Miracle-dz/UniFAR-FTUs huggingface dataset:
Seston and Dissolved Organic Carbon Dynamics in a Southern Appalachian Stream

Suspended paniculate matter (seston) and dissolved organic carbon (DOC) were stud- ied along a 6.4-km section of a southern Appalachian headwater stream from July 1978 to August 1979. Samples were collected at six sites encompassing stream orders 1-4 and a 635 m elevation change. Nonstorm concentration of particulate organic matter (POM) measured as ash-free dry mass (AFDM) ranged from 0.53-3.68 mg/L during the study. No significant changes in seston concentration occurred from upstream to downstream sites, and only one site had concentrations significantly different from the others. Significant seasonal trends in seston concentrations existed over all stations, and these were associated with corresponding hydrograph changes. During the first storm following leaf-fall both seston concentration (AFDM 22.5 mg/L) and particle size in transport increased. Non- storm DOC/particulate organic carbon (0.45 x POM) ratios average =1. DOC concentrations (mg/L) increased over the first 2 km of stream but remained relatively constant farther downstream. The increase was largely due to high molecular mass fractions. Seven size classes of seston were measured, and discriminant analysis was used to assess longitudinal changes in particle size distribution. The largest and two smallest size classes increased in relative abundance downstream while the four intermediate classes decreased. Although the mean particle size decreased downstream, the ratio of coarse particulate organic matter (CPOM)/fine particulate organic matter (FPOM) increased down- stream. We suggest that CPOM/FPOM ratios do not necessarily reflect downstream reductions in mean particle size. CPOM/FPOM ratios and downstream changes in mean particle size should be viewed as separate phenomena. The ratio of benthic CPOM/suspended CPOM decreases downstream, which is apparently attributable to the lack of retention devices in higher order streams. Food quality available to collector organisms, as indicated by adenosine triphosphate (ATP) measurements, was highest in the two smallest (0.45-43 /^m) seston size classes. No apparent relationship existed between ATP and percent organic matter in the various seston size classes.
Improved Polymerase Chain Reaction-Based Mitochondrial Genotype Assay for Identification of the Africanized Honey Bee (Hymenoptera: Apidae)

Abstract A polymerase chain reaction (PCR)-based restriction fragment-length polymorphism (RFLP) assay was developed that discriminates among the 4 mitotypes found in North, Central, and South American honey bee racial groups—eastern European (Apis mellifera ligustica Spinola, caucasica Gorbachev, and carnica Pollman), western European (A. m. mellifera Linnaeus), Egyptian (A. m. lamarckii Cockerell Lepeletier), and sub-Saharan African (A. m. scutellata). Before the development of this assay, 13% of southern Californian feral bees collected before the arrival of the Apis mellifera scutellata (Africanized) race were found to contain a non-European mitochondrial genotype that could not be distinguished from that of A. m. scutellata. DNA sequence analysis suggests the unusual mitotype to be that of A. m. lamarckii. An RFLP polymorphism was identified that distinguished this subspecies from all others present in North America. This polymorphism was not found in any of 96 bees collected primarily in Mexico and Central America. Thus, the Egyptian mitochondrial type is either absent or extremely rare in these regions. The PCR assay also distinguishes A. m. lamarckii from 2 other north African racial types, A. m. intermissa Buttel-Reepen and A. m. sahariensis Baldensperger.
Diet attributes of lactating ewes at pasture using faecal NIRS and relationship to pasture characteristics and milk production

SUMMARY In order to assess the diet of lactating ewes fed at pasture and the relationship of diet quality to pasture characteristics and milk production (MP), 12 lactating ewes were monitored during five lactation cycles (LCs). Individual faecal samples were collected three times per LC and scanned using a Foss NIRSystem 6500 monochromator. The organic matter digestibility (OMD), organic matter intake (OMI), digestible OMI (DOMI) and the chemical composition of the herbage ingested, i.e. the crude protein (CP) content of the herbage ingested (CPi) and the acid detergent fibre and lignin contents of the herbage ingested (ADFi and ADLi), were determined. The MP of the ewes and the pasture characteristics were measured and their relationships with diet quality were analysed. OMI and DOMI were higher during the first and the fourth LC (P<0·01). OMD and CPi were higher during the second and the fifth LC (P<0·01). MP varied with OMI (P<0·01) and with DOMI (MP=0·1362×DOMI0·53, R2=0·40, P<0·001), whereas it was negatively correlated with OMD (r=−0·46, P<0·001). OMD and CPi were both positively correlated with the CP content of the pasture (r=0·25, P<0·03; r=0·50, P<0·001), whereas the ADFi was negatively correlated with CP content (r=−0·48, P<0·01). The variation in OMI, DOMI and MP, on the one hand, and OMD and CPi, on the other, throughout the different LCs illustrates the importance of measuring several parameters when evaluating diets at pasture.
Betta hendra - a new species of fighting fish (Teleostei: Osphronemidae) from Kalimantan Tengah (Borneo, Indonesia)

