Miracle-dz/UniFAR-FTUs huggingface dataset:
Micropropagation of grapevine (Vitis vinifera L.) seedless cultivar 'Parvana' through lateral bud development

Factors affecting successful establishment in vitro, rapid proliferation, rooting and acclimatization of grapevine seedless cultivation 'Parvana' were studied. A treatment combination of 2.0 % calcium hypochlorite for 7 minutes plus 70 % ethanol for 3 minutes was found to be effective with 75.0 % of aseptic culture establishment in vitro. The highest number of new microshoots (4.5) was obtained in a culture medium (Gambourg's B5 modification) supplemented with 0.6 mg∙L-1 BAP + 0.2 mg∙L-1 KIN + 0.5 mg∙L-1 GA3. Presence of GA3 in combination with BAP and KIN promoted elongation of shoots. A concentration of 0.4 mg/l IAA in half strength of MS (Murashige and Skoog) proved to be the best for rooting (84.4 % root induction, 4.66 roots with 7.9 cm length). In vitro rooted plantlets were successfully acclimatized, with 82.2 % survival rate in plastic pots containing garden soil, sand and peat moss(1:1:1). In this study an efficient micro propagation technique of grapevine seedless cultivar 'Parvana' was successfully achieved through lateral bud culture. Such a technique would be useful for large scale plant production and in vitro conservation.
Gradual enrichment of 15N with humification of diets in a below‐ground food web: relationship between 15N and diet age determined using 14C

Summary 1Stable nitrogen (N) isotope has been widely used to disentangle food webs and to infer trophic positions of organisms based on an assumption that the stepwise enrichment occurs along trophic levels. The enrichment of 15N in soil organisms with diet humification has also been reported, but the underlying mechanism has not been fully examined. 2To examine the effect of diet humification on 15N, we estimated the stable N isotope ratios and diet ages of earthworms and termites. These organisms feed on organic matter with various degrees of humification, ranging from undecomposed plant materials to humified organic matter (soil organic matter), in a gallery forest and a savanna in the Ivory Coast. We defined diet age as the time elapsed since carbon (C) in the diet of earthworms and termites was fixed from atmospheric CO2 by photosynthesis; it was estimated by comparing the radiocarbon (14C) content of these organisms to atmospheric 14CO2 records. 3Stable N isotope ratios increased along the humification gradient of diets, and values for earthworms and termites varied from 1·8‰ to 9·9‰ and from –1·5‰ to 15·9‰, respectively. Epigeic (litter-feeding) earthworms had younger diet ages (2–4 years), whereas endogeic (soil-feeding) earthworms generally exhibited older diet ages (5–9 years). Grass-feeding termites had young diet ages (2 years), and wood/soil-feeding termites had the oldest diet ages (c. 50 years). Soil-feeding termites were similar in diet age (7–12 years) to wood feeders (8–11 years), with the exception of one species (18–21 years) that consumes large-diameter wood. 4A significant positive relationship was found between diet ages and stable N isotope ratios of the two groups in the savanna. This relationship held in the gallery forest when termites feeding on woody tissues were not considered. These results show that the stable N isotope ratios of organisms can increase with diet age, unless C in the diet has been stored as organic matter, such as woody tissue, that is able to age without being subject to humification processes. 5Given that above-ground food webs are often sustained directly by material and energy flow from below-ground food webs, in addition to trophic interactions, gradual enrichment of 15N with the humification of below-ground diets should be considered when interpreting stable N isotope ratios of terrestrial food webs.
Characterization and optimization of antigen-specific T cell responses during ex vivo expansion of melanoma tumor-infiltrating lymphocytes

