Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional characterisation of ABC-type metal ion uptake systems in the staphylococci

Previously, the sitABC operon of S. epidermidis has been shown to be regulated in response to the extracellular concentration of both iron and manganese, though the identity of the true substrate for this putative ABC-type import system remains to be determined. Through the course of these investigations, the metal binding characteristics of the substrate binding component, SitC, were investigated further. Recombinant protein was over-expressed and purified as an oligomeric form. The metal binding properties of purified SitC were studied using circular dichroism (CD) spectroscopy, which demonstrated a primary specificity for Mn2+ ions with additional lower affinities for Fe2+ and Zn2+ ions. Hill analysis showed metal ion binding proceeded with dissociation constants within the micromolar range and with the strongest degree of cooperativity with Mn2+. As only a single metal ion binding site is expected to reside within SitC this cooperativity was proposed to occur intermolecularly. Inductively coupled plasma atomic emission spectroscopy (ICP-AES) revealed dissociation between metal ions and SitC with Mn2+ almost completely dissociating, and which may be due to conformational changes required to relay the substrate(s) through the transport system. A molar ratio of bound metal ion to protein approaching 1:1, suggests SitC possesses only a single metal ion binding site. These data suggest SitABC may function primarily in manganese uptake. MntC from S. aureus is regarded as an orthologue of SitC, and which has previously been shown by mutational analysis to function solely in manganese accumulation. An amino-terminal truncate of MntC (His(6)-MntC-N) was over-expressed also in an oligomeric form and the metal binding properties compared to SitC using CD analysis. Using this method, His(6)-MntC-N demonstrated cooperative primary specificity for Mn2+, with secondary affinity for Zn2+ and Cu2+ but no evidence of Fe2+ binding was apparent. These data support the previous hypothesis that SitC and MntC are orthologous in their primary metal ion specificity, though attempts to provide confirmatory functional evidence through mutational analysis of sitABC were unsuccessful.
Seeds handbook: biology, production, processing, and storage.

SEED BIOLOGY Seed Morphology and Development Seed Dormancy Seed Germination Seed Viability and Longevity SEED PRODUCTION Basic Principles of Seed Production Cereal Crops Pulse Crops Oilseed Crops Vegetable Crops Flowers and Ornamental Crops Sugar and Fiber Crops Grasses and Forage Legumes SEED PROCESSING AND STORAGE TECHNOLOGY Drying, Cleaning, and Upgrading Seed Treatment Seed Packaging and Handling Seed Transportation and Storage Seed Testing Seed Marketing and Distribution Seed Certification and Legislation NEWER SEED BIOTECHNOLOGIES Seed-Production Industry Micropropagation Synthetic Seed Biotechnology Transgenic Seeds, Plants, and Crops Loss Reduction Biotechnology of Seeds World Food Security: Future Challenges
Performance of sole and intercropped pigeonpea (Cajanus cajan) as influenced by land configuration, post-monsoon irrigation and phosphorus fertilization

A field experiment conducted at New Delhi during 2001 - 02 on a sandy loam soil analysing low in soil available P revealed that broad-bed and furrow system of planting recorded higher biomass and grain yield of pigeonpea (Cajanus cajan (L.) Millsp), pigeonpea equivalent yield, N and P uptake, water use efficiency, net returns, and P use efficiency over flat planting. Post-monsoon irrigation at 0.4 IWJCPE ratio gave higher biomass and grain yield of pigeonpea, pigeonpea equivalent yield, N and P uptake, net returns, and P use efficiency, but lower water-use efficiency and residual P at harvest over uninigated pigeonpea. The blackgram (Vigna mungo L. Hepper) intercropping did not affect yield and nutrient uptake in pigeonpea, but recorded higher pigeonpea equivalent yield, net returns, and water and P use efficiency. The soil had lower available P status at harvest after intercropping as compared with sole pigeonpea. Application of P up to 17.2 kgha enhanced biomass and grain yield of pigeonpea and grain yield of blackgram, total N and P uptake in the cropping system, P use efficiency and residual soil P at harvest. However, 34.4 kg Piha recorded higher biomass yield of blackgram, pigeonpea equivalent yield, net returns and water-use efficiency.
Silvical characteristics of Aquilaria agallocha Roxb.

