Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular phylogeny of Abyssocladia (Cladorhizidae: Poecilosclerida) and Phelloderma (Phellodermidae: Poecilosclerida) suggests a diversification of chelae microscleres in cladorhizid sponges

Vargas, S. , Erpenbeck, D. , Göcke, C. , Hall, K. A. , Hooper, J. N. A. , Janussen, D. & Wörheide, G. (2012) Molecular phylogeny of Abyssocladia (Cladorhizidae: Poecilosclerida) and Phelloderma (Phellodermidae: Poecilosclerida) suggests a diversification of chelae microscleres in cladorhizid sponges. —Zoologica Scripta, 42, 106–116.
Association of insect life stages using DNA sequences: the larvae of Philodytes umbrinus (Motschulsky) (Coleoptera: Dytiscidae)

Abstract. Insect life stages are known imperfectly in many cases, and classifications are based often on only one or a few semaphoronts of a species. This is unfortunate as information in alternative life stages often is useful for scientific study. Although recent examples of DNA in taxonomy have emphasized the identification of indistinguishable species, such sequence data facilitate the association of life history stages and hold considerable promise in phylogenetic analysis, evolutionary studies, diagnostics, etc. These concepts are discussed here and an example is provided from diving beetles (Dytiscidae: Coleoptera). Three unknown larval specimens of an apparent species of Laccophilinae collected in Namibia were associated with the species Philodytes umbrinus (Motschulsky) using DNA sequence data. An 806‐bp portion of the gene cytochrome oxidase I was sequenced from the unknown larvae. Several identified adult specimens of species of Laccophilinae from Namibia were also sequenced, including two P. umbrinus specimens and specimens from four Laccophilus Leach species. Additional species of Laccophilus from other areas of the world also were sequenced, as were specimens of Agabetes acuductus (Harris), Australphilus saltus Watts, Neptosternus boukali Hendrich & Balke and a species of Laccodytes Régimbart. Parsimony analysis resulted in two most parsimonious trees with the unknown larva unambiguously resolved in a group with both adult specimens of P. umbrinus (bootstrap value = 100%). The average pairwise p‐distance between the unknown larva and adult P. umbrinus specimens averaged 0.09% (0–0.14%), compared with an average divergence between other conspecifics in the analysis of 0.24% (0–0.82%) and an overall average divergence between species of 13.49% (1.90–19.86%). Based on this, the unknown larvae were assigned to P. umbrinus. The larvae are diagnosed and described and their relationship with other Laccophilinae is discussed.
The Effect of Photoperiod on β-glucuronidase Gene Expression under Control CaMV-35S Promoter in Transgenic Lettuce

We investigated the effects of different photoperiods on the expression level of GUS genes regulated by the CaMV-35S promoter in leaf lettuce (Lactuca sativa L. cv. ‘Greenwave’) for a recombinant protein production system. A leaf disk experiment and a cultivation experiment were conducted in different photoperiods. A linear relationship (R2=0.9934) was observed between the lengths of photoperiods and GUS activities per unit fresh weight in the leaf disk experiment. This result indicates that the expression of the CaMV-35S promoter during a photoperiod was much more enhanced than that during a dark period. In the cultivation experiment, a longer photoperiod helped not only to enhance the growth of a lettuce plant but also to increase its GUS activity. As a result, GUS activity per plant under the 24:0 h photoperiod was significantly (P‹0.05) higher than that under the 16:8 and 8:16 h photoperiods. However, the question remains whether these results for GUS-CaMV-35S promoter can be applied to other recombinant proteins or promoters. Further studies are thus required to establish a practical strategy for designing an efficient recombinant production system in a plant factory.
Rapid Cold-Branding of Salmon and Trout with Liquid Nitrogen

Liquid nitrogen (at −196 C) was successfully used as a coolant in a simple, inexpensive, and rapid method of marking salmon and trout with a metal branding tool. The marks, applied to as many as 650 fish per hour per marker, were consistently clear and readily identifiable for at least 14 months after application. No mortalities could be attributed to the branding technique among 4000 yearling coho salmon held for 2 months after marking.
Songs, genetics, and morphology: revealing the taxonomic units in the European Cicadetta cerdaniensis cicada group, with a description of new taxa (Hemiptera: Cicadidae)

