Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining the TRAF6/P62 Interactome for Preferred Substrates and Target Ubiquitination Sites: Developing a “Code Hypothesis”

It has been more than 30 years since the initial report of the discovery of ubiquitin as an 8.5 kDa protein of unknown function expressed universally in living cells. And still, protein modification by covalent conjugation of the ubiquitin molecule is one of the most dynamic posttranslational modifications studied in terms of biochemistry and cell physiology. Ubiquitination plays a central regulatory role in number of eukaryotic cellular processes such as receptor endocytosis, growthfactor signaling, cell-cycle control, transcription, DNA repair, gene silencing, and stress response. Ubiquitin conjugation is a three step concerted action of the E1-E2-E3 enzymes that produces a modified protein. In this review I investigate studies undertaken to identify both ubiquitin and SUMO (small ubiquitin-related modifier) substrates with the goal of understanding how Lysine selectivity is achieved. The SUMOylation pathway though distinct from that of ubiquitination, draws many parallels. Based upon the recent findings, I present a model to explain how an individual ubiquitin ligase may target specific Lysine residue(s) with the co-operation from a scaffold protein. * Published in J Proteomics Bioinform. 2009 Jul 24; 2:316.
Strategies for the Identification of Posttranslational Modifications in Biopharmaceuticals by Mass spectrometry

Protein based therapeutics are emerging as the largest class of new chemical entities being developed in drug industry. Presently there are approximately 140 therapeutic proteins approved and additional 500 are in clinical trials and people who use these drugs worldwide are over 250million. Recombinant technologies used for large scale production leads to modifications of proteins depending on expression systems. Although there are number of posttranslational modifications known, the most common form of protein posttranslational modification is glycosylation. During glycosylation, monosaccharides are attached to the protein side chain and form a glycoprotein. Glycosylation can either be an N-linked or Olinked depending on the expression system. The glycosylation pattern of a protein also depends on number of factors such as expression system, media, pH, cell density and age, which makes the structural diversity of glycoproteins vast and impossible to predict. In biological processes, glycosylation plays an important role in immune defense, fertilization, viral replication, parasitic infection, cell growth, and inflammation and cell-cell adhesion. In case of pharmaceutical glycoproteins, glycosylation affects stability of protein conformation, immunogenicity, clearance rate, and protection from proteolysis and improves protein solubility.
COMPARISON OF NATURAL AND EXPERIMENTAL HOST RANGE OF BEET SEVERE CURLY TOP, BEET CURLY TOP IRAN AND TOMATO YELLOW LEAF CURL VIRUSES

Beet curly top Iran virus (BCTIV, genus Becurtovirus ) and Beet severe curly top virus (BSCTV-IR, genus Curtovirus ) induce beet curly top disease in different regions of Iran. In addition to sugar beet, tomato and pepper are important hosts of these viruses. Also tomato yellow leaf curl disease (TYLCD) is a serious disease of tomato in Iran. The Iranian isolate of Tomato yellow leaf curl virus (TYLCV-(Ab)), a severe strain of TYLCV (genus Begomovirus ), is a major component of TYLCD in southern Iran. Until now, no information is available regarding comparative host range of these viruses. To determine the natural hosts of BSCTV-IR, BCTIV and TYLCV-(Ab), samples of sugar beet, tomato, pepper, turnip and spinach were collected from different regions in Fars province. For the experimental host range determination, a number of plants were grown in the greenhouse and their seedlings were agroinoculated with the infectious clone of each virus. The results showed that BSCTV-IR has a wider natural and experimental host range compared to BCTIV. These results indicated that member of Solanaceae, Brassicaceae, Fabaceae and Amaranthaceae are most frequently infected by BSCTV-IR and BCTIV. Natural host range of TYLCV-(Ab) seemed to be very narrow as, in the present study, this virus was isolated only from tomato. However, under greenhouse conditions, bean, nasturtium, petunia, redroot pigweed, datura, night shade and ground cherry were found to be infected by this virus.
Identificação de Fungos Emboloradores em Madeira de Pinus spp. em Laboratório

