Miracle-dz/UniFAR-FTUs huggingface dataset:
The function of E2F6 in the Polycomb complex

The E2F family of transcription factors are known cell cycle regulators that function at the G1/S transition. Unlike other E2Fs, E2F6 does not activate transcription and is not regulated by pocket protein binding. Instead, this protein appears to repress transcription through the recruitment of the Polycomb Group (PcG) complex. This complex is responsible for the maintenance of Hox gene expression patterns during development and thus ensures the correct anterior-posterior segmentation of the embryo. Genetic ablation of PcG proteins leads to posterior transformations of the axial skeleton as well as other developmental abnormalities such as hematopoietic, cerebellar and smooth muscle defects. The PcG complex has been implicated in cell cycle control since several of its members, including the oncoprotein Bmi 1, appear to repress the transcription of p1 6INK4 A and pI 9 ARF. In order to determine the biological function of E2F6, we have generated and characterized E2f6'mice and mouse embryonic fibroblasts (MEFs). The mutant mice are viable and survive into adulthood with similar lifespan as their littermate controls. Furthermore, the E2f6 null MEFs are indistinguishable from wild-type MEFs in asynchronous proliferation, cell cycle re-entry from quiescence, senescence and E2F target genes expression levels. These findings suggest that E2F6 does not play a major role in cell cycle control or that its function can be compensated by the action of other factors. In fact, preliminary results from combined loss of E2f6 and Bmil suggest that E2F6 may take part in the Bmi 1-mediated control of the cell cycle. Furthermore, we found that the loss of E2F6 results in posterior axial skeleton transformations that are reminiscent of the Bmil-deficient mice defects. The study of the E2f6;Bmil compound mutant mice revealed a dosage-dependent synergism between E2F6 and Bmi 1. These results indicate that E2F6 participates in segmentation during murine development. As a whole, our work has provided proof that E2F6 is a bonafide Polycomb Group protein and, at the same time, has opened the field to a number of interesting questions. Thesis supervisor: Jacqueline A. Lees Title: Professor of Biology
Species composition and life forms of epiphytic bryophytes in old-growth and secondary forests in Mt. Ailao, SW China.

Epiphytes constitute it Major component of tropical forests. However, human caused disturbances can alter the structure and diversity of epiphyte community. We Surveyed and compared the diversity and distribution of epiphytic bryophytes on host free trunks within 0.2m above ground in two old-growth and three secondary forests in Xujiaba, Mt. Ailao, SW China, in order to see whether disturbed forests have lower diversity and to identify environmental variables that can influence epiphyte distribution. We recorded 176 species in total 38 families. Meteoriaceae was the dominant families ill terms of species richness (24 species). Species richness did not differ between old-growth and secondary forests, however, beta diversity indexes were severely reduced in secondary forests. The life forms differed ill preferences to some forest types: fail (moss) and rough mat (moss) preferred old-growth forests, while turf (moss) was, commoner in secondary forests. The degree Of abundance of CWD (Coarse Woody Debris), atmospheric relative humidity, the roughness and water-holding capacity of host bark were the four environmental variables found to be significantly influencing the distribution of life forms in epiphytic bryophytes in the study area. Although secondary forests were similar to old-growth forests in epiphytic diversity, the absence of particular bark features in trees in secondary forest limited the growth of certain life form groups. Besides retaining CWD ill old-growth forest, forest management should encourage the protection and rehabilitation of trees with special bark features to enhance the diversity of epiphytic bryophytes.
Prevalence of Thermophilic Campylobacter spp. in Turkey Meat and Antibiotic Resistance of C. jejuni Isolates

The objectives of this study were to determine the prevalence of thermophilic Campylobacter spp. in turkey meat samples by conventional cultivation method, to confirm the Campylobacter jejuni, Campylobacter coli, and Campylobacter lari isolates by the detection of specific genes with polymerase chain reaction (PCR), and to find out the antimicrobial susceptibility of the C. jejuni isolates using disc diffusion method. In the present study, thermophilic Campylobacter spp. were in 123 of 270 (45.6%) turkey meat samples. Among the isolates, 109 (40.4%) were C. jejuni and 11 (4.1%) were C. coli as identified by conventional cultivation technique and verified by PCR assay. Prevalence of thermophilic Campylobacter spp. was higher in warm months than cold months. In the study, 104 (95.4%) of the C. jejuni isolates were found resistant to azithromycin, while 103 (94.5%) to erythromycin, 40 (36.7%) to tetracycline, 19 (17.4%) to ciprofloxacin and 10 (9.2%) to nalidixic acid. Practical Applications Thermophilic Campylobacter is one of the major causes of human gastroenteritis worldwide and the present study emphasizes the importance of turkey meat as an important thermophilic Campylobacter spp. source from a public health point of view. Although antimicrobial therapy is suggested for human campylobacteriosis, an increase in antibiotic resistance of Campylobacter jejuni, isolates from human cases and animals were reported. In the present study, prevalence of thermophilic Campylobacter spp. in turkey meat and the antibiotic resistance profiles of the C. jejuni isolates were reported.
Ectomycorrhiza of Pinus radiata (D. Don 1836) in New Zealand — an above- and below- ground assessment

