Miracle-dz/UniFAR-FTUs huggingface dataset:
Thraustochytrids: A neglected agent of the marine microbial food chain

The base of the pelagic microbial food chain consists of bacterioplankton and mycoplankton (mostly thraustochytrids), the latter having drawn less attention. In a rather simplistic formulation, bacterioplankton is regarded as the harvester of autochthonous (marine) dissolved organic material exuded from phytoplankton, while mycoplankton is seen to be the scavenger of refractory dissolved organic material which is often allochthonous (riverine). This study presents a case study report on the abundance of thraustochytrids (mycoplankton) and bacterioplankton in the discharge area of River Shimanto, Northwestern Pacific, Japan. Thraustochytrid cells were stained with acriflavine and counted directly by epifluorescence microscopy. Thraustochytrids were found in the surface water at a density of 0.9 to 3.6 x 10 3 cells l -1 , with an overall average of 2.5 x 10 3 cells l -1 . Distribution of thraustochytrids was correlated to (or controlled by) river discharge as depicted by lowered salinity. On the other hand, abundance of bacterioplankton, 1.2 to 1.4 x 10 9 cells l -1 , showed no significant correlation with river discharge. Thraustochytrids may grow on terrestrial organic matter in the riverine input, which is often refractory to degradation, and play a role in enhancing carbon cycling in the estuarine and coastal areas.
Blumeria graminis f. sp. hordei virulence frequency and the powdery mildew incidence on spring barley in the Wielkopolska province

Powdery mildew caused by fungi Blumeria graminis f. sp. hordei is one of the most common barley diseases in Polish me- teorological conditions. The powdery mildew fungus is made up of different races and forms that are highly specialized. Barley cul- tivars might be resistant to a certain race of the mildew fungus, but susceptible to another race. Development of the disease is rapid in temperatures from 12 to 20°C, and in humid weather. The aim of the two-year experiment was to assess B. graminis f. sp. hordei virulence frequency and powdery mildew occurrence on five spring barley cultivars. Virulence frequency of the pathogen depended on place and term of exposition. The occurrence of powdery mildew on spring barley cultivars depended on virulence frequency of the pathogen and weather conditions.
Generalist predators in organically and conventionally managed grass-clover fields: implications for conservation biological control

Organically managed agroecosystems rely in part on biological control to prevent pest outbreaks. Generalist predators (Araneae, Carabidae and Staphylinidae) are a major component of the natural enemy community in agroecosystems. We assessed the seasonal dynamics of major generalist predator groups in conventionally and organically managed grass–clover fields that primarily differed by fertilisation strategy. We further established an experiment, manipulating the abundant wolf spider genus Pardosa, to identify the importance of these predators for herbivore suppression in the same system and growth period. Organic management significantly enhanced ground-active spider numbers early and late in the growing season, with potentially positive effects of plant cover and non-pest decomposer prey. However, enhancing spider numbers in the field experiment did not improve biological control in organically managed grass–clover fields. Similar to the survey results, reduced densities of Pardosa had no short-term effect on any prey taxa; however, spider guild structure changed in response to Pardosa manipulation. In the presence of fewer Pardosa, other ground-running spiders were more abundant; therefore, their impact on herbivore numbers may have been elevated, possibly cancelling increases in herbivore numbers because of reduced predation by Pardosa. Our results indicate positive effects of organic farming on spider activity density; however, our survey data and the predator manipulation experiment failed to find evidence that ground-running spiders reduced herbivore numbers. We therefore suggest that a positive impact of organic fertilisers on wolf spiders in grass–clover agroecosystems may not necessarily improve biological control when compared with conventional farming.
NF‐κB activation upregulates fibroblast growth factor 8 expression in prostate cancer cells

Fibroblast growth factor 8 (FGF8) is over‐expressed in prostate cancer (CaP) correlating with high‐grade disease and reduced survival. The role of acetylation in transcriptional regulation of FGF8 was investigated using the histone deacetylase (HDAC) inhibitor Trichostatin A (TSA).
The synthesis and anti‐acetylcholinesterase activities of (+)‐physostigmine and (+)‐physovenine *

(+)‐Physostigmine and (+)‐physovenine have been synthesized. The anti‐acetylcholinesterase activities of these two bases, which have been investigated in vitro using erythrocyte acetylcholinesterase, have been found to be much lower than the corresponding activities of the alkaloids (‐)‐physostigmine and (‐)‐physovenine. Possible reasons for these activity differences are discussed.
Expression of CCAAT enhancer binding protein-alpha (C/EBP alpha) in the rat ovary: implications for follicular development and ovulation.

