Miracle-dz/UniFAR-FTUs huggingface dataset:
Antifungal effect of some plant extracts on Alternaria alternata and Fusarium oxysporum

In vitro studies were carried out to test the antifungal activity of 5 plant extracts; Cinnamomum zeylanicum (Cinnamon), Cymbopogon proximus (Halfa barr), Laurus nobilis (Laurel), Persea americana (Avocado) and Zingiber officinale (Ginger) performed with either cold distilled water (CDW) or boiling (BDW) on two pathogenic fungi, Alternaria alternata and Fusarium oxysporum. The results revealed that plants extracts especially those performed with CDW had a strong antifungal activity with significant inhibition on the growth of the 2 tested fungi and their hydrolytic enzymes, β-glucosidase, pectin lyase and protease. Extracts of Halfa barr and ginger were the most effective to inhibit the growth of the tested fungi followed by avocado, cinnamon and laurel. Findings from this study confirmed that plant extracts can be used as natural fungicides to control pathogenic fungi, thus reducing the dependence on the synthetic fungicides. Halfa barr, which was found to be the most efficient extract (75% inhibition), might be a promising material for controlling these fungi.
High resolution analysis of mating systems: inbreeding in natural populations of Pinus radiata

Pinus radiata has a history of population bottlenecks and is currently restricted to five relatively small populations, three in mainland California, and two on islands off the coast of Baja California. Using highly polymorphic microsatellite markers and a newly developed statistical approach, we were able to estimate individual inbreeding coefficients and can thus analyse the mating system with high resolution. We find a bimodal distribution of inbreeding coefficients: most individuals result from selfing whereas few (in the mainland populations) to a modest number (in the island populations) are likely selfed. In most other pine species and presumably in the ancestral P. radiata population, occurrence of mature selfed individuals would be impossible because of the high genetic load. We therefore conclude that inbreeding depression has been purged in P. radiata and that the mating system has changed as a consequence.
Seasonal pattern of germination and seed longevity in the invasive species Heracleum mantegazzianum

We investigated the effects of different temperature regimes and dry storage on germination of H. mantegazzianum (Apiaceae, native to Caucasus) seeds in the laboratory and linked the results with studies of seasonal seed bank depletion in a common garden experiment and under field conditions. Seeds were collected at seven sites in the Slavkovský les region, Czech Republic, cold-stratified for 2 months and germinated at seven temperature regimes. Under all temperature regimes, fresh seeds germinated to significantly higher percentages than older (1, 2, 3 years) seeds. For all storage lengths, seeds germinated best at alternating day/night temperatures of 20/5 °C. The length of the germination period had a significant effect only at low constant temperatures of 2 and 6 °C, where germination percentage increased between 2 and 6 months. Seasonal germination exhibited a distinct pattern, with rapid depletion of seed bank by the first spring after seed burial. Non-dormant seeds were present in the soil early in spring and late in autumn. The higher summer temperatures prevented dormancy breaking and another cold period of at least two months below 10 °C was needed to bring non-germinated seeds out of dormancy. The results suggest that (1) seed dormancy of H. mantegazzianum was not completely broken until the first spring, but that some seeds re-enter or retain dormancy during high summer temperatures and that (2) the threshold needed for breaking the dormancy was achieved gradually during the cold autumn and winter months. However, in a small fraction of seeds the dormancy breaking process took several years. Of seeds buried in 10 different regions of the Czech Republic, on average 8.8% survived 1 year, 2.7% 2 years and 1.2% remained viable and dormant after 3 years of burial. The ability of even small fraction of H. mantegazzianum seeds to survive for at least 3 years can result in re-invasion of this species into controlled sites.
An update on sequenced chloroplast genomes of Bryophytes

The sequencing of complete chloroplast genome of Marchantia polymorpha paved the way to know the structure and organization of chloroplast genomes of other plants. Since then ~747 chloroplast genomes have been sequenced. However, in comparison to the tracheophytes, a small number of complete chloroplast genome sequences of bryophytes are available (only 4 liverworts, 6 mosses and 2 hornwort). This review represents an update on sequenced chloroplast genomes of bryophytes.
Typage moléculaire du complexe d'espèces Fusarium solani et détermination de son mécanisme de résistance au voriconazole : Molecular typing of Fusarium solani species complex and determination of its resistance mechanism to voriconazole

