Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving fruit size and quality of low yielding and small fruited pear cultivars with benzyladenine and gibberellin applications

Summary This study was conducted to determine the effects of benzyladenine (BA) and BA plus gibberellin (GA) treatments on fruit size and quality of ‘Akca’ pear (Pyrus communis), a low yielding and a small fruited summer variety. Pear trees were sprayed to run off 14 d after full bloom with BA (50, 100 and 150 ppm) or BA+GA4+7 (concentrations of each chemical; 12.5, 25, and 50 ppm). Fruits were harvested and evaluated in terms of fruit size and quality parameters. Higher concentrations of BA+GA4+7 (25 and 50 ppm) and the medium concentration of BA (100 ppm) increased fruit weight, fruit diameter and fruit length. The highest fruit weights and the highest fruit lengths were obtained from 25 ppm BA+GA4+7 and 50 ppm BA+GA4+7 treatments. Compared to weight of control fruit (48.85 g), 25 ppm BA+GA4+7 applications resulted in a 20.2% increase in fruit weight (58.71 g). ‘Akca’ pear showed different responses to BA and BA + GA4+7 applications. In 25 and 50 ppm BA + GA4+7 treatments, the increases in fruit weight were accompanied by heavy reductions in yield (54.3% and 59.9%, respectively), while in 100 ppm BA EiieaOEnaee�aioa n�iaua�ea��O�cOE
Dehiscensicoridae fam. nov. (Insecta: Heteroptera: Pentatomomorpha) from the Upper Mesozoic of Northeast China

A new family of insects is described from the Lower Cretaceous Yixian Formation in western Liaoning Province, China. Dehiscensicoridae Du, Yao & Ren fam. nov. comprises five new genera and five new species: Dehiscensicoris sanctus Du, Yao & Ren gen. et sp. nov., Pingquanicoris punctatus Du, Yao & Ren gen. et sp. nov., Changirostrus maculatus Du, Yao & Ren gen. et sp. nov., Crassiantenninus minutus Du, Yao & Ren gen. et sp. nov. and Minuticoris brunneus Du, Yao & Ren gen. et sp. nov. A cladistic analysis based on a combination of fossil and extant morphological characters is used to hypothesize the phylogenetic status of the new family, allowing the reconstruction of the interfamily relationships within the Coreoidea (sensu lato) which were found to be: Pyrrhocoroidea + (Dehiscensicoridae fam. nov. + (Coreoidea + (Idiostoloidea + Lygaeoidea))). http://zoobank.org/urn:lsid:zoobank.org:pub:E501B670-AF36-408C-8B9D-466B330BA775
Reports of Cladonia magyarica and C. humilis in Manitoba

Abstract. The genus Cladonia is widely distributed around the world. Since the section Cladonia contains species complexes that are difficult to distinguish, the distributions of species within these complexes are even less well-known than others. The cup-forming species, Cladonia magyarica, is morphologically similar to C. pyxidata and C. pocillum; and C. humilis is morphologically similar to C. conista and C. chlorophaea. Both species, C. magyarica and C. humilis, have not been previously reported for Manitoba, but their distribution ranges fall very close to the province, and they grow in habitats that are present in southern Manitoba. The goal of this paper was to report the presence of C. magyarica and C. humilis in Manitoba representing range extensions for both species, and to show morphological differences among them and their close allies present in the same geographic locations. The morphological differences between C. magyarica and C. pyxidata include squamules inside the cup and a significantly taller podetium and wider cup diameter in C. magyarica than C. pyxidata. Cladonia magyarica also differs from C. pyxidata in possessing atranorin in addition to fumarprotocetraric acid, in every specimen we collected. Atranorin and fumarprotocetraric acid were also shown to be present in C. humilis, but C. humilis has soredia covering the podetium, which is not present in the aforementioned taxa.
Effect of Trichoderma and fungicide on seedling establishment and yield performance of dry direct seeded boro rice

