Miracle-dz/UniFAR-FTUs huggingface dataset:
SCF SKP2B - AND KPC1-DEPENDENT DEGRADATION OF CYCLIN-DEPENDENT KINASE INHIBITOR KRP1 AND CELL CYCLE REGULATION IN ARABIDOPSIS THALIANA

In animals and fungi, cyclin-dependent kinase inhibitors play a key role in cell cycle regulation by inhibiting the activities of cyclin-dependent kinase/cyclin complexes. However, little is known about the role of this group of proteins in plant cell cycle regulation. To gain insight into the mechanisms by which the plant cell cycle is regulated, I studied the cyclin-dependent kinase inhibitor KRP1 in Arabidopsis. The role of KRP1 in pericycle activation during lateral root initiation and in cell cycle regulation and how ubiquitinmediated protein degradation regulates KRP1 protein turnover were investigated. My results show that KRP1 plays an important role in the regulation of pericycle activation during lateral root initiation. KRP1 interacts with the CDKA;1/CYCD2;1 complex in planta and functions in the G1-S transition of the cell cycle. KRP1 is an unstable protein in planta and its degradation depends on the 26S proteasome. Further, an SCF complex composed of CUL1 and SKP2b regulates KRP1 degradation. These results suggest that SCF targets KRP1 for degradation by the 26S proteasome to regulate the G1-S transition of the cell cycle. In addition to SCFmediated KRP1 degradation, KRP1 degradation is also regulated by the
Distribution patterns of the sublittoral epibenthic assemblages on a rocky shoal in the Ligurian Sea (NW Mediterranean)

Acquiring baseline data on highly diverse communities such as coralligenous ones is very valuable in order to determine possible shifts in communities and define strategies for their preservation. Distribution of sciaphilic epibenthic communities belonging to the `coralligene de la roche littorale´ was investigated at 30 photostations from 17 to 24 m depth on a rocky shoal off the island complex in the Gulf of La Spezia (Ligurian Sea, NW Mediterranean). Four communities displayed a sharp zonation: Paramuricea clavata characterised deeper, vertical surfaces, whereas on horizontal and medium inclination, sediment-covered substrata, Leptogorgia sarmentosa , together with Eunicella singularis and Eunicella verrucosa , characterised the upper stratum of the deeper community. Shallow vertical walls were characterised by a facies with sponges and zoantharians, whereas community dominated by large, massive colonies of Pentapora fascialis with a basal stratum of sciaphilic algal species patched with sediment on shallow rocky slopes of medium inclination. Bathymetric distribution of assemblages is influenced by high seawater turbidity (mean annual transparency: 11.9 ± 5.7 m at the western site, 6.2 ± 1.6 m at the eastern site), which induces a shift of the upper limit of distribution of these facies to unusually shallow depths. Quantitative data provide a baseline on the study site that will be useful to understand the influence of not only biotic and abiotic factors, but also mass-mortality events, particularly on these communities characterised by high resilience.
Characterisation of Potential Antimicrobial Targets in Bacillus spp. I. Aminotransferases and Methionine Regeneration in Bacillus subtilis

Abstract : The aminotransferases involved in the final step of methionine recycling from methylthioadenosine have been examined in the gram-positive bacterium Bacillits subtilis. Homogenates of this bacterium were able to convert ketomethiobutyrate to methionine, utilising leucine, isoleucine, valine, phenylalanine, tyrosine, and alanine as preferred amino donors. Unlike other organisms examined to date in this context, B. subtilis was found to contain no aspartate aminotransferase or tyrosine aminotransferase sequences with structural homology to subfamily Ia aminotransferases. Instead, in B. subtills, the six putative homologues of aspartate aminotransferase were found to be members of the If subfamily. Five of these six sequences were cloned and expressed, with only the ykrV gene product capable of producing methionine from ketomethiobutyrate. However, this enzyme only catalysed the reaction using glutamine as an amino donor. Two putative branched-chain amino acid aminotransferases from family III were also cloned and expressed, and both were found to produce methionine from ketomethiobutyrate using branched-chain and aromatic amino acids. Of these two enzymes, the ybgE gene product was the most active and had kinetic constants consistent with it being the enzyme responsible for the majority of methionine regeneration in this organism. The ybgE gene product could be inhibited uncompetitively by the aminooxy compound canaline, with a Ki of 48 muM. In addition, canaline inhibited the in vitro growth of B. subtilis in minimal medium with an IC50 of 37 muM and an MIC of 500 muM. Growth inhibition in nutrient broth was negligible.
Examining synergistic effects of TDZ and TIBA on adventitious shoot induction in Dianthus caryophyllus L. leaf explants.