The development of follicles from the antral to the preovulatory stage in the mammalian ovary involves both proliferation and differentiation of cells. These processes are coordinated by endocrine, paracrine, and autocrine factors in a time- and cell-specific pattern. Each stage of development is characterized by expression of specific genes the products of which are involved in different cellular processes, e.g., signal transduction (cAMP-dependent protein kinases), steroidogenesis (cytochrome P450 enzymes). At the nuclear level, the signaling pathway from external stimuli converges to modify the mechanisms of transcription factors. One such factor, CCAAT enhancer binding protein-alpha (C/EBPalpha), participates in differentiation processes of several organs, e.g., liver, adipose tissue, and gut. We have previously demonstrated that C/EBPalpha is expressed in rat ovarian follicles in a cell-, time-, and hormone-specific manner. This increase in granulosa cells was concomitant with the more differentiated phenotype. The aim of the present study was to explore the function of C/EBPalpha in the rat ovary. To achieve this, the expression of C/EBPalpha in follicular cells was attenuated in vivo by the local administration of antisense oligonucleotides (AS) into the ovarian bursa, i.e., the sac-like structure surrounding the ovary of immature rats. This administration resulted in an impaired response to subsequent injections of exogenous gonadotropins (PMSG, hCG) with an attenuated expression of C/EBPalpha protein and finally a decreased ovulation rate. Furthermore, the morphology of the AS-treated ovary was altered with large, oocyte-containing follicles at a time when ovaries exposed to sense (S) oligonucleotides demonstrated newly formed corpora lutea. AS also affected the expression of the proto-oncogene c-myc, which was elevated by this treatment. The administration of S was without effects. Thus, C/EBPalpha seems to be a necessary factor for follicular development in the rat ovary.
Rapid Estimation of Heat Accumulation from Maximum and Minimum Temperatures

A method is presented for estimating heat accumulation by using daily maximum and minimum temperatures and assuming the sine curve as an approximation of the diurnal temperature curve. A table is given for estimating heat accumulation for a given day, and a computer program is described for accumulating heat units over a 1—year period. The technique permits the use of an upper as well as a lower threshold and has a precision in the order of ± 5%.
Feltleaf Willow‐Snowshoe Hare Interactions: Plant Carbon/Nutrient Balance and Floodplain Succession

This experiment was designed to determine if winter browsing by snowshoe hares is a potentially important control over primary succession on floodplains of Alaskan rivers. In a 2 x 2 x 2 factorial experiment, I increased nutrient availability by NPK fertilization, decreased light intensity with shade cloth, and clipped winter-dormant feltleaf willow (Salix alaxensis) to simulate severe snowshoe hare browsing. After 3 yr of fertil- ization, 1 yr of clipping, and 1 yr of shading, the 240 experimental plants were measured for height growth and current-year twig production, and their winter-dormant twigs were bioassayed for palatability to snowshoe hares and analyzed chemically. With one exception, both fertilization and shading increased the palatability of twigs in comparison to twigs of control plants. Moreover, shade had a comparatively strong effect on the palatability of stump sprouts of clipped plants. Both fertilization and shade generally reduced the concentrations of soluble carbohydrate and phenolics in winter-dormant twigs of unclipped plants. However, only shade significantly affected the concentrations of soluble carbohydrate and phenolics in twigs of clipped plants. These results indicate (1) that the palatability and chemical defenses of winter-dormant S. alaxensis are sensitive to plant carbon/nutrient balance and (2) that the effects of soil fertility and light intensity on plant carbon/nutrient balance vary with respect to browsing history. Although severe clipping increased production of current-year twig biomass it greatly reduced plant height. These results imply that severe browsing of winter-dormant willow growing on flood- plains of interior Alaskan rivers, such as occurs at some points during snowshoe hare cycles, may result in reduced height growth of willow. I suggest that such a reduction in height growth may result (1) in shading of floodplain willow by alder and (2) in a shade-caused increase in the palatability of willow stump sprouts. Furthermore, I suggest that this increase in the palatability of shaded willow may be a partial control over the shift from willow dominance to alder dominance that occurs in the late shrub stage of primary succession on floodplains of interior Alaskan rivers.
Genetic evidence for an undescribed species previously considered as Sillago sihama from the northern Red Sea

