Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Trichoderma isolates from Philippine rice fields by UP-PCR and rDNA-ITS1 analysis: identification of UP-PCR markers

Forty-two isolates of Trichoderma from rice fields in four provinces in the Philippines were characterized using rDNA-ITS1 analysis and universally primed polymerase chain reaction (UP-PCR). Two groups were clearly distinguishable on the basis of length and restriction pattern of the internal transcribed spacer (ITS) region of the ribosomal DNA and UP-PCR banding profiles using UP primer, L45. The 40 isolates comprising the largest group were very similar with respect to their UP-PCR banding profiles and were assigned to Trichoderma harzianum Rifai following morphological identification of four of the isolates. The two isolates belonging to the second group were identified as Trichodermaviride Pers. ex. Gray on the basis of their morphology, rDNA-ITS1 analysis and distinct UP-PCR banding profiles. One of the T. harzianum isolates with good cellulolytic and competitive saprophytic abilities was analysed using single and pair-wise combinations of UP primers in order to distinguish it from the remaining 41 isolates. A suitable diagnostic marker was identified and this marker will be valuable for monitoring the isolate in field tests. Zusammenfassung Zweiundvierzig Trichoderma-Isolate aus Reisfeldern vier philippinischer Provinzen wurden mittels rDNA-ITS1-Analyse und Universally Primed PCR (UP-PCR) charakterisiert. Basierend auf der Lange und dem Restriktionsmuster der Internal-transcribed-spacer-(ITS-)Region der ribosomalen DNA und den UP-PCR-Bandenprofilen bei Verwendung des UP-Primers L45 waren zwei Gruppen deutlich unterscheidbar. Die grosiere Gruppe bestand aus 40 Isolaten, die sehr ahnliche UP-PCR-Bandenprofile aufwiesen und nach morphologischer Bestimmung von vier Isolaten der Art Trichoderma harzianum Rifai zugeordnet wurden. Die beiden Isolate der zweiten Gruppe wurden basierend auf Morphologie, rDNA-ITS1-Analyse und von der ersten Gruppe verschiedener UP-PCR-Bandenprofile als Trichoderma viride Pers. ex Gray bestimmt. Eines der T. harzianum-Isolate mit guten zellulolytischen und konkurrenzstarken saprophytischen Eigenschaften wurde durch Einzel-und Paarkombinationen von UP-Primern analysiert, um es von den ubrigen 41 Isolaten unterscheiden zu konnen. Ein geeigneter diagnostischer Marker wurde identifiziert und kann wertvoll sein, um das Isolat bei Feldversuchen zu detektieren.
Imbibition behavior of soybean (Glycine max (L.) Merrill) accessions with different testa characteristics.

The imbibition behavior of 18 soybean accessions with a wide range of seed size and testa color was examined. In two accessions, the presence of an intact testa did not reduce the rate of water uptake, and provided no protection against imbibition damage. In one black-seeded accession, seeds soaked with the testa intact had a higher rate of water uptake than embryos without testas due to the loose adherence of the testa, hence creating a wide gap that allowed free water to be trapped between embryos and testa. In the other black-seeded accession, a delayed-permeability testa characteristic was associated with low levels of imbibition damage. Wetting and drying of seeds increased the rate of the water uptake, but this effect could not be attributed entirely to a loosening of the seed coat to the embryo due to the presence of ruptures in the testa surface. Although adherence of the testa to the embryo could play an important role in controlling water uptake in soybeans, it appeared to be difficult to measure or quantify its role per se.
The phylogenetics and systematics of Physaria kingii (Brassicaceae)

The subspecies of Physaria kingii (S. Watson) O’Kane and Al-Shehbaz (Brassicaceae) have historically been a difficult group to delimit taxonomically based on morphology, geography, and ecology. The taxa have been moved between genera as well among varieties, subspecies, and full species many times over. This study addressed the systematics relationships of the subspecies of P. kingii using a combination of molecular (both nuclear and chloroplast DNA sequences), morphological, geographical, and ecological data. Three non-coding DNA regions were chosen: the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and the chloroplast rps intron and the chloroplast ndhC-trnV intergenic spacer. Eighty-seven aligned sequences in total were selected and networks were constructed using SplitsTree for exploratory data analyses to identify any genealogical discordance for each of the regions in addition to a combined chloroplast region. With the prior knowledge of possible hybridization among P. k. subsp. kaibabensis, P. k. subsp. wardii (formerly included within P. k. subsp. latifolia), along with other taxa in the genus found on the Kaibab Plateau, P. arizonica, and P. purpurea, three networks for the ITS region were included to attempt to identify if hybridization is involved and, if so, to determine the maternal taxa. Additionally, Bayesian analyses were completed using each of the regions in addition to combining the chloroplast sequences. The nuclear and chloroplast regions produced statistically different results, so were not combined. The subspecies were not monophyletic and will remain as subspecies of P. kingii. There was a single taxonomic change, separating P. wardii from P. kingii subsp. latifolia and moving P. wardii to a subsp. of P. kingii.
Global patterns and environmental correlates of high‐priority conservation areas for vertebrates

