Miracle-dz/UniFAR-FTUs huggingface dataset:
The global dynamics of CDK substrate phosphorylation in a simplified CDK network

Cyclin-CDK complexes initiate S-phase and mitosis, but how these events are temporally separated is not fully understood. In S. pombe a single Cyclin-CDK is sufficient to order the cell cycle. Understanding how and when CDK substrates are phosphorylated, during the cell cycle, will inform how CDK orders cell cycle events. To this end, I have combined in vivo chemical inhibition of CDK and phosphoproteomics to study the behaviour of CDK-mediated phosphorylation. Hundreds of CDK-dependent phosphorylation events have been identified and their cell cycle phosphorylation dynamics quantified. CDK substrates falls into three categories: i) the vast majority become phosphorylated during mitosis, ii) S-phase substrates, which are first phosphorylated at G1/S and are stable until mitosis, and iii) biphasic substrates that increases in phosphorylation at both transitions but peak at G2/M. All three classes are dephosphorylated simultaneously at mitotic exit. S-phase substrates are more sensitive to CDK activity in vivo than mitotic substrates. The causal relationship between CDK activity, substrate phosphorylation, and cell cycle fate is corroborated by the fact that when the timing of substrate phosphorylation is reordered, the order of cell cycle events is correspondingly reorganised. These data argue that rising CDK activity orders the cell cycle via the attainment of substrate-specific thresholds. Low activity results in S-phase substrate phosphorylation, and the initiation of DNA synthesis, whilst higher CDK activity results in mitotic substrate phosphorylation and chromosome segregation. Furthermore, the timing of mitotic substrate phosphorylation during G2/M correlates with sensitivity to CDK activity, indicating that passage through sequential CDK activity thresholds orders substrate phosphorylation, and likely mitotic events, during the entry into mitosis. Phosphoproteomic analysis also indicates that G1/S cyclins contribute mainly to the accumulation of CDK activity, and that phosphorylation by other mitotic kinases is organised into sequential waves, allowing the amplification and diversification of CDK signalling.
Effects of Maternal Dietary Yeast Supplementation on Foal Growth and Microbial Diversity of the Hindgut in Quarter Horse Mares and Their Offspring

ii Dedication . v Acknowledgments. vi Vita . vii List of Tables . xi List of Figures . xii Chapter 1: Literature Review . 1 Development of the Foal Gastrointestinal Tract and the Microbial Environment . 4 Intestinal Microbial Ecosystem of the Horse . 5 Factors Affecting the Intestinal Microbial Ecosystem of the Horse . 12 Dietary Supplements . 18 Effect of Maternal Diet on Offspring’s Growth and Development . 27 Chapter 2: Effects of a Live Yeast Supplement on the Gastrointestinal Microflora in Quarter Horse Mares and Their Offspring . 3
Correction for Reprogramming of murine and human somatic cells using a single polycistronic vector, by Bryce W. Carey

Correction for ‘‘Icy insights from emperor penguins,’’ by Colleen Cassady St. Clair and Mark S. Boyce, which appeared in issue 6, February 10, 2009, of Proc Natl Acad Sci USA (106:1691–1692; first published February 4, 2009; 10.1073/pnas.0812940106). The authors note that due to a printer’s error in the Fig. 1 legend, the two panels were credited incorrectly. The corrected legend and its figure appear below.
The Effect of Tax Avoidance, Real and Accrual Earnings Management on Cost of Equity

: This research aims to examine the effect of tax avoidance, accrual earnings management, and real earnings management on the cost of equity. The independent variables used in this study are tax avoidance measured by abnormal book-tax differences (ABTD), earnings accrual management as measured by performance-adjusted current discretionary accruals (PACDA), and real earnings management measured by abnormal discretionary expense and abnormal production cost. Meanwhile, the dependent variable used is the cost of equity as measured by the equity cost formula. The equity cost formula is obtained by summing the book value per share in period t plus the earnings per share in the period t+1 then subtracted from the stock price in period t which is divided by the share price in period t. The population in this study were manufacturing companies listed on the Indonesia Stock Exchange from 2012 to 2016. Samples were taken using the purposive sampling method. This study uses panel data regression analysis techniques. The results showed that tax avoidance had a significantly positive effect on the cost of equity while accrual earnings management and real earnings management had no effect on the cost of equity.
Chitinase production by endophytic Streptomyces aureofaciens CMUAc130 and its antagonism against phytopathogenic fungi