Abstract The augmentation of traditional taxonomy by the addition of genetic methods, particularly DNA analysis, has revealed that many species that appeared identical morphologically throughout their distribution range are actually divided into two or more genetically distinct species. The whiting, Sillago sihama, is a fish that was considered to be of a wide Indo-Pacific distribution. Not long ago, what was considered to be S. sihama invaded the Mediterranean from the Red Sea via the Suez Canal. In our study we sequenced a 655-bp region of the mitochondrial cytochrome c oxidase subunit I gene (COI) from Hong Kong, southern Red Sea and Mediterranean populations of Sillago. We discovered that the first two (HK and southern Red Sea) are genetically similar while the sequencing of the Mediterranean population shows a significant divergence, confirming the existence of two distinct species. We further sequenced a segment of 178 bp (of the 655 bp) from a formaldehyde-fixed specimen from the northern Red Sea (Gulf of Suez) and found it to be identical to that of the Mediterranean population. We were thus able to confirm that the northern Red Sea population is the source for the invading population. The mitochondrial control region (D-loop) analysis of the Mediterranean population revealed that all 38 specimens have a single mitochondrial haplotype.
Efficiency of Orius minutus for control of Tetranychus urticae on selected potato cultivars

The influence of host plant traits of five potato cultivars: Savalan, Agria, Morene, Kondor and Diamant on the population density of two-spotted spider mite (TSM) Tetranychus urticae Koch, and ovipositional preference, predation rate and life history parameters of its predator Orius minutus L. were studied under laboratory conditions (23 ± 1°C, 50 ± 5% RH and 14L:10D). The density of TSM adults on Savalan, Agria and Morene was significantly lower than on Kondor and Diamant. In both no-choice and free-choice experiments, the females of the predator laid more eggs on TSM-infested leaves of Savalan (6 eggs/leaf and 24 eggs/plant) than on Agria, Morene, Kondor and Diamant. In predation rate experiments, the females of O. minutus consumed more TSM on the infested leaves of Savalan (32 TSM/predator during 48 hours) than on Agria, Morene, Kondor and Diamant. In performance experiments, the predator nymphs developed faster when reared on TSM-infested leaves of Savalan (16 days) than on Kondor and Diamant. Moreover, the survival rate, from egg to adult, of O. minutus on TSM-infested leaves of Savalan (52.8%) was better than on Kondor and Diamant. The fecundity of O. minutus reared on TSM-infested leaves of Savalan (11.7 eggs/female) was significantly higher than on Agria, Morene, Kondor and Diamant. The intrinsic rate of natural increase and the population growth rate of O. minutus were highest when reared on TSM-infested leaves of Savalan (rm = 0.089 day−1 and λ = 1.094 day−1). These results suggest that using Savalan cultivar integrated with O. minutus could result in improved efficacy of this predator and lead to effective and more sustainable management of T. urticae in potato fields.
The role of DNA polymerase eta in determining cellular responses to chemo-radiation treatment

