Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information

Summary: A variety of specialist databases have been developed to facilitate the study of allergens. However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains

Assessment of the Albumin-Bilirubin (ALBI) Grade as a Prognostic Indicator for Hepatocellular Carcinoma Patients Treated With Radioembolization.

OBJECTIVE: As the utility of Child-Pugh (C-P) class is limited by the subjectivity of ascites and encephalopathy, we evaluated a previously established objective method, the albumin-bilirubin (ALBI) grade, as a prognosticator for yttrium-90 radioembolization (RE) treatment for patients with hepatocellular carcinoma (HCC). MATERIALS AND METHODS: A total of 117 patients who received RE for HCC from 2 academic centers were reviewed and stratified by ALBI grade, C-P class, and Barcelona Clinic Liver Cancer stage. The overall survival (OS) according to these 3 criteria was evaluated by Kaplan-Meier survival analysis. The utilities of C-P class and ALBI grade as prognostic indicators were compared using the log-rank test. Multivariate Cox regression analysis was performed to identify additional predictive factors. RESULTS: Patients with ALBI grade 1 (n=49) had superior OS than those with ALBI grade 2 (n=65) (P=0.01). Meanwhile, no significant difference was observed in OS between C-P class A (n=100) and C-P class B (n=14) (P=0.11). For C-P class A patients, the ALBI grade (1 vs. 2) was able to stratify 2 clear and nonoverlapping subgroups with differing OS curves (P=0.03). Multivariate Cox regression test identified alanine transaminase, Barcelona Clinic Liver Cancer stage, and ALBI grade as the strongest prognostic factors for OS (P\u3c0.10). CONCLUSIONS: ALBI grade as a prognosticator has demonstrated clear survival discrimination that is superior to C-P class among HCC patients treated with RE, particularly within the subgroup of C-P class A patients. ALBI grade is useful for clinicians to make decisions as to whether RE should be recommended to patients with HCC

A high-throughput immobilized bead screen for stable proteins and multi-protein complexes

We describe an in vitro colony screen to identify Escherichia coli expressing soluble proteins and stable, assembled multiprotein complexes. Proteins with an N-terminal 6His tag and C-terminal green fluorescent protein (GFP) S11 tag are fluorescently labeled in cells by complementation with a coexpressed GFP 1–10 fragment. After partial colony lysis, the fluorescent soluble proteins or complexes diffuse through a supporting filtration membrane and are captured on Talon® resin metal affinity beads immobilized in agarose. Images of the fluorescent colonies convey total expression and the level of fluorescence bound to the beads indicates how much protein is soluble. Both pieces of information can be used together when selecting clones. After the assay, colonies can be picked and propagated, eliminating the need to make replica plates. We used the method to screen a DNA fragment library of the human protein p85 and preferentially obtained clones expressing the full-length ‘breakpoint cluster region-homology' and NSH2 domains. The assay also distinguished clones expressing stable multi-protein complexes from those that are unstable due to missing subunits. Clones expressing stable, intact heterotrimeric E.coli YheNML complexes were readily identified in libraries dominated by complexes of YheML missing the N subunit

