Miracle-dz/UniFAR-FTUs huggingface dataset:
Micropropagation of Strawberry (Fragaria ananassa) through runner culture

In vitro propagation of strawberry was conducted at the Biotechnology Lab. of BARI, Joydebpur, Gazipur. For shoot induction, five BAP concentrations viz., 0.0 (Control), 0.5, 1.0, 1.5, and 2.0 mg/l and for root induction four IBA concentrations viz., 0.0 (Control), 0.5, 1.0, and 1.5 mg/l were used. The highest average number of shoots (7) and the highest average length (3.34 cm) of shoot was observed at the concentration of 0.5 mg/l BAP. The highest average number of leaves (5) was also observed at the same concentration. Among the five rooting concentrations, IBA @ 0.5 mg/l showed the best performance in all the parameters studied. The highest number (6) of roots/culture and the longest (3.05 cm) roots were also obtained from this concentration. Half strength MS media without IBA concentration did not show any response regarding root induction. DOI: http://dx.doi. org/10.3329/bjar.v38i3. 16973 Bangladesh J. Agril. Res. 38(3): 467-472, September 2013
EVALUATION OF CARCASS TRAITS OF HEREFORD STEERS THROUGH ULTRASOUND IN DIFFERENT NATIVE PASTURE: PARTIAL RESULTS

Beef quality traits can be influenced by different finishing diets which can be assessed in the carcass of the live animal through ultrasound technique. The aim of this study was assess the influence of different pastures in the carcass traits of Hereford steers. Were evaluated the carcasses of 36 steers divided into 3 different sorts of pasture: native pasture (T1), fertilized native pasture (T2) and improved fertilized native pasture (T3). The carcass traits assessed were live weight (W, kg), rib eye area (REA, cm 2 ), backfat thickness (BF, mm) and rump fat thickness (RF, mm). There was highly pasture* time of year effect for all pasture sorts and in all carcass traits. The live weight of the steers were also significantly different among the treatments, 269.66, 306.06 and 333.91 kg respectively T1, T2 and T3 (P 0.05) for REA (35.33, 37.31 cm 2 ), BF (1.06,1.23 mm) and RF (0.82, 1.11 mm) , respectively. T3 carcass traits were significantly divergent from T1 and T2 for REA (41.33 cm 2 ), BF (1.87 mm) and RF (1.61 mm). Improved fertilized native pasture demonstrated be the best alternative for animal finishing diets resulting in better carcass traits.
Hydrodynamics and larval dispersal: a population model of Acanthaster planci on the Great Barrier Reef

This paper presents results of a modelling study of the large-scale population dynamics of Acanthaster planci in the central Great Barrier Reef. Dispersal patterns generated by larval transport models are used to drive the simulation. Population flow through the reef matrix during outbreaks is simulated by using an elementary representation of the starfish life cycle. Features of the results include the following: (I) Population patterns generated by the model are consistent with observations of starfish outbreaks. (2) The overall impact of starfish populations undergoing an outbreak on the reef system decreases with a southward shift in the location of initial outbreaks. (3) Within the central Great Barrier Reef, outbreak populations of starfish generally occur more frequently on the inner- and central-matrix reefs than on the outer-matrix reefs.
The influence of maternal effects in larval survival on fishery harvest reference points for two life-history patterns

Increased larval viability with increased spawner age (i.e., maternal effects) have been observed in Atlantic cod (Gadus morhua) and Pacific rockfish (Sebastes spp.) stocks. Analytical results from a Beverton–Holt recruitment model indicate density-independent maternal effects affected the relative stock productivity and fishing rate reference points. We simulated populations based on Pacific cod (Gadus macrocephalus) and Pacific ocean perch (Sebastes alutus) to explore how estimates of reference points Fmsy and Fcrash are affected by maternal effects and potential interactions with life-history pattern, recruitment autocorrelation, and exploitation rate. Estimates of Fmsy and Fcrash were made from populations with maternal effects using either total larvae (proportional to eggs) or viable larvae (incorporating the maternal effect). Maternal effects have the largest impact upon estimated population productivity at high fishing rates. Estimates of Fmsy and Fcrash for cod were also affected by autocorrelate.
The Food and Feeding Biology of Common Terns Wintering in Argentina: Influence of Environmental Conditions