DNA polymerase η (pol η), a crucial component of the cellular translesion synthesis pathway, allows cells to bypass and thereby temporarily tolerate DNA damage. Inherited deficiency of pol η, as reported in the variant form of xeroderma pigmentosum, predisposes to UV light-induced skin cancers. To date, pol η is the only DNA polymerase shown to exhibit a causal link to the formation of cancers in humans. However, the role of pol η in the cellular response to forms of DNA damage other than UV-induced lesions is largely unknown. In the first part of this thesis, it is shown that cells deficient in pol η are resistant to ionising radiation. Deficiency in the polymerase was associated with accumulation of cells in S phase of the cell cycle. Cells deficient in pol η demonstrated increased homologous recombination-directed repair of DNA double-strand breaks created by ionising radiation, and depletion of the homologous recombination protein X-ray repair cross-complementing protein 3 (XRCC3), abrogated the radioresistance observed in pol η-deficient cells compared to pol η-complemented cells. These findings suggest that homologous recombination mediates S phase-dependent radioresistance associated with pol η-deficiency. In the second part of this thesis, it is shown that pol η-deficient cells have increased sensitivity to the chemotherapeutic compound, oxaliplatin, compared to pol η-deficient expressing cells, but not to the drug 5-fluorouracil that is usually administered in combination with oxaliplatin in the clinical setting. Despite the importance of pol η for cellular survival following exposure to oxaliplatin, the drug did not upregulate the enzyme after either short-term or long-term exposure. Inhibition of pol η activity by siRNA-mediated knockdown of the protein sensitised cells to oxaliplatin treatment, and partially reversed acquired resistance in oxaliplatin-resistant tumour cell lines. These data suggest that pol η is an interesting target whose function can potentially be interfered with to optimise oxaliplatin-based chemotherapy. In the third part of this thesis, clinical samples obtained from oesophageal cancer patients before and after treatment with oxaliplatin-containing chemotherapy were analysed for POLH mRNA levels encoding pol η protein. Malignant tissue specimens obtained before treatment demonstrated a significantly higher level of POLH mRNA than matched normal oesophageal tissue samples. Contrary to the preclinical data, high POLH mRNA expression before therapy was shown to correlate with increased overall and disease-free survival of the patient cohort in the clinical trial. Additionally, patients with high POLH mRNA-expressing cancers had better therapeutic responses (measured by PET-CT) to oxaliplatin-based treatment than those with low levels. These data suggest that POLH mRNA expression should be tested as a biomarker to predict survival and therapeutic responses in oesophageal cancer patients treated with oxaliplatin-containing chemotherapy.
The AMP‐activated protein kinase activator AICAR does not induce GLUT4 translocation to transverse tubules but stimulates glucose uptake and p38 mitogen‐activated protein kinases α and β in skeletal muscle

The AMP‐activated protein kinase (AMPK) pathway participates in the metabolic effects of contraction on muscle glucose uptake. We have shown that contraction increases both GLUT4 translocation to the cell surface and p38 mitogen‐activated protein kinase (p38 MAPK) activity. The latter pathway may be involved in the activation of GLUT4. Here we investigated whether the AMPK activator AICAR increases glucose uptake by inducing translocation of GLUT4 and/or by activating the p38 MAPK pathway. AICAR infusion into glucose‐clamped rats increased muscle glucose uptake and GLUT4 translocation from an intracellular fraction to the plasma membrane but not to T‐tubules. AICAR also caused recruitment of the transferrin receptor to the plasma membrane and increased [125I]‐transferrin uptake in isolated muscle. AICAR treatment in vivo or in vitro activated both p38 MAPKα and β (1.6‐ to 2.8‐fold) in EDL muscles with a time course identical to that of stimulation of AMPK and glucose transport. The p38 MAPK inhibitor SB203580 abrogated the stimulatory effect of AICAR on glucose uptake. These results suggest that AICAR increases muscle glucose uptake by two mechanisms: 1) inducing selective recruitment of GLUT4 to the plasma membrane, and 2) activating p38 MAPKα and β, which may be involved in the activation of GLUT4—Lemieux, K. , Konrad, D. , Klip, A. , Marette, A. The AMP‐activated protein kinase activator AICAR does not induce GLUT4 translocation to transverse tubules but stimulates glucose uptake and p38 mitogen‐activated protein kinases α and β in skeletal muscle. —Lemieux, K. , Konrad, D. , Klip, A. , Marette, A. The AMP‐activated protein kinase activator AICAR does not induce GLUT4 translocation to transverse tubules but stimulates glucose uptake via p38 mitogen‐activated protein kinases α and β in skeletal muscle. FASEB J. 17, 1658–1665 (2003)
Plant community composition and disturbance in Caspian Fagus orientalis forests: which are the main driving factors?