Betta hendra spec. nov. is described from Kalimantan Tengah, Borneo, Indonesia. It is a bubble-nesting fighting fish of the B. coccina species group. The new species differs from the other members of the group by a bright greenish iridescent colour on the flanks and unpaired fins. It is distinguished from its geographical neighbour species B. uberis by a lower number of dorsal-fin rays (10–12 versus 14–17).
Expression of human immunoglobulin E ε chain cDNA in E.coli

Using the cDNA of human epsilon chain, three expression plasmids that code directly the constant portion of the epsilon chain (C epsilon 1-C epsilon 4, C epsilon 2-C epsilon 4 and C epsilon 3-C epsilon 4 domains) were constructed. These epsilon chain peptides were synthesized in E. coli under the control of the trp promoter-operator. The bacterially produced peptides have the antigenicity of human epsilon chain and gave the molecular weights equal to the values calculated from the amino acid sequence of the constructed plasmids.
Fast Microwave-based DNA Extraction from Vegetative Mycelium and Fruiting Body Tissues of Agaricomycetes for PCR Amplification

In this study, we tested a microwave-based DNA extraction method for subsequent DNA amplifications by PCR on vegetative mycelia and mushrooms of different Agaricomycetes. The extraction method requires tiny amounts of fungal material, is rapid and achieved within minutes, why it is superior to classical extraction methods which are work-intensive and require larger amounts of starting material, hours of time for performance and in addition specific expensive and hazardous chemicals for cell lysis and DNA purification. The microwave method with highest reliability is suitable for vegetative mycelium harvested from fresh and also from aged fungal cultures. It is especially attractive for slowgrowing species of which larger amounts of mycelium are difficult to obtain from. The method is further applicable with success rates between 76.9% and 90.9% to fleshy mushrooms over a wide range of families of Agaricomycetes, both in fresh as well as in dried form, and also to firm young and older fruiting bodies of more robust leathery, corky and woody textures. Also noncultivable species can thus be accessed for DNA analyses. Finally, we show that also fungal infested plant material such as millet, straw, wood and bark can be used. However, here the success depends on freshness of the material and on presence of sufficient surface mycelium.
Honey bee attractants and pollination in sweet orange, Citrus sinensis (L.) Osbeck, var. Pera-Rio

This experiment studied the frequency and behavior of insects on sweet orange flowers, Citrus sinensis (L.) Osbeck, their effect on fruit production (quantity and quality), nectar and pollen collection, and the effectiveness of different attractants. Over three consecutive years, the most frequent visitor to the flowers was Apis mellifera (Africanized). Flowers visited less than ten times showed low fructification. Fruit production was 35.30% greater in uncovered flowers. Fruit mean weight was much greater in uncovered (180.2g) than in covered flowers (168.5g). Fruits from the covered were more acid (1.411g of citric acid/100ml of juice) than the uncovered flowers (1.164g of citric acid/100ml of juice). The number of seeds per bud was higher in the uncovered (1 seed/bud) than in the covered treatment (0.8 seed/bud). Bee-HereR, eugenol, geraniol, citral, and lemon grass extract, mainly diluted in water, were effective in attracting honeybees to orchards. However, these compounds were less effective when diluted in sugar syrup. The same products had variable attractiveness to honeybees in different years.
Validation and incorporation of leaf rust resistance genes Lr9, Lr19, Lr24 and Lr26 through molecular markers in wheat (Triticum aestivum L.)