ПЕРВЫЙ КЛИНИЧЕСКИЙ ОПЫТ ПРИМЕНЕНИЯ КОЛОНОК ДЛЯ ЛПС-АДСОРБЦИИ «ТОКСИПАК» В ЛЕЧЕНИИ ПАЦИЕНТОВ С СЕПСИСОМ

Endotoxicosis is one of the main factors of the pathogenesis of multiple organic dysfunctions in gram-negative sepsis, induced by the accumulation of lipopolysaccharides - wall components of gram-negative bacteria. In vitro removal of them (LPS-adsorption) promotes better treatment outcomes in sepsis patients. Development and introduction of the Russian tools for LPS-adsorption becomes more crucial. Objective: to evaluate the efficiency and safety of the column of Toxipak for endotoxin removal, manufactured by POCARD Ltd. Materials and methods: 7 adult sepsis patients who had LPS-adsorption were included into the study. The changes of the following parameters were monitored in the patients: temperature, pulse, arterial pressure, respiration rate, central venous pressure, oxygen saturation, hourly rate of diuresis, oxygenation index was calculated, hematologic and biochemical blood parameters were tested as well as coagulation system rates, endotoxin level, C-reactive protein (CRP), procalcitonin, and interleukins (IL) 1, 6, 8. Criteria of the system inflammatory response and SOFA score were used for the comprehensive evaluation of clinical status. The adverse events, duration of stay in the intensive care ward and 18- and 24-day mortality were followed up during manipulations. Results: the studied column provided no negative effect on the cellular and biochemical composition, main parameters of clotting system and acid-base balance of blood. Its use resulted in the reduction of endotoxin (LPS) (by 64%), CRP (by 14%), IL-1 (by 38%) in blood, increase of oxygenation index, and renal function improvement. LPS adsorption promoted the reduction of clinical and laboratory signs of system inflammatory response, and severity of organ dysfunction (from 6.0 to 3.0 as per SOFA score) in patients with sepsis and septic shock. Conclusion: Toxipak column is safe and efficient for removal of endotoxins from blood. Одним из основных факторов патогенеза множественной органной дисфункции при грамотрицательном сепсисе является эндотоксикоз, обусловленный накоплением липополисахаридов – компонентов стенки грамотрицательных бактерий. Их экстракорпоральное удаление (ЛПС-адсорбция) способствует улучшению результатов лечения пациентов с сепсисом. Разработка и внедрение в практику отечественных устройств для ЛПС-адсорбции является актуальной задачей. Цель: провести оценку эффективности и безопасности колонок «Токсипак» для удаления эндотоксинов производства ЗАО НПФ «ПОКАРД». Материал и методы: в исследование включено 7 взрослых пациентов с сепсисом, которым выполнено 10 ЛПС-адсорбций. У пациентов в динамике измеряли температуру тела, пульс, артериальное давление, частоту дыхания, центральное венозное давление, сатурацию кислорода, почасовой темп диуреза, рассчитывали индекс оксигенации, в крови определяли гематологические и биохимические показатели, показатели системы свертывания, уровень эндотоксина, С-реактивного белка (СРБ), прокальцитонина, интерлейкинов (ИЛ) 1, 6, 8. Для интегральной оценки клинического статуса использовали критерии системной воспалительной реакции и шкалу SOFA. Оценивали нежелательные явления в ходе проведения процедур, длительность пребывания в отделении реанимации и интенсивной терапии, 14- и 28-дневную летальность. Результаты: изученные колонки не оказывали отрицательного влияния на клеточный и биохимический состав крови, основные показатели системы свертывания и кислотно-основное состояние крови. В результате их использования в крови достоверно уменьшилась концентрация эндотоксинов (ЛПС) (на 64%), СРБ (на 14%) и ИЛ-1 (на 38%), повысился индекс оксигенации, улучшилась функция почек. ЛПС-адсорбция способствовала ослаблению клинических и лабораторных проявлений системной воспалительной реакции, снижению выраженности органной дисфункции (с 6,0 до 3,0 баллов по шкале SOFA) у пациентов с сепсисом и септическим шоком. Вывод: колонки «Токсипак» эффективно удаляют из крови эндотоксины и являются безопасными.

Сравнение эффектов селективной плазмофильтрации, плазмодиафильтрации с системами MARS и Prometheus при лечении печеночной недостаточности

The mortality of patients with hepatic failure remains high. Often the patient's life can be saved only with extracorporeal liver support (ELS). ELS systems – MARS® и Prometheus® have proved their efficacy but their widespread use is constrained by their very high cost. Introduction in clinical practice of new affordable ELS systems is a topical issue. The objective: to compare clinical and laboratory effects of selective plasma exchange (SPE), plasmadialfiltration (PDF) with use of the selective membrane plasma separators EvaclioTM and MARS® and Prometheus® (FPSA) systems in the treatment of liver failure. Subjects and methods: 15 extracorporeal procedures of each type were performed in 52 patients with acute liver failure (14) and acute-on-chronic liver failure (38): MARS, FPSA, PDF, SPE with use of Evaclio ЕС-2C, and ЕС-3C, ЕС-4C. The clinical and laboratory parameters (total, direct and indirect bilirubin, total protein, albumin, creatinine, urea, etc.), severity of the condition according to MELD score were determined before and after the session and the next morning. Changes, side effects and complications of procedures were assessed and compared. Results. Reduction of concentration of direct bilirubin was comparable with FPSA, PDF and SPE on Evaclio ЕС-3C20 и ЕС-4C20 (38-42%), indirect bilirubin – with PDF and SPE on Evaclio ЕС-3C20 и ЕС-4C20 (29-34%). Low-molecular metabolites (urea, creatinine) were better removed with FPSA (35-44%) and PDF (40-42%). The reduction of their concentration with SPE was insignificant. The reduction of albumin level was the highest with FPSA (10.2%) and SPE on Evaclio ЕС-4C20 (14.3%). All investigated ELS methods did not exert a significant influence on the basic parameters of blood coagulation and quantity of blood cells. No side effects and complications were observed. Conclusion: Selective plasma exchange and plasmadiafiltration are generally comparable in clinical and laboratory effects in the treatment of liver failure with MARS and Prometheus system provided significantly lower costs.Летальность пациентов c печеночной недостаточностью остается высокой. Часто спасение жизни пациента возможно только с использованием экстракорпоральной детоксикации (ЭКД). Системы экстракорпоральной поддержки печени MARS® и Prometheus® продемонстрировали свою эффективность, однако их широкому использованию препятствует очень высокая стоимость. Внедрение в клиническую практику новых, более доступных методов ЭКД является актуальной задачей. Цель: сравнение клинических и лабораторных эффектов процедур селективной плазмофильтрации (СПФ), плазмодиафильтрации (ПДФ) с использованием фракционаторов плазмы EvaclioTM, систем MARS® и Prometheus® (FPSA) при лечении печеночной недостаточности. Материалы и методы: 52 пациентам с острой (14) и декомпенсацией хронической печеночной недостаточности (38) выполнено по 15 экстракорпоральных процедур: MARS, FPSA, ПДФ, СПФ с использованием фракционаторов Evaclio ЕС-2C, ЕС-3C, ЕС-4C. До, сразу после и на следующее утро исследовались клинические и лабораторные (билирубин и фракции, общий белок, альбумин, мочевина, креатинин и др.) показатели, тяжесть состояния по шкале MELD. Оценивались и сравнивались их динамика, побочные эффекты и осложнения процедур. Результаты. Уменьшение концентрации прямого билирубина было сравнимо при FPSA, ПДФ и СПФ на Evaclio ЕС-3C20 и ЕС-4C20 (38‒42%), непрямого билирубина – при ПДФ и СПФ на Evaclio ЕС-3C20 и ЕС-4C20 (29‒34%). Низкомолекулярные метаболиты (мочевина и креатинин) лучше всего удалялись при FPSA (35‒44%) и ПДФ (40‒42%). Снижение их концентрации при СПФ было незначительным. Снижение уровня альбумина было наибольшим при FPSA (10,2%) и СПФ на Evaclio ЕС-4C20 (14,3%). Все исследованные методы ЭКД не оказывали существенного влияния на основные показатели системы свертывания и клеточный состав крови. Побочных реакций и осложнений не отмечено. Вывод. СПД и ПДФ по клиническим и лабораторным эффектам не уступают системам MARS® и Prometheus® при существенно меньшей стоимости