Recent acoustic studies have revealed that Cicadetta montana (Scopoli, 1772), which was once thought to be asingle widespread Palaearctic cicada species, is actually a complex of many taxa. Although some song patternsare very distinct, others comprise groups of closely related species, as in the case of Cicadetta cerdaniensis Puissant& Boulard, 2000, Cicadetta cantilatrix Sueur & Puissant, 2007, and Cicadetta anapaistica Hertach, 2011.Seven spatially or behaviourally isolated metapopulations belonging to this song group from Italy and Switzerlandwere detected and investigated using acoustic, molecular, and morphological methods. Taxonomic decisionsin this group are challenging because of a lack of truly diagnostic morphological characters, variously colouredmorphs, qualitatively intermediate song patterns in contact zones, and strong temperature dependence of songdurationcharacters. Molecular genetic studies suggest rapid speciation resulting in incomplete lineage sorting andintrogression. It is only by using multiple sources of data that species can be delimited. The new species Cicadettasibillae sp. nov. and the new subspecies Cicadetta anapaistica lucana ssp. nov. were described using the microstructureof the male calling songs. Cicadetta sibillae sp. nov. occurs from southern Switzerland to centralItaly, and is the most abundant cicada in the Northern Apennine. Cicadetta anapaistica lucana ssp. nov. isendemic to a small southern Italian distribution range, and seems to be threatened by habitat loss and fragmentation.There is strong evidence that current distribution patterns and phylogenetic relationships of the Cicadettacerdaniensis group are linked to speciation events in Pleistocene glacial refugia in the Italian, Iberian, and Balkanpeninsulas.
Gendered business activities in family farm forestry: From round wood delivery to health service

Abstract The development of non-wood forest products and services has been put forward as a means for business diversification and development of rural areas. However, the well-documented male dominance in traditional family farm forestry (FFF) is considered to restrain women's involvement in forestry activities, and thus hamper new enterprising businesses. Given the gender structure in traditional forestry, it is hypothesised that women are more likely to engage in less traditional activities than men. Through a cluster analysis of data from the Swedish Farmers Association's member survey, typical combinations of forest-related business activities were identified. The representation of women and men as operational managers within each activity was assessed. Results show that traditional forestry is the main task for both male and female FFF owners, however, women engage more often than men in service-oriented business activities. The main conclusion is that the prevailing pattern on the labour market, with women predominately within service and care professions, seems to be reproduced within FFF businesses. The results are further discussed in relation to owner types and possible impact on FFF restructuring and rural development.
Paraphaeosphaeria barrii , a new species on Yucca schidigera from Mexico

Paraphaeosphaeria barrii , a new species of the genus found on Agavaceae , is described from leaves of Yucca schidigera collected in Baja California, Mexico. The Coniothyrium anamorph is briefly described from cultured ascospores. This species was found to be most closely related to P. conglomerata, P. filamentosa , and P. quadriseptata all of which are from Agavaceae , produce 3 or 4 septate ascospores and pigmented, non-septate conidia from holoblastic, percurrently proliferating conidiogenous cells.
A decline in the abundance and condition of a native bivalve associated with Caulerpa taxifolia invasion

Caulerpa taxifolia is a fast-spreading invasive seaweed that threatens biodiversity in temperate Australian estuaries. To date, little is known about its effects on infauna. In the present study, we describe variation in demographic and life-history traits of the abundant infaunal bivalve, Anadara trapezia, in C. taxifolia and uninvaded habitats (seagrass and unvegetated sediments) at multiple sites across three estuaries in south-eastern New South Wales. Densities of A. trapezia were always lower in C. taxifolia than on unvegetated sediment, and lower in C. taxifolia than in seagrass at three out of four sites where they were compared. Dry tissue weight of A. trapezia was also lower in C. taxifolia than on unvegetated sediment at most sites, but was only lower in C. taxifolia than in seagrass at one of four sites. Populations were dominated by larger individuals (>45 mm length), but smaller individuals (35–45 mm length) were more common in C. taxifolia and seagrass. A. trapezia shell weight and morphology was variable and appeared weakly affected by invasion. Generally, our findings are consistent with the hypothesis that A. trapezia is negatively affected by C. taxifolia. However, C. taxifolia invasion appears complex and, at some places, its effects may not differ from those of native seagrass. There is a need for manipulative studies to understand the mechanisms underlying the effects of C. taxifolia on infauna.
Rationale of driven element geometric parameters for herbicides applying in foam composition