The objective of this study was to identify the species of mold fungi in untreated wood of Pinus spp. stored at laboratory conditions in Pelotas, Rio Grande do Sul, Brazil. For this purpose, 10 Pinus spp. wood samples were randomly selected for fungal structures identification by morphological spores and subsequently, these were isolated and sent elongation factor 1-alpha (EF-1α) sequencing for molecular identification. Five isolates were obtained from the genus Trichoderma and one isolate of Fusarium. These were identified by molecular analysis as belonging to the species T. atroviride and F. solani, respectively.
1er informe técnico sobre el estado de la diversidad biológica en áreas relacionadas con el recurso agua de interés para proyecto 2-OP15, sitios de la provincia de Guantánamo

PROYECTO NACIONAL CONTRAPARTE: “Conservación y uso sostenible de la Diversidad Biológica en ecosistemas Forestales y ganaderos bajo Manejo Sostenible de Tierras (MST) en Guamuhaya y Cuenca del Cauto”. PROGRAMA: USO SOSTENIBLE DE LOS COMPONENTES DE LA DIVERSIDAD BIOLÓGICA EN CUBA. Instituto de Ecología y Sistemática, AMA_CITMA. Editora: Lucia Hechavarria Schwesinger, Herbario Nacional de Cuba (HAC) AUTORES 1. Ricardo Rosa Angulo, Herbario Nacional de Cuba (HAC): Diversidad Vegetal. 2. Ana América Socarrás, Ecología funcional: Mesofauna del suelo. 3. Grisel Cabrera, Ecología funcional: Macrofauna del suelo. 4. Ramona Oviedo Prieto, Herbario Nacional de Cuba (HAC): Diversidad Vegetal.
Modified-Chronic Disease Score (M-CDS): Predicting the individual risk of death using drug prescriptions

Background Estimating the morbidity of a population is strategic for health systems to improve healthcare. In recent years administrative databases have been increasingly used to predict health outcomes. In 1992, Von Korff proposed a Chronic Disease Score (CDS) to predict 1-year mortality by only using drug prescription data. Because pharmacotherapy underwent many changes over the last 3 decades, the original version of the CDS has limitations. The aim of this paper is to report on the development of the modified version of the CDS. Methods The modified CDS (M-CDS) was developed using 33 variables (from drug prescriptions within two-year before 01/01/2018) to predict one-year mortality in Bologna residents aged ≥50 years. The population was split into training and testing sets for internal validation. Score weights were estimated in the training set using Cox regression model with LASSO procedure for variables selection. The external validation was carried out on the Imola population. The predictive ability of M-CDS was assessed using ROC analysis and compared with that of the Charlson Comorbidity Index (CCI), that is based on hospital data only, and of the Multisource Comorbidity Score (MCS), which uses hospital and pharmaceutical data. Results The predictive ability of M-CDS was similar in the training and testing sets (AUC 95% CI: training [0.760–0.770] vs. testing [0.750–0.772]) and in the external population (Imola AUC 95% CI [0.756–0.781]). M-CDS was significantly better than CCI (M-CDS AUC = 0.761, 95% CI [0.750–0.772] vs. CCI-AUC = 0.696, 95% CI [0.681–0.711]). No significant difference was found between M-CDS and MCS (MCS AUC = 0.762, 95% CI [0.749–0.775]). Conclusions M-CDS, using only drug prescriptions, has a better performance than the CCI score in predicting 1-year mortality, and is not inferior to the multisource comorbidity score. M-CDS can be used for population risk stratification, for risk-adjustment in association studies and to predict the individual risk of death.
Gastric Calcifying Fibrous Tumor: An Easy Misdiagnosis as Gastrointestinal Stromal Tumor—A Systemic Review