Ectomycorrhizal (ECM) species identity, richness and diversity of the exotic plantation species Pinus radiata were investigated in a nursery and stands of different ages (2, 8, 15 and 26 years of age) in the North Island of New Zealand over the course of two years. ECM species were identified by morphology and molecular (restriction fragment length polymorphism (RFLP) and DNA sequencing) analysis. Eighteen ECM species were observed above-ground, 19 ECM species below-ground. Inocybe sindonia, Lactarius rufus, Pseudotomentella sp. , Pseudotomentella tristis, Rhizopogon pseudoroseolus, R. luteorubescens, Tomentella sp. and Wilcoxina mikolae were recorded as ECM associates of P. radiata in New Zealand for the first time. Species richness and diversity of ECM fungi associated with P. radiata in New Zealand were low compared to native forests in the Northern Hemisphere but comparable to other exotic plantations in the Southern Hemisphere.
The Specificity of a Weak γδ TCR Interaction Can Be Modulated by the Glycosylation of the Ligand

The γδ T cell clone LBK5 recognizes the MHC molecule IEk. Here, we demonstrate that the affinity of this interaction is weaker than those typically reported for αβ TCRs that recognize peptide/MHC complexes. Consistent with our previous finding that peptide bound to the IE molecule does not confer specificity, we show that the entire epitope for LBK5 is contained within the polypeptide chains of the molecule, centered around the polymorphic residues 67 and 70 of the IE β-chain. However, LBK5 recognition is profoundly influenced by the N-linked glycosylation at residue 82 of the IE α-chain. Since infected, stressed, or transformed cells often change the posttranslational modifications of their surface glycoproteins, this finding suggests a new way in which γδ T cell Ag recognition can be regulated.
Critical Role of Tumor Necrosis Factor-α and NF-κB in Interferon-γ-induced CD40 Expression in Microglia/Macrophages*

CD40 is a member of the tumor necrosis factor (TNF) receptor superfamily. CD40 expression on antigen-presenting cells (including macrophages and microglia) is crucial for T-cell activation. Aberrant expression of CD40 has been associated with autoimmune inflammatory diseases such as multiple sclerosis and rheumatoid arthritis. We have recently shown that the cytokine interferon (IFN)-γ is the most potent inducer of CD40 expression in macrophages and microglia, and this induction is mediated by the IFN-γ-activated transcription factor STAT-1α and constitutively expressed PU.1 and/or Spi-B. In this study, we have discovered that a major component of IFN-γ-induced CD40 expression involves the endogenous production of the cytokine TNF-α. The inclusion of anti-TNF-α-neutralizing antibody significantly inhibits IFN-γ-induced CD40 mRNA and CD40 promoter activity. IFN-γ-induced CD40 protein expression is attenuated in TNF-α-deficient microglia and can be restored with exogenous TNF-α. Site-directed mutagenesis studies demonstrate that three of the four NF-κB elements in the CD40 promoter are required for IFN-γ-induced CD40 promoter activity. IFN-γ treatment leads to the activation of NF-κB in a time-dependent manner, which is inhibited in the presence of anti-TNF-α-neutralizing antibody. These results indicate that IFN-γ-induced TNF-α production and subsequent NF-κB activation are integral parts of the mechanism of IFN-γ-induced CD40 expression.
COMPARISON OF FOUR DNA EXTRACTION METHODS FROM INVASIVE FRESHWATER BIVALVE SPECIES (MOLLUSCA: BIVALVIA) IN ROMANIAN FAUNA