Molecular markers for the leaf rust resistance genes Lr9, Lr19, Lr24, rye specific chromatin (1BL.1RS translocation, Lr26), and Lr28 were validated in the parental lines of wheat (Triticum aestivum L.). The markers for Lr9, Lr19 and Lr26 were able to discriminate the lines with specific genes/chromatin from the lines that did not carry these genes. The Lr24 marker showed polymorphism between positive and negative controls but in white grained genotypes the amplified band was faint and inconsistent as compared to red seeded lines. The marker used for detecting Lr28 was not polymorphic among the tested carrier and non-carrier lines. The markers of Lr19 and Lr24 were utilized for authenticating the presence of specific genes in the advanced breeding lines whereas rye-chromatin specific marker was used for marker assisted selection of Lr26. Genetic stocks with combined resistance genes Lr19 + Lr26 + 5r25 + 5r31 + Yr9 + Yr27 and Lr24 + Lr26 + 5r24 + 5r31 + Yr9 + Yr27 were developed in the background of PBW 343 with the aid of pedigree information, host-pathogen interaction and molecular marker.
Growth and yield of anthurium in response to sawdust mulching

The objectives of the study were to analyze the effect of sawdust mulch on the: (1) soil characteristics; (2) growth and flower yield of the anthurium cv. 'Apalai'. Assay was conducted in a totally randomized design in subdivided plots, with five treatments and eight replications. The treatment consisted of five volumes of sawdust 0, 20, 40, 60 and 80L m-2, distributed over the bed, every three months. Soil, plants and flower stalks were evaluated during two years. Soil temperature, moisture, organic matter, bulk density and water retention conditions were improved, while the leaf area of plants and the yield of flower stalks were increased when the soil were mulched with sawdust. In addition to increasing soil organic matter, however, no change occurred in the level of nutrients in plants. Sawdust also improved the dimension of flower stalks. Application of 40L m-2 of sawdust every three months is recommended.
Din+ (‘invertase’) activity in Gram-negative bacteria

The H2 region, encoding one of the flagellar antigens of Salmonella typhimurium and the controlling elements of phase variation has been subcloned into the broad-host-range plasmid, RP4. Due to a deletion within the H2 region, the ‘invertase’ normally encoded by the hin gene is absent. This plasmid was transferred into a number of Gram-negative bacteria, and a hin complementary (din) activity detected in some.
Remote video-camera traps measure habitat use and competitive exclusion among sympatric chimpanzee, gorilla and elephant in Loango National Park, Gabon

Abstract: Species commonly exist in sympatry, yet ecological studies are often based on a single species approach while ignoring the impact of sympatric competitors. Over 13 mo we used 24 remote video-camera traps to monitor habitat use of sympatric chimpanzee, gorilla and elephant in four different habitat types in Loango National Park, Gabon. Habitat use by each species was predicted to vary according to seasonal changes in food availability and precipitation. Increased interspecific competition between the three species was expected at times of reduced resource availability, leading to exclusion of the inferior competitor. Supporting the predictions, species abundance per habitat showed seasonal variation: all three species responded positively to increased fruit availability in all habitats, but the response was only significant for gorilla in mature forest and elephant in coastal forest. Responses to rainfall varied, with the chimpanzee responding negatively to rainfall in swamp forest, the gorilla responding positively to rainfall in coastal and secondary forest, and the elephant responding positively to rainfall in mature forest. Elephant presence resulted in competitive exclusion of the apes under certain conditions: the chimpanzee was excluded by the elephant where fruit availability was low, whereas the gorilla was excluded by the elephant in areas of low herb density despite high fruit availability. Our results emphasize the value of applying a multi-species, longer-term approach to studying variation in habitat use among sympatric species and highlight the impact competitors can exert on one another's distribution.
Effects of over-expressing the AgGPPS2 gene in Salvia stenophylla (Burch. ex Benth) on terpenoid biosynthesis

ii Opsomming . iv Scientific publications from the dissertation . vii Dedication . ix Acknowledgements . x Table of contents. xii Table of figures . xvi List of tables . xxi List of acronyms. xxiv Chapter One . 1 General introduction . 1 1.1 Medicinal plant use . 1 1.2 Medicinal Salvia . 3 1.3 Outline of the thesis . 4 1.4 References . 6 Chapter Two . 9 Literature review . 9 2.1 Salvia stenophylla (Burch. ex Benth.) . 9 2.2 Production of secondary compounds . 12 2.3 Medicinal Properties of Salvia . 13 2.3. 1 Pharmacology and phytochemistry of S. stenophylla essential oil14 2.3. 2 Pharmacology of polar fraction . 18 2.4 Salvia biotechnology . 19 2.5 Medicinal plant farming . 20 Stellenbosch University http://scholar.sun.ac.za
Finding common ground: Centralizing responsiveness within a multisite initiative