Poor seedling establishment and seedling mortality is the major barrier to optimum stand establishment in dry direct seeded boro rice. Experiments were carried out at the Agronomy Field Laboratory, Bangladesh Agricultural University (BAU), Mymensingh, Bangladesh during January to June 2013 to study the effect of Trichoderma and fungicide application on seedling establishment and yield performance of dry direct seeded Boro rice. The experiment comprised ten treatment combinations of Trichoderma and fungicides viz. seed treatment with Trichoderma (M 1 ), seed treatment with Trichoderma +spraying of Thiovit (M 2 ), seed treatment with Trichoderma + spraying of Propiconazole (M 3 ), seed treatment with Trichoderma + spraying of Thiovit and Propiconazole (M 4 ), spraying of Thiovit (M 5 ), spraying of Propiconazole (M 6 ), seed treatment with Thiovit + spraying of Propiconazole (M 7 ), seed treatment with Propiconazole + spraying of Thiovit (M 8 ), spraying of mixture of Thiovit and Propiconazole (M 9 ), and control (no fungicide or Trichoderma ) (M 10 ). The experiments used Randomized Complete Block Design (RCBD) with three replications. Experiment revealed that seed treatment with Trichoderma harzianum followed by spraying of Thiovit gave the highest yield of rice. The study concludes that Trichoderma and then application of sulphur fungicide at 20 days after sowing could be practiced for ensuring high seedling establishment and yield of rice under dry direct seeded system in boro season. J. Bangladesh Agril. Univ. 14(1): 37-42, June 2016
Terrestrial photogrammetry: a non‐destructive method for modelling irregularly shaped tropical tree trunks

Irregularly shaped trees including trees with buttresses, flutes or stilt roots are frequent in tropical forests. The lack of an international standard to measure the diameter of such trees leads to high uncertainties in biomass estimation, tree growth and carbon budget monitoring. In this study, we developed a new method based on terrestrial close‐range photogrammetry for measuring and modelling irregular stems. This approach is cheap and easy to implement in the field as it only requires a camera and a graduated rod. We validated the approach with destructive cross‐section measurements along the stem of three buttressed trees. To demonstrate the broader utility of this method, we extended the validated approach to 43 additional trees belonging to two species: Celtis mildbraedii (Ulmaceae) and Entandophragma cylindricum (Meliaceae). Based on the three dimensional models, we computed shape indices for each tree, and we analysed the stem morphology of the two species. Finally, we analysed some standardized predictors for the estimation of above‐ground biomass. We found a high concordance between diameters derived from the photogrammetric process and destructive diameter measurements along the stem for the three calibration trees. We found that C. mildbraedii develop much stronger irregularities than E. cylindricum. We also identified a large intraspecific variation in trunk morphology for E. cylindricum. The basal area at 1·3 m height (Darea130) seems to be a more robust predictor for biomass estimates (lowest Akaike information criterion and relative squared error) than diameter measured above buttresses (DAB) or diameter at breast height estimated from available taper model. Finally, Darea130 might be estimated with a good precision [root mean square error (RMSE) < 5%] with linear model based on the field measurements DAB and the perimeter of the convex hull of the buttresses at 1·3 m height (Dconvhull130). In this study, we showed the high potential of the photogrammetry for measuring and modelling irregular stems. Photogrammetry could then be used as a non‐destructive measurement tool to produce correction factors for standardizing the diameter of irregular stems at a reference height which is a key issue in tree growth monitoring and biomass change estimation.
Physiological and genomic characterization of thermophilic methanotrophic archaea and their partner-bacteria