Abstract The aim of this study was to analyze the variability observed in the food and feeding biology of the Common Tern (Sterna hirundo) in relation with environmental factors operating in nonbreeding season in Argentina at different spatial and temporal scales. Fish constituted more than 60% of the diet of the Common Tern in terms of biomass in all years, while insects never exceed 40%. A total of 25 fish species and nine insect species (Orders Coleoptera, Lepidoptera, Odonata and Hemiptera) were found in the diet. In four of six years, terns preyed more on marine fish (68%) while in 2001-02 terns foraged mostly on freshwater species (60%). Estuarine fish species were eaten in all years (>10%). Freshwater prey were found only in seasons with high local rainfall. Local wind-speed had a significant effect on the daily proportion of insects and fish prey found in the diet, with more insects (hence less fish) consumed on days with high winds. La Plata River overflow seasons were correlated with negatives values of the Southern Oscillation Index (SOI). We found less estuarine fish (e.g., Whitemouth Croacker, Pejerrey Silverside) after a month with a low SOI value. A positive trend was also observed between La Plata river outflow and more marine fish in the Common Tern diet. The observed environmental variability in winter quarters and the fluctuation in the use of different food sources may affect the individual quality of terns and not only the survival of individuals during the nonbreeding season but also the timing of migration or breeding performance of adults during the following reproductive season.
Characterization of Human FSH Isoforms Reveals a Nonglycosylatedβ -Subunit in Addition to the Conventional Glycosylatedβ -Subunit

Human FSH consists of a mixture of isoforms that can be separated on the basis of differences in negative charge conferred by variations in the numbers of sialic acid residues that terminate oligosaccharide branches. Western analysis of human FSH isoforms separated by chromatofocusing revealed the presence of two human FSHβ isoforms that differed in size. A low mol wt human FSHβ isoform was associated with all FSH isoform fractions. A high mol wt human FSHβ isoform was associated with the more acidic fractions and increased in relative abundance as the pI decreased. Characterization of representative human FSHβ isoforms by mass spectrometry and automated Edman degradation revealed a low mol wt isoform that was not glycosylated. A high mol wt isoform was N-glycosylated at Asn residues 7 and 24. These results indicate that pituitary human FSH consists of two classes of molecules: those that possess a nonglycosylated β-subunit and those that possess a glycosylated β-subunit. Glycoprotein hormones are known t.
Fertilization and development: The stages at which human fertilization arrests: microtubule and chromosome configurations in inseminated oocytes which failed to complete fertilization and development in humans

The goal of fertilization is the union of one, and only one, sperm nucleus with the female pronucleus within the activated oocyte. For this to occur successfully, several events must transpire, including the incorporation of the entire spermatozoon into the oocyte, the completion of meiotic maturation with the extrusion of the second polar body, the metabolic activation of the previously quiescent oocyte, the decondensation of the sperm nucleus and the maternal chromosomes into the male and female pronuclei respectively, and the cytoplasmic migrations of the pronuclei, which bring them into apposition. Defects in any of these events are lethal to the zygote and might prove to be causes of infertility. In this study, the microtubules and DNA were imaged in inseminated human oocytes that had been discarded as unfertilized. The presence and number of incorporated sperm tails were also documented using a monoclonal antibody specific for the posttranslationally modified acetylated-α-tubulin found in the tail, but not the oocyte, microtubules. An analysis of 211 oocytes from failed in-vitro fertilizations from 58 patient couples resulted in the determination of several previously undetectable phases at which fertilization arrests : (i) metaphase II arrest ; (ii) arrest after the successful incorporation of the spermatozoon ; (iii) arrest after the formation of the sperm aster ; (iv) arrest during mitotic cell cycle progression ; and (v) arrest during meiotic cell cycle progression. Data on polyspermy and arrested embryonic development are also presented. These results have implications for the diagnosis and treatment of female, as well as male, infertility. They also provide a rationale for the reasonable use of intracytoplasmic sperm injection (ICSI) therapy, although they suggest that cases intractable to this approach will be found. Concerns are raised about the use of seemingly 'unfertilized' but inseminated oocytes for subsequent re-inseminations, ICSI or even research, since the fertilization process might have arrested after sperm penetration. These results demonstrate that the proper union of the parental genomes requires a series of cytoskeletal-mediated events on the oocyte surface and within the oocyte proper, and that failure at any phase results in the arrest of human fertilization.
Inter-populations genetic and morphological diversity in three Silene (Caryophyllaceae) species