Treatment of metastatic melanoma with tumor reactive T cells (adoptive T cell therapy, ACT) is a promising approach associated with a high clinical response rate. However, further optimization of this treatment modality is required to increase the clinical response after this therapy. ACT in melanoma involves an initial phase (pre-REP) of tumor-infiltrating lymphocyte (TIL) expansion ex vivo from tumor isolates followed by a second phase, “rapid expansion protocol” (REP) generating the billions of cells used as the TIL infusion product. The main question addressed in this thesis was how the currently used REP affected the responsiveness of the CD8 T cells to defined melanoma antigens. We hypothesized that the REP drives the TIL to further differentiate and become hyporesponsive to antigen restimulation, therefore, proper cytokine treatment or other ways to expand TIL is required to improve upon this outcome. We evaluated the response of CD8 TIL to melanoma antigen restimulation using MART-1 peptide-pulsed mature DC in vitro. Post-REP TILs were mostly hyporesponsive with poor proliferation and higher apoptosis. Phenotypic analysis revealed that the expression of CD28 was significantly reduced in post-REP TILs. By sorting experiment and microarray analysis, we confirmed that the few CD28 post-REP TILs had superior survival capacity and proliferated after restimulation. We then went on to investigate methods to maintain CD28 expression during the REP and improve TIL responsiveness. Firstly, IL-15 and IL-21 were found to synergize in maintaining TIL CD28 expression and antigenic responsiveness during REP. Secondly, we found IL-15 was superior as compared to IL-2 in supporting the long-term expansion of antigen-specific CD8 TIL after restimulation.
Large sharks and plastic debris in KwaZulu-Natal, South Africa

In total, 28 687 large sharks were caught between 1978 and 2000 in the nets that protect users of the popular swimming beaches of KwaZulu-Natal, South Africa, against shark attack. Over this 23-year period, 53 sharks (0.18% of the catch) were found with polypropylene strapping bands around the body. Less than 1% of the individuals from each of eight species were entangled in this manner. The dusky shark Carcharhinus obscurus was the most frequently entangled species, with 27 individuals (0.47% of the species catch). There was an increase in the incidence of entangled C. obscurus with time. Those examined in the laboratory were significantly underweight. Although entanglement may ultimately result in death, the low incidence recorded in this study is unlikely to affect the populations of sharks concerned. A total of 60 sharks (0.38% of those with recorded stomach contents) had ingested plastic debris. The most common items were packets or sheets. There was no increase in the ingestion of plastics with time. The highest frequency of occurrence was in the tiger shark Galeocerdo cuvier, with 38 individuals (7.5% of tiger sharks examined).
Biomass and stem volume equations for tree species in Europe

A review of stem volume and biomass equations for tree species growing in Europe is presented. The mathematical forms of the empirical models, the associated statistical parameters and information about the size of the trees and the country of origin were collated from scientific articles and from technical reports. The total number of the compiled equations for biomass estimation was 607 and for stem volume prediction it was 230. The analysis indicated that most of the biomass equations were developed for aboveground tree components. A relatively small number of equations were developed for southern Europe. Most of the biomass equations were based on a few sampled sites with a very limited number of sampled trees. The volume equations were, in general, based on more representative data covering larger geographical regions. The volume equations were available for major tree species in Europe. The collected information provides a basic tool for estimation of carbon stocks and nutrient balance of forest ecosystems across Europe as well as for validation of theoretical models of biomass allocation.
A Chemical-Genetic Study of EphB Receptor Tyrosine Kinase Signaling in the Developing Nervous System