Methane is a potent greenhouse gas and its atmospheric concentration is strongly influenced by microbial processes. In anoxic marine environments 80% of the methane is oxidized by anaerobic microorganisms leading to reduced oceanic methane emissions. This anaerobic oxidation of methane (AOM) is coupled to sulfate reduction and is mediated by microbial consortia of anaerobic methane-oxidizing archaea and partner bacteria. The physiology of the consortia is incompletely understood but is thought to base on a metabolic interdependency of the partners, a syntrophy. The research presented in this PhD thesis focused on the physiology and genomic profile of AOM consortia, in particular on the microorganisms that are active at elevated temperatures (thermophiles). The thermophilic AOM is performed by a unique consortium of ANME-1 archaea and HotSeep-1 bacteria. In Chapter II we describe physiological studies and gene expression experiments with thermophilic AOM consortia and propose a syntrophy of AOM via direct exchange of reducing equivalents. In support of this hypothesis we visualized cell-to-cell connections in these consortia that we suggest to function as conductive nanowires in interspecies electron transfer. For the thermophilic bacterial partner, HotSeep-1 we obtained an ANME-1-free enrichment culture using hydrogen as alternative energy source, and by physiological and genomic investigation we show in Chapter III that this bacterial partner grows as chemolithoautotrophic sulfate reducer. Based on phylogenetic analysis we propose that HotSeep-1 presents a novel species, Candidatus Desulfofervidus auxilii. ANME-1, the archaeon participating in thermophilic AOM, belongs to a large group of uncultured organisms, which are known to have reversed the methanogenesis pathway to metabolize methane. The metabolic diversity among members of the ANME-1 group is still widely unexplored. In a comparative genome analysis of different ANME-1 in Chapter IV we show central aspects of their metabolism including a modified methanogenesis pathway and abundant cytochromes possibly relevant for electron transfer. Environments of AOM activity and in vitro AOM enrichments are dominated by AOM consortia, but other microorganisms sustain as low abundant community whose function is not well understood. In Chapter V we show the cultivation of methanogens and sulfur disproportionating bacteria from AOM enrichments. In conclusion the work of this PhD thesis has advanced our understanding of the functioning of thermophilic AOM, while further detailed comparative approaches are necessary to comprehend AOM syntrophy in all its detail and diversity.
Using stable isotope analysis to study the diet of Gilchristella aestuaria larvae: preliminary insights into the foodwebs of six South African estuaries

South African estuarine systems are becoming increasingly altered by anthropogenic and environmental factors, but the consequences of such changes for these systems are still not fully understood. The most common approach for evaluating the ecological status of aquatic systems is studying their associated foodwebs. Due to their high abundance and important ecological role, the larvae of estuarine round herring Gilchristella aestuaria (Gilchrist, 1913) are key candidates for examining the foodweb structure and function of southern African estuaries. The foodwebs and trophic interactions of G. aestuaria larvae in six estuaries in South Africa were compared using larvae sampled in November 2013 and analysed using δ13C and δ15N and Bayesian isotopic mixing models. The main prey type for G. aestuaria larvae in all estuaries was zooplankton. We found a high similarity among the Kariega, Gamtoos, Great Fish and Sundays estuaries in terms of consumers and potential sources for both δ13C and δ15N signatures. Significant differences were found in δ13C values among marine-dominated estuaries, such as the Kromme Estuary, and the more freshwater-dominated systems. In addition, in the Kromme Estuary particulate organic matter was very important in the diet of G. aestuaria larvae. Our results suggest that both food availability and physical environmental parameters strongly affect the diet and condition of G. aestuaria and, consequently, the entire foodweb in the system.
EFFECT OF SOME PLANT DENSITIES PATTERNS AND NITROGEN FERTILIZER RATES ON COTTON YIELD, ITS COMPONENTS AND FIBRE PROPERTIES FOR HYBRID COTTON 10229 X GIZA 86 UNDER EARLY AND LATE SOWING