Background and Objectives: Calcifying fibrous tumor (CFT) in the stomach is extremely rare and is easily misdiagnosed as a gastrointestinal stromal tumor (GIST). This study aims to determine the best method to differentiate between gastric CFT and GIST after a systemic review and meta-analysis. Materials and Methods: A systematic search of articles using electronic databases (MEDLINE, EMBASE, and LILACS) was conducted and resulted in 162 articles with 272 CFT cases published from January 1988 to September 2019. Results: Of these cases, 272 patients, 60 patients with gastric CFT (32 men and 28 women, mean age 49.2 years) were analyzed. The mean tumor size was 2.4 cm in patients with gastric CFT. Both endoscopic ultrasound (EUS) and computed tomography (CT) findings revealed well-defined (100% vs. 77.8%), heterogeneous (100% vs. 77.8%), iso-hypoechoic (71.4% vs. 33.3%), and calcified (85.7% vs. 77.8%) lesions, respectively. The majority of patients (53.3%) were symptomatic, with the most common symptom being abdominal discomfort (55.6%). None of the patients with gastric CFT showed recurrence after treatment, and most patients received nonendoscopic treatment (56%, n = 28/50). Both age and tumor size were statistically significant in patients with gastric CFT than GIST (49.2 vs. 65.0 years and 2.4 vs. 6.0 cm; both p < 0.001). The ratio of children among patients with CFT (5%) and GIST (0.05%) was also significantly different (p = 0.037). The calcification rates of gastric CFT had significantly higher calcification rates than GIST on images of EUS and CT (85.7% vs. 3.6% and 77.8% vs. 3.6%; both p < 0.001). Conclusions: Compared with patients with GIST, patients with gastric CFT were younger, had smaller tumor size, and were symptomatic. Furthermore, gastric CFT was well-defined, heterogeneous in the third layer, and had high calcification rates on the images.
The role of the thymus in COVID-19 disease severity: implications for antibody treatment and immunization

ABSTRACT The thymus is a largely neglected organ but plays a significant role in the regulation of adaptive immune responses. The effect of aging on the thymus and immune senescence is well established, and the resulting inflammaging is found to be implicated in the development of many chronic diseases including atherosclerosis, hypertension and type 2 diabetes. Both aging and diseases of inflammaging are associated with severe COVID-19 disease, and a dysfunctional thymus may be a predisposing factor. In addition, insults on the thymus during childhood may lead to abnormal thymic function and may explain severe COVID-19 disease among younger individuals; therefore, measurement of thymic function may assist COVID-19 care. Those with poor thymic function may be treated prophylactically with convalescent serum or recombinant antibodies, and they may respond better to high-dose or adjuvanted COVID-19 vaccines. Treatments inducing thymic regeneration may improve patients’ overall health and may be incorporated in COVID-19 management.
The Arabidopsis transcription factor ERF13 negatively regulates defense against Pseudomonas syringae

Author(s): Chia, Kimberly F. | Abstract: Food security is a function of, among other factors, plant health. Because people subsist on a small number of key crops in many parts of the world, disease epidemics among such crops can have dire ramifications. It therefore behooves us to learn more about the plant immune system in order to better protect crops and safeguard the food supply. Many studies on plant immunity have focused in on the role of phytohormones, particularly salicylic acid (SA), jasmonic acid (JA), and ethylene (ET), in negotiating defense strategies against pathogens with different lifestyles. Our work addresses the role of AtERF13, an Arabidopsis ethylene response factor previously found to enhance abscisic acid (ABA)-mediated responses to abiotic stress. We found in proteome profiling of plant immune signaling that S168- phosphorylated ERF13 increases concurrent with early effector-triggered immunity mediated by the R protein RPM1. Using quantitative luminescence assays to measure the growth of bioluminescent bacteria in planta, we determined that overexpression of ERF13 induces susceptibility to the bacterial pathogen Pseudomonas syringae. We also found that ERF13 overexpression promotes chlorosis and inhibits plant growth. Semi-quantitative RT- PCR analysis furthermore demonstrated that ERF13 stimulates the expression of PDF1.2a, a JA/ET-inducible pathogenesis-related gene. We conclude that ERF13 lies at a junction in the signaling pathways of SA, JA, ET, and ABA, and that it promotes susceptibility to P. syringae by negotiating the crosstalk between these hormones which shapes and tailors the plant defense response
Chapter 2:Natural Occurrence of Masked Mycotoxins

This chapter describes recent knowledge of the occurrence of the major masked mycotoxins, principally those derived from deoxynivalenol, zearalenone and fumonisin. The occurrence of several minor masked mycotoxins is described and summaries of quantitative data from some large-scale surveys are provided. Some factors that might influence the formation of masked mycotoxins are discussed.
Results of the fecal immunochemical test in a colorectal cancer screening program in Mexico.

