Miracle-dz/UniFAR-FTUs huggingface dataset:
Response of benthic algae to environmental gradients in an agriculturally dominated landscape

Benthic algal communities were assessed in an agriculturally dominated landscape in the Central Columbia Plateau, Washington, to determine which environmental variables best explained species distributions, and whether algae species optima models were useful in predicting specific water-quality parameters. Land uses in the study area included forest, range, urban, and agriculture. Most of the streams in this region can be characterized as open-channel systems influenced by intensive dryland (nonirrigated) and irrigated agriculture. Algal communities in forested streams were dominated by blue-green algae, with communities in urban and range streams dominated by diatoms. The predominance of either blue-greens or diatoms in agricultural streams varied greatly depending on the specific site. Canonical correspondence analysis (CCA) indicated a strong gradient effect of several key environmental variables on benthic algal community composition. Conductivity and % agriculture were the dominant explanatory variables when all sites (n = 24) were included in the CCA; water velocity replaced conductivity when the CCA included only agricultural and urban sites. Other significant explanatory variables included dissolved inorganic nitrogen (DIN), orthophosphate (OP), discharge, and precipitation. Regression and calibration models accurately predicted conductivity based on benthic algal communities, with OP having slightly lower predictability. The model for DIN was poor, and therefore may be less useful in this system. Thirty-four algal taxa were identified as potential indicators of conductivity and nutrient conditions, with most indicators being diatoms except for the blue-greens Anabaena sp. and Lyngbya sp.
Tall Fescue Fertilized with Alum-Treated and Untreated Broiler Litter: Runoff, Soil, and Plant Nutrient Content

ABSTRACT Land application of poultry litter as fertilizer may lead to impaired surface and ground water quality. An experiment was conducted at Crossville, AL to study the effects of alum [Al2(SO4)3 · 14H2O] treatment of broiler litter on the yield and nutrient uptake of tall fescue (Festuca arundinaceae) and the nutrient content of runoff water exited from treated plots. Alum was used at the rate of 0, 545 and 1090 kg per 1464 m2 (12 m × 122 m) of the poultry house. The low rate is the one recommended by Natural Resource Conservation Service (NRCS) in Alabama. Soil samples were collected from the research plots at the beginning of the experiment and at the end of each growing season from 0–7.5, 7.6–15, and 16–30 cm depth. Runoff samples were collected from each plot after each rainfall event that caused runoff. Alum treatments had no effect on tall fescue dry matter yield, and the herbage nutrient concentrations were within acceptable limits. We observed significant reductions in the runoff concentrations of NH4-N (28.6 mg L−1 for untreated litter vs. 15.0 mg L−1 for alum-treated litter), total P (11.5 mg L−1 vs. 5.1 mg L−1), soluble reactive P (10.4 mg L−1 vs. 4.7 mg L−1), and particulate P (1.9 mg L−1 vs. 0.8 mg L−1). This practice should receive serious consideration as a method of reducing the adverse environmental impact of broiler chicken production when the litter is applied to pasture land.
Nutritive value of tillers and morphological components on deferred and nitrogen fertilized pastures of Brachiaria decumbens cv. Basilisk

This work was carried out aiming to evaluate the nutritional value of tillers and the morphological components on deferred and nitrogen-fertilized pastures of Brachiaria decumbens cv. Basilisk. Two experiments were performed in randomized block designs with three repetitions and subdivided plot scheme. In the first experiment, combinations among nitrogen doses (0, 40, 80 and 120 kg/ha) were performed either with the morphological components (green leaves, green stem, dead leaves and dead stem) or with tiller categories (vegetative and reproductive) of the pasture. In the second experiment, the combinations of the deferring periods (73, 95 and 116 days) with the tiller categories (vegetative and reproductive) were studied. N-fertilization increased neutral detergent fiber (NDF) percentage in the green stem and the content of crude protein (CP) in green leaves, dead leaves, and green stem. N-fertilization also increased CP percentages in the vegetative and reproductive tillers, as well as the NDF content in vegetative tillers. A higher deferring period resulted in an increment of the NDF percentage and a reduction of crude protein percentage in the vegetative and reproductive tillers. Nitrogen dose and the deferring period alter the nutritional value of the morphological components and the tillers of the pastures of B. decumbens cv. Basilisk. For deferring of pastures, management actions that result in higher percentages of green foliar blade and vegetative tiller in the pasture contribute to improve the nutritional value of the deferred forage.
Synaptotagmin VII splice variants α, β, and δ are expressed in pancreatic β‐cells and regulate insulin exocytosis