The aim of the present investigation was to study the combined effect of cytokinin thidiazuron (TDZ) and auxin-transport inhibitor 2,3,5-triiodobenzoic acid (TIBA) on adventitious shoot induction in leaf explants of carnation (Dianthus caryophyllus) cultivar ‘Master’. In this study, various concentrations and combinations of TDZ and TIBA were used for induction of adventitious shoots in leaf explants. The explants showed adventitious shoot regeneration (12.33%) on modified Murashige and Skoog’s (MS) medium supplemented with 1.0 mg/l TDZ and 1.0 mg/l TIBA while highest frequency of shoot regeneration was observed on MS medium supplemented with 1.0 mg/l TDZ and 0.5 mg/l TIBA (18.33%). Increase in shoot number as well as shoot length was observed with progressive subculturing of shoots. Subculturing of adventitious shoots gave highest average number of shoots (10.22). Shoots were subsequently rooted on MS medium devoid of any phytohormones, supplemented with activated charcoal and rooted plantlets were successfully acclimatized. The combined effects of cytokinin TDZ and auxin transport inhibitor TIBA were found to promote shoot multiplication in vitro and prolonged exposure of shoot cultures to TIBA was not found detrimental to shoot growth and multiplication.
The sustainability of managing the environmental process of agglomerating smelter by-products

2 ACKNOWLEDGEMENTS . 4 TABLE OF CONTENTS . 5 LIST OF FIGURES . 8 LIST OF TABLES . 9 CHAPTER 1: NATURE AND SCOPE OF STUDY . 10 1.
Elk forage utilization within rested units of rest-rotation grazing systems

Elk (Cervus elaphus) have been repeatedly observed to prefer rested units within rest-rotation grazing systems. Given the logistical and financial investments associated with the maintenance of these systems, elk herbivory within rested units is a potential source of conflict. Elk forage utilization was determined during the summers of 1994 and 1995 at the forest-grassland ecotone of 3 rest-rotation grazing allotments in south-central Utah's Fishlake National Forest. Average phytomass within areas protected from and subjected to elk herbivory was not statistically different in June and August 1994. Average phytomass within caged areas was greater (P < 0.20) than that within areas subjected to elk use in 2 of 3 rested units in June-July 1995 (14.1 and 35.6% utilization) and August 1995 (34.7 and 42.0% utilization). June-to-August forage regrowth, however, was 31.3 and 33.0% greater in 1995 than in 1994 within caged and uncaged areas, respectively.
FAKTOR YANG BERHUBUNGAN DENGAN KEPATUHAN PENGGUNAAN ALAT PELINDUNG DIRI PADA PEKERJA AREA MID PROYEK 88 AVENUE