More than three hundred isolates of endophytic actinomycetes were screened for their potential for chitinase production. The strain identified as Streptomyces aureofaciens CMUAc130 was the most effective amongst those investigated. This isolate was selected for a more detailed study of chitinase production and its effectiveness in fungal cell wall lysis. Production of the chitinase was optimal with 1% colloidal chitin concentration, at 30-40 °C, pH 6.5-7.0 and 100-150 rev min -1 shaking. N-acetylglucosamine was a good inducer and expression of the enzyme complex was repressed by several mono- and disaccharides including lactose, mannose, glucose, cellobiose, arabinose, raffinose, sucrose, xylose and fructose. Addition of pectin, starch and carboxymethyl cellulose to the colloidal chitin-containing medium, increased chitinase production. The enzyme tolerated a wide range of temperature (30-50 °C) and pH (5.5-8). Among various divalent cations Hg 2+ Cd 2+ and Ni 2+ completely inhibited the purified enzyme while Mg 2+ stimulated its activity. The crude or purified enzyme had potential for cell wall lysis of many phytopathogenic fungi tested.
Estandarización del protocolo de desinfección para la micropropagación de Aspidosperma polyneuron

Aspidosperma polyneuron is a species native to the Neotropics, in countries like Colombia, Venezuela, Peru, Brazil, Argentina and Paraguay, typical of semi-deciduous forests, catalogued since 1998 by the IUCN as "Endangered (EN)", because its natural populations were subjected to an intense exploitation for timber and its habitat was seriously degraded by agricultural and silvopastoral activities. The difficulties for its natural regeneration and the rooting of cuttings, make the in vitro culture an efficient tool to counteract the reproductive difficulties that it presents. However, the presence of pollutants that affect the viability of the explants needs the development of protocols that allow the in vitro establishment of this species. The objective of this research was to achieve aseptic establishment and the induction of callogenesis in explants of A. polyneuron, by evaluating different disinfection treatments. The expants were obtained from individuals of natural regeneration, in the Municipality of Armero in the Department of Tolima, which were immersed in distilled water with a drop of Tween® 80 for each 100 ml, for 10 minutes and then rinsed with sterile distilled water. There were used as disinfectant agents, sodium hypochlorite and mercury dichloride in different concentrations and times of immersion. Among the used explants: buds, nodal segments and leaf blades, the last one was selected for its capacity of producing friable and green callosity, for which a disinfection with mercury dichloride (HgCl2) 0.125% for 10 minutes was enough for contamination control and low indexes of oxidation.
Bi‐phasic pattern of brachial artery flow mediated dilation in response to a 20min step increase in shear rate

OBJECTIVE‐ to characterize brachial artery (BA) flow mediated dilation (FMD) in response to a 20min step increase in shear stress. BA diameter and mean blood velocity (MBV) were measured with Doppler ultrasound in 16 healthy subjects. A maintained target MBV was created by controlled release of BA compression upstream of heat‐induced forearm vasodilation. Two stimulus magnitudes were investigated;
In vitro antimicrobial activity of essential oils from mediterranean Apiaceae, Verbenaceae and Lamiaceae against foodborne pathogens and spoilage bacteria