Background Colorectal cancer (CRC) is one of the main five causes of morbidity and mortality by oncologic diseases in our country and worldwide. Recently, fecal immunochemical test (FIT) has proven to be a noninvasive screening test that allows to select patients most likely to have a pre-malign lesion in order to perform a colonoscopy. Objective To report the findings of a CRC screening program using FIT in our country population. Method A multicentric study was performed, by inviting open population older than 50 years to participate in a CRC screening. Quantitative FIT specific for human hemoglobin was used, with a cut point of 100 ng/ml or higher to consider as positive. Those patients with positive results were asked to undergo a colonoscopy. In the cases where polypoid lesions were found, biopsies were performed. Results In total, 751 FIT were processed, and 51 (6.8) of those were positive, with a rate of 15.9 premalign lesions for 1,000 individuals, and 1.3 patients with CRC for every 1,000. Conclusions The present study matches worldwide reports, supporting the initiative of establishing a formal and standardized CRC screening program in the public health sector.
Neuropathogenesis in COVID-19

To the Editor: SARS-CoV-2 or COVID-19 is a new human coronavirus that emerged in Wuhan, China in late 2019 and is currently causing a pandemic (1, 2). With the possibility of future outbreaks of the disease, it may manifest with diverse clinical characteristics and different severity, as has been seen with other viruses. COVID-19 belongs to a large family of RNA viruses that have been considered a global health problem because they have a remarkably high transmissibility potential and sometimes invade the CNS (3–5). Because of the rapid expansion of a virus that until now was unknown, it is important to understand the mechanisms by which COVID-19 generates CNS disease. Understanding CNS involvement in the disease is especially challenging and current theories of pathogenesis include direct neuroinvasion, crossing of the blood–brain barrier (BBB) by the virus, and a nicotinic hypothesis.
Ecosystem Services, Physiology, and Biofuels Recalcitrance of Poplars Grown for Landfill Phytoremediation

Long-term poplar phytoremediation data are lacking, especially for ecosystem services throughout rotations. We tested for rotation-age differences in biomass productivity and carbon storage of clones Populus deltoides Bartr. ex Marsh × P. nigra L. ‘DN34′ and P. nigra × P. maximowiczii A. Henry ‘NM6′ grown for landfill phytoremediation in Rhinelander, WI, USA (45.6° N, 89.4° W). We evaluated tree height and diameter, carbon isotope discrimination (Δ), and phytoaccumulation and phytoextraction of carbon, nitrogen, and inorganic pollutants in leaves, boles, and branches. We measured specific gravity and fiber composition, and determined biofuels recalcitrance of the Rhinelander landfill trees versus these genotypes that were grown for biomass production on an agricultural site in Escanaba, MI, USA (45.8° N, 87.2° W). ‘NM6′ exhibited 3.4 times greater biomass productivity and carbon storage than ‘DN34′, yet both of the clones had similar Δ, which differed for tree age rather than genotype. Phytoaccumulation and phytoextraction were clone- and tissue-specific. ‘DN34′ generally had higher pollutant concentrations. Across contaminants, stand-level mean annual uptake was 28 to 657% greater for ‘NM6′, which indicated its phytoremediation superiority. Site-related factors (not genotypic effects) governed bioconversion potential. Rhinelander phytoremediation trees exhibited 15% greater lignin than Escanaba biomass trees, contributing to 46% lower glucose yield for Rhinelander trees.
Hazard Perception and Prediction test for walking, riding a bike and driving a car: “Understanding of the global traffic situation”

To “put oneself in the place of other road users” may improve understanding of the global traffic situation. It should be useful enabling drivers to anticipate and detect obstacles in time to prevent accidents to other road users, especially those most vulnerable. We created a pioneering Hazard Perception and Prediction test to explore this skill in different road users (pedestrians, cyclists and drivers), with videos recorded in naturalistic scenarios: walking, riding a bicycle and driving a car. There were 79 participants (30 pedestrians, 14 cyclists, 13 novice drivers and 22 experienced drivers). Sixty videos of hazardous traffic situations were presented, divided into 2 blocks of 30 videos each: 10 walking, 10 riding a bicycle, 10 driving a car. In each situation presented, we evaluated the performance of the participants carrying out the task of predicting the hazard and estimating the risk. In the second block, after they had carried out the task, we gave them feedback on their performance and let them see the whole video (i.e., checking what happened next). The results showed that the holistic test had acceptable psychometric properties (Cronbach’s alpha = .846). The test was able to discriminate between the different conditions manipulated: a) between traffic hazards recorded from different perspectives: walking, riding a bicycle and driving a car; b) between participants with different user profiles: pedestrians, cyclists and drivers; c) between the two test blocks: the first evaluation only and the second combining evaluation with this complex intervention. We found modal bias effects in both Hazard Perception and Prediction; and in Risk Estimation.
Discovery of lipoic acid-4-phenyl-1H-pyrazole hybrids as novel bifunctional ROCK inhibitors with antioxidant activity