Pembangunan gedung mid proyek 88 Avenue Surabaya memiliki berbagai potensi bahaya meliputi bahaya fisik, kimia, biologi, ergonomi dan psikologi. Alat Pelindung Diri merupakan salah satu upaya pengendalian bahaya. Pemakaian Alat Pelindung Diri (APD) telah menjadi suatu kewajiban bagi seluruh pekerja. Penelitian ini bertujuan untuk mengetahui faktor yang berhubungan dengan APD pemakaian Alat Pelindung Diri pada pekerja area mid proyek 88 Avenue. Penelitian ini bersifat obervasional analitik dengan desain cross sectional. Jumlah sampel adalah 62 pekerja yang didapat melalui random sampling. Variabel yang diteliti adalah karakteristik pekerja (umur, tingkat pendidikan dan masa kerja), faktor presdisposisi (pengetahuan dan sikap kerja), faktor pemungkin (ketersediaan APD) dan faktor pendorong (dorongan petugas K3 dan rekan kerja). Hasil penelitian menunjukan bahwa dari total sampel 62 pekerja, sebagian besar tidak patuh terhadap pengggunaan APD sebanyak 40 pekerja (64,5%). Pekerja paling banyak berada pada rentang umur25-30 tahun (37,1%) , memiliki latar belakang pendidikan SMP (40,3%), serta telah bekerja selama 4-5 bulan(33,9%). Kebanyakan pekerja memiliki pengetahuan baik mengenai APD (40%) dan memiliki sikap peduli terhadap penggunaan APD (48%). Pekerja (67,7%) menyatakan bahwa ketersediaan APD sudah baik. Tidak adanya dorongan dari petugas K3 yang berupa pelatihan mengenai penggunaan APD (71%) melainkan hanya ada penyuluhan (88,7%), pengawasan (83,9%), pemberian sanksi (80,6%). Selain itu, terdapat dorongan dari rekan kerja berupa menegur rekan kerja jika mengetahui tidak menggunakan APD (87%). Dari sebelas variabel yang diteliti masa kerja, pengetahuan, pelatihan dan pemberian sanksi merupakan faktor yang berhubungan dengan kepatuhan penggunaan Alat Pelindung Diri (APD), sedangkan faktor lainnya tidak terdapat hubungan dengan kepatuhan penggunaan APD. Berdasarkan hasil penelitian saran yang dapat diberikan adalah menambahkan jumlah sumber daya manusia untuk petugas K3, menambahkan pemasangan sign mengenai APD untuk meningkatkan pengetahuan pekerja, mengadakan pelatihan mengenai penggunaan APD secara rutin yang bertujuan untuk meningkatkan pengetahuan pekerja dan mempertegas pemberian sanksi terhadap pekerja yang tidak patuh terhadap penggunaan APD.
microRNA expression in colorectal tumours : identification of novel mechanisms of gene regulation

Colorectal cancer is a major cause of cancer-related death in the UK, in part as a consequence of a failure to detect the disease at its early stages and also to treatment failure due to the development of drug and radiation resistance. MicroRNAs (miRNAs), small non-coding RNAs, regulate the expression of tumour suppressor genes and oncogenes including KRAS and may influence cancer development and drug and radiation response in colorectal cancer. MiRNAs therefore have potential as biomarkers of disease progression and treatment response. Quantitative real time PCR analysis, in the form of Taqman Low Density Array (TLDA) miRNA cards, was firstly used to prolife colorectal adenomas, cancers and matched normal mucosae and isogenic KRAS mutant and wild-type colorectal cancer cell lines to identify potential candidate miRNAs that regulate KRAS signalling and are involved in colorectal cancer progression. The over-expression of miR-224 was identified to be an early and persistent event in colorectal cancer as it was increased in colorectal adenomas and cancers compared to patient-matched normal tissue. MiR-224 expression was also increased in KRAS WT cells compared to mutant cells and in KRAS/BRAF WT colorectal cancers compared to BRAF mutant cancers. MiR-224 knockdown in KRAS WT cells increased the amount of GTP-bound activated KRAS, increased ERK 1/2 phosphorylation and also increased cellular 5-FU sensitivity thus mimicking a KRAS mutant phenotype. MiR-224 knockdown also reduced cell
Mechanism of Dorso‐Ventral Axis Specification in Nuclear Transplanted Eggs of Xenopus laevis

The rotation of subcortical cytoplasm relative to egg surface (“subcortical rotation”, 28) is known to specify the dorso‐ventral axis of fertilized Xenopus eggs. However, except for brief descriptions (14, 15), no information has been provided on the process of the dorso‐ventral axis specification in nuclear transplanted Xenopus eggs. This study shows that (i), among the events that occur in association with dorso‐ventral axis specification in fertilized Xenopus eggs, only the subcortical rotation occurs in a normal manner in both nuclear transplanted and non‐nuclear transplanted (enucleated) Xenopus eggs, (ii), in these eggs, there is no factor that appears to affect the direction of subcortical rotation as the sperm entry point does in fertilized eggs: neither the site of pricking for activation nor that of injection for nuclear transplantation affects the direction of the subcortical rotation in those eggs and (iii) the subcortical rotation in nuclear transplanted eggs predicts very precisely the direction of their dorso‐ventral axis as it does in fertilized eggs. These results suggest that matured Xenopus oocytes have a cytoplasmic potential to induce subcortical rotation along a particular meridian in the absence of a sperm aster and that the subcortical rotation induced by this cytoplasmic potential specifies the dorso‐ventral axis in nuclear transplanted Xenopus eggs as in fertilized eggs.
Advances in the study of flavonoids in Ginkgo biloba leaves.