Le complexe d'especes Fusarium solani regroupe des champignons phytopathogenes egalement impliques en pathologie humaine dans des infections parfois profondes et souvent de mauvais pronostic. Dans un premier temps, une methode de MLST, s'appuyant sur 5 genes de menage a donc ete developpee. Validee sur 51 isolats epidemiologiquement distincts, cette methode stable et reproductible presente un pouvoir discriminant de 99,1 %. Apres comparaison a la technique de reference utilisee en phylogenie, un schema consensus a 8 loci a ete propose. Dans un second temps, une etude de la sensibilite de ce pathogene a l'amphotericine B et au voriconazole a ete menee par deux techniques d'evaluation des CMI : microdilution CLSI M38-A2 et bandelettes E-test. Devant le paradoxe entre une sensibilite diminuee in vitro au voriconazole et la recommandation de cette molecule pour le traitement curatif de la fusariose humaine, des mecanismes de resistance ont ete explore. L'hypothese d'un phenomene d'efflux n'a pas ete retenue alors que celle d'une modification de la cible, la 14 alpha sterol demethylase, peut etre envisagee apres la description de differentes mutations pour les isoformes CYP51A, B et C%%%%Fusarium solani species complex includes phytopathogenic fungi also involved in human infections with poor prognosis. Firstly, MLST method, based on five housekeeping genes has been developed. This method has been validated on 51 isolates epidemiologically distinct, and has been shown to be stable and reproducible and provides a discriminating power of 99.1%. After comparison with the reference technique used in phylogeny, a consensus method with 8 loci has been proposed. Secondly, a study of the susceptibility to amphotericin B and voriconazole has been conducted with two MIC determination methods : CLSI M38-A2 microdilution and E-test. The paradox between decreased susceptibility to voriconazole in vitro and recommendation of this molecule for the curative treatment of Fusarium infections has lead to the exploration of resistance mechanisms. The hypothesis of an efflux phenomenon has not been retained whereas a change in the target, the sterol 14 alpha demethylase may be considered following the description of different mutations on proteins CYP51A, B and C
A biogeoclimatic analysis of Nothofagus cunninghamii (Hook.) Oerst. in southeastern Australia

The geographical limits of Nothofagus cunninghamii are highly correlated with climate and appear to be more or less in equilibrium with the climate of the present century in all but one of the areas of its present range. It is suggested that suitable climates for the species occur in the highlands of northeastern Victoria and southern New South Wales, beyond its present range, and it is possible that it occurred within the predicted area prior to the last ice age. It is suggested that populations of N. cunninghamii along the northeastern edge of its present range in the Central Highlands of Victoria may be migrating northeast along a narrow corridor of apparently suitable climate to re-occupy the postulated former range. The rate of migration would be expected to be extremely slow because of the poor dispersal ability of the species and the adverse impact of recurrent fires.
Identificación y fluctuación poblacional de insectos polinizadores en palma aceitera (Elaeis guineensis Jacquin) en el sur del lago de Maracaibo, estado Zulia, Venezuela

Oil palm (Elaeis guineensis Jacq.) is the oil crop that produces the most oil quantity per area unit and it could cover -in the futurethe vegetable oil demand in Venezuela. The oil palm high productivity is the result of a permanent production of bunches, which depends in high measure of pollinating insects. In this research, pollinating insect’s population fluctuation was studied, with the purpose to know the current situation of these insects, as native ones as those introduced. Systematic surveys were carried out between December 2002 and November 2003, on a 3 years old oil palm plantation, located in «Francisco Javier Pulgar» municipality, Zulia state. Samples were taken from male inflorescences in anthesis (MIA) and in the female inflorescences in anthesis (FIA), traps were placed to capture the insects; which were identified per species and they were counted for. Also, a register of the monthly rainfall and temperature of area was made. The main species found were Elaeidobius kamerunicus Faust, E. subvittatus Faust and M. costaricensis Gillogly. Thrips hawaiiensis Morgan was also observed and one Smicripidae coleopteron. Among the climatic variables studied, rainfall affected the pollinating insect’s population, because dry conditions caused a decrease of pollinating activity in Elaeidobius and the M. costaricensis species. At the same time it was observed that the E. kamerunicus and the M. costaricensis were more commonly found in relation to the FIA and MIA, respectively.
A Comparison of Machine Learning Species Distribution Methods for Habitat Analysis of the Korea Water Deer (Hydropotes inermis argyropus)

