piglets born to gilts having between about 0·3 and 0·7 of their VLDL as subfraction 2. This observation suggests a simple measurement that could be used in the selection of sows for a breeding programme. The proportion of subfraction 2 fell throughout pregnancy in each of three genetic lines measured and only returned to pre-pregnant values after weaning: these changes did not correlate with the changes in the lipid composition of plasma VLDL measured during pregnancy and lactation. The findings suggest a role for the VLDL subfractions in controlling the nutrition of the neonatal pig.
Variation in Shell Morphology of the Western Pond Turtle (Actinemys Marmorata Baird and Girard) from Three Aquatic Habitats in Northern California

Abstract Intraspecific variation in turtle life-history traits has been well documented for many turtle species; however, comparative studies of such traits for the Western Pond Turtle (Actinemys marmorata) are lacking. Here we compare three years of morphometric data on A. marmorata from three study sites in northern California. Our study sites represent various habitat types where A. marmorata can be found and include foothill creeks (BCCR), valley sloughs (SR), and human-made canals (HS). We used maximum carapace length (MCL) as a measure of overall body size and found that A. marmorata differed in body size among sites. For all sites combined, males were significantly larger in mean MCL than females. Among the three sites, both mean male and female body sizes were significantly different (HS > SR > BCCR). Within sites, males were larger than females at SR and HS, but no difference was found between males and females at BCCR. Controlling for body size (MCL), A. marmorata in the foothill creek habitat were flatter and narrower than those in both the valley slough and human-made canal habitats. The observed variation in body size among sites could possibly be caused by differences in prey availability, water temperature, or microhabitat characteristics. Although we have no hard evidence to explain our observed size differences in A. marmorata, we suggest that phenotypic plasticity is responsible for determining maximum size at maturity. Additionally, it is unclear at this time whether fusiform, or compressed shell shape, in A. marmorata offers any adaptive significance in lotic environments.
A gene for social immunity in the burying beetle Nicrophorus vespilloides?

Some group-living species exhibit social immunity, where the immune system of one individual can protect others in the group from infection. In burying beetles this is part of parental care. Larvae feed on vertebrate carcasses which their parents smear with exudates that inhibit microbial growth. We have sequenced the transcriptome of the burying beetle Nicrophorus vespilloides and identified six genes that encode lysozymes – a type of antimicrobial enzyme that has previously been implicated in social immunity in burying beetles. When females start breeding and producing antimicrobial anal exudates, we found that the expression of one of these genes was increased by ∼1000 times to become one of the most abundant transcripts in the transcriptome. We conclude that we have likely identified a gene for social immunity, and that it was recruited during evolution from a previous function in personal immunity.
First record of Batrachochytrium dendrobatidis on amphibians in Romania

The project was financed by the Hungarian Scientific Research Fund (OTKA K77841) granted to JV. TH was supported by the strategic grant POSDRU/89/1.5/S/58852, Project “Postdoctoral programme for training scientific researchers” cofinanced by the European Social Fund within the Sectorial Operational Program Human Resources Development 2007–13.
Dynamics of biologically fixed N in legume-cereal rotations: a review

Agronomically significant N yield responses of cereals following grain legumes compared with cereal monoculture are frequently measured. The positive N response of the cereal has been attributed to the transfer of biologically fixed N, to N-sparing under the antecedent legume, and to less immobilisation of nitrate during the decomposition of legume residues. Methods for estimating the transfer of biologically fixed N in rotations, and for separating the N benefit into fixed N and non-fixed N components, are reviewed. Available data indicate that both sources of N contribute to the N benefit. The role of the grain legume in the gain or drain of soil N is evaluated by considering the balance between symbiotic dependence and N harvest index, as well as long-term changes in total soil N. Several 15N-based techniques for direct estimation of inputs of biologically fixed N to the soil N pool are reviewed. N balances in grain legume-cereal rotations may be positive or negative depending on the legume species, symbiotic performance, and agronomic factors.
EFFECTS OF DESERT WILDFIRES ON DESERT TORTOISE (GOPHERUS AGASSIZII) AND OTHER SMALL VERTEBRATES