The article is devoted to the construction of the driven element for subsoil band applying of liquids in crop growing since one of the most important tasks of agricultural production is maximum crop yields obtaining. This problem solution is possible only under condition of the active use of crops protection from diseases and pests. Nowadays the chemical method of plants protection is the most effective and allocated, that is plants treatment in which liquid means of protection are its main part. They can be applied in two ways: the surface (with subsequent laying or without it ) and the subsoil ones. Disadvantages of surface applying are the following: some portion of the working liquid is lost unproductively exposed to evaporation, weathering, photochemical decomposition and so on, in most cases the preparation applied on the surface, acts only against vegetative plants, that is during a short-term period. That is why such treatments are called chemical weeding. Finally all above listed things result in decreasing of total treatment effectiveness and environment contamination. To some extent above mentioned problems can be solved under condition of subsoil pesticide application. The driven element geometric parameters of which were proved in the article was developed to raise the cultivated area quality.
First laboratory confirmation of Xylophilus ampelinus in Slovenia.

Bacterial blight of grapevine is caused by a slow-growing bacterium Xylophilus ampelinus . It has been suspected to occur in Slovenia on the basis of visual observation of characteristic symptoms in the 1960s. In the present study, symptoms were recorded in an infected vineyard during three consecutive years (2002/2004). Samples from this vineyard were tested by nested-PCR and isolation of bacteria on media was attempted. In the first year, angular lesions on leaves were highly expressed and an isolate morphologically similar to X. ampelinus was obtained from one sample. It was purified and identified as X. ampelinus using biochemical and nutritional tests, fatty acid analysis, immuno-fluorescence, nested PCR and partial sequencing of the 16S rRNA gene. The 16S rDNA sequence showed 99‐100% homology to known sequences of X. ampelinus strains, including the type strain. Pathogenicity of the isolate was confirmed in tissue-cultured and potted grapevine plants. In the following two years, symptoms of bacterial blight were only faintly expressed. Using isolation on media and nested-PCR, 23 and 17 extracts prepared from 10 and 8 grapevines, respectively, were analysed. In 2003, no positive sample was found, but X. ampelinus was again isolated and identified by colony morphology and nested-PCR in 2004.
Les méthodes d'analyse de ségrégation en mélange et d'association marqueur-trait révèlent des marqueurs AFLP communs de résistance à la septoriose chez un ancien blé dur de Tunisie

Septoria tritici blotch (STB) caused by the fungus Mycosphaerella graminicola is currently the major foliar disease of durum wheat in Tunisia. Most of the Tunisian elite cultivars show little or no resistance to this pathogen. Recently, some Tunisian landraces including 'Agili' have been identified as highly resistant to the virulent STB pathotype, 'Tun06'. In order to identify amplified fragment length polymorphism (AFLP) markers associated with resistance to STB, we used bulk segregant analysis (BSA) in two F3 biparental populations derived from crosses between the resistant durum wheat accession 'Agili' and the susceptible cultivars 'Karim' and 'Khiar' and Association Mapping (AM) in a collection of 110 old durum wheat landraces. Out of the 24 EcoRI/MseI primer combinations tested, 4 were polymorphic between resistant and susceptible DNA pools. Screened on the parents and 9 to 12 progenies from each bulk, these polymorphic AFLP primer combinations revealed EcoACT/MseCTC-241, EcoACA/MseCTT-128, and EcoAGG/MseCTC-104 as specific alleles to resistant individuals suggesting their linkage to a gene for resistance to STB. Binary logistic regression analysis on the diversity panel showed that two AFLP markers out of the three identified by BSA were significantly associated with the resistance. EcoACT/MseCTC-241 was the significantly associated allele at P < 7.10-8 and was identified at a genetic distance of 1.2 cM to the resistance gene. This result indicates the efficiency of using landrace populations to detect potential markers for qualitative resistance.
Determination of Erythroid Cells in Unincubated Chick Blastoderm