EphB receptor tyrosine kinases regulate cell-cell contacts throughout nervous system development, mediating processes as diverse as axon guidance, topographic mapping, neuronal migration and synapse formation. EphBs bind to a group of ligands, ephrin-Bs, which span the plasma membrane, thus allowing for bidirectional signaling between cells. Since EphBs are capable of multiple modes of signaling, and since they regulate numerous interdependent stages of development, it has been challenging to define which signaling functions of EphBs mediate particular developmental events. To overcome this hurdle, we developed an approach combining chemical biology with genetic engineering to reversibly inhibit EphB receptors in vivo. By mutating a residue in the receptor’s ATP-binding pocket, we rendered its kinase activity sensitive to reversible inhibition by PP1 analogs that do not inhibit wild type receptors. We engineered triple knockin mice bearing this mutation in which the kinase activity of EphB1, EphB2, and EphB3 can be rapidly, reversibly, and specifically blocked. Since we are able to block the kinase activity of EphBs while leaving their scaffolding and reverse signaling capabilities intact, we can precisely isolate the role of the kinase domain. In addition, acute inhibition can circumvent the developmental compensation that may
Effect of High-pressure Treatment on Polyphenoloxidase Activity of the Agaricus Bisporus Mushroom

High pressure treatments (100-500 Mpa/4 °C/10 min) were carried out on freshly sliced mushrooms ( Agaricus bisporus ) and on liquid extract. Pressure above 200 MPa led to respiratory activity loss, significant enzymatic browning and polyphenoloxidase (PPO) activation in treated mushrooms. Increasing pressure from 200 to 500 MPa enhanced the PPO activation (in whole tissue and in liquid extract). Stabilization of mushroom by high-pressure (HP) alone cannot be considered. A combination of HP with thermal or chemical treatments is found necessary.
Response to Comments by Timpson et al. and Yu et al.

The lack of association of the abnormal spindle-like microcephaly associated (ASPM) and Microcephalin (MCPH1) genes with brain size or intelligence described by Timpson et al. has been reported previously, including by our own group. Moreover, as in most studies of selection, our analyses were entirely independent of phenotypic association. We also respond to the previously published comment by Yu et al., which argued that ASPM has not undergone positive selection.
Influence of Nisin and Lauryl Arginine Ester Against Some Foodborne Pathogens in Recombined Feta and Processed Spread Cheese

The aim of this study was to evaluate the impact of nisin with lauryl arginine ester (LAE) or their combination by 1: 3 (w/w) on cheese preservation. The study was carried out against the most common foodborne pathogens in recombined feta cheese (RFC) and processed cheese spread (PCS). Combination of nisin with LAE has higher synergistic preservative effect on different widespread foodborne pathogens such as Bacillus subtilis, Clostridium sporogenes and Escherichia coli compared with individual one. The most sensitive strain was E. coli with an effective minimal inhibition concentration (MIC) of 400 ppm, whereas the former spore-forming bacterial strains were totally inhibited using 700 ppm from the combination, respectively. Synergistic combination blend was added by its recommended MIC (700 ppm) in the manufacture of both RFC and PCS. The results indicated that it is efficient enough to inhibit the growth of the most common foodborne pathogens in cheese after their storage for 7 days (RFC) and 30 days (PCS). Practical Applications Inhibiting the foodborne pathogens by the addition of lauryl arginine ester (LAE) and nisin together by 1: 3 (w/w) increased the cheese quality. However, the possibility of contamination of traditional cheese during the preservation in terms of food safety can be controlled by the addition of the two mentioned additives (i.e., LAE and nisin) and can be manufacture and distribute in the dairy industries.
Convergent functional groups. 4. Recognition and transport of amino acids across a liquid membrane

Description d'un recepteur modele sous forme d'une cle moleculaire, comprenant des domaines ionique, aromatique et hydrophobe. Ces particularites permettent la reconnaissance specifique des aminoacides comportant des chaines secondaires aromatiques et donnent un moyen de les extraire, a partir de l'eau a pH neutre. Cette selectivite s'etend aux phenomenes de transport
Receptor cluster formation during activation by bacterial products