Abstract We report the results of standardized surveys to determine the effects of wildfires on desert tortoises (Gopherus agassizii) and their habitats in the northeastern Mojave Desert and northeastern Sonoran Desert. Portions of 6 burned areas (118 to 1,750 ha) were examined for signs of mortality of vertebrates. Direct effects of fire in desert habitats included animal mortality and loss of vegetation cover. A range of 0 to 7 tortoises was encountered during surveys, and live tortoises were found on all transects. In addition to desert tortoises, only small (<1 kg) mammals and reptiles (11 taxa) were found dead on the study areas. We hypothesize that indirect effects of fire on desert habitats might result in changes in the composition of diets and loss of vegetation cover, resulting in an increase in predation and loss of protection from temperature extremes. These changes in habitat also might cause changes in vertebrate communities in burned areas.
The distribution of insect pests on crops of oil-seed rape (Brassica napus L.) and the damage they cause

Summary During 3 years the distribution of pests on ten crops of winter rape and two of spring rape, and the damage they caused, has been determined. During immigration the adults of all pests infested crop edges more than crop centres, particularly on large crops, irrespective of the presence of wind breaks. The proportion of M. aeneus and G. assimilis at the crop edge gradually diminished as they moved further into the crop, and their larvae and pods with C. assimilis emergence holes were more evenly distributed over the crops than the adults. Damage by M. aeneus was not the only cause of podless stalks. The larvae of D. brassicae were largely confined to the edges of crops; split pods were largely but not solely confined to the edges. In winter rape crops correlations were found between the percentage of podless stalks per plant and the number of M. aeneus present, and the percentage of pods infested with C. assimilis larvae and the adult C. assimilis population. In two fields infested with D. brassicae the diminution in the proportion of split pods from crop edge to crop centre was positively correlated with diminution in the number of adult D. brassicae.
Fossil and Extant Western Hemisphere Boragineae, and the Polyphyly of “Trigonotideae” Riedl (Boraginaceae: Boraginoideae)

Abstract Boraginaceae tribe Trigonotideae comprises a heterogenous assemblage of taxa, many of which have been shown to belong to widely divergent lineages in Boraginaceae in the recent past, with some taxa now assigned to three of the four currently recognized tribes of the Boraginaceae s. s. , namely the Cynoglosseae, Echiochileae, and Lithospermeae. The systematics of Moritzia and Thaumatocaryon, the only endemic South American genera of Boraginaceae, have been controversially discussed in the past, and their most recent placement was in Trigonotideae. The present study investigates the phylogenetic relationships of “Trigonotideae” based on micromorphology and molecular data (ITS including 5.8S rRNA, and the trnL-trnF spacer). Molecular data show that “Trigonotideae” are polyphyletic, and none of its members is at all closely related to Trigonotis itself. Moritzia and Thaumatocaryon are closely allied to each other and are the sister group of the Old World Boragineae. Flowers, pollen, and fruit morphology strongly support this systematic placement. Extant (native) Boragineae are absent from North America and had not previously been reported from South America, whereas members of the Cynoglosseae, Echiochileae, and Lithospermeae have been reported from both continents. Moritzia and Thaumatocaryon are thus the only native representatives of Boragineae in the Americas and represent an unexpected western Eurasian/South American disjunction. However, several (widespread and abundant) fossil taxa from the Cenozoic of North America (especially species of †Prolithospermum) can be confidently placed into Boragineae. Extant Moritzia /Thaumatocaryon likely go back to a lineage which reached North America from Europe and then migrated into South America, with subsequent extinction in North America.
Effects of Plot Size and Census Interval on Descriptors of Forest Structure and Dynamics