The inter-populations morphological and genetic variations were studied in three species of Silene ( Silene indeprensa , Silene gynodioica and Silene crispans) of the section Auriculatae , which grow and form several populations in different regions of Iran. Morphological analysis of variance (ANOVA) and analysis of molecular (AMOVA) analyses showed the species distinctness. Unweighted paired group with arithmetic average (UPGMA) clustering of morphological characters and neighbor-joining (NJ) tree of molecular features almost separated the species from each other. In S. gynodioica , Soltaneiyes and Gheydar populations differed from the other populations in both morphological and molecular features, and in case of S. indeprensa , Ghorkhood and Hezarmasjed populations differed significantly from the other populations in both morphological and molecular features. Therefore, these populations are considered as a new subspecies in these two species. Some of the populations showed the presence of specific inter-simple sequence repeat (ISSR) band/locus, indicting genetic divergence of the populations possibly either due to local adaptations or genetic drift. Mantel test performed did not show significant correlation between morphological/molecular distance and geographical distance of the populations studied. Keywords: Diversity, ISSR, morphometry, Silene
Spatiotemporal Changes in Fish Assemblages of Los Terreros Creek, an Isolated Stream System in Headwaters of the Lerma River, Central Mexico

Abstract Los Terreros Creek, a reservoir-fragmented tributary in the upper Lerma River system of central Mexico, was sampled at four localities in wet (2001) and dry (2002) seasons to evaluate spatial and temporal patterns of fish assemblages, the conservation status of native fishes, and prevalence of exotic species. Two of five species present were non-native; the common carp (Cyprinus carpio) and the shortfin silverside (Chirostoma humboldtianum). Fish assemblages formed a strong gradient largely separating the lentic, reservoir-impacted, locality (downstream-most site) from the remaining lotic sites. The two most-upstream sites were not distinguishable based on structure of fish assemblages. Three of five species showed significant spatial variation in abundance. The Aztec shiner (Aztecula sallaei) occurred only at the lotic sites and the two species of silversides (Chirostoma) occurred only at the lentic site. Temporal trends in assemblages were less evident, but assemblages in the dry season had lower mean species-richness and mean abundance values. Analysis of distance matrices based on assemblages, site-specific environmental conditions, and spatial structure indicated that a strong, spatially structured environmental gradient was significantly associated with fish assemblages in the wet season, but not assemblages in the dry season. Los Terreros Creek still supports an assemblage of native fish that is typical for the upper Lerma River system. However, this relict system remains threatened by anthropogenic activities including changes in land use and further introduction of exotic species.
Misinterpreting the Internal Rate of Return in Sustainable Forest Management Planning and Economic Analysis

Sustainable forest management planning includes accounting for revenues and costs that accrue throughout time. While debate continues as to the how to account for these cash flows, the most used techniques are net present value, benefit cost ratios, and internal rate of return (irr). Managing forests sustainably depends critically on interpreting the results and management implications of these techniques accurately. It is appealing to equate the irr with a market-derived rate of return given its definition. Unfortunately, its mathematical derivation does not support this interpretation and past use of irr often illustrates this confusion and misinterpretation. The irr only reflects the amount and timing of the net cash flows for a given venture and does not include any social, economic, or other external factors found in market-derived discount rates. Therefore, the irr does not reflect an appropriate rate of return or opportunity cost of capital for sustainable forest management. My purpose is to provide a theoretical argument that can be used to help correct this misinterpretation and stimulate discussions on the economics of sustainable forest management.
The role of L3T4 in recognition of Ia by a cytotoxic, H-2Dd-specific T cell hybridoma