The Response of Lactococcus lactis to Membrane Protein Production

Background: The biogenesis of membrane proteins is more complex than that of water-soluble proteins, and recombinant expression of membrane proteins in functional form and in amounts high enough for structural and functional studies is often problematic. To better engineer cells towards efficient protein production, we set out to understand and compare the cellular consequences of the overproduction of both classes of proteins in Lactococcus lactis, employing a combined proteomics and transcriptomics approach. Methodology and Findings: Highly overproduced and poorly expressed membrane proteins both resulted in severe growth defects, whereas amplified levels of a soluble substrate receptor had no effect. In addition, membrane protein overproduction evoked a general stress response (upregulation of various chaperones and proteases), which is probably due to accumulation of misfolded protein. Notably, upon the expression of membrane proteins a cell envelope stress response, controlled by the two-component regulatory CesSR system, was observed. Conclusions: The physiological response of L. lactis to the overproduction of several membrane proteins was determined and compared to that of a soluble protein, thus offering better understanding of the bottlenecks related to membrane protein production and valuable knowledge for subsequent strain engineering.

Cashew nut allergy: clinical relevance and allergen characterisation

Cashew plant (Anacardium occidentale L.) is the most relevant species of the Anacardium genus. It presents high economic value since it is widely used in human nutrition and in several industrial applications. Cashew nut is a well-appreciated food (belongs to the tree nut group), being widely consumed as snacks and in processed foods by the majority of world's population. However, cashew nut is also classified as a potent allergenic food known to be responsible for triggering severe and systemic immune reactions (e.g. anaphylaxis) in sensitised/allergic individuals that often demand epinephrine treatment and hospitalisation. So far, three groups of allergenic proteins have been identified and characterised in cashew nut: Ana o 1 and Ana o 2 (cupin superfamily) and Ana o 3 (prolamin superfamily), which are all classified as major allergens. The prevalence of cashew nut allergy seems to be rising in industrialised countries with the increasing consumption of this nut. There is still no cure for cashew nut allergy, as well as for other food allergies; thus, the allergic patients are advised to eliminate it from their diets. Accordingly, when carefully choosing processed foods that are commercially available, the allergic consumers have to rely on proper food labelling. In this sense, the control of labelling compliance is much needed, which has prompted the development of proficient analytical methods for allergen analysis. In the recent years, significant research advances in cashew nut allergy have been accomplished, which are highlighted and discussed in this review.This work was supported by FCT/MEC through national funds and co-financed by FEDER, under the Partnership Agreement PT2020 with grant no. UID/QUI/50006/2013–POCI/01/ 0145/FEDER/007265. Joana Costa is grateful to FCT post-doctoral grant (SFRH/BPD/102404/2014) financed by POPH-QREN (subsidised by FSE and MCTES).info:eu-repo/semantics/publishedVersio