A major challenge for the emerging discipline of conservation biogeography is to identify conservation areas and understand the factors and processes that govern the spatial distribution of those areas. We aimed to identify high‐priority conservation cells (HPCC) – 1° cells that efficiently represent species – for amphibians, birds and mammals at the global extent, to identify the environmental variables associated with conservation priority, and to evaluate how well the areas of highest species richness correspond to these high‐priority areas.
Length–length and length-weight relationships and condition factor of nine freshwater fish species of Nageshwari, Bangladesh

The research carried out the length-length relationships (LLR), length-weight relationship (LWR) and condition factor of nine freshwater small indigenous species viz. G. giuris, E . Danricus, M . pancalus , L . guntea, C. fasciatus, P. sophore, H . Fossilis, C . punctatus and M. cavasius from the waterbodies of Nageshwari, Bangladesh. Relationships among different body lenght parameters of each species were found highly significant with all “r” values being >0.900. LWRs were obtained on the form of TW = aTL b . The “b” values range from 2.65-3.03. The parameter “b” of the length-weight relationship equation showed higher value (>3) only for G. giuris and C. fasciatus . Rest of the specimens showed lower value ( 9.00 . The Fulton’s condition factors showed positive growth tendency for five specimens viz. G. giuris, C. fasciatus, P. sophore, C. punctatus, M. cavasius; and negative tendency for four specimens viz. E . danricus, M . pancalus , L . guntea , and H . Fossilis .
Cloning, characterisation, and expression analysis of an oleosin gene in coconut (Cocos nucifera L.) pulp

Summary Oleosins are structural proteins found in oil bodies, organelles found in the cells of plant tissues with a high oil content that undergo extreme desiccation as part of their maturation process. Oleosins stabilise oil bodies. In this paper, a full-length cDNA sequence homologous to oleosin, a seed-storage oil-body protein, from coconut (Cocos nucifera L.) was identified from cDNA libraries during fruit development and characterised. The gene, termed Coco-Ole, contained an open reading frame of 375 bp encoding a polypeptide of 125 amino acids. The predicted amino acid sequence of coconut oleosin had a molecular mass of 13.0 kDa, and showed 92% (AAF76238.1) and 67% (AAC02239.1) sequence similarity to oil palm (Elaeis guineensis Jacq.) and rice (Oryza sativa) oleosin proteins, respectively. The amino acid sequence clustered in the same branch as oil palm in the cladogram, but was distant from other species. The results of semi-quantitative RT-PCR indicated that the Coco-Ole gene was expressed only in the pulp, and its expression increased significantly during pulp development. Compared with fluctuations in oil content, expression of the Coco-Ole gene was consistent with the anabolism of oil during pulp development. The cloning and sequencing of the Coco-ole gene provides a new marker for studies on oil body biogenesis and fruit development in coconut.
A REVIEW OF THE FISH GENUS PARASCOLOPSIS (NEMIPTERIDAE) OF THE WESTERN INDIAN OCEAN, WITH DESCRIPTION OF A NEW SPECIES FROM THE NORTHERN RED SEA

ABSTRACT The western Indian Ocean species of the deep-water fish genus Parascolopsis (Nemipteridae) are reviewed. Four species, including a new species, are recorded from the western Indian Ocean: P. aspinosa (Rao and Rao) occurs in the northwestern Indian Ocean, including the Gulf of Aden, southern Red Sea, and Persian Gulf, and also in the Andaman Sea, in depths of 20–300 m; P. eriomma (Jordan and Richardson) is widespread in the Indo-West Pacific, including the Red Sea and Gulf of Oman, in depths of 59–264 m; P. townsendi Boulenger occurs in the northwestern Indian Ocean, including the Gulf of Aden, Gulf of Oman, and Arabian Sea, in depths of 94–225 m; and the new species, P. baranesi, occurs in the Gulf of Aqaba, northern Red Sea, in depths of 160–500m.
An overview of female reproductive traits in South American Mabuya (Squamata, Scincidae), with emphasis on brood size and its correlates