Synaptotagmins (SYT) are calcium‐binding proteins that participate in regulated exocytosis. Although SYTI to IX isoforms are expressed in insulin‐producing cell lines, hitherto only SYTIX has been associated with native β‐cell insulin granules and implicated in exocytosis. SYTVII was also proposed to regulate insulin exocytosis, but its subcellular location and number of alternative splice variants produced remain controversial. Only transcripts of SYTVII α, β, and a novel splice variant δ are expressed in β‐cells and INS‐1E cells. Western blotting revealed that INS‐1E cells predominantly produced SYTVII α and low levels of SYTVII β, whereas SYTVII δ was undectable. The protein colocalized with insulin granules but not with synaptic‐like microvesicles. Overexpression of SYTVII α resulted in decreased insulin granule content with a concomitant translocation of the variant to the plasma membrane, while SYTVII β retained largely a granular pattern. Overexpressed SYTVII δ exhibited a distribution different to that of insulin granules and inhibited exocytosis when assessed by whole cell patch clamp capacitance recording. Silencing of SYTVII α by targeted RNA interference suppressed secretion, while repression of β slightly increased release. Our results demonstrate that SYTVII is expressed on insulin granules and that only SYTVII α is implicated in exocytosis under physiological conditions. — Gauthier, B. R. , Duhamel, D. L. , Iezzi, M. , Theander, S. , Saltel, F. , Fukuda, M. , Wehrle‐Haller, B. , Wollheim. C. B. The synaptotagmin VII splice variants α, β, and δ are expressed in pancreatic β‐cells and regulate insulin exocytosis FASEB J. 22, 194–206 (2008)
Reassessment of diversity and analysis of distribution in Tulipa (Liliaceae) in Uzbekistan

The diversity and distribution of the genus Tulipa in Uzbekistan are discussed; 34 taxa of Tulipa are recognized in Uzbekistan. The taxa were mapped using GIS software and their distributions were analyzed. Six species are endemic to the country. A national check-list of Tulipa was created based on the classification developed by Zonneveld (2009). ‘Hot spot’ areas of tulip diversity in Uzbekistan are western Tien-Shan (18 taxa), the western Pamir–Alay mountains (18 taxa) and the Turan lowland (5 taxa). An assessment of rare tulip species according to IUCN red list categories and criteria was performed for the first time for Uzbekistan. Evaluation of the latest classification of Tulipa clearly shows that further studies are required to arrive at a natural classification of the genus.
Revision of the subfamily Leucochloridiinae Poche, 1907 (Trematoda: Brachylaemidae).

The literature dealing with the subfamily Leucochloridiinae Poche, 1907 is vast. An era of confusion in the identification of species in the genus Leucochloridiumn Carus, 1835 prevailed during the several decades preceding and following the turn of the century largely because of a disregard for the significance of the arrangement of the genital glands in the known species. 'Maximilian Braun apparently had small appreciation of the significance of the internal morphology of the various species which he examined within this genus, for in a series of papers (1901, 1902) that influenced many workers he reduced all known species to synonymy with Leucochloridium macrostomum (Rudolphi, 1803). The genus Leucochloridium has been critically treated taxonomically only by Witenberg (1925) who, because of his emphasis on host specificity, made some serious errors of judgment, in recognition and synonymy of several species. He rejected practically all the taxonomic conclusions presented in the literature by the earlier workers when he placed many of the species therein described in the category of species dubiae until the time "wenn eine umstandliche Revision der Typen ihre Stellung im System festellen wird. " A foundation for a thorough revision of the concepts regarding the taxonomy of this genus was laid by Szidat (1936) who restudied Rudolphi's material deposited in the Berlin Museum and redescribed and validated two of Rudolphi's species, D. macrostomum and D. holostomum. He also pointed out that the species identified by Zeller (1874) and Heckert (1889) as D. macrostomum and so accepted for more than 60 years were distinct and different from Rudolphi's D. macrostomum and D. holostomum. He recognized three morphological types of Leucochloridium, namely: distomes with the genital glands in a straight line represented by D. macrostomum Rud. , distomes with the genital glands in a triangle similar to the species of Heckert (1889) and Zeller (1874), and those with these glands in a triangle and with an intracaecal uterus similar to D. holostomumn Rud. On
REPLY TO COMMENT ON THE LIFE CYCLE AND TOXICITY OF PFIESTERIA PISCICIDA REVISITED 1