Aquilaria agallocha (Agar-wood) is a very valuable tree of North-eastern region of India and is distributed along foot-hills of evergreen and semi-evergreen forests. The tree flowers and fruits at an age of 7 to 9 years. The capsules ripen in second week of June and 1500 seed weigh to a kg. Seed germinates in 10 to 12 days and is viable for 30 days. Initial germination is 65% and it reduces to 5% after three weeks. Regular plantations are not raised due to uncertainty of agar-wood formation. Agar-wood formation is regarded as a pathological product. Many workers have studied agar formation since 1929 but could not work out a suitable technique for agar-wood formation. Agar tree is attacked by a defoliator (larvae of family Thyrididae) which can be controlled by spraying 0.1% Fenitrotbion or Thiodon.
Alterations in Retinoic Acid Receptors in Non-Small Cell Lung Cancer and Their Clinical Implications

The nuclear retinoic acid receptor may play a critical role in the process of lung carcinogenesis. Alteration or loss of nuclear retinoic acid receptors (RARs) has been associated with progression in premalignant and malignant tissues and it is associated with malignant transformation in human cells. Vitamin A derivates, such as retinoic acid, have emerged as adjuvant to therapy in several types of cancer with favorable effects. Retinoic acid regulates the expression of target genes through the binding and activation of RARs, inhibiting growth proliferation. Diverse studies have evaluated different retinoids alone or in combination with chemotherapy in lung cancer, from which results have been controversial with benefits observed only in the subpopulation with high levels of triglycerides. Additionally, several large randomized trials using retinoids to prevent tobacco-related cancer have failed; due to the latter the use of retinoids in clinical trials remains controversial. However they could reduce the risk of cancer development in non-smokers. There is evidence that retinoids have different effects on lung cancer; still the identification of biomarkers could determinate their benefits as preventive or therapy agents. This review describes the RAR alterations during the development of Non-Small Cell Lung Cancer and sets out the importance of several cancer treatments with retinoid compounds.
Diagnóstico das áreas de preservação permanente das microbacias hidrográficas do município de Bandeirantes – Paraná

A expansao das fronteiras agricolas, o desenvolvimento industrial e o aumento dos indices populacionais demandaram aumentos substanciais na producao de alimentos. Estes fatores levaram a degradacao crescente dos recursos naturais. A devastacao das areas de florestas ao longo dos rios e corregos, entorno das nascentes e topos de morros, no passado, obrigam sua recomposicao, por forca de lei, como areas de preservacao permanente (APP). Este trabalho teve por objetivo delimitar as microbacias do municipio de Bandeirantes, mensurar as areas de preservacao permanente, total e existentes, ao longo dos cursos d’agua, nascentes e topo de morros e identificar o uso conflitivo destas areas. Utilizou-se o sistema de informacao geografica SPRING 4.1, imagem do Landsat ETM+, bandas 2, 3, 4 e 5, base cartografica do IBGE, escala 1:50000 e fotografias aereas, escala 1:25000. Verificou-se que o municipio apresenta 8,6% das APPs com mata ciliar, sendo 11,38%, 8,21% e 5,25% referentes a rios, corregos e nascentes, respectivamente. As APPS referentes a topo de morros e declividades superiores a 100% tem area equivalente a 24,94 ha e 8,7 ha, no entanto 100% destas areas encontram-se sem mata. As microbacias que apresentaram menor indice de APP foram aquelas com melhor aptidao agricola.
Acquired abnormalities of chromosome 21 in acute lymphoblastic leukaemia