The viviparous New World Mabuya (Reptilia, Scincidae) are characterized by a peculiar suite of reproductive traits associated with an extreme degree of matrotrophy and a specialized placenta. We gathered information on female reproductive traits of South American Mabuya based on a compilation of literature data plus original information on two species (Mabuya dorsivittata and Mabuya macrorhyncha). Considering brood size, we identified one “large-brooded” group (brood sizes up to eight to ten) and one “small-brooded” group (brood sizes up to four to six). Brood size tended to be positively correlated with female body size among species, although the correlation is not as strong as it is within species. There were some general trends for the reproductive ecology of New World Mabuya, such as early sexual maturation, brood sizes of usually four to six young, and parturition occurring around the dry–wet season transition.
Physiology of Flower Formation

Adaptation to Photoperiod . Interactions of External Factors . Reversion to Vegetative Growth . Genetics of Flower Formation .
PATTERNS OF MORPHOLOGICAL AND REPRODUCTIVE VARIATION IN STENONEMA MAYFLIES (EPHEMEROPTERA: HEPTAGENIIDAE) IN EASTERN LAKE HURON

Abstract Significant variation in the morphology of late-instar nymphs of Stenonema tripunctatum (Banks) in Lake Huron could not be ascribed to their proximity to warm-water plumes originating from the Bruce Nuclear Power Development, by either multivariate or univariate analyses of size and shape. Major sources of variation in S. tripunctatum were developmental state and sex. Nymphs collected just prior to emergence had low values of transverse measurements in anterior regions (inter-orbital width, prothoracic width), whereas males and females were separated by these measurements and other components of head geometry. No significant effects of thermal exposure were found in the reproductive development of S. tripunctatum, but this species is most commonly found below depths at which thermal-plume effects are expected. Based on a small but representative sample, ultimate-instar nymphs of Stenonema vicarium (Walker) from a depth of 3 m contained significantly fewer eggs and allocated a significantly lower proportion of biomass (dry weight) to reproduction in locations with higher temperatures. Résumé D'après des analyses uni- ou multivariates de grandeur et de forme, la variation significative dans la morphologie des stades tardifs des nymphes de Stenonema tripunctatum (Banks) dans le lac Huron n'a pas pu être attribuée à leur proximité aux panaches d'eau chaude provenant du développement de la centrale nucléaire Bruce. Les sources principales de variation dans S. tripunctatum étaient dans le stade de développement et le sexe. Les valeurs des mesures transverses des régions antérieures (largeur inter-orbital et largeur prothoracique) des nymphes prélevées juste avant emergence étaient basses, tandis que les mâles et les femelles étaient séparés par ces mesures et d'autres composants de la géométrie de la tête. Aucun effet significatif à l'exposition thermale sur le développement reproductif de S. tripunctatum n'a été trouvé, cependant cet espèce est trouvée le plus souvent sous la profondeur où les effets de la panache thermale sont attendus. Basé sur un petit échantillon représentif, les nymphes de Stenonema vicarium (Walker) provenant d'une profondeur de 3 m contenaient significativement moins d'oeufs et allouaient une proportion significativement plus basse de biomasse (poids sec) à la reproduction dans des endroits à températures plus élevées.
A Rapid and Sensitive Method for Direct Detection of Erwinia amylovora in Symptomatic and Asymptomatic Plant Tissues by Polymerase Chain Reaction

Fire blight is a destructive disease of apple and pear trees and other rosaceous plants caused by the Gram-negative bacterium Erwinia amylovora. Several molecular detection procedures described for this plant pathogen are either too time consuming, too insensitive or impractical when handling a large number of samples routinely. Here, we describe a modified protocol of the REDExtract-N-AmpTM Plant polymerase chain reaction kit for the detection of E. amylovorain planta and demonstrate that it provides simplicity, high sensitivity, speed and high throughput potential. A total of 951 samples collected in Austria were tested with the modified protocol and the standard protocol of our laboratory to validate the accuracy of this detection method.
First data on the helminth fauna of a locally distributed mountain frog, “Tavas frog” Rana tavasensis Baran & Atatür, 1986 (Anura: Ranidae), from the inner-west Anatolian region of Turkey