The recognition of bacterial products, such as lipopolysaccharide (LPS) by the innate immune system lead to a strong pro-inflammatory response that can eventually lead to fatal sepsis syndrome in humans. Although CD14 and TLR4 have been identified as the key molecules involved in LPSinduced signal transduction, accumulating evidence indicates that multiple receptors are also involved. Our group has recently identified a cluster of receptors, involving heat-shock proteins 70 and 90, chemokine receptor 4 as well as growth differentiation factor 5, that are formed following LPS stimulation. In addition, we present data demonstrating that these molecules associate with TLR4 and accumulate in membrane microdomains following LPS ligation. Our results suggest that the entire bacterial recognition is based around the recruitment of multiple signalling molecules, in addition to CD14 and TLRs, within the lipid rafts. We propose that different combinational associations of receptors within activation clusters determine the different responses to a variety of bacterial stimuli.
The interaction of phylloxera infection, rootstock, and irrigation on young Concord grapevine growth

Concord roots are moderately resistant to phylloxera, which form nodosities on the fine roots and weaken the root system. Rootstocks and vineyard floor management both have the potential to eliminate or reduce the effect of phylloxera in New York Concord vineyards. Young, container-grown Concord grapevines were used to evaluate the interaction between rootstock (own-rooted, Couderc 3309), irrigation, and phylloxera infection on vine growth. Phylloxera inoculation alone caused a 21 % decrease in vine dry mass and lack of irrigation (mid-day stem water potential: -0.9 to -1.0 M Pa) alone caused a 34 % decrease in vine dry mass. The combination of phylloxera stress and water stress was additive and caused a 54 % decrease in vine dry mass. Because C3309 rootstock is resistant to phylloxera, the grafted vines showed a response to irrigation but not phylloxera inoculation. This container study shows the potential benefits of irrigating own-rooted Concord grapevines or the use of rootstocks without irrigation to withstand phylloxera infection.
Temporal variation in the reproductive pattern of blood cockle Anadara antiquata from Pakistan (northern Arabian Sea)

Sex ratios, size frequency, and reproductive patterns of blood cockle Anadara antiquata were studied from Sonmiani and Phitti Creek, Pakistan, from May 2004 to April 2005. At both sites, the overall sex ratio was significantly in favor of females. The population of A. antiquata at Sonmiani consisted of cockles of 31-80 mm in size and that at Phitti Creek of 21-100 mm in size; however, the majority of specimens were of 51-70 mm in size at both sites. Four stages of gametogenesis were identified in male and female cockles: 1) developing, 2) ripe, 3) spawned out, and 4) resorbing. No hermaphrodites or specimens with undifferentiated sex were found in the present study. The gametogenic activity in males and females occurred year-round, with greater intensity during January to March and low activity in December at both Sonmiani and Phitti Creek in female cockles, as indicated by low gonad index values of females in these months.
Multiple Minisequencing Screen for Seven Southeast Asian Nondeletional α-Thalassemia Mutations

α-Thalassemia is the most common globin disorder in the world, and the severe forms are especially prevalent among Southeast Asians. It is a disorder of absent or reduced production of α-globin chains resulting from mutations in the α-globin gene cluster on chromosome 16p13.3. Most α-thalassemia mutations involve deletions of one (−α) or both (− −) α-globin genes, whereas point mutations within the α-globin genes (αTα or ααT) are much less frequent. Nonetheless, the number of point mutations that have been described has been steadily increasing, with >40 identified to date (1)(2). The importance of nondeletional α-thalassemia mutations is underscored by the observation that patients with nondeletional hemoglobin (Hb) H disease (αTα/− −) are generally more severely affected and more likely to require transfusions compared with deletional Hb H disease patients (−α/− −) (3). There have also been a few reports of Hb H disease caused by homozygosity or compound heterozygosity of nondeletional mutations involving the α2-globin gene (αTα/αTα) (1)(3). Additionally, nondeletional Hb H disease involving the α2 codon 30 or codon 59 mutation can cause the fatal Hb H hydrops fetalis syndrome, especially if associated with large ζ-α-globin gene deletions (4). In certain regions of Southeast Asia, nondeletional Hb H disease can account for as many as 50% of all Hb H disease patients (3). Several specific and reliable molecular tests have previously been developed to diagnose and screen the most common deletional (5)(6) and nondeletional (7)(8) α-thalassemia mutations. We now describe a multiplex minisequencing assay to detect seven Southeast Asian nondeletional mutations: Hb Constant Spring (α2 codon 142 TAA→CAA), Hb Pakse (α2 codon 142 TAA→TAT), Hb Quong Sze (α2 codon 125 CTG→CCG), α2 codon 0 Δ1bp (−T), α2 …
Estimators for successive forest sampling with partial replacement