The intrachromosomal amplification of chromosome 21 (iAMP21) was identified as a novel and prognositically important acquired chromosomal abnormality in childhood acute lymphoblastic leukaemia (ALL). It is defined by multiple copies of the RUNX1 gene, as seen by fluorescence in situ hybridisation (FISH), localised to a single abnormal duplicated chromosome 21 [dup(21)]. The morphological form of this chromosome is highly variable between patients and currently the only reliable method of detection is FISH with probes to RUNX1. Studies of 48 iAMP21 patients using detailed FISH techniques and array-based comparative genomic hybridisation highlighted an extensive region of chromosome 21 involvement. A minimum common region of amplification, between 33.19 and 39.80Mb, including RUNX1 was identified, together with a minimum common region of deletion, between 46.54 and 46.92Mb, in 100% and 77% of patients, respectively. This study established that there were unique patterns of imbalance, with evidence of deletions, inversions and amplification, displayed on the dup(21), between individual patients. This provided evidence of an abnormality that may have arisen from a breakage-fusion-bridge mechanism, possibly initiated by loss of a telomere. Results indicated that iAMP21 represents a distinct genetic subgroup of childhood ALL and is not secondary to a cryptic abnormality of chromosome 21. Two possible variant cases were identified both involving chromosome 15. The abnormality can be distinguished from other numerical abnormalities of chromosome 21 by exploiting the unique pattern of gain, amplification and deletion seen in these patients. This allowed for the development of diagnostic tests based on copy number using either FISH or multiplex ligation dependent probe amplification (MLPA), both of which successfully identified iAMP21 patients.
Effect of genetic and proteomic variation in field isolates of Mycoplasma hyopneumoniae on virulence, diagnosis and prevention of disease in the pig

The purpose of these studies was to investigate the implications of variability in virulence, genetics and antigenic profiles among field isolates of Mycoplasma hyopneumoniae. Increased virulence was compared with in vitro and in vivo growth characteristics of the organism and with immune parameters in the pig, although none was found to be significantly correlated. The impact of proteomic and genetic variation among field isolates on diagnostic assays was examined by both in vivo and in vitro studies. Three enzyme-linked immunosorbent assays (ELISAs) used in the United States were compared and shown to not detect all isolates of M. hyopneumoniae equally. Similarly, polymerase chain reaction (PCR) assays were tested against a panel of M. hyopneumoniae field isolates and it was shown that some isolates are not detected by all published PCR assays. Therefore, two new real-time PCR assays were developed that appear to be both sensitive and specific for M. hyopneumoniae. The ability of a commercial vaccine to protect against field isolates of M. hyopneumoniae was evaluated in a challenge study using two recent field isolates. One isolate produced nearly twice as many macroscopic lung lesions as the other isolate, but vaccinated pigs had less pneumonia compared to non-vaccinated pigs in both challenge groups. Together these results demonstrate that differences exist among isolates of M. hyopneumoniae in the field at the genetic and antigenic level and that these differences impact the virulence of the organism, diagnostic capabilities in the pig, and the prevention of M. hyopneumoniae-associated disease.
Humans and climate as drivers of algal community change in Windermere since 1850

1. Historical archives, published data sets and lake sediments from the North and South Basins of Windermere were analysed to reconstruct changes in the lake and catchment since 1850 and determine the drivers of limnological variability. 2. Pastoral sheep farming has remained the dominant form of agriculture since 1850, but there was a decline in horse numbers (because of agricultural mechanisation), an increase in nitrogen fertiliser use and a doubling in sheep numbers since the 1950s. The human population in the Windermere catchment almost quadrupled between 1801 and 1921 coincident with the arrival of the railway in 1847, which led to urban expansion, sewer and piped water installation (since ∼1860s) and the development of sewage treatment systems (after 1886). 3. C : N ratios and stable isotopes of carbon in 210Pb-dated sediment cores suggested that land disturbance increased the transport of terrestrial carbon to sediments of both basins after 1870, but algae increasingly contributed to the sediment matrix after ∼1890. Nitrogen-stable isotope ratios generally declined in both basins consistent with an increase in an isotopically light source such as atmospheric N deposition or synthetic fertilisers. 4. Chlorophyll and carotenoid pigments in sediment cores showed that algal production increased gradually in the North Basin from ∼1890 to 1940 to be maintained at higher abundance thereafter. South Basin pigments changed most markedly ∼1860 (increase in cyanobacterial pigments), ∼1945 (increase in siliceous algal and chlorophyte pigments) and ∼1987 (increase in cyanobacterial pigments). 5. Redundancy and variance partitioning analyses suggested that sewage influx and the modernisation of agriculture were strongly and positively correlated with algal abundance. However, climate variables were a secondary driver of algal change in both lake basins. 6. Enrichment of the lake was caused by a combination of increases in population (after 1847), more efficient sewage disposal, intensification of agriculture and atmospheric deposition of N, which led to a greater than fivefold increase in primary production in the North Basin and marked shifts in algal communities of the South Basin. 7. After enrichment, lake phytoplankton responded markedly to fluctuations in climate. High precipitation in January–March led to lower abundance of siliceous algae (mostly Asterionella formosa) in both lake basins, possibly because A. formosa inocula were diluted, thus limiting the spring diatom bloom. 8. This combined palaeolimnological and archival study has shown that eutrophication of Windermere occurred before the start of the lake monitoring programme in 1945, but that nutrient enrichment enhanced the lake response to meteorological change. Therefore, future management of Windermere should aim for baseline conditions similar to those existing c. 1850 and consider that the control of eutrophication is essential in building resilience to future climate change.
Understanding the Cellular Response to Cytosolic Cytochrome c