A total of 8 specimens of Rana tavasensis Baran & Atatur, 1986 (Tavas frog) were collected in Denizli Province (inner-west Anatolia, or the eastern part of the Aegean region), Turkey, in 2008 and 2009 and were examined for the first time for helminths. All 8 frogs were infected with 1 or more helminths. The helminth fauna of R. tavasensis comprised 3 species: 1 species of Digenea [Haplometra cylindracea (Zeder, 1800) Looss, 1899], 1 species of Nematoda [Cosmocerca ornata (Dujardin, 1845)], and 1 species of Acanthocephala [Acanthocephalus ranae (Schrank, 1788) Luhe, 1911)]. R. tavasensis represents a new host record for each of the observed helminth species in Turkey.
Regulation of Mo-cofactor, NADH- and NAD(P)H-specific nitrate reductase activities in the wild type and two nar-mutant lines of barley (Hordeum vulgare L.)

Seedlings of three genotypes of barley, Hordeum vulgare L. , cv. Winer, were grown in nutrient solutions for 12 d: (a) Wt, the wild type; (b) Chlo19 and (c) Chlo29, two nitrate reductase (NR) deficient nar-mutants. Nar-mutant plants grown in nitrate developed about 5-24% of NADH-NR (EC 1.6.6.1.) activity level characteristic of the Wt. The NR in vitro assays in which NADH or NADPH were used as electron donors showed that the two mutant lines contained a mixture of NADH-specific and NAD(P)H-bispecific (EC 1.6.6.2.) NRs. Chlo19 had a very low level of MoCo activity as compared to Chlo29 and Wt. Chlo19 appeared to be mutated in a MoCo gene rather than in the genes coding for the nitrate NR apoenzyme. NAD(P)H-NR was found in the shoots and roots of both mutants but only in the roots of Wt. Several aspects of the regulation of NADH and NAD(P)H specific NRs in plants of the barley cv. Winer genotypes are discussed. MoCo was a strong limiting factor for NR biosynthesis in nitrate-fed plants of Chlo19, but less limited in N-starved and ammonium-fed plants. Biomass production by the three genotypes was similar during first 12 d after germination, regardless of the level of NR detected in vitro. Mutant plants may be able to supply the nitrogen required for growth with only 5-24% of the NR level of the WT.
Two new records of powdery mildews with their effectiveness on three ornamentals in Turkey

In this study, two new species of powdery mildews together with disease severities measured at four different growing stages were identified on three ornamental species in the Aanliurfa district of Turkey. Observations and measurements were made on natural and experimental stands. On natural stands, 15, 85 and 100% disease rates were determined on Fuchsia regia, Calendula officinalis and Zinnia elegans, respectively. Powdery mildews of C. officinalis and Z. elegans were identified as Podosphaera xanthii(Oidium subgenus Fibroidium). Disease symptoms were observed from early seedling to late maturing stages on Z. elegans, and from pre flowering to maturing stages on C. officinalis. The mildew pathogen of Fuchsia regia was identified as Leveillula taurica. This ornamental species appear to be resistant to this respected powdery mildew agent during summer, but somewhat susceptible in the early autumn. In addition, upper leaves were observed the only section displaying the disease. Key words: Podosphaera xanthii, Leveillula taurica, ornamentals, disease severity.
Assessment of Plant Diversity and Associated Mycorrhizal Fungi in the Mined-out Sites of Atlas Mines in Toledo City, Cebu for Bioremediation

The diversity of plant and mycorrhizal fungi within the 35,000-ha of the Atlas Mines in Toledo, Cebu, was surveyed with the goal of rehabilitating their mined-out area through bioremediation (the use of dominant plants and mycorrhizal fungi present in area to contain/reduce pollutants). From five one km transect lines in five sites, the survey indicated that the vegetation was classified as a disturbed grass-shrubland-savanna-agroforest plant community with tree plantations in rehabilitated sites. Plant composition comprised 69 species belonging to 66 genera and 35 families which include trees, shrubs, herbs, creepers, vines, agricultural or agroforest crops. Fruit bodies of ectomycorrhizal fungi (ECMF), namely: Pisolithus, Scleroderma, Thelephora and Boletellus were found under Acacia auriculiformis, A. mangium, Eucalyptus urophylla and E. camaldulensis. Pisolithus were the most dominant. For arbuscular mycorrhizal fungi (AMF), out of 50 plants collected, 10-100% roots of Lycopodium, Saccharum spontaneum, Nephrolepsis, Acacia mangium and Stachytarpheta jamaicensis were colonized by AMF. All roots of S. jamaicensis were colonized solely by Glomus sp. Pithecellobium dulce harboured the highest spore density (2,575 spores/plant/30g dry soil), consisting of Glomus (42%), Acaulospora (24%) and Entrophospora (37%). Muntingia calabura was the only plant associated with Glomus, Gigaspora, Scutellospora, Acaulospora and Entrophospora, though with low spore population. Glomus was the most prevalent among the AMF. The above AMF and ECMF can be mass-produced as biofertilizers for use in bioremediation of mined-out sites and other areas with similar conditions.
Insect phylogenomics: new insights on the relationships of lower neopteran orders (Polyneoptera)