In this paper we propose an evaluation of four DNA extraction methods in terms of DNA quantity, quality and success of the subsequent PCR amplifications of nuclear and mitochondrial loci. Individuals from the following freshwater invasive mussels in Romania were used to asses the efficiency of the DNA extraction methods: Dreissena polymorpha, Dreissena bugensis, Sinanodonta woodiana and Corbicula fluminea. While the manual method provided the highest amount of DNA, the subsequent PCR manipulation showed variable success rate, possible because of the phenol contamination of the samples. The commercial kits assayed performed equally well with the subsequent PCR manipulations of the isolated DNA. Resume. On a compare quatre methodes pour l'extraction de l'ADN qui provenait des especes suivantes, envahissantes en Roumanie: Dreissena polymorpha, Dreissena bugensis, Sinanodonta woodiana et Corbicula fluminea. Les methodes commerciales essayees ont fourni de l'ADN en concentrations variables mais d'une qualite suffisante pour l'amplification par PCR. La methode manuelle (protocole de Sokolov) a fourni une plus grande quantite d'ADN, mais celui-ci etait contamine par du phenol, ce qui a rendu l'amplification par PCR difficile a realiser.
Does money in adulthood affect adult outcomes

This report examines the evidence on whether money in adulthood has a causal impact on wider adult outcomes. Individuals with less income tend to do worse on a range of indicators than those with more, including measures of physical health and subjective well-being. Would more money in itself make a difference? Or are these differences driven by other, associated factors (education, more satisfying work), or by long-term factors too well-established to shift with a boost to income during adulthood?
Histopathological assessment of wheat seedling tissues infected by Fusarium pseudograminearum

Histopathological assessment of infection by the crown rot pathogen Fusarium pseudograminearum in wheat seedling tissues was performed using fluorescence microscopy. The coleoptiles and leaf sheaths of four host cultivars of differing susceptibility were examined. Leaf sheaths were most frequently penetrated via stomata, indicated by initial lesions forming at the guard cells. Internally, cell wall penetration was facilitated by penetration structures which appeared as hyphal swellings or septate foot-shaped appressoria. Colonization of leaf sheaths resulted in the re-emergence of hyphae from stomata on both surfaces of the sheath. These hyphae are hypothesized to have two major roles; first as exploratory hyphae for colonization of new tissues, and secondly as sites of profuse conidial production. The formation of conidia on the leaf sheath surface was only recorded on the most susceptible bread wheat genotype. No other major differences in host‐pathogen interactions were observed among these cultivars. Almost all cell types in the leaf sheath tissues were extensively colonized, except for the vascular bundles and silica cells. This investigation provides the first comprehensive assessment of F. pseudograminearum infection structures and growth patterns during the infection of wheat seedlings.
Cholinergic receptor subtypes functional regulation in spinal cord injured monoplegic rats

S/ SCIENTIFIC PRESENTATIONS 1. Chinthu Romeo, Nandhu M S and C.S. Paulose. Down regulation of Acetylcholine receptor in the spinal cord of spinal cord injured rats: Treatment with Neurotransmitters combination and Bone marrow cells. National conference on Biotecnology for human development, Vellore Institute of Technology, Vellore. November, (2009). 2. Chinthu Romeo, Anitha Malat, Jayanraynan. S, Korah P Kuruvilla, Smijin Soman and C S Paulose. Enhanced Malate dehydrogenase, Glutamate dehydrogenase, Arginase and Cholesterol in herbal formulation treated rats: A molecular study. Modern methods in herbal drug development, Bharat Matha College, Cochin. July, (2010). 3. Chinthu Romeo, Anju T R and C S Paulose. Down regulation of muscarinic m1 receptor in the cerebellum of spinal cord injured rats: bone marrow cells and neurotransmitters supplementation. Indian Ageing congress held at Banaras Hindu University, Varanasi, India. November, 2010. 4. Roshni Thomas, Anju TR, Chinthu Romeo and C S Paulose. Alterations in cortical cholinergic functions and Bax expression in mediating long term cognitive impairment in neonatal rats exposed to hypoxia. Annual meeting of society for Biotechnologists, India and National symposium on innovations in Biotechnology2010, SRM University, Chennai, September, (2010). 5. Smijin soman, Chinthu Romeo, Anitha Malat. Hippocampal oxidative damage in pilocarpine induced temporal lobe epilepsy: Neuroprotective effects of Withania somnifera and Withaniolide-A. International Academy of Neuroscience, Banaras Hindu University, November, (2010).
Revisión del MSLQ : veinticinco años de evaluación motivacional