Portions the size of 1/6 to 1/32 part of unincubated blastoderm cultured in an albumen‐salineagar solid medium form erythroid cells under conditions which suppress normal co‐ordinated movements for mesoderm induction. Anterior and posterior regions of unincubated blastoderm have the same potentiality to form erythroid cells. The marginal zone seems to be the contributor of prospective erythroid cells. Portion 1/16 part of unincubated blastoderm forms morphologically distinct erythroid cells of the primitive and definitive lines as in normal development in ovo. It seems progenitor cell(s) is pre‐programmed to a particular pattern of differentiation and/or includes differentiation to various erythroid cell types as an obligatory step. This system provides novel experimental possibilities in the study of erythroid cell determination and differentiation.
Correcting Bias Introduced by Aerial Counts in Angler Effort Estimation

Abstract A critical part of most any roving angler survey is angler effort estimation. Various methods have been proposed and implemented to calculate this important parameter, and one of the most effective methods for estimation over large areas utilizes aerial counts of anglers. In this paper, we describe effort estimation methodology used for a creel survey conducted by the Pennsylvania Fish and Boat Commission in the lower Juniata River and lower and middle Susquehanna River during 2007. Daytime angler effort estimates were calculated using an augmented aerial survey, which includes both aerial counts and data collected by creel agents on the ground. Interview angler effort data obtained via a modified roving ground survey were used to produce estimates of daily effort distributions, which were then used to expand instantaneous aerial counts to daily effort estimates. We present two ratios that ameliorate biases introduced by the aerial survey. An angler-to-people ratio calculated from the ground data.
Modeling regional variation in riverine fish biodiversity in the Arkansas-White-Red River basin

Abstract The patterns of biodiversity in freshwater systems are shaped by biogeography, environmental gradients, and human-induced factors. In this study, we developed empirical models to explain fish species richness in subbasins of the Arkansas–White–Red River basin as a function of discharge, elevation, climate, land cover, water quality, dams, and longitudinal position. We used information-theoretic criteria to compare generalized linear mixed models and identified well-supported models. Subbasin attributes that were retained as predictors included discharge, elevation, number of downstream dams, percent forest, percent shrubland, nitrate, total phosphorus, and sediment. The random component of our models, which assumed a negative binomial distribution, included spatial correlation within larger river basins and overdispersed residual variance. This study differs from previous biodiversity modeling efforts in several ways. First, obtaining likelihoods for negative binomial mixed models, and thereby av.
The cure model: an improved way to describe seed germination?

Onofri A, Mesgaran MB, Tei F & Cousens RD (2011). The cure model: an improved way to describe seed germination? Weed Research51, 516–524. Summary Traditional methods of data analysis (anova and linear/non-linear regression) may often not be appropriate for datasets resulting from seed germination/emergence assays. One major problem is that they take the form of ‘time to event’ data with censoring, i.e. the event is only known to have occurred within an interval of time. Parametric survival models have, therefore, been proposed as appropriate alternatives. These, in turn, have the disadvantage that they assume that all the seeds will germinate at some future time, conflicting with the fact that a proportion of ungerminated viable seeds is frequently observed at the end of an experiment. The ‘cure’ model, which we present here, has been used in cancer research as an extension to parametric survival models, to account for a final fraction of individuals that is cured from the disease under study and will not die because of that cause. We show that the ‘cure’ model holds the potential to be used successfully in germination assays, as an extension to non-linear regression and conventional accelerated failure time (AFT) models, with several logical improvements in terms of distributional assumptions and censoring. By way of selected examples, it is shown that the ‘cure’ model can separate the effect of factors/covariates on germination capacity (final germination percentage) from that on germination velocity (germination rate) and uniformity (synchrony of germination), which may represent an advantage from a biological point of view.
Enhancement of germ cell apoptosis induced by ethanol in transgenic mice overexpressing Fas Ligand