In this reflective analysis, I describe the conditions that led the leaders of a multisite initiative to adapt their program model towards a framing that centralized responsiveness as an organizing value. After reflecting on how this shift affected the initial evaluation plan, I provide a synopsis of how we went about revising our evaluation strategy. The reimagined approach centred on eliciting and characterizing various site-specific aspects of culture and context that may influence outcomes attainment across the multisite initiative. This approach enabled comparative analysis of the various innovative, place-based expressions of the initiative across its sites. Reframing the evaluation strategy also enabled future comparative mixed methods study of maximal variation cases and qualitative comparative analysis of specific conditions related to outcomes attainment. Findings suggest that evaluators would benefit from embracing adaptive change in programs and expecting heterogeneity in multisite initiatives.
A dye-binding assay for the spectrophotometric measurement of transparent exopolymer particles (TEP)

Large transparent exopolymer particles (TEP) are found abundantly in the ocean and play an important role in many fields of marine ecology. Quantification of TEP by light microscopy, however, is labor-intensive and slow. Here we introduce a simple, semiquantitative method to determine the concentration of TEP colorimetrically. In this method TEP are first stained with alcian blue. The dye complexed with TEP is then redissolved and measured spectrophotometrically. Several independent tests of the method show that the concentration of TEP measured spectrophotometrically compares well with parallel light microscope counts. Fractionation experiments confirm that TEP are not generated as an artifact of filtration. Field data show that the concentration of TEP in different oceanic environments ranges from 10 to 500 μg liter -1 xanthan equivalent depending on season, depth, and plankton community composition.
Simplification and optimization of media ingredients for enhanced production of CMCase by newly isolated Bacillus subtilis NA15

Cellulose degrading bacterium was isolated from composting biomass and identified as Bacillus subtilis on the basis of phenotypic fingerprint using GEN III MicroPlateTM and 16S ribosomal RNA (rRNA) gene sequence analysis. 16S rRNA gene sequence similarity analysis showed 99% similarity with Bacillus subtilis. The screening of 11 nutrients was done using Plackett‐Burman design to explicate the parameters that significantly influence the carboxy methyl cellulase (CMCase) production. Maximum CMCase production of 0.47 U/mL was obtained using response surface methodology with carboxy methyl cellulose (CMC): 18 g/L, peptone: 5 g/L, yeast extract: 5 g/L and MnCl2: 0.5 g/L. The model predicted the maximum CMCase activity (0.45 U/mL), which was in good agreement with the experimental value of 0.47 U/mL showing sevenfold increase as compared to unoptimized medium. Presence of MnCl2 in the medium significantly enhanced the CMCase production. © 2014 American Institute of Chemical Engineers Environ Prog, 34: 533–541, 2015
INFLUENCE OF WEATHER CONDITIONS ON HONEY BEE VISITS (Apis mellifera carnica) DURING SUNFLOWER (Helianthus annuus L.) BLOOMING PERIOD

The objective of the investigation was to determine influence of weather conditions on activity of honey bees during blooming time of six sunflower hybrids. The investigation was carried out in 2002 growing season at Kneževi Vinogradi located in Baranja country, north-eastern edge of Croatia.Honey bees communities were moved to the field trial site inside Langstroth-Rooth's bee-hives. Honey bees visiting sunflower head inflorescence was measured at 100, 200, and 300 meters by counting honey bees four times a day (9.00 am, 11.00 am, 1.00 pm, and 5.00 pm). The influence of weather conditions was analysed by Spearman correlation coefficient. Results of the investigation show significant differences regarding honey-bee visit to the head inflorescences in six hybrids, as well as significant influence of air temperature, humidity, precipitation, minimum and maximum air temperature, as well as wind strength.
A model of phytoplankton acclimation to iron–light colimitation