Understanding the Cellular Response to Cytosolic Cytochrome c by Carrie Elizabeth Johnson Department of Pharmacology and Cancer Biology Duke University Date:_______________________ Approved: ___________________________ Sally Kornbluth, Supervisor ___________________________ Donald McDonnell ___________________________ Robert Wechsler-Reya ___________________________ Gerard Blobe ___________________________ Salvatore Pizzo An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology and Cancer Biology in the Graduate School of Duke University 2009
Rethinking integration: Superdiversity in the networks of transnational individuals

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Influence of ultrasound during wheat gluten hydrolysis on the antioxidant activities of the resulting hydrolysate

Summary Wheat gluten was hydrolysed by Alcalase 2.4L under ultrasound. Different antioxidant assays in vitro, such as ferrous ion-chelating activity, reducing power, inhibition of linoleic acid emulsion peroxidation and 2,2′-azinobis (3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) radical scavenging activity, were employed to evaluate the antioxidant activities of the wheat gluten hydrolysate (WGH) obtained. It was found that WGHL (WGH which was obtained by low frequency (LF) ultrasound) exhibited the strongest antioxidant activities, with an EC50 value of 0.513 mg mL−1 for ferrous iron-chelating activity, as well as a high and dose-dependent reducing power. In the linoleic acid system, a longer induction time indicated a significant decrease of lipid peroxidation. In addition, WGH also exhibited notable ABTS radical scavenging activity. A good correlation was observed between antioxidant activities and the amount of WGH, but a poor correlation was observed between antioxidant activities and degree of hydrolysis. The molecular weight distribution of WGH was affected by ultrasonic frequency and WGHL had the highest proportion of peptide fractions of molecular weight 3000–500 Da. All the results showed that the WGH treated by ultrasound had strong antioxidant activities and low molecular weight.
Effect of environmental factors on the flight activity of Trialeurodes vaporariorum (Westwood) under greenhouse conditions

The flight activity of the greenhouse whitefly Trialeurodes vaporariorum (Westwood) was monitored over a 3‐year period in greenhouses containing tomato and zucchini crops. The environmental factors affecting its flight activity and dispersal were analyzed. Among the climatic variables, temperature had a positive impact on T. vaporariorum flight, whereas relative humidity had only a weak effect. More flights were made during the morning and afternoon, with fewer flights occurring when the temperature was above 25°C in greenhouses containing zucchini or above 30°C in those containing tomato; no flights were recorded when the temperature was 12.30°C in either setting. Flight typology, classified as short, long or dispersal, and covering a few centimeters to more than 2–3 m, was influenced by the vegetative condition of the plants. As the plants aged and declined in condition, the number of short flights decreased, whereas the number of long and dispersal flights increased. Based on these results, we can conclude that the dispersal of T. vaporariorum in greenhouses containing either tomato or zucchini crops is generally influenced by environmental factors, which also affect the type of flight, with a trade‐off between short and long dispersal flights. However, adult dispersal is driven not only by temperature, but also by other factors, such as conspecific density and time of the day. Therefore, producers must consider such factors when aiming to reduce the dispersal of pest insects within greenhouses and, thus, to maintain the productivity of their crops.
Damage thresholds and population dynamics of Meloidogyne chitwoodi on carrot (Daucus carota) at different seed densities