야생동식물 서식지 보전 연구는 통합적인 생물다양성 관리 전략으로서 주목받고 있다. 국내 종조사자료 및 환경공간정보 여건을 고려할 때 종출현정보에 최적화된 것으로 알려져 있는 GARP 모형과 Maxent 모형이 서식지 분석에 가장 적합한 것으로 판단된다. 국내 적용가능성을 확인하기 위해 충청도 삽교천 일원을 대상으로 고라니( Hydropotes inermis argyropus)에 대한 기계학습식 모형을 적용하였다. 종출현지점은 3차 전국자연환경조사, 환경변수는 문헌조사를 통해 10개를 도출하였다. 분석 결과 Maxent 모형과 GARP 모형은 각각 전체 면적의 16.3%, 27.1%를 고라니 서식지로 예측하였다. 종분포모형 정확도(훈련/검증)는 Maxent 모형(0.85/0.69)이 GARP 모형(0.65/0.61)보다 높게 분석되고 Spearman 순위 상관계수 역시 Maxent 모형(r=0.71, p<0.01)이 GARP 모형(r=0.55, p<0.05)보다 높게 분석되었다. 이는 대상지의 특성과 대상종에 따라 달라질 수 있으므로 상황에 따라 적절한 모형을 적용하는 것이 바람직할 것으로 판단된다.
Weed Control in Field Corn (Zea mays) with RPA 201772 Combinations with Atrazine and S-Metolachlor1

Abstract: The premix atrazine + S-metolachlor is commonly used to control a wide range of weeds in corn, but it is weak on velvetleaf and several other broadleaf species. RPA 201772, used at reduced rates in combination with atrazine + S-metolachlor, may improve the weed control spectrum. In field studies at Urbana and Dekalb in 1998 and 1999, RPA 201772 was combined with a premix of atrazine at 1,820 g ai/ha and S-metolachlor at 1,408 g ai/ha to compare RPA 201772 rate effects on corn injury, weed control, and yield. RPA 201772 was applied at 0, 26, 53, 78, 105, and 132 g ai/ha early preplant (EPP), preplant incorporated (PPI), and preemergence (PRE). Compared with atrazine + S-metolachlor alone, RPA 201772 combinations did not improve giant foxtail control. However, RPA 201772 at 26 or 53 g/ha increased control of redroot pigweed, common lambsquarters, ivyleaf morningglory, common ragweed, giant ragweed, and velvetleaf in some environments. At Urbana in both years, RPA 201772 at 26 g/ha in combination with atrazine + S-metolachlor increased velvetleaf control 15% compared with the premix alone. RPA 201722 at 26 to 78 g/ha decreased velvetleaf densities with all application methods. Greater weed control and higher corn yield occurred in treatments applied PRE or PPI compared with EPP applications, except where conditions were dry after PRE applications. This research demonstrates the benefit of RPA 201772 at low rates for broadleaf weed control with less potential for crop injury compared with high RPA 201772 rates. Nomenclature: RPA 201772 (proposed common name, isoxaflutole), 5-cyclopropyl isoxazol-4-yl-2-mesyl-4-trifluoromethylphenyl ketone; common lambsquarters, Chenopodium album L. #3 CHEAL; common ragweed, Ambrosia artemisiifolia L. # AMBEL; giant foxtail, Setaria faberi Herrm. # SETFA; giant ragweed, Ambrosia trifida L. # AMBTR; ivyleaf morningglory, Ipomoea hederacea (L.) Jacq. # IPOHE; redroot pigweed, Amaranthus retroflexus L. # AMARE; velvetleaf, Abutilon theophrasti Medicus # ABUTH; corn, Zea mays L. Additional index words: HPPD inhibitor, isoxaflutole, reduced herbicide rates. Abbreviations: DAE, days after emergence; DAT, days after treatment; EPP, early preplant; PPI, preplant incorporated; PRE, preemergence.
Differences in the susceptibility among silkworm, Bombyx mori (Lepidoptera: Bombycidae), strains to the entomopathogenic fungus, Beauveria brongniartii and the mode of inheritance of the susceptibility