This study was designed to explicitly formulate the effect of census interval and plot size on the variability of descriptors of tropical forest structure (stand density, basal area, aboveground biomass [AGB]) and dynamic (tree growth, mortality and recruitment rates, biomass fluxes). A unique dataset from a broad plot network (37.5 ha) surveyed every 2 yr over a 16‐yr period was used to develop and parameterize a new statistical model predicting the coefficients of variation for each forest descriptor. More than 90 percent of the inherent variability of these coefficients was predicted using a simple model including plot size and census interval in a Bayesian modeling framework. All descriptors of forest structure varied by <10 percent for plot sizes >2 ha. Among the descriptors of forest dynamics, AGB loss was the most variable. The number of 6.25 ha plots required to estimate its mean, over a 16‐yr period, within a 20 percent error of the mean remains above four. This contrasts with a relative constant flux of biomass entering the plot through tree growth and tree recruitment. Tree growth was remarkably well estimated with <15 percent variability for a 2‐yr census in a plot of 2 ha. This study provides an easy method to assess dataset limitations in efforts to estimate descriptors of forest structure and dynamic, which is of primary importance to decipher any clear consequences of global change in tropical forests.
Detection of mutations in quinolone-resistant determining regions in clinical isolates of Escherichia coli from Saudi Arabia

Since the use of fluoroquinolone antibiotic in clinical practice was introduced about two decades ago, quinolone-resistant E. coli strains are being isolated with increasing frequency. This study devotes to determine the resistance rate of fluoroquinolones for 112 Escherichia coli isolates from Prince Salman Hospital, Riyadh and to detect the mutations in the quinolone resistance-determining region (QRDR) of gyrA and parC in the fluoroquinolones resistant isolates. The resistance rate of ciprofloxacin for E. coli isolates was 37.5%. We have determined QRDR of the gyrA and parC genes of ciprofloxacin resistant E. coli (MIC 2-64 mg/L). A single mutation in gyrA (Ser TCG-83 → → → →Leu TTG) was detected in the isolate with a reduced susceptibility to ciprofloxacin (MIC 2 mg/L). Three mutations were detected in E. coli isolates with ciprofloxacin MIC ≥16 mg/L. Double mutations in gyrA (Ser-83 → → → →Leu and Asp-87 →Asn) and a single mutation in parC (Ser-80 →Ile). This study suggests, that in clinical isolates of E. coli , DNA gyrase is a primary target of quinolones, that only a single amino acid change at Ser-83 in GyrA is sufficient to generate high-level resistance to nalidixic acid and to decrease susceptibility to ciprofloxacin, and that the accumulation of amino acid changes in GyrA and the simultaneous presence of the ParC alterations play a central role in developing high-level resistance to ciprofloxacin.
Studies of the trafficking of the insulin-responsive glucose transporter, GLUT4, in 3T3-L1 adipocytes

The translocation of GLUT4 from intracellular stores to the plasma membrane in response to insulin accounts for the large insulin-mediated glucose uptake in muscle and fat tissue. A defect of this translocation mechanism is evident in individuals with insulin resistance and type 2 diabetes. Hence, understanding the molecular basis of GLUT4 localisation and recycling is important in order to assist the design of rational therapies for the treatment of this disease.Here, we have used iodixanol gradient analysis to examine the intracellular distribution of GLUT4. By this method intracellular GLUT4 could be separated into two pools one of which is highly insulin sensitive, and corresponds to "GLUT4 storage vesicles" (GSV), while the other is less insulin sensitive and is of endosomal origin. We further show that during differentiation of 3T3-L1 fibroblasts into adipocytes, the formation of the GSV compartment appears to be driven by the expression of GLUT4.SNARE proteins are involved in the fidelity of GLUT4 translocation, but little is known about how these proteins may be altered in insulin resistance. Using insulin-resistant 3T3-L1 adipocytes, we show that SNARE protein levels are increased. The potential importance of this observation is discussed. Using iodixanol gradient analysis we also found that the downregulation of GLUT4 known to occur in insulin-resistant 3T3-L1 adipocytes is predominantly from the GSV compartment. The implications of these data for the aetiology of insulin resistance are discussed.
Spatial and Temporal Pattern of Caddisfly Distribution at a Mesohabitat Scale in two Patagonian Mountain Streams Subjected to Pastoral Use