Four field experiments were conducted at Sakha Agriculture Research Station, Kafr El-Sheikh Governorate during 2011 and 2012 seasons. Early and late sowing experiemnts were carried out in the first season and repeated in the second season. These experiments were conducted to study the response of hybrid cotton 10229 x Giza 86 to agricultural systems, i.e., 43077 plants/fed. (65 cm ridge width and 30 cm hill spacing on one side), 36923 plants/fed. (65 cm ridge width and 35 cm hill spacing on one side), 48000 plants/fed. – (100 cm ridge width and 35 cm hill spacing on two sides) and 42000 plants/fed. (100 cm ridge width and 40 cm hill spacing on two sides) and nitrogen levels of 45, 60 and 75 kg/fed. Plants were thinned to two plants per hill after the formation of the second true leaf. Two of these experiments were carried out for the early sowing (15 April), but the other two experiments for the late sowing (15 May). The treatments carried out in the early planting also applied in the late sowing. The results can be summarized as follow: 1. Increasing plant population density significantly increased final plant height, number of monopodia, number of sympodia per plant, number of main stem internodes/plant, nodal position of first sympodium, shedding percentage, number of open bolls and unopen bolls/plant, boll weight and seed cotton yield (kentar/fed.) in the two seasons. However, earliness percentage and percentage of plant losses/fed. significantly decreased by increasing plant density. 2. There were significant differences among the three nitrogen levels, in all growth, earliness characters and yield and its components. Application of 75 kg N/fad. produced the highest values of plant height, number of monopodia and sympodia/plant, number of main stem internodes/plant, nodal position of the first sympodium, number of open and unopen bolls, boll weight and seed cotton yield (kentar/fed.), while the lowest nitrogen level (45 kg N/fed.) produced the lowest values of earliness %, shedding % and stand losses % at harvest. Seed index, lint percentage and fiber properties insignificantly affected by all treatments. The interaction between agricultural systems and nitrogen levels attained insignificant effect on all traits. 3. The results showed that late sowing took the same direction as early planting and were higher values for the number of bolls, boll weight, yield and its components. In general, it can be stated that early sowing (15 April) of hybrid cotton 10229 x Giza 86 with 75 kg N/fed. and higher density 48000 plants/fed (100 cm ridge width and 35 cm hill spacing on two sides) induced higher seed cotton yield.
Identification of membrane associated proteins as potential markers for the DLKP clonal subpopulations

Lung cancer is one of the major causes of cancer death worldwide, it represents a heterogeneous group of tumours with distinct morphological, histological and molecular features reflected by varied clinical outcome and response to treatment. DLKP is a cell line originating from a lymph node metastasis of a primary lung tumour histologically described as a “poorly differentiated squamous cell carcinoma”. DLKPSQ, DLKPI and DLKPM are three distinct subpopulations derived from DLKP, which are morphologically and phenotypically different from each other. The research outlined in this thesis aims to identify membrane associated proteins that could be used as potential markers for the DLKP clones, but also to identify potentially novel proteins associated with lung cancer. Cell surface protein isolation and label-free mass spectrometry analysis were performed on proteins isolated from DLKP and the DLKP clones. Eight proteins were successfully validated in the DLKP clones; AHNAK, HDGF, ROBO2, SLIT2, ALCAM, IQGAP1, INA and SPR, using Western blot analysis, Immunofluorescence and Immunocytochemistry. Their expression was also investigated in various tumour types and representative cell lines. SPR is associated with poor survival of patients with Luminal A and basal-like breast cancers and also shows high expression across triple negative breast cancer subtypes. siRNA mediated knockdown studies of three candidate proteins. ALCAM, INA and SPR knockdown led to a significant reduction in the invasion and migration of DLKPM cells, indicating a potential functional role for these proteins in lung cancer invasion/migration. A pilot in vivo study using severe combined immune-deficient (SCID) mice to investigate the growth of DLKP and its clones resulted in all four cell lines forming tumours following implantation. Tumours derived from DLKP and DLKPI were the fastest growing and largest tumours, DLKPM formed smaller solid tumours following an initial lag phase, while DLKPSQ formed large, highly vascularised tumours. Immunohistochemical analysis of the xenografts derived from all four cell lines revealed; strong Ki67 immunoreactivity, negligible CD31 immunoreactivity and strong N-cadherin immunoreactivity. Explant culture revealed a significant reduction in migratory capacity of DLKPSQ cells, but also a significant reduction in invasion/migration of DLKPM cells. Western blot analysis and immunohistochemical analysis indicated that expression of SLIT2, ALCAM, IQGAP1, INA and SPR were maintained in vivo. The research presented demonstrates that proteomic analysis of cell surface isolates from the DLKP variants can lead to the identification of proteins with potential functional roles in cancer. AHNAK, SLIT2, ALCAM, and SPR were identified as potential markers capable of distinguishing between each of the DLKP clones. In addition, SPR may represent a novel target for triple negative breast cancer. The DLKP cell line model could also prove to be an invaluable model to study the effects of potential novel therapeutics in lung cancer, in vivo.
Plant communities and ecosystem processes in a succession-altitude matrix after shifting cultivation in the tropical montane forest zone of northern Borneo