This study aims at presenting a revision of the development and subsequent adaptations and applications of the Motivated Strategies for Learning Questionnaire (MSLQ). And the main areas of expertise that have been reached in the field of motivation and self-regulation since their beginnings. The development of the MSLQ took 10 years of work and it is considered Paul Pintrich's main legacy. The MSLQ was created from a motivational and self-regulational sociocognitive framework. The carried out revision evidences the validity and interest for the MSLQ 25 years after it first appeared as well as the need for its revision after the occurred social changes and the conducted statistical analysis.
Gonadal Development and Gametogenic Cycle of the Equilateral Venus, Gomphina veneriformis (Bivalvia: Veneridae)

Gonadal development and gametogenic cycle of the equilateral venus, Gomphina collected in the coastal waters of Gangneung, Gangwon-do, Korea were investigated by means of histological method from March 2001 to February 2002. Sex of the clam was dioecious. The gonads are composed of a number of gametogenic follicles. The gonad index (GI) was reached the maximum in June (3.87), and the minimum in August (0.66). The condition index (CI) was reached the maximum in May (0.051), and the minimum in January (0.028). The gametogenic cycle of the clam could be divided into five stages inactive (September to November), early active (November to March), late active (April to May), ripe (June and July) and spent/degenerative stage (July to August). Sex ratio (male/female) was 1:0.9.
Effects of melatonin and cortisol on vitellogenin and estrogen receptor α mRNA expression in 17β-estradiol stimulated Atlantic salmon (Salmo salar) hepatocytes

Knowledge regarding the influence of external and internal factors on teleost fecundity may contribute to increased production and efficiency in aquaculture. Teleost plasma cortisol levels may be elevated in response to stress, potentially affecting reproduction through a negative impact on vitellogenesis. Melatonin (MEL), on the other hand, is shown to have protective effects in organisms, and large amounts of MEL has been observed in the gastrointestinal tract (GIT) in various species, hence finding its way to the liver. The subject of this thesis was to document the MEL concentration in Atlantic salmon (Salmo salar) vena portae, and compare this to MEL in the circulating blood. Further, the effect of MEL and cortisol on 17beta-estradiol (E2) stimulated vitellogenin (Vtg) mRNA expression in hepatocytes from Atlantic salmon, was investigated in vitro. The presence of MEL in vena portae was documented, seemingly independent of light conditions and pineal MEL levels. A decrease in Vtg mRNA expression was observed in hepatocytes exposed to cortisol after preincubation with E2 and MEL. This effect was not seen in hepatocytes exposed to cortisol after preincubation with E2 alone.
Effect of chicken genotype on growth performance and feed consumption in the development of broiler lines

This experiment was conducted to assess the effect of chicken genotype on the growth performance, feed intake and feed efficiency of the progenies resulting from pure, straight and reciprocal cross of Giriraja (Gr) and Alpha chickens. Data obtained on body weight, body length, breast girth, keel length, feed intake and feed efficiency were analyzed using general linear models analysis of variance. Generally, all growth traits and feed consumption characteristics were significantly affected (P < 0.05) by chicken genotype. Growth traits and feed intake increased as birds advanced in age. Giriraja X Giriraja purebred chickens had the highest body weight, breast girth, feed intake and feed conversion efficiency through out the experimental period. However, the progenies resulting from the reciprocal crosses of Alpha X Gr had significant higher body weight and keel. Also, the feed conversion efficiency of the reciprocal crosses were better than the dihybrid cross progenies. The results therefore suggest that the superiority exhibited by the Giriraja could be utilized to improve the growth performance of the indigenous chicken thereby speed up desirable progress in the improvement of the indigenous broiler line. Key words: Chicken, Crossbred, Feed consumption, Genotype, Growth trait, Purebred
The effect of nitrogen fertilization and stage of plant development on the mass and quality of sweet basil leaves [Ocimum basilicum L.]

the effect of nitrogen fertilization in various rates and the stage of plant development (beginning and full bloom) on the mass of leaves of three sweet basil cultivars (‘Dark Opal’, ‘Mittelgross’ and ‘Wala’) as well as the content of total N, chloroplast pigments and essential oil in leaves were estimated. it was found that nitrogen fertilization significantly increased the mass of leaves, the chloroplast pigment content and the yield of essential oil whereas the effect of the stage of plant development on above parameters depended on the cultivar.
A data-driven method for selecting candidate reference sites for stream bioassessment programs using generalised dissimilarity models