Entomopathogenic fungi have attracted public attention as an effective material for microbial control of pest insects. In Japan, B. brongniartii isolated from the yellowspotted longicorn beetle, Psacothea hilaris (Pascoe) (Coleoptera: Cerambycidae), is used to control the mulberry and fig tree pest P. hilaris; a citrus tree pest, the white-spotted longicorn beetle, Anoplophora malasiaca (Thomson) (Coleoptera: Cerambycidae), and the Japanese angelica tree pest, the udo longicorn beetle, Acalolepta luxuriosa (Bates) (Coleoptera: Cerambycidae). The isolates of B. brongniartii from P. hilaris are known to have high pathogenicity to the three longicorn beetles, but low pathogenicity to silkworms (Kawakami, 1978; Shimane and Kawakami, 1993). Therefore, the use of the B. brongniartii isolates to control the longicorn beetles in mulberry fields is allowed even during the silkworm rearing season. The pathogenicity of the isolates has usually been tested using hybrid strains of silkworm commonly reared in silkworm farmhouses. When the fourth instar larvae of F1 hybrid of Japanese No.145 × Chinese No.146 were inoculated by dipping into a conidial suspension (10-10 conidia/ml), all the treated larvae survived (Shimane and Kawakami, 1993). In case of F1 hybrid of Chinese No.12 × Japanese No.124, 40.7% of the newly hatched larvae died and all the second to fifth instar larvae survived at higher concentration (10 conidia/ml) (Kawakami, 1978). However, the pathogenicity of B. brongniartii to parent strains of silkworm has not yet been investigated. And the resistant mechanisms of silkworm against B. brongniartii have not been inevestigated. Therefore, we examined the susceptibilities of 22 parent strains of silkworm to an isolate of B. brongniartii to elucidate resistant mechanisms of silkworm against B. brongniartii. There were large variations in susceptibility among the silkworm strains in either case the conidial suspension was applied topically by dipping or by injection. This paper provides insight into the mode of heredity for susceptibility to B. brongniartii based on the difference in susceptibility of a susceptible strain, a resistant strain and their progenies.
SNARE proteins in human mast cells

Mast cells form an integral part of both innate and adaptive immunity; they help to orchestrate the inflammatory immune response through the release of a variety of inflammatory mediators [1]. Adverse reaction to allergens can lead to activation of mast cells, causing degranulation and release of a range of pro-inflammatory mediators contributing to the onset of allergy [2]. The most studied activation pathway in the adaptive immune response of mast cells is through the Immunoglobulin E (IgE) cell surface receptor FcεRI. Crosslinking of FcεRI leads to degranulation and de novo synthesis of mediators [3]. Every eukaryotic cell undergoes constitutive secretion. Alongside this general process, cells such as neuronal endocrine and immune cells, including mast cells, perform regulated secretion. This enables the cell to rapidly release mediators stored in secretory granules upon stimulation by a particular extracellular ligand. Mediators released fall into two categories; pre-formed, contained within these secretory granules; monoamines such as histamine as well as many proteases [4, 5], and de novo synthesized that are released through the constitutive secretory pathway, including prostaglandins, leukotrienes, cytokines and chemokines [6, 7]. Elucidating the mechanisms of mast cell mediator release is imperative for understanding many disease processes; however, knowledge of the precise mechanisms by which mast cell exocytosis is controlled remains elusive. The aim of this study was to identify and characterise Soluble NSF attachment protein receptor (SNARE) proteins involved in the release of inflammatory mediators in human mast cells. Using LAD 2 human mast cells and primary human lung mast cells (HLMCS), expression of a variety of syntaxins and Vesicle associated membrane proteins (VAMPs), as well as the ubiquitously expressed SNAP-23 were found. To study the roles of individual VAMPs in exocytosis a novel technique utilising pH sensitive pHluorins was developed. Using VAMPs tagged with pHluorins, the cellular distribution of VAMP-3 and VAMP-8 containing vesicles and their behaviour upon IgE stimulation in live cells was monitored. In unstimulated cells, VAMP3 and 8 were found to have distinct cellular distributions. Upon IgE stimulation both VAMP-3 and VAMP-8 containing vesicles translocated to the membrane and underwent membrane fusion, consistent with roles in exocytosis. However, their responses showed distinct time courses and calcium dependences. Importantly the VAMP-3 vesicle pool could be selectively targeted with a botulinum neurotoxin serotype B (BoNT)/B LC construct and in doing so inhibited the release of IL-6. The findings in this study support the notion that distinct vesicle pools, defined in part by expression of VAMP-3 and VAMP-8, regulate the release of inflammatory mediators from mast cells and that BoNTs might provide a novel means of targeting the release of chronic inflammatory mediators from mast cells for treatment of chronic inflammatory diseases.
Thermal Physiology, Phenology, and Distribution of Tree Frogs