We developed and calibrated a dynamic model for cellular carbon, chlorophyll (Chl), and iron under iron‐light colimitation. The model allows growth rate and two other state variables (Fep :C and Chl : C) to be described as functions of light intensity and the free iron concentration (Fe'). The model requires specification of the values of nine parameters. We obtained values for these parameters using published experimental results for Thalassiosira pseudonana using a combination of a random parameter initialization and a golden section search to minimize the cost function. The tuned model explained 95% of the variability in the observations of growth rate, 94% in Chl : C, and 90% in Fep : C. Although the model is applicable to both balanced and unbalanced growth conditions, data were only available for balanced growth; thus, the dynamics of state variables during unbalanced growth conditions could not be investigated. A limitation in calibrating the model was in the scarcity of suitable experimental data sets under well‐defined environmental forcing. This points to the need for new experimental work on iron‐limited cultures, including measurements of photosynthesis‐light curves and the dynamic responses to changed Fe' and light intensity. This phytoplankton growth model provides a physiological treatment of iron‐light colimitation for implementation within ocean biogeochemical models. By including both growth rate and elemental stoichiometry (e.g., Fep : C) as state variables, the model can be applied to assess both rate and yield limitation.
Common data standards for recording relevés in field survey for vegetation classification.

In the framework of the European Vegetation Survey common data standards are proposed for recording phytosociological releves for syntaxonomical classification. The authors wish to establish the notion that common data standards for recording phytosociological data can only be advantageous for advancing the credibility and application of vegetation science, and may stimulate other projects.
An intravenous replenishment of salivary components decrease water intake and increases feed intake in freely drinking large-type goats fed on dry forage

This research utilized two treatments to investigate if feed intake is reduced by changes in humoral factors induced by dry forage feeding in large-type goats given free access to water. In the control treatment (NI), a solution was not infused. The artificial parotid saliva i.v. infusion (ASI) treatment consisted of an i.v. infusion of artificial parotid saliva in order to replenish NaHCO3 and fluids lost from the blood to the rumen due to increased saliva secretion volume during initial stages of dry forage feeding. The ASI treatment significantly mitigated the decreases in circulating plasma volume caused by saliva secretion. Thirst was lower in the ASI-treated group, as indicated by the lower water intake (NI, 3894 mL 2 h-1; ASI, 3100 mL 2 h-1). Decreases with time in dry forage intake were significantly reduced by the ASI treatment (2134g 2 h-1) compared with the NI control (1756 g 2 h-1). These results indicate that under free drinking conditions, dry forage intake of large-type goats may likely be .
Latitudinal diversity gradients for brachiopod genera during late Palaeozoic time: links between climate, biogeography and evolutionary rates

Aim The latitudinal diversity gradient, in which taxonomic richness is greatest at low latitudes and declines towards the poles, is a pervasive feature of the biota through geological time. This study utilizes fossil data to examine how the latitudinal diversity gradient and associated spatial patterns covaried through the major climate shifts at the onset and end of the late Palaeozoic ice age. Location Data were acquired from fossil localities from around the world. Methods Latitudinal patterns of diversity, mean geographical range size and macroevolutionary rates were constructed from a literature-derived data base of occurrences of fossil brachiopod genera in space and time. The literature search resulted in a total of 18,596 occurrences for 991 genera from 2320 localities. Results Climate changes associated with the onset of the late Palaeozoic ice age (c. 327 Ma) altered the biogeographical structure of the brachiopod fauna by the preferential elimination of narrowly distributed, largely tropical genera when glaciation began. Because the oceans were left populated primarily with widespread genera, the slope of the diversity gradient became gentle at this time, and the gradient of average latitudinal range size weakened. In addition, because narrowly distributed genera had intrinsically high rates of origination and extinction, the gradients of both of these macroevolutionary rates were also reduced. These patterns were reversed when the ice age climate abated in early Permian time (c. 290 Ma): narrowly distributed genera rediversified at low latitudes, restoring steep gradients of diversity, average latitudinal range size and macroevolutionary rates. Main conclusions During late Palaeozoic time, these latitudinal gradients for brachiopods may have been linked by the increased magnitude of seasonality during the late Palaeozoic ice age. Pronounced seasonality would have prevented the existence of genera with narrow latitudinal ranges. These results for the late Palaeozoic ice age suggest a climatic basis for the present-day latitudinal diversity gradient.