The aim of this work was to investigate the antimicrobial activity of twelve essential oils, against Gram-positive and Gram-negative bacteria, for a potential use in food industry. The antimicrobial activity of essential oils was determined by an agar diffusion method against food borne pathogens and spoilage bacteria. Further, bacteriostatic and bactericidal concentrations were determined for each strain that evidenced sensitivity to the oils. All the oils showed bacteriostatic and bactericidal activity against Escherichia coli O157:H7 and Salmonella Typhimurium, while Brochotrix thermosphacta was inhibited by eight of 12 tested oils. Finally, the pathogenic microorganism Listeria monocytogenes and lactic acid bacteria strains were affected only by thyme, oregano and vervain oils. The essential oils considered in this research showed a satisfactory antimicrobial activity. The essential oils could be used for the development of novel systems for food preservation.
Isolation and Identification of Concrete Environment Bacteria

This paper presents the isolation and molecular method for bacteria identification through PCR and DNA sequencing. Identification of the bacteria species is required in order to fully utilize the bacterium capability for precipitation of calcium carbonate in concrete. This process is to enable the addition of suitable catalyst according to the bacterium enzymatic pathway that is known through the bacteria species used. The objective of this study is to isolate, enriched and identify the bacteria species. The bacteria in this study was isolated from fresh urine and acid mine drainage water, Kota Tinggi, Johor. Enrichment of the isolated bacteria was conducted to ensure the bacteria survivability in concrete. The identification of bacteria species was done through polymerase chain reaction (PCR) and rRDNA sequencing. The isolation and enrichment of the bacteria was done successfully. Whereas, the results for bacteria identification showed that the isolated bacteria strains are Bacillus sp and Enterococus faecalis.
Biochemical characterisation of indian durum wheats

Eight varieties of durum wheat-PDW 233, MACS-9, HI-8498, A-9-30-1, Raj 911, Raj 1555 having good quality characteristics and Bijagayellow, NIDW-15 having poor quality characteristics have been characterized for their gluten components which govern their dough properties. The protein content in these varieties varied from 11.1% to 13.8% and the β-carotene content from 4.1 to 5.85 ppm with maximum in PDW-233 and minimum in A-9-30-1. A 45 kD polypeptide was present only in the good quality durum varieties. PCR amplification of the genomic DNA from the selected varieties using LMW glutenin gene specific primers, however, showed no polymorphism between the good and poor quality varieties under study.
Cryopreservation of Fruit Crop Genetic Resources— Implications for Maintenance and Diversity during Conservation

Even though the importation of fruit crop germplasm to North America coincided with and perhaps reached a zenith during the earliest phases of colonization and settlement, a national organized system of conservation did not emerge until the late 1970s. Serious concern that the maintenance and conservation of this important resource required national coordination and commitment led to the establishment of several clonal repositories to accommodate most of the fruit crops with production potential in North America (Brooks and Barton, 1983). In recent years, it has become apparent that a comprehensive conservation program for fruit crop genetic resources will probably best be accomplished by developing storage systems for organs and tissues under controlled conditions to compliment the clonal repositories. Cryopreservation of appropriate tissues and organs is one option. The potential for long-term storage in a stable condition using cryopreservation is appealing for several reasons, including improved efficiency and the potential for long-term storage. However, there is a need for more research to answer questions pertaining to long-term viability, genetic stability with various systems and tissues, improved protocols, and basic cell survival mechanisms at the biochemical and biophysical level. Accordingly, in this report, 1 will initially attempt to outline some current conservation strategies in light of present programs and conclude with comments on recent research on cryopreservation of fruit crop genetic resources and the potential application to conservation of these resources.
Growth inhibition of the stored fish (Ethmalosa fimbriata) fungus Aspergillus flavus, exposed to extracted essential oils from Callistemon citrinus and Ocimum canum