Ginkgo biloba flavonoids are one of the most popular herbal supplements, taken for their perceived “memory enhancing” properties. In this paper, the current studies of Ginkgo biloba flavonoids from leaves is been reviewed. Flavonoids are derived from the products of the shikimate and acetate-malonate pathways. Flavonoid concentration in G. biloba leaves is not only regulated by the involvement of genes, but also by other factors, such as photosynthesis, tree age, season, extent of leaf maturity, plant seed-load, the reproductive ways of nursery stock and the variety, time, quantity of fertilizer application and so on. Ecological factors influence flavonoid concentration primarily during the young stage of ginkgo development. Among all ecological factors, light and temperature are the most important. Great progress in producing flavonoids by means of biological technology and chemical synthesis has been made. Comments and analysis on the methods of increasing flavonoid content in G. biloba leaves were made in this review. Key words: Ginkgo biloba, flavonoid, mechanism of control, external synthesis.
The energy requirement for maintenance and production of laying hens.

Respiration experiments were applied to fasting laying hens in an attempt to estimate the 'heat expenditure for synthesis' of eggs from body reserves. The equation H = 85.2 X W0-75 + 16.6 was found for the regression from heat production (H) to meta­ bolic weight (W0-75). It was concluded from this regression equation that about 20 kcal of heat are evolved in the production of every 100 kcal of egg substance from body substance. Energy balance experiments were then conducted on a total of 37 laying hens fed ad libitum in batteries. From these experiments a calculation was made of the regression from the energy balance (Y) to the intake of metabolizable energy (X), both calculated per unit of metabolic weight (W0-75). In the case of a negative total balance (B), a cor­ rection of 0.2 B was applied to the amount of heat evolved. The regression equation found was Y = 0.642 X-65.7. It was concluded from this regression equation that under the experimental conditions the efficiency of utilization of the metabolizable energy for production was 64.2 °/o (± 5.5%) and the maintenance requirement 102 ± 7.6 kcal kg—0-75. The results of the experiment were compared with entirely parallel experiments under practical conditions (birds kept in batteries and on litter). Considerable discrepancies were found between the results of the two experiments. It was assumed that the most likely cause of these discrepancies was a difference in environmental conditions as a result of which the birds' maintenance requirement during the practical experiments may have been higher.
Proteoliposome Proton Flux Assays Establish Net Conductance, pH-Sensitivity, and Functional Integrity of a Novel Truncate of the M2 Ion "Channel" of Influenza A

Proteoliposome Proton Flux Assays Establish Net Conductance, pHSensitivity, and Functional Integrity of a Novel Truncate of the M2 Ion ―Channel‖ of Influenza A Emily Peterson Department of Physiology and Developmental Biology Master of Science A novel truncate of Influenza A M2 protein (residues 22-62), incorporated into a uniquely tailored proteoliposome proton uptake assay, demonstrated proton flux more characteristic of an ion transporter than a traditional ion ―channel. ‖ The liposome paradigm was essential for testing the conductance activity of this M2 truncate at a range of extraphysiological pHs appropriate for channel vs. transport function determination. In addition to transportertypical proton flux, M2(22-62) showed the key characteristics of functional integrity: selective proton uptake into liposomes and block of uptake by amantadine. Two sets of proteoliposome proton flux assays were carried out, Set 1 at pH values of 6.5, 6.0. 5.5, 5.0, and 4.5; Set 2 at pH values of 6.25, 6.0, 5.75, 5.5, 5.25, 5.0, and 4.75. Observed flux rates followed a proton transport saturation curve similar to that observed in mouse erythroleukemia cells 1 . Proton transport was maximal at pH 5.5 in Set 1 (139 H + /second/tetramer) and at pH 5.75 in Set 2 (43 H + /second/tetramer). Amantadine block was strongest at pH 5.5 in Set 1 and 6.25 in Set 2, and apparent desensitization of the protein severely reduced proton flux and amantadine sensitivity below pH 5.5 in both sets of experiments. Decreased external pH increased proton uptake with an apparent pKa of 6 (Set 1) or 6.5 (Set 2). These data indicate acid activation of M2(22-62) between pH 5.5-6, optimal amantadine block between pH 5.5-6.25, and a loss of peptide functionality between pH 5.9-4.7.
Second Chromosomes and Megaplasmids in Bacteria