Seasonal and latitudinal gradients in the thermal sensitivity of jumping performance have been examined in 10 species of hylids representing five different seasonal and distributional categories. Among temperate species, low-temperature performance is best in early-breeding northern species, intermediate in later-breeding northern species, and worst in southern species. Subtropical and tropical species have progressively higher critical thermal minima, but their thermal performance curves are not much different from those of southern temperate species in other respects. Critical upper thermal limits on jumping performance are much less variable than are lower limits, and the critical thermal minimum (CTmin) is not correlated with the critical thermal maximum (CTmax) in our sample. Effectively, CTmax is relatively inflexible, and consequently an improvement in low-temperature performance (reduction in L80, the lowest temperature at which frogs can attain 80% of maximal performance) results in a widening of the thermal breadth of performance at or above some arbitrarily selected standard (e.g., B80, 80% of maximal performance). The strong negative correlation between L80 and B80 in our sample of hylids is not found in lizards. Differences in thermal sensitivity of jumping performance are strongly correlated with naturally experienced minimum body temperatures. The thermal sensitivity of locomotion may itself be (or may be correlated with) a mechanism underlying distributional differences and temporal partitioning of habitat among frogs. We suggest that some aspects of the community organization of hylids, such as breeding phenology and the depauperate faunas of high latitudes, are constrained at least in part by thermal physiology. Ecological consequences of this constraint are currently being investigated.
Expression of Bacterial β-Galactosidase in Animal Cells

A recombinant plasmid containing the gene for bacterial β-galactosidase, situated close to the simian virus 40 early promoter, has been constructed. Transfection of CHO, L, and COS-1 cells with this plasmid led to the expression and appearance of the enzyme. Using this system, we have developed a series of promoter cloning vehicles capable of accepting promoter signals for animal genes.
Frequent fuel-reduction burning: the role of logs and associated leaf litter in the conservation of ant biodiversity

Frequent low-intensity fires are used in management of Australian forests to reduce fuel loads and protect natural resources and human property. Low-intensity fires are typically patchy and unburned litter microhabitats are often associated with large objects such as logs, which may act as refuges both for vertebrate and for invertebrate fauna. The aim of this study was to determine whether ants were using unburned leaf litter microhabitats associated with logs as a refuge after fire. The study was carried out in Bulls Ground State Forest, New South Wales, Australia, where experimentally burned and unburned sites had previously been established. Species richness and abundance of ants in leaf litter did not differ between habitats adjacent to logs and away from logs, in burned and unburned sites. Fifteen of the 42 ant species were found in all four habitats, and contributed 94% of total ant abundance. Every habitat had a group of unique species, which together made up 30% of the total species richness. There was also a distinct group of species that was not found in the leaf litter associated with the burned/open habitat. However, as 45% of all species were found in low abundance (less than 10 individuals), care must be taken in inferring patterns for these groups. When functional groups were used to assess community structure, ‘cryptic’ species were found to be common in all habitats, whereas ‘subordinate Camponotini’ were found in burned habitats only. This study indicates that in an area where frequent burning is applied on a broad scale, preserving a range of microhabitats, including those associated with retained logs, may make a substantial contribution to conserving ant biodiversity.
Species-specific effects of four preservative treatments on oocytes and ovarian material of Atlantic cod (Gadus morhua), haddock (Melanogrammus aegleflnus), and American plaice (Hippoglossoides platessoides)

The lack of information concerning the preservation of ovarian material of fish species inhibits standardization of methods for determining fecundity and measuring oocytes. The effects of four preservatives (10% phosphate-buffered formalin, modified Gilson’s solution, 70% ethanol, and freezing) on ovarian material weight and oocyte size were quantified for prespawning Atlantic cod (Gadus morhua), haddock (Melanogrammus aeglefinus), and American plaice (Hippoglossoides platessoides). Effects of preservation were similar between Atlantic cod and haddock but different between Atlantic cod and American plaice for nearly all comparisons. Although all treatments affected the weight of ovarian material, freezing caused the most change and formalin caused the least. Such signif icant species-specific effects should be quantified in the calculation of life history characteristics, such as fecundity, to minimize error. This is one of few studies dedicated to evaluating the effects of preservation on oocytes and ovarian material and is the first to evaluate multiple preservatives on species.