The aim of this study was to evaluate the antifungal effects of essential oils from Callistemon citrinus and Ocimum canum against Aspergillus flavus. Major components in the oil of C. citrinus were 1,8-cineole (60.6%), α-pinene (18.5%), limonene (5.0%) and α-terpineol (5.0%). The oil of O. canum was mainly composed of 1.8-cineole (20.8%), linalol (14.3%), eugenol (11.9%), terpinen-4-ol (7.4%) and germacrene D (4.9%). Inhibition of the mycelia growth of A flavus increased significantly (p < 0.05) with the essential oils concentrations. Positives correlations were observed between inhibition percentages and the concentration of C. citrinus (p < 0.001; r = 0.873) and O. canum oils (p< 0.001; r = 0.768). O. canum oil was fungicide at 325 ppm while C. citrinus was fungistatic at all the tested concentrations with the highest inhibition percentage means of 89.74 %. Antifungal activity of the essential oil of O. canum was significantly (p < 0.001) higher than that of C. citrinus. Antioxidant activity of O. canum (49.3 mol/l) was significantly (p < 0.001) higher than that from C. citrinus (5.0 mol/l). These observations suggest the possible exploitation of the oils from O.canum and C.citrinus as potential approach for smoked Ethmalosa fimbriata preservation against A. flavus. Key words: Antifungal effects, Aspergillus favus, Ethmalosa fimbriata, essential oils.
The presence of lectins in bacteria associated with the Azolla-anabaena symbiosis

Cell extracts from the Azolla-Anabaena system are known to cause agglutination of erythrocytes, and if lectins, which are carbohydrate-binding proteins, are involved in the establishment of the Azolla-Anabaena-bacteria symbiosis, they may play any role in it. In order to clarify this situation, we have isolated and identified six different bacterial strains contained in the leaf cavities of two Azolla species (A. Jiliculoides and A. pinnata). From these symbiotic bacteria lectin extracts were prepared, treated with polyvinylpolypyrrolidone (PVPP), and analyzed by SDSp AGE that, for each analyzed bacterial strain, revealed several protein bands whose molecular masses varied between 50 and 142 kDa. The protein extracts, with and without PVPP treatment, were also used in haemagglutination tests, and showed a positive reaction. The results of this study indicate that lectins are involved in the haemagglutination activity of the extracts recovered from the symbiotic bacteria present in the system Azolla-Anabaena.
Frequency-dependent hoarding by Sciurus carolinensis occurs with seeds of similar perceived value

Seed predation and rodent foraging behaviors depend on frequency of available seeds and seed traits. However, the interaction of frequency of seed availability and seed traits adds a new level of complexity to granivore–seed dynamics. We conducted experiments with eastern gray squirrels (Sciurus carolinensis) designed to elucidate the frequency × trait interaction. We hypothesized that frequency-dependent caching should occur only among pairs of seeds that are relatively similar in attributes that affect their perceived value as a storable food item. We also tested whether caching decisions were dependent on seeds already cached, a variable rarely considered in seed dispersal studies. Frequency-dependent seed caching occurred when seeds of relatively similar value (Juglans regia and Castanea mollissima) were paired. For this seed pair, caching decisions by S. carolinensis were dependent on seeds already cached such that squirrels tended to cache seeds that were either rare in the environment or in the cache. When seeds of very different caching values were paired (Juglans nigra and Corylus americana), a strong preference for the high-value seed was observed, but no frequency-dependent selection. We conclude that in pairings of seeds of differential caching value, the highly preferred seed is cached regardless of frequency of availability. In contrast, when seeds of similar value are paired, rarer (more common) seeds are cached at a higher (lower) rate than expected, and this behavior potentially stabilizes seed survival across available seed types leading to increased tree diversity. Our results indicate that caching of seeds by squirrels, and by implication recruitment of seedlings into plant populations, is likely driven by complex interactions between the relative frequency of seeds and their traits. We expect similar patterns to occur in any system in which foragers select among resource types that vary in perceived value.
Systems Biology Approaches to Evaluate Disease Modularity