Abstract: Plant communities and ecosystem processes in seres at multiple altitudes in the tropical montane forest zone of northern Borneo were studied to understand the patterns and mechanisms of the secondary succession after shifting cultivation. A total of 25 stands (and additional three stands) were sampled with stand ages ranging from 2 to 55 y after slash and burn at altitudes between 900 and 1400 m asl. Plant species composition, above-ground biomass (AGB), chemical properties of soils, litter and foliar samples were investigated in each stand. A TWINSPAN analysis classified five plant communities primarily as a sere but with two altitudinal communities in the later successional phase. AGB accumulated steadily at the rate of 2.42 Mg ha−1 y−1 during the succession for the first 55 y due to the ontogenetic development of plants as well as plant community shifts. At the onset of secondary succession, pool of soil NO3-N and soil total P was high probably because burning caused flushes of minerals originating from the burnt plant materials. Pool of soil NO3-N and soil total P decreased with increasing stand age during the succession. Leaf-litter N:P ratios of dominant species significantly increased with increasing stand age suggesting disproportionately greater P deficiency than N deficiency in the later successional phase. It is suggested that tree species shifted to those of greater P-use efficiency during succession in response to decreasing soil P availability. We conclude that the interaction of altitude with the reduction of soil N and P availability was related to the altitudinal split of plant communities in the later phase, while pioneer communities were wide-ranging across altitudes reflecting richer soil nutrients.
The role of lysine-67 in a class C β-lactamase is mainly electrostatic

By using site-directed mutagenesis, the conserved Lys-67 residue situated three positions after the active-site Ser of a class C beta-lactamase was replaced by Arg or Gln. The Lys-67-Gln protein was nearly inactive. Although severely impaired, the Lys-67-Arg mutant exhibited an appreciable activity above pH 7.5 and, for some poor substrates of the wild-type enzyme, the kcat. values were even increased. The properties of the Lys-67-Arg mutant were studied by both steady-state and transient-state kinetic methods with a variety of compounds representing distinct classes of available substrates. With beta-lactam substrates, the kcat. /Km values reflecting the efficiency of the acylation step (k+2/K) were decreased 25-100-fold. When the individual values could be measured, k+2 was not significantly altered, but K was found to be strongly increased, a result most likely explained by a corresponding increase in the k+1/k-1 ratio. These results, combined with the much stronger impairment of the Lys-67-Gln mutant, can be interpreted by attributing an electrostatic role to the positive ammonium group of the Lys-67 side chain.
Relevance of environmental impact categories for perennial biomass production

The decarbonization of the economy will require large quantities of biomass for energy and biomaterials. This biomass should be produced in sufficient quantities and in a sustainable way. Perennial crops in particular are often cited in this context as having low environmental impacts. One example of such crops is miscanthus, a tall perennial rhizomatous C4 grass with high yield potential. There are many studies which have assessed the global warming potential (GWP) of miscanthus cultivation. This is an important impact category which can be used to quantify the environmental benefit of perennial crops. However, the GWP only describes one impact of many. Therefore, the hypothesis of this study was that a holistic assessment also needs to include other impact categories. A life cycle assessment (LCA) with a normalization step was conducted for perennial crops to identify relevant impact categories. This assessed the environmental impact of both miscanthus and willow cultivation and the subsequent combustion for heat production in eighteen categories using a system expansion approach. This approach enables the inclusion of fossil reference system hot spots and thus the evaluation of the net benefits and impacts of perennial crops. The normalized results clearly show the benefits of the substitution of fossil fuels by miscanthus or willow biomass in several impact categories (e.g. for miscanthus: climate change −303.47 kg CO2 eq./MWhth; terrestrial acidification: −0.22 kg SO2 eq./MWhth). Negative impacts however occur, for example, in the impact categories marine ecotoxicity and human toxicity (e.g. for miscanthus: +1.20 kg 1.4‐DB eq./MWhth and +68.00 kg 1.4‐DB eq./MWhth, respectively). The results of this study clearly demonstrate the necessity of including more impact categories than the GWP in order to be able to assess the net benefits and impacts of the cultivation and utilization of perennial plants holistically.