It was suggested that chronic ethanol exposure could result in testicular germ cell apoptosis, but the mechanism is still unclear. In the present study, we use a model of transgenic mice ubiquitously overexpressing human FasL to investigate whether Fas ligand plays a role in ethanol-induced testicular germ cell apoptosis. Both wild-type (WT)mice and transgenic (TG) mice were treated with acute ethanol (20% v/v) by introperitoneal injection for five times.After ethanol injection, WT mice displayed up-regulation of Fas ligand in the testes, which was shown by FITCconjugated flow cytometry and western blotting. Moreover, TG mice exhibited significantly more apoptotic germ cells than WT mice did after ethanol injection, which was demonstrated by DNA fragmentation, PI staining flow cytometry and TUNEL staining. In addition, histopathological examination revealed that degenerative changes of epithelial component of the tubules occurred in FasL overexpressing transgenic mice while testicular morphology was normal in wild-type mice after acute ethanol exposure, suggesting FasL expression determines the sensitivity of testes to ethanol in mice. In summary, we provide the direct evidences that Fas ligand mediates the apoptosis of testicular germ cells induced by acute ethanol using FasL transgenic mice.
Winter Oilseed Crops after Soybeans as Tools for Weed Management in Brazilian Savannah Cropping Systems

We aimed with this study to evaluate the potential of oilseed crops planted following soybean, in terms of their ability to inhibit the occurrence of weed species under Brazilian Savannah cropping systems. The long-term experiment was installed in 2010 at Dourados, MS, Brazil, and in completely randomized blocks design with five replications with 12 × 24 m plot size. For three consecutive years (2010/11, 2011/12 and 2012/13), soybeans were planted in all the area by October/November being harvested in February/March, when previously marked plots were planted in April with: (1) radish (Raphanus sativus); (2) rapeseed (Brassica napus); (3) crambe (Crambe abyssinica); (4) winter fallow-no plantation after soybeans. In all years the same crop was repeated at the same plots, with no crop rotation. Phytosociological characterization of weed species was carried out in winter (after oilseeds harvest), pre-planting and post-emergence of soybean for the three years. Relative abundance, frequency and dominance, as well as the importance value for each species, was obtained. Areas were also intra-characterized by the coefficients of Simpson, Shannon-Weiner and Shannon-Weiner’s Evenness Proportion, and areas were compared for species dissimilarity with Jaccard’s presence-only coefficient, by multivariate cluster analysis. Oilseed crops definitely contribute for sustainable weed management as a cultural tool. The most important oilseed crop weeds in the Savannah-like region of Brazil were Amaranthus hybridus, Richardia brasiliensis, Lepidium virginicum, Leonotis nepetifolia and Hybanthus parviflorus. After three years of repetitive crop succession, some weeds were selected, and rotation in Winter is advised at least every two or three years.
Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum)

A standard karyotype based on N-banding, C-banding, and modified C-banding has been constructed for Triticum aestivum L. 'Chinese Spring'. An idiogram and a nomenclature system have been developed for the description of individual bands. Nomenclatural rules have been proposed for the description of chromosomal structural aberrations and polymorphic bands in other wheat cultivars. As a rule each short arm (S) and a long arm (L) consists of a series of dark bands (C-bands) and light bands (mainly euchromatic) and by definition there are no interbands. In some cases, each arm has been subdivided into two or more regions. The description of a band requires designation of a chromosome number, arm (S or L), region, and band. The region number is separated from the band number by a decimal point. Except for arms 1AS, 3AL, 4AS, and 6AS, all wheat chromosome arms have one or more intercalary C-bands and are divisible into three or more bands. It is hoped that the proposed karyotype and nomenclature system will be .