Key issues with defining reference condition for stream bioassessment are (1) equivocal definitions of ‘minimally disturbed’ pressure criteria and wide-ranging approaches to site selection, (2) highly modified regions where near-pristine areas do not exist, leading to management decisions based on inconsistent and unquantified benchmarks and (3) costly field campaigns associated with ‘extensive spatial survey’ approaches. We used generalised dissimilarity modelling (GDM) to classify stream segments into ecotypes, and transparently and efficiently define candidate reference conditions for the Ecosystem Health Monitoring Program (EHMP) assessment area in south-eastern Queensland, a highly modified region with a complex biogeographic history. We modelled fish presence–absence data from 396 sites with GIS-based natural and anthropogenic predictors. Stream segments were classified into ecotypes using the GDM-transformed natural variables so that (1) reference-site selection adequately covered the β-diversity of the study area and (2) we could evaluate the validity of incorporating sites from neighbouring catchments outside of the EHMP assessment area. Relationships between selected anthropogenic variables (the river disturbance index and %stream connectivity) and fish assemblages were used to define pressure criteria and map candidate reference conditions. We conclude by describing a new framework that can be used to select indicator-specific reference sites by GDM and a stratified, probabilistic sampling design.
On Turkish Cerambyx Linnaeus, 1758 with zoogeogrephical remarks (Coleoptera: Cerambycidae: Cerambycinae).

Cerambyx (Coleoptera: Cerambycidae: Cerambycinae). ABSTRACT: All taxa of the genus Cerambyx Linnaeus, 1758 in Turkey and the whole world are evaluated. The genus is also discussed in detail. The main aim of this catalogic work is to clarify current status of the genus in Turkey. New faunistical data are given in the text. A key for Turkish Cerambyx species is also given in the text.
Bt rice: practical steps to sustainable use.

In 1996, maize, cotton, and potato farmers in the USA became the first farmers in the world to grow transgenic insect-resistant cultivars. These cultivars contain genes from the bacterium Bacillus thuringiensis (Bt) that encode insecticidal proteins known as delta-endotoxins. Delta-endotoxins have two properties that are essential for toxins used in transgenic crops: they are highly toxic to certain insect pests, and they are generally safe for human consumption (NRC 2000). Bt crops have been a large commercial success. In 1999, 11.7 million ha of Bt crops were grown by farmers in 10 countries, including Australia, Canada, China, South Africa, Spain, and the USA (James 1999). Many laboratories around the world have transformed rice with Bt genes and have evaluated their effectiveness under greenhouse conditions (e.g., Cheng et al 1998, Datta et al 1998, Maqbool et al 1998). No Bt rice varieties have yet been released to farmers, but field testing began at two sites in China in 1998 (Datta 1999, Ye et al 2000). The target pests for control by Bt rice are caterpillars, most importantly the yellow stem borer (YSB, Scirpophaga incertulas), the striped stem borer (SSB, Chilo suppressalis), and leaffolders such as Cnaphalocrocis medinalis. It has not been possible to produce rice with high resistance to these pests through conventional breeding, although short-duration semidwarf varieties are generally less damaged by stem borers than are traditional varieties (Khan et al 1991).
A new highly efficient beta-glucosidase from the novel species, Aspergillus saccharolyticus

Several process steps are used for production of cellulosic ethanol from biomass raw materials such as pre‐treatment, enzymatic hydrolysis, fermentation, and distillation. Use of streams within cellulosic ethanol production was explored for on‐site enzyme production as part of a biorefinery concept. In order to discover the most suitable fungal strain with efficient hydrolytic enzymes for lignocellulose conversion, a screening of 64 fungal isolates from environmental samples was carried out. These strains were examined in a plate assay for lignocellulolytic activities. Of the 64 isolates, 25 were selected for further enzyme activity studies using a stream derived from the bioethanol process. The filter cake that is left after hydrolysis and fermentation was the substrate chosen as the medium for enzyme production. Five of the 25 isolates were further selected for synergy studies with commercial enzymes, Celluclast 1.5L and Novozym 188. Finally, two strains, IBT25747 (Aspergillus niger) and AP (unidentified), were found as promising candidates for on‐site enzyme production where the filter cake was inoculated with the respective fungus and in combination with Celluclast 1.5L used for hydrolysis of pretreated biomass. A R T I C L E I N F O