The oriental beech forests along the southern Caspian Sea shores of Iran are characterized by high biodiversity and high ecological value. However, there is little information concerning factors governing community composition and the presence and abundance of invasive plants. In the present study we aimed to evaluate the main drivers of community composition, diversity, and establishment of invasive plants in disturbed and undisturbed Fagus orientalis communities. We sampled 104 vegetation releves in undisturbed and disturbed sites of the "Kheiroud Investigation Forest" in northern Iran and collected data on a large number of environmental variables concerning soil properties, light conditions, and topography. Data analysis consisted of a forward selection of significant explanatory variables followed by partial CCA analyses. Additionally, we carried out indicator species analysis of groups of releves affected by different disturbance types and analyzed effects of disturbance on species richness, diversity, and evenness using general linear models. CCA results showed that disturbance, soil properties, light conditions and elevation explained 22.6% of the total variation in floristic composition. Gap and gap + grazing were the most important disturbance types affecting community composition. Disturbance had significant but rather weak effects on species richness, evenness, and the Shannon index. The most obvious effect of disturbance was on species composition, as revealed by significant groups of indicator species for different disturbance types. Most of the indicator species in grazed sites were unpalatable, poisonous, and creeping species, which are avoided by cattle. Grazing led to decreased abundance of indicator species and species characteristic of old-growth Fagus forests. The most intensive disturbance type "harvesting + gap + grazing" was associated with invasion by native vascular plant species not typically found in beech forests (apophytes).
Distribution of Birds in the Jeju Seonheul Gotjawal Region, a Survey Site of Long-term Ecological Study

The study on the avifauna of the Seonheul Gotjawal region of Jeju-do (Is.), a survey site of long-term ecological study, was conducted between February of 2011 and January of 2012. A total of 54 species and 1,039 individuals of birds were observed, with 30 species and 164 individuals observed during spring, 31 species and 174 individuals during summer, 30 species and 206 individuals during fall and 28 species and 868 individuals during winter. In terms of dominant species, Mandarin Duck (Aix galericulata) was the most dominant at 500 individuals (48.12%), followed by Rook (Corvus frugilegus) at 250 individuals (24.06%), Black-billed Magpie (Pica pica) at 36 individuals (3.46%), Barn Swallow (Hirundo rustica) at 34 individuals (3.27%) and Great Tit (Parus major) and Japanese White-eye (Zosterops japonicus) at 26 individuals (2.50%) each. The overall species diversity was 1.95, with the value 2.69 during spring, 2.87 during summer, 2.81 during fall and 1.29 during winter. The species diversity was low during the winter, because Mandarin Duck (Aix galericulata) and Rook (Corvus frugilegus) were observed at a relative high level when compared to other species, at 500 individuals and 250 individuals respectively. Government protected species included 8 natural monument species, such as Mandarin Duck (Aix galericulata), Common Kestrel (Falco tinnunculus), Peregrine Falcon (Falco peregrinus), Cinereous Vulture (Aegypius monachus), Eurasian Sparrowhawk (Accipiter nisus), Northern Goshawk (Accipiter gentilis), Lesser Cuckoo (Cuculus poliocephalus) and Fairy Pitta (Pitta nympha), and 8 endangered species of Japanese Night Heron (Gorsachius goisagi), Peregrine Falcon (Falco peregrinus), Cinereous Vulture (Aegypius monachus), Crested Honey Buzzard (Pernis ptilorhychus), Northern Goshawk (Accipiter gentilis), Eurasian Sparrowhawk (Accipiter nisus), Fairy Pitta (Pitta nympha) and Black Paraside Flycatcher (Terpsiphone atrocaudata). Since subtropical birds, such as Japanese Night Heron (Gorsachius goisagi), White-bellied Green Pigeon (Treron sieboldii) and Chestnut-winged Cuckoo (Clamator coromandus) were observed during the study, there is a need for a continuous monitoring of their migratory pattern and breeding.
Lactobacillus Plantarum: Characterization of the Species and Application in Food Production

Lactobacillus plantarum is a heterofermentative microaerophilic Gram-positive microorganism, with rod morphology, occurring singly or grouped in short chains. This species has well accepted GRAS status and numerous strains of L. plantarum have been isolated from different ecological niches including meat, fish, fruits, vegetables, milk, and cereal products. L. plantarum has been used as a starter culture in various food fermentation processes contributing to the organoleptic properties, flavour, and texture. Due to production of lactic acid and other antimicrobial compounds, L. plantarum also contributes to the safety of the final products. In this article, we overview the history of description of L. plantarum and biochemical properties, methods for identification and applications in food production.