The branching pattern of the diverse lower neopteran insect lineages (Polyneoptera: cockroaches, mantids, earwigs, grasshoppers, phasmids etc.) is the least resolved problem in insect systematics. Despite the accumulation of various morphological and molecular datasets, the proposed phylogenetic relationships within Polyneoptera remain unstable. In this study we investigate these relationships based on a new transcriptome data matrix covering almost all polyneopteran orders, except for Mantophasmatodea, Grylloblattodea and Mantodea. The data conclusively support a monophyletic Polyneoptera, thus corroborating previous findings from (i) recent large gene studies with smaller taxon sampling and (ii) comprehensive protein coding gene analyses across all insect lineages, and, consequently, rejecting the paraphyletic lower neopteran group suggested by various morphological characters and rRNA gene analyses. The inclusion of several phylogenetically ambiguous polyneopteran orders (Zoraptera, Dermaptera, Plecoptera, Phasmatodea and Embioptera) allows us to further test alternative phylogenetic relationships within Polyneoptera. Previously suggested clades are significantly rejected: Parametabola (= Zoraptera + Paraneoptera), Mystroptera (= Embioptera + Zoraptera) and Orthopterida (= Orthoptera + Phasmatodea). Although the lower neopteran orders are so far only supported as a monophyletic group by autapomorphies in wing base characters, phylogenomic analyses consistently provide further strong support. However, despite the use of this large dataset, several polyneopteran orders still show unstable positions within a monophyletic Polyneoptera.
A tool to assess the influence of management practices on grassland surface macrofaunas

We present a method for involving the invertebrate fauna into nature management by the selection of species indicating effects of fertilization, mowing and grazing on the surface macrofauna of grasslands. Low fertilization levels result in the highest numbers of individuals. Grazing results in lowered diversity and a decrease in number of species as compared with no management and with mowing. Mowing results in higher numbers of individuals compared with no management and with grazing. Indicator species are given for assessing the main difference between grasslands which turns out to be fertilization/yield, and grazing. Management effects on the surface macrofauna, the usefulness of the method, and the indicator species concerned are discussed.
Drought-induced changes in the accumulation of boiling-soluble proteins (p40, GST, HSP90) in the grains of drought-tolerant and drought-sensitive cultivars of Triticum aestivum

Abstract. Approximately 70% of crop yield losses are caused by abiotic stresses, with drought being the most serious threat to crop production in many areas of the world. Plants have developed physiological and biochemical responses at multiple levels to allow them to grow and survive under drought stress. Among these, hydrophilins (BSPs, proteins soluble after boiling), representing 0.2% of the total genome, play an important role in the stress adaptation in plants. In this study, we examined the effect of drought on BSPs at different developmental stages of leaves and seeds in drought-tolerant (cv. PBW 175) and drought-susceptible (cv. PBW 621) cultivars of Triticum aestivum. The BSP profiles of seeds were outlined via SDS-PAGE followed by immunoblot analysis using anti-HSP (heat shock protein-90), anti-GST (glutathione S-transferases) and anti-p40 (protein 40). In SDS-PAGE profile, BSPs were detected in a genotype- and treatment-dependent manner. Notably, no BSPs were detected in shoots at any stage, whereas in seeds, many BSPs were detected, indicating organ-specific regulation of BSPs. In western blotting, the induced accumulation of protein bands Bsp40-51 and 59 and presence of differential band of BsHSP44 under drought conditions was observed only in tolerant cv. PBW 175, not in sensitive cv. PBW 621, indicating the roles of such proteins in drought-stress adaptation. BSPs were accumulated at different developmental stages in a cultivar- and stage-dependent manner. The induced expression of different BSPs under drought conditions in tolerant cv. PBW 175 implies the relevance of these BSPs under drought conditions. Notably, the different BSPs were also expressed under normal growth and developmental stages at 57 and 76 days post-anthesis, implying their key role in earlier stages and maturity of grain development.