This chapter reviews some aspects of the many major secondary DNA replicons that have been characterized from organisms that possess multireplicon genomes. Nonprimary replicons are often referred to as secondary chromosomes if they are essential for cell viability or as megaplasmids. A modern source of ambiguity in genomic biology is whether certain replicons represent megaplasmids or second chromosomes. Multircplicon genomes in bacteria could conceivably arise by a number of mechanisms, but two general mechanisms seem most plausible. A major secondary replicon may derive from an ancestral chromosome via an excision event where the excised DNA possesses an origin of replication that is either a duplicated copy of the oriC region or a second, redundant origin that was previously resident on that part of the ancestral chromosome. Chromosome I has an origin of replication typical of other bacterial chromosomes, and the region encodes the dnaA, dnaN, recF, and gyrA genes. A greater proportion of chromosome II is also devoted to genes encoding transporters and solute binding proteins and to genes encoding enzymes required in central intermediary metabolism. The linear chromosome encodes exoC and other genes required for synthesis of several cell surface polysaccharides and also the cellulose synthesis genes that are required for host attachment. Copies of genes required for the synthesis of some amino acids and for certain enzyme cofactors are carried uniquely on the megaplasmid as are the flagellar genes.
Molecular origin of the antifungal action of Amphotericin B - computational approach

Systemic fungal infections are an increasing threat, especially in immunocompromised patients. One of the problems is a lack of good antifungal agents. Amphotericin B (AmB), the oldest antifungal antibiotic, has been widely used in the clinical treatment for over 50 years, due to its many superior properties. Nevertheless, it is not a good therapeutic agent because of its high toxicity. The rational design of the AmB derivatives with the better safety profile is hindered since, despite extensive experimental work, the mechanism of action of AmB at the molecular level is not clear. AmB is known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores. It is also accepted that the presence of sterols in the membrane is essential for the AmB membrane-disruptive activity. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against the mammalian membranes with cholesterol. As shown experimentally, the induction of increased membrane permeability coincides with the appearance of aggregated species of AmB. Thus, the aggregation of AmB molecules in a phospholipid bilayer is crucial for the drug’s activity. The main goal of the present thesis is elucidation of the possible early stages of the AmB aggregation in a lipid bilayer, i.e., formation of (i) AmB/sterol complexes and (ii) AmB dimers. According to the well-known “primary complex” model, AmB and sterol molecules form binary complexes, which subsequently assemble into a barrel-stave channel. In the present thesis, conventional atomistic molecular dynamics simulations as well as free energy calculations are used to study the formation of these putative AmB/sterol complexes in a lipid bilayer. The results obtained confirm the formation of specific AmB/ergosterol complexes and indicate the enhanced affinity of AmB for ergosterol than for cholesterol. The energetic and structural origin of this affinity difference is also determined and its significance for the mechanism of action of AmB is discussed. It is known that AmB self-aggregation in a phospholipid bilayer plays a major role in the AmB activity. To provide an insight into the molecular nature of this process, I report a molecular dynamics free energy study of AmB head-to-head dimerization in a phospholipid bilayer. The results demonstrate that although AmB dimers are formed in all the systems studied, they are significantly less favorable in the bilayer with ergosterol than in the cholesterol-containing or sterol-free ones. The molecular determinants of this difference are investigated and its consequences for the AmB membrane activity are discussed.
New oligidic production diet for Lygus hesperus Knight and L. lineolaris (Palisot de Beauvois).

A new oligidic (undefined) diet for rearing Lygus hesperus Knight (Heteroptera: Miridae) and L. lineolaris (Palisot de Beauvois) is described. The diet (referred to as Nl diet) is a semisolid slurry that accommodates the solid-to-liquid feeding habits of Lygus spp. The Nl diet consists of an “entomophage component” (cooked, whole chicken eggs, chicken egg yolks, sugar, and yeast) combined with plant components (soy bean flour, wheat germ, lima bean meal, and soy lecithin). Biological fitness estimates for L. hesperus indicated that mean biomass production per cage, adult wet and dry weights, survival to the adult stage, and egg production were significantly greater for the Nl diet than for the existing standard, Debolt (1982) diet. The ingredients in the Nl diet cost about ⅛ those in the Debolt diet, and preparation requires less than ½ of the labor. The cost of diet for production per 1000 eggs was approximately $0.004 compared to $0.04 for an equal number of eggs from Debolt diet. Recent work, started a.