A series of lipoic acid (LA) and 4-phenyl-1H-pyrazole hybrids as bifunctional Rho-associated kinase (ROCK) inhibitors were designed, synthesized and evaluated. Compound 15 is identified to be a novel potent bifunctional ROCK inhibitor with antioxidant activity and neuroprotection.
Regional response of grassland productivity to changing environment conditions influenced by limiting factors

Regional differences and regulatory mechanisms of vegetation productivity response to changing environmental conditions constitute a core issue in macroecological researches. To verify the main limiting factors of different macrosystems [temperature-limited Tibetan Plateau (TP), precipitation-limited Mongolian Plateau (MP), and nutrient-limited Loess Plateau (LP)], we conducted a comparative survey of the east-west grassland transects on the three plateaus and explored the factors limiting regional productivity and their underlying mechanisms. The results showed that aboveground net primary productivity (ANPP) of LP (109.10 ± 16.76 g m−2 yr−1) was significantly higher than that of MP (66.71 ± 11.11 g m−2 yr−1) and TP (57.02 ± 10.59 g m−2 yr−1). The response rate of ANPP with environmental changes was different among different plateaus, being closely related to the main limiting factors. On MP, this was precipitation, on LP it was temperature and nutrients, and on TP, it was non-specific, reflecting restriction by the extremely low temperature. After autocorrelation screening of environmental factors, different regions exhibited different productivity response mechanisms. MP was mainly influenced by temperature and precipitation, LP was influenced by temperature and nutrient, and TP was influenced by nutrient, reflecting the modifying effect of the main limiting factors. The effect of each regional environment on ANPP was 72.56% on average and only 27.18% after simple regional integration. The regional model could optimize the simulation error of the integrated model, and the relative deviations in MP, LP, and TP were reduced by 31.76%, 17.22%, and 2.23%, respectively. These findings indicate that the grasslands on the three plateaus may have different or even the opposite mechanisms to control productivity.
Microsatellites markers to study genetic relationships among cowpea (Vigna unguiculata) genotypes

Genetic diversity and phylogenetic relationships among 48 cowpea [Vigna unguiculata (L.) Walp. ] genotypes collected from different places in India were evaluated using simple sequence repeat molecular markers. A set of 40 primer combinations developed from cowpea genomic/expressed sequence tags and evaluated for their ability to detect polymorphisms among the various cowpea genotypes. Eleven primer combinations detected polymorphisms; sixteen primer combinations were monomorphic, with the remaining 13 primer sets failing to yield PCR amplification products. From one to 5 alleles were found among the informative primer combinations. The genetic diversity of the sample varied from 0.02 to 0.39 (mean = 0.205). The polymorphic information content ranged from 0.12 to 0.86 (mean = 0.49). The inter-cluster representatives of distant clusters (based on morphological and molecular markers) would be more useful for choosing the parents in cowpea breeding programmes.
Fractionation and distribution of calcium in sprouting and non-sprouting potato tubers

Autoradiographs of potato tubers (Solatium tuberosumL. cv. Mans Piper) grown in the presence of “Ca revealed high activity in the periderm, vascular ring (predominantly xyiem), phloem bundles and pith. It is calculated that only 40 per cent of tubeT Ca entered directly through the periderm and the possibility of import via the phloem is discussed. Chemical fractionation procedures showed that more than 90 per cent of tuber Ca could be considered to be in a physiologically active form and very little in the form of insoluble components such as calcium oxalate. Microautoradiography confirmed the infrequent occurrence of specialized calcium oxalate-containing cells. When tubers were sprouted in trays in the dark water-soluble forms of “Ca were preferentially transported to the sprout Greater depletion occurred from the outermost tissues of the tuber but there was no indication of preferential mobilization from tissues immediately adjacent to the sprouting region. Sprouts which developed sub-apical tip necrosis showed a positive gradient of “Ca from the tip to the base.