for sedentary and free-living nematodes. The tolerance limits for yield loss were 0.34, 0.62 and 0.50, while that of quality were 0.012, 0.142 and 0.813 second-stage juveniles (J2) (g dry soil) −1 at increasing seed densities, respectively. The minimum yield (m), increased with seed density: 0.25, 0.30 and 0.50; the minimum quality yield was 0.10, 0.08 and 0.15 J2 (g dry soil) −1 at increasing seed densities, respectively. Both maximum multiplication rates and maximum population densities increased with increasing seed density but were generally low. Carrot cv. Nerac can be considered a bad host for M. chitwoodi.
Restoration of coelomocytes in the earthworm Dendrobaena veneta

We have previously shown that Dendrobaena veneta belongs to the earthworm species which possesses two main cohorts of coelomocytes, namely amoebocytes and autofluorescent eleocytes, the latter storing moderate amounts of riboflavin. The aim of the present experiments performed at 17oC was to follow the restoration of amoebocytes and eleocytes, as well as riboflavin stores in eleocytes after experimental extrusion of coelomocyte-containing coelomic fluid through the dorsal pores induced by electrostimulation (4.5V, 1 min). The analyses were conducted using a combination of cell counts, flow cytometric detection of eleocytes, and spectrofluorimetric measurements of riboflavin in coelomocyte lysates. It has been found that the depleted coelomocyte system recovers slowly. The number of amoebocytes reaches the level characteristic of that in undisturbed worms in 4 weeks, while the number of elecytes is still below the control level 6 weeks after extrusion. The amount of riboflavin stored in recovering chloragocytederived eleocytes is higher than that in mature eleocytes for at least 4 weeks.
Small but not ephemeral: newly discovered species of Aphelinidae and Trichogrammatidae (Insecta: Hymenoptera: Chalcidoidea) from Eocene amber

New species of fossil Aphelinidae and Trichogrammatidae are described from middle Eocene (Lutetian) Baltic amber (41.3–47.8 Ma). A new subfamily, two new genera and three new species of Aphelinidae are described, with comments on their placement: Phtuaria fimbriae gen.n. , sp.n. in Phtuariinae subf.n. , Glaesaphytis interregni gen.n. , sp.n. and Centrodora brevispinae sp.n. These represent the first described true fossil Aphelinidae. Four new species of Trichogrammatidae are described: Mirufens illusionis sp.n. , Palaeogramma eos gen.n. , sp.n. , Pterandrophysalis plasmans sp.n. and Szelenyia terebrae sp.n. , thus expanding our knowledge of fossil Trichogrammatidae beyond the single previously described species. The presence of recognizable extant genera of Aphelinidae and Trichogrammatidae in the Eocene suggests that the morphology of these genera has been relatively invariant despite highly variable conditions during and since the Eocene.
Somatic Embryogenesis and Plant Regeneration from Juice Vesicles of Mexican Lime (Citrus aurantifolia L.)

Callus production, somatic embryogenesis and plant regeneration were achieved from juice vesicles of Mexican lime. First, three types of culture media, Murashige and Skoog (MS), Murashige and Tucker (MT) and Grosser and Gmitter (H+H) and different levels of 2,4-Dicholorophenoxy acetic acid (2,4-D) were used to study their effects on production and proliferation of embryogenic calli from juice vesicles. Second, for initiation of somatic embryos from embryogenic calli, five different media and twenty combinations of growth regulator treatments were investigated. Results showed that MS medium supplemented with 0.5 mg/l 2,4-D produced maximum embryogenic calli. In MT and H+H media, maximum calli were obtained with 0.5 and 1.5 mg/l 2,4-D, respectively. Somatic embryos were formed only by the use of MT medium containing 500 to 700 mg/l malt extract. Embryos germinated and completed their growth on MS medium supplemented with 1.0 mg/l Gibberlic acid (GA3) and 0.02 mg/l α-Naphthalene acetic acid (NAA). Maximum shoot length and leaf number were observed when 1.0 mg/l GA3 was added to the MS medium. Plantlets were transferred into pots containing of 1:2:2 volume ratio of soil mixture (sand, peat moss and perlite, respectively) and the rate of survival was 100%.