The coefficient of variation of forest stand volume can remain approximately constant over successive measurements. This consideration was exploited to provide an efficient estimator of the mean timber volume on the current occasion when sampling with partial replacement (SPR) on two occasions. For even-aged and normally distributed forest populations, the gains in precision were shown to be in the range of 8 to 200% when using the modified SPR estimator of the current mean volume.
CHARACTERIZATION OF ATYPICAL CLAVIBACTER MICHIGANENSIS subsp. MICHIGANENSIS POPULATIONS IN GREENHOUSE TOMATOES IN ITALY

SUMMARY The quarantine bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) is the agent of tomato bacterial canker (TBC), one of the most destructive bacterial diseases of this crop, that causes severe economic losses worldwide. During a recent outbreak of TBC in Sicily (insular Italy), it was impossible to amplify the pat-1 gene by PCR with CMM5/CMM6 primers from affected greenhouse-grown plants from three farms, although Cmm-like colonies were consistently isolated. Microlog metabolic profile, 16S rDNA sequencing and the positive amplification of other Cmm DNA targets supported the identification of the strains as Cmm, suggesting the occurrence of a population lacking the virulence gene pat-1. A detailed phenotypic and molecular characterization of these Cmm strains and their virulence to tomatoes, as compared with Cmm reference strains is reported in this study. Pathogenicity tests revealed the strains under study were able to induce TBC, although delayed wilting symptoms were observed. Strains with or without pat-1 were undistinguishable, based on disease indexes.
The ABC's of Cell Division: Regulation of Peptidoglycan Amidase Activity during Cytokinesis in Escherichia coli

The bacterial cell wall, composed of peptidoglycan (PG), is an essential component of the cell envelope. This macromolecular structure fortifies the cell membrane, determines cell shape, and helps prevent osmotic lysis. The synthesis and remodeling/recycling of this polymer is mediated by PG synthases and hydrolases, respectively. Proper control of the PG hydrolases is particularly important since misregulation of these enzymes can lead to lethal breaches in the cell wall. Surprisingly, however, the precise molecular mechanisms governing the activities of these enzymes remain poorly understood. To help understand how PG hydrolases are regulated, I examined how their activity is controlled during cytokinesis in Escherichia coli. One important class of PG hydrolases necessary for cell division is the LytC-type amidases (AmiA, AmiB and AmiC). These enzymes require activation by the LytM factors EnvC and NlpD. My work focused on elucidating the mechanism by which the LytM factors activate the amidases. Using a genetic enrichment strategy, I isolated amiB misregulation mutants. Interestingly, the mutations mapped to a region of AmiB found only in cell separation amidases. Structural analysis of an AmiB ortholog indicates that this region corresponds to an alpha-helical domain that appears to occlude the active site. Thus, activation of the amidases by the LytM factors likely occurs via a conformational change that displaces the regulatory helix from the active site.
Sources of variation in reflectance spectrophotometric data: a quantitative analysis using avian eggshell colours

1. The evolution of coloration has generated some of the most diverse and variable phenotypes, both within and between species, in animals and plants. The objective quantitative assessment of the physical, chemical and perceptual basis of coloration has been greatly improved by the application of portable full‐spectrum spectrophotometers to measure reflectance data. Yet, the analysis and interpretation of physical measures of colour spectra must be conducted within the constraints of the uncertainty regarding the relative impacts of methodological vs. biological sources of variation.