Free‐living, marine dinoflagellates are typified by a well‐defined, haplontic life cycle with relatively few stages. The most unusual departure from this life cycle is one reported for the heterotrophic dinoflagellate Pfiesteria piscicida Steidinger et Burkholder. This species is alleged to have at least 24 life cycle stages including amoebae and a chrysophyte‐like cyst form ( Burkholder et al. 1992 , Burkholder and Glasgow 1997a ) not previously known in free‐living marine dinoflagellates. Litaker et al. (2002) redescribed the life cycle of P. piscicida from single‐cell isolates and found only life cycle stages typical of free‐living marine dinoflagellates. The discrepancy between these observations and the life cycle reported in the literature prompted a rigorous study to resolve the life cycle of P. piscicida. Burkholder and Glasgow (2002) took exception to this study, arguing that Litaker et al. (2002) misunderstood the life cycle of P. piscicida and ignored recent publications. We present a rebuttal of their criticisms and suggest a simple way to resolve the discrepancies in the P. piscicida life cycle.
Reply: Assessment of Significant Change in BMD: An Equivalent Approach

To the Editor: We appreciate the statistical comments of Nguyen and Eisman and welcome the opportunity to discuss this issue again. With regards to their comments, there seems to be a misunderstanding of the underlying statistical model adopted for the analysis of our data. As shown below, Nguyen and Eisman’s mathematical derivations are perfectly equivalent to those we presented. First of all, as explained in the bone mineral density (BMD) measurements section the two repeated measurements performed on each patient of groups 1 and 2 were realized not more than 1 hour apart. Therefore our data are not a ‘‘series of BMD measurements x1, x2, x3, . ,xt21, xt’’ as assumed by Nguyen and Eisman. They are replicate measures of BMD, as usually done for reproducibility studies, which means that there is no organic change between them. The underlying statistical model then is a one-way random effects model, a frequently adopted model for reproducibility studies, which we already described in the Appendix section. If we namex1j and x2j the two measures associated to the jth subject, we assume that they are distributed as follows:
Maximum temperatures over Slovenia and their relationship with atmospheric circulation patterns

1 University of Novi Sad, Faculty of Sciences, Climatology and Hydrology Research Centre, Serbia; e-mail: dragan.milosevic@dgt.uns. ac.rs 2 University of Novi Sad, Faculty of Sciences, Center for Spatial Information of Vojvodina Province, Serbia 3 University of Maribor, Faculty of Arts, Department of Geography, Slovenia 4 University of Novi Sad, Faculty of Sciences, Department of Geography, Tourism and Hotel Management, Serbia
Molecular systematics of the Cactaceae

Bayesian, maximum‐likelihood, and maximum‐parsimony phylogenies, constructed using nucleotide sequences from the plastid gene region trnK‐matK, are employed to investigate relationships within the Cactaceae. These phylogenies sample 666 plants representing 532 of the 1438 species recognized in the family. All four subfamilies, all nine tribes, and 69% of currently recognized genera of Cactaceae are sampled. We found strong support for three of the four currently recognized subfamilies, although relationships between subfamilies were not well defined. Major clades recovered within the largest subfamilies, Opuntioideae and Cactoideae, are reviewed; only three of the nine currently accepted tribes delimited within these subfamilies, the Cacteae, Rhipsalideae, and Opuntieae, are monophyletic, although the Opuntieae were recovered in only the Bayesian and maximum‐likelihood analyses, not in the maximum‐parsimony analysis, and more data are needed to reveal the status of the Cylindropuntieae, which may yet be monophyletic. Of the 42 genera with more than one exemplar in our study, only 17 were monophyletic; 14 of these genera were from subfamily Cactoideae and three from subfamily Opuntioideae. We present a synopsis of the status of the currently recognized genera. © The Willi Hennig Society 2011.
Vertical point quadrat sampling and an extinction factor to calculate leaf area index