Substrate, flow type, nutrients, aquatic vegetation, organic matter, and caddisfly community structure were studied at two low order streams (Glyn and Nant y Fall) subjected to pastoral use in the Patagonian mountains. At both sites, we examined the effect of habitat type (boulder-pebble with and without filamentous algae, cobble-pebble, gravel-sand, leaf-pack, the submerged macrophytes Myriophyllum quitense and Isoetes savatieri) and season (high and low water period) on caddisfly assemblages. Benthic particulate organic matter (BPOM) ranged between 4.6 and 472 g m–2, all allochtonous detrital fractions were significantly higher at leaf-packs at Glyn, whereas M. quitense habitats supported more BPOM and macrophytes biomass at Nant y Fall. As expected, boulder-pebble sustained higher Trichoptera richness than M. quitense and gravel-sand, moreover all habitats showed higher density than M. quitense at Nant y Fall. According to our results at least nine caddisfly species exhibited some habitat preference with boulder-pebble and cobble-pebble the most selected habitat. These particular habitats sustained more than 68% of the total caddisfly species. Multidimensional scaling ordination highlighted differences in composition per habitat for both sites showing a clear distinction among depositional and erosional habitats. Substrate, flow type, detritus biomass were important predictors defining assemblages. Based upon our findings, those anthropogenic actions or stressors that change hydraulic as well substrate attributes in mountain streams such as stock trampling, dredging, clearing of riparian areas, will reduce caddisfly richness. These results are relevant for outline management and conservation biomonitoring and schemes in headwater Patagonian streams as well as other similar environments worldwide (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
FLOWER-VISITING BEES AND WASPS IN SINGAPORE PARKS (INSECTA: HYMENOPTERA)

In 2012 from February to June, a study was conducted by the National Biodiversity Centre, National Parks Board (NParks) to document the diversity and community of flower-visiting insects in seven parks. The insect orders recorded in the study are Blattodea, Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, and Orthoptera. Of these seven orders, Hymenopterans were the most abundant and diverse with 93 species from 13 families recorded, comprising 50 species of bees from four families, 24 species of wasps from seven families, and 19 species of ants (Formicidae). Among the 50 species of bees include six possible new records for Singapore. This paper presents the bees and wasps recorded from the study together with their respective species of flowers visited.
Improved methods for predicting individual leaf area and leaf senescence in maize (Zea mays)

The ability to predict leaf area and leaf area index is crucial in crop simulation models that predict crop growth and yield. Previous studies have shown existing methods of predicting leaf area to be inadequate when applied to a broad range of cultivars with different numbers of leaves. The objectives of the study were to (i) develop generalised methods of modelling individual and total plant leaf area, and leaf senescence, that do not require constants that are specific to environments and/or genotypes, (ii) re-examine the base, optimum, and maximum temperatures for calculation of thermal time for leaf senescence, and (iii) assess the method of calculation of individual leaf area from leaf length and leaf width in experimental work. Five cultivars of maize differing widely in maturity and adaptation were planted in October 1994 in south-eastern Queensland, and grown under non-limiting conditions of water and plant nutrient supplies. Additional data for maize plants with low total leaf number (12-17) grown at Katumani Research Centre, Kenya, were included to extend the range in the total leaf number per plant. The equation for the modified (slightly skewed) bell curve could be generalised for modelling individual leaf area, as all coefficients in it were related to total leaf number. Use of coefficients for individual genotypes can be avoided, and individual and total plant leaf area can be calculated from total leaf number. A single, logistic equation, relying on maximum plant leaf area and thermal time from emergence, was developed to predict leaf senescence. The base, optimum, and maximum temperatures for calculation of thermal time for leaf senescence were 8, 34, and 40 degrees C, and apply for the whole crop-cycle when used in modelling of leaf senescence. Thus, the modelling of leaf production and senescence is simplified, improved, and generalised. Consequently, the modelling of leaf area index (LAI) and variables that rely on LAI will be improved. For experimental purposes, we found that the calculation of leaf area from leaf length and leaf width remains appropriate, though the relationship differed slightly from previously published equations.