Biological systems are in a constant process of innovation as an essential precondition to evolve. For this reason, the emergence of phenotypic variation is an inherent property of complex adaptive systems. Even though living systems acquire robustness to internal and external disturbances during the evolutionary process, pathological conditions entail impairments to their functionality. This is the rationale for studying biomedical issues according to the organizational properties of biological systems, with the aim of understanding the mechanisms of diseases. I first discuss the theoretical background that is suitable for the research included in this Thesis, such as my own interpretation of systems biology, the current theories about the origin of the biological modularity and some evolutionary considerations that concern in the genotype-phenotype relationships. In this section, I also argue the use and the development of integrative systems biology methods that should be addressed to evaluate disease modules: computational models (i.e. mathematical and network-based models) and other standardized efforts (ontologies and different databases with biological and biomedical data). Then, I enunciate the hypothesis and declare the objectives that motivated this research: i) mathematical modelling based on kinetic law formalism for studying the functional modularity of the metabolism; ii) the development of a workflow to integrate metabolic and kinetic data from different databases for metabolic modelling; iii) the evaluation of the functional coherence in phenotypic relationships between disease-causing genes by using network-based analysis; iv) the development of an integrative framework of biomedical information; v) the use of network medicine approaches to study the phenotypic and genotypic relationships in a heterogeneous group of patients with genetic syndromes. Finally, the results derived from the research carried out in this Thesis are included in the form of already published articles and manuscripts (either submitted or in preparation).
On empty islands and the small-island effect

Aim The small-island effect (SIE) has become a widely accepted part of the theoretical framework of island biogeography. A major criticism of SIE studies is the exclusion of empty islands from analyses. However, the generality and underlying factors determining the role of empty islands in generating SIEs remain obscure because few published datasets include islands with no species. The aim of this study was thus to evaluate the prevalence and underlying factors determining the role of empty islands in generating SIEs. Location Global. Methods We compiled 278 datasets that included empty islands. For each dataset, we compared the fit of a logarithmic model with two breakpoint models separately for all the islands and for datasets excluding empty islands to determine the role of empty islands in generating SIEs. We then employed multinomial logistic regressions and an information-theoretic approach to determine which combination of island characteristics was important in determining the role of empty islands in generating SIEs. Results Among 211 datasets with adequate fits, the exclusion of empty islands changed the evidence for an SIE in 68 cases (32.2%). SIEs were quite prevalent, both for all the islands (104 cases, 49.3%) and for datasets excluding empty islands (73 cases, 34.6%). Our results were not consistent with the hypothesis that excluding empty islands would increase the evidence for an SIE. Model selection and relative variable importance indicated that the number of empty islands, the minimum area of empty islands and area ratio were important variables that determined the role of empty islands in generating SIEs. Main conclusions Our study demonstrates that the effect of empty islands in generating SIEs is quite prevalent. The exclusion of empty islands is thus an important methodological shortcoming for the detection of SIEs. We conclude that, for the robust detection of SIEs, empty islands should not be excluded in future studies.
Molecular assessment of invasive Carrageenophyte Kappaphycus alvarezii from India based on ITS-1 sequences

This is the first report on the molecular systematic characterization of the invasive red alga Kappaphycus alvarezii in India. Cultivated for the production of carrageenan around the Gulf of Mannar, southeast India, this exotic alga is causing havoc in coastal ecosystems by invading the habitats of a number of endemic species, especially soft corals. We have sequenced the nuclear ribosomal DNA internal transcribed spacer 1 barcode of this introduced species. In our phylogenetic analyses using Bayesian inference and maximum likelihood, this alga clustered within a well-supported clade of K. alvarezii of mixed geographic origin. Phylogenetic analyses were congruent in their separation of K. alvarezii and Kappaphycus striatum. Analyses also suggest that this species might have originated in the Malay Archipelago and spread elsewhere. Our results provide insights into the evolutionary and biogeographic patterns of this alga around the world.
Diagnostic approaches to reproductive failure in pigs

If the answer to each of these is “no,” then the likelihood that infectious disease is a factor in the reproductive failure is very low. At that point, infectious disease should move to the background and other causes of reproductive failure to the foreground. Even though I will discuss disease diagnosis first, I cannot stress enough that unless the above clinical signs are observed, chances of recovering a significant infectious agent are extremely remote.