Abstract The appropriateness of a correction factor to derive leaf area index (LAI) from contact frequency using vertically-inserted point quadrat sampling was investigated. Point quadrat data were collected in a grid pattern over 72 individual shrubs and grass plots comprising eight common Great Basin scrub species of widely divergent ecology and canopy form. Destructive sampling and intercept measurements were used to determine LAI values. Extinction coefficients were then calculated from paired LAI and contact frequency. For all eight species, this extinction coefficient was statistically equivalent to 0·5 as a result of spherical leaf angle distribution, permitting LAI estimation simply by multiplying contact frequency by 2.
Less diverse forest is more resistant to hurricane disturbance: evidence from montane rain forests in Jamaica

1 Are more diverse ecosystems more or less resistant to disturbance? Does diversity increase in a forest after being hit by a hurricane? We answer these questions using a 30‐year study of four Jamaican forests, which differ in soil fertility and diversity, and which were hit by Hurricane Gilbert in 1988; the decades were: pre‐Gilbert (1974–84), Gilbert (1984–94), and post‐Gilbert (1994–2004). 2 Diversity (Shannon index) was always higher in the three forests (Col H′ 3.00, Mull H′ 2.91 and Slope H′ 2.99) on more fertile soils (C : N ratios 10–13, N : P 16–24), and significantly lower in the Mor forest (H′ 2.26) with the least fertile soil (C : N ratio 24, N : P ratio 44). Diversity increased during the Gilbert decade in two of the more diverse forests (Mull and Slope), it did not increase in the least diverse, Mor forest. The overall increase in diversity during the Gilbert decade was due to the recruitment of eight, mostly light‐demanding, species and the increased abundance of uncommon species. 3 We used turnover rates (the average of mortality and recruitment of stems) as a measure of resistance. We equate low turnover with high resistance to hurricane damage. Turnover increased during the Gilbert decade in all forests, but increased more in the three more diverse forests (Mull 1.5% year−1 1974–84 to 3.1% year−1 1984–94; Slope 1.3–2.6; Col 1.5–3.2); than in the least diverse Mor forest (1.2–1.9). 4 Stem diameter growth rates pre‐Gilbert were very low in all forests and were lowest in the Mor forest (Mor 0.3 mm year−1, Mull 0.4, Slope 0.5, Col 0.6). They increased during the Gilbert decade and remained, in the post‐Gilbert decade, double those of the pre‐Gilbert decade (Mor 0.6 mm year−1, Mull 0.6, Slope 0.8, Col 1.1). Smaller stems increased growth more than larger stems. The stems recruited during the Gilbert and post‐Gilbert decades grew faster than those present in 1974. 5 Thus, in montane forest in Jamaica the least diverse forest was most resistant to hurricane damage, and although there was a strong similarity in species rank abundances over 30 years including a hurricane, the hurricane increased diversity.
Ficus religiosa L.: callus, suspension culture and lectin activity in fruits and in vitro regenerated tissues.

Ficus religiosa L. is a tree of immense cultural heritage in Asian countries. It is respected by followers of many religions and faiths. Fruits of Ficus religiosa L. are the ‘figs’ and possess many medicinal properties reported in ethnomedicinal and pharmacological studies. These medicinal properties range from antidiabetic, anticancer, anticonvulsant, antimicrobial, antiviral and antioxidant activities. In the figs, pollination takes place with ‘wasp’. Till date no work on ‘fruit tissue culture’ has been reported in this species. For the first time the callus cultures have been developed using ‘fig fruits’. Fruit callus was multiplied on solid medium using 2 mm to 3 mm diameter fruits. During the present study, lectin/hemagglutinin activity was detected in fruits and fruit callus extracts for the first time. Both In vivo fruits (figs) and In vitro fig callus were used to assay the hemagglutinin activity using pronase treated and untreated rabbit blood erythrocytes. Fruit extract showed 4-8 times more hemagglutination activity in presence of pronase treated erythrocytes. It is the first report of callus/suspension culture and detection of thermostable (up to 70oC) hemagglutinin/lectin from fruits in this species. Preliminary biochemical characterization of the lectin activity e.g. metal ion requirement, EDTA, pH and temperature stability was carried out during the present study. Original Research Article British Biotechnology Journal, 4(2): 215-227, 2014 216
Differential sensitivity of neurosecretory and non‐neurosecretory neurones of an aphid to sucrose during fixation for electron microscopy