The expression of T4/T8 surface markers on human T cells and of L3T4/Lyt-2 on murine T cells has lead to the association of these surface markers with recognition of either class II or class I major histocompatibility complex (MHC) antigens. It has been suggested that these T cell surface antigens interact with MHC antigens. We have examined the role of L3T4 in the recognition of Dd by the T cell hybridoma, 3DT52.5. This T cell hybridoma was found to be specific for the N/Cl domain of Dd. The recognition of a class I antigen by an Lyt-2- , L3T4+ T cell hybridoma allowed the separate evaluation of interactions between L3T4/Ia and the T cell antigen receptor, Dd. Recognition by this hybridoma resulted in the production of interleukin 2 (IL-2) and cytolytic activity. Antibody blocking experiments have demonstrated that L3T4 was involved in triggering the effector function of 3DT52.5 only on Ia+ stimulator or target cells. We have demonstrated that an L3T4+, Dd-specific T cell hybridoma, 3DT52.5, uses the L3T4 molecule to directly interact with nonpolymorphic Ia determinants.
Brassinosteroids Denigrate the Seasonal Stress through Antioxidant Defense System in Seedlings of Brassica juncea L.

The present work has been undertaken to study the effect of exogenously application of 24epiBL and 28-homoBL on soluble protein, proline contents and antioxidant defense system of Brassica juncea L. RLM 619 under the influence of seasonal stress. It was observed that 24epiBL and 28-homoBL treatment enhance the soluble protein, dry weight and shoot length of B. juncea seedlings under seasonal stress. If seeds treated with the different concentrations (10 -6 , 10 -8 and 10 -10 M) of 24-epiBL and 28-homoBL revealed batter growth, protein and proline contents as compare to untreated seedlings. Similarly the activities of antioxidant enzymes SOD, CAT, APOX, DHAR, PPO and Auxinases were enhanced by the application of different concentration of both brassinosteroids, whereas MDA content was decrease with both brassinosteroids treatments. Then we have concluded that both brassinolides have the seasonal stress ameliorative properties in B. juncea seedlings grown under the influence of seasonal stress. This study culminates to the role of brassinolides as an anti-stress property for protection of plant from various types of stresses.
Isolation of symbiosomes and the symbiosome membrane complex from the zoanthid Zoanthus robustus

A. Kazandjian, V.A. Shepherd, M. Rodriguez-Lanetty, W. Nordemeier, A.W. D. Larkum and R.G. Quinnell. 2008. Isolation of symbiosomes and the symbiosome membrane complex from the zoanthid Zoanthus robustus. Phycologia 47: 294–306. DOI: 10.2216/07-23.1 The zoanthid Zoanthus robustus was used as a model organism to develop procedures for isolating pure symbiosomes and symbiosome membranes. The symbiosome is comprised of a zooxanthella (Symbiodinium sp.) cell that divides rarely and is separated from the host gastrodermal cytoplasm by a symbiosome multimembrane complex. Devising a method to isolate membranes at the interface between the symbiotic partners is a critical first step in characterising the molecular components involved in the metabolic trafficking necessary to sustain an effective symbiosis. After zoanthid gastrodermal cells were extracted, symbiosomes were released by mechanical disruption, recovered by centrifugation, and then purified using discontinuous sucrose gradient centrifugation. The material forming the membrane complex around symbiosomes proved highly resistant to disruption. Methods used to dissociate this interface from symbionts included (1) Triton X-100 detergent solubilisation, (2) osmotic shock with mechanical disruption, and (3) vigorous mechanical disruptions, where powerful shearing forces were used, combined with a series of sucrose density gradient centrifugation steps. The lipophilic styryl fluorochrome FM 1-43, at a concentration of 30 µM, selectively labelled the symbiosome membrane complex, both for isolated symbiosomes and those in hospite. Other cell membranes, including plasma membranes, endoplasmic reticulum, tonoplast, and organelle membranes, were not visibly labelled at this concentration. The selective labelling of the symbiosome membrane complex remained stable even after long exposure times (3 h). At 30 µM concentration, FM 1-43 also labelled symbiosome membrane fragments isolated using methods (1), (2) and (3). Method (3) proved to be the most effective in producing a fraction enriched in FM-143-labelled membrane material, which we call a symbiosome membrane complex. Transmission electron microscopy, together with confocal and conventional epifluorescence microscopy of the FM 1-43-stained preparations, was used to validate the purity of symbiosome preparations and to infer the complexity of the symbiosome membrane complex. This membrane complex has regions where the membranes contributed by the alga are appressed, and punctate regions whose function remains unclear.
Electrophoretic karyotypes of the phytopathogenic Pyrenophora graminea and P. teres