The Group 1 neurosecretory cells and a proportion of the non‐neurosecretory cells in the protocerebrum of the aphid Megoura viciae show gross differences in preservation when sucrose is used to increase the osmolarity of a glutaraldehyde primary fixative and an osmium tetroxide secondary fixative. The neurosecretory cells are well preserved whilst a proportion of the non‐neurosecretory cells are shrunken and electron dense, the proportion of affected cells increases with the concentration of sucrose used. This difference is not seen when either the primary or the secondary fixatives are used alone, when a mixture of the primary and secondary fixatives is used or when the osmotic pressure is increased with inorganic salts.
Crop damage by granivorous birds despite protection efforts by human bird scarers in a sorghum field in western Kenya

Cereal crop damage from granivorous birds poses a serious food security problem for subsistence farmers in sub-Saharan Africa. In this region, farmers may rely on human ‘bird scarers’ to limit crop damage. Here we report feeding behaviour and crop damage patterns caused by Village Weavers Ploceus cucullatus and African Mourning Doves Streptopelia decipiens during four days in a 0.12 ha sorghum field protected by two full-time bird scarers in western Kenya. Despite the scarers’ efforts, almost 60% of the seed was lost before harvest. Bird abundance was largely determined by the presence of the bird scarers, with seed loss patterns being a function of distance from these people. Throughout the day, an average of 18 weavers (maximum 120) was present on the crop in any five-minute period. The number of mud projectiles thrown at the birds per 15 min showed only minor diurnal fluctuations, further suggesting that seed eaters attacked the crop throughout the day. Village Weaver individuals took an average 16 seeds per visit, whereas dove individuals took 32 seeds (maximum 105 and 455, respectively). Our study illustrates that avian crop pests can be extremely persistent and, even with consistent diurnal bird scaring activity, severely damage a small crop field. Bird scarers need to be active throughout daylight hours and patrol both the centres and edges of fields to create maximum disturbance to foraging seed eating birds. Further research is needed in order to investigate effects of local- and landscape-level land use patterns on the feeding behaviour of crop pests and the effectiveness of crop protection measures.
Characterization of a new potyvirus isolated from peanut (Arachis hypogaea)

During a survey of viruses of peanuts in South Africa a mechanically transmissible virus was isolated from a plant exhibiting chlorotic ringspots and blotches on the leaves. Typical potyvirus-like flexuous particles were detected by electron microscope examination. Pinwheel-shaped and laminated inclusions in ultrathin sections, reaction with a monoclonal antibody directed to a potyvirus common epitope, a single 33 kDa coat protein and aphid transmission using Myzus persicae all confirmed that the virus was a subdivision II member of the Potyviridae. Host range studies suggested that the virus was none of the previously reported potyviruses of peanuts or of subdivision II potyviruses. The serological relationships of the virus were studied using a range of 17 antisera to potyviruses in ELISA and immunosorbent electron microscopy (ISEM). The isolate reacted weakly with antisera to plum pox virus and bean yellow mosaic virus in ISEM only. Nucleotide sequence of a 624 bp DNA product was obtained following immuno-capture with a potyvirus common epitope antiserum, cDNA synthesis and PCR amplification with potyvirus specific primers which amplify the 3′ untranslated region and a part of the coat protein gene. The sequence was only distantly related to a number of potyviruses, whether amino acid or nucleotide sequences were used for comparisons. It is proposed that the virus be named peanut chlorotic blotch virus and be accepted as a new member of the genus Potyvirus in the family Potyviridae.
External and internal fungal flora of pine sapwood (Pinus sylvestris L.) specimens in above-ground field tests at six different sites in south-west Germany

Abstract The occurrence of fungal species on pine sapwood samples obtained from an above-ground field test study was analysed by terminal restriction fragment length polymorphism (T-RFLP), cloning, and sequencing. Samples were taken from eight double-layer set-ups that were exposed to the environment at six different locations in south-west Germany. The occurrence of fungal species was correlated with decay intensity and rot types on one hand, and characteristics of the test sites, such as precipitation, average temperature and height above sea level on the other hand. In total, 62 different fungal species were found based on T-RFLP, cloning and sequencing. Of the 39 species that were found four or more times, 30 were ascomycetes, five were basidiomycetes, and four could not be classified. The most common fungus found in this study was Coniochaeta ligniaria ((Grev.) Cooke), a soft rot fungus that occurred in 87 of 152 samples (57%). No single factor at the test sites seemed to be decisive for the abundance of fungal species or decay intensity. Within the first years of this study, soft rot fungi was found more frequently in pine sapwood specimens than basidiomycetes.