Contour-clamped homogeneous electric field has been applied to analyse genome size and organisation of two important pathogens of barley, Pyrenophora graminea and P. teres. Electrophoretic karyotypes of four P. graminea isolates resolved 6–8 chromosomal bands, depending on the isolate, while the one P. teres isolate analysed contained six chromosomal bands. Chromosome length polymorphism was observed among P. graminea isolates. For both fungi the chromosomes ranged from 1.6 to more than 6 Mb, with chromosomes larger than 6 Mb migrating as a single band within the compression zone of the gel.
Homology modeling deduced tridimensional structure of Bacillus thuringiensis Cry1Ab18 toxin

Cry1Ab18 is an δ-endotoxin produced by Bacillus thuringiensis strain. Till date the detailed mechanism of this toxin action is unclear. Therefore, solution of the three-dimensional structure of all Cry1 family members would be desirable for a comprehensive understanding of the initial mechanisms that underlie the toxicity of this type of toxin. Here, we predict a theoretical structural model of the newly reported Cry1Ab18 δ-endotoxin, using a homology modeling technique with the structure of Cry1Aa toxin molecule (resolution 2.25A). Cry1Ab18 resembles Cry1Aa toxin by sharing a common three-domain structure. Domain I is composed of nine α helixes and one small β strand, domain II is composed of nine β strands and two α helixes and domain III consists of two α helixes and eleven β strands. This model supports the existing hypotheses of receptor insertion and will further provide the initiation point for the domain swapping experiments aimed towards improving protein toxicity, and will help in the deeper understanding of the mechanism of action of common toxins.
Species spread and persistence: Implications for experimental design and habitat re‐creation

Abstract The patterns of species establishment, persistence and spread in a long‐term experiment investigating the re‐creation of chalk grassland using different seed mixtures on ex‐arable land were analysed with the intention of providing enhanced re‐creation/restoration prescriptions and a critique of experimental designs. Species had a wide range of behaviours; (1) species that did not establish from seed e.g. Blackstonia perfoliata, (2) establishment but poor persistence in closed sward e.g. Hieracium pilosella, (3) establishment and persistence but little spread e.g. Onobrychis viciifolia and (4) good establishment and spread over all treatments e.g. Centaurea nigra and Trisetum flavescens. Persistence appeared greater in species with lower germination rates in both light and dark. Spread was greater in species with higher seed mass and lower dark germination rates. However, results from small‐plot experiments should be critically analysed. Though initial results show the potential for re‐establishment of vegetation, subsequent vegetation dynamics may be more closely related to the invasion of species from other treatments than the original species sown. Experimental designs should employ either large plots and/or wide guard rows to extend their useful life span. Long‐term data show which species are useful for cost‐effective restoration. Some species need to be sown over the whole area to provide cover (a ‘grass matrix’) and competition with arable weeds. Others need to be sown over wide areas as they spread poorly. Some species can be sown at low densities or in small patches as they have the ability to spread in closed vegetation. Nomenclature:Clapham et al. (1987).
Intro

The purpose of this text is to begin the process of developing a working familiarity with some of these key mathematical concepts. As your studies in the life sciences become more specialized you will naturally find that certain mathematical fields receive more emphasis than do others. We hope that we will have laid a foundation that will allow you to deepen your understanding as the need to do so arises.