Rule-based modelling provides an extendable framework for comparing candidate mechanisms underpinning clathrin polymerisation

Abstract Polymerisation of clathrin is a key process that underlies clathrin-mediated endocytosis. Clathrin-coated vesicles are responsible for cell internalization of external substances required for normal homeostasis and life –sustaining activity. There are several hypotheses describing formation of closed clathrin structures. According to one of the proposed mechanisms cage formation may start from a flat lattice buildup on the cellular membrane, which is later transformed into a curved structure. Creation of the curved surface requires rearrangement of the lattice, induced by additional molecular mechanisms. Different potential mechanisms require a modeling framework that can be easily modified to compare between them. We created an extendable rule-based model that describes polymerisation of clathrin molecules and various scenarios of cage formation. Using Global Sensitivity Analysis (GSA) we obtained parameter sets describing clathrin pentagon closure and the emergence/production and closure of large-size clathrin cages/vesicles. We were able to demonstrate that the model can reproduce budding of the clathrin cage from an initial flat array

Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (,23%) than the other two, COPI (,9%) and COPII (,8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest major roles for this structural property in shaping the differences of evolutionary adaptability in the three routes

Molecular architecture of the Nup84–Nup145C–Sec13 edge element in the nuclear pore complex lattice

Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport. These massive protein assemblies are modular, with a stable structural scaffold supporting more dynamically attached components. The scaffold is made from multiple copies of the heptameric Y complex and the heteromeric Nic96 complex. We previously showed that members of these core subcomplexes specifically share an ACE1 fold with Sec31 of the COPII vesicle coat, and we proposed a lattice model for the NPC based on this commonality. Here we present the crystal structure of the heterotrimeric 134-kDa complex of Nup84–Nup145C–Sec13 of the Y complex. The heterotypic ACE1 interaction of Nup84 and Nup145C is analogous to the homotypic ACE1 interaction of Sec31 that forms COPII lattice edge elements and is inconsistent with the alternative 'fence-like' NPC model. We construct a molecular model of the Y complex and compare the architectural principles of COPII and NPC lattices.National Institutes of Health (U.S.) (Grant GM77537)Pew Charitable Trusts (Scholar Award

Therapeutic efficacy in a hemophilia B model using a biosynthetic mRNA liver depot system

DNA-based gene therapy has considerable therapeutic potential, but the challenges associated with delivery continue to limit progress. Messenger RNA (mRNA) has the potential to provide for transient production of therapeutic proteins, without the need for nuclear delivery and without the risk of insertional mutagenesis. Here we describe the sustained delivery of therapeutic proteins in vivo in both rodents and non-human primates via nanoparticle-formulated mRNA. Nanoparticles formulated with lipids and lipid-like materials were developed for delivery of two separate mRNA transcripts encoding either human erythropoietin (hEPO) or factor IX (hFIX) protein. Dose-dependent protein production was observed for each mRNA construct. Upon delivery of hEPO mRNA in mice, serum EPO protein levels reached several orders of magnitude (>125 000-fold) over normal physiological values. Further, an increase in hematocrit (Hct) was established, demonstrating that the exogenous mRNA-derived protein maintained normal activity. The capacity of producing EPO in non-human primates via delivery of formulated mRNA was also demonstrated as elevated EPO protein levels were observed over a 72-h time course. Exemplifying the possible broad utility of mRNA drugs, therapeutically relevant amounts of human FIX (hFIX) protein were achieved upon a single intravenous dose of hFIX mRNA-loaded lipid nanoparticles in mice. In addition, therapeutic value was established within a hemophilia B (FIX knockout (KO)) mouse model by demonstrating a marked reduction in Hct loss following injury (incision) to FIX KO mice

Санітарно-мікробіологічні показники питної води тваринницьких ферм

The article presents data on the study of sanitary and microbiological indicators of drinking water of livestock farms. The criteria for sanitary and hygienic assessment of water from a microbiological point of view are the total amount of microflora and the presence or absence of Escherichia coli, the definition of pathogenic microorganisms, including salmonella, which characterize its fitness for consumption by animals. The main purpose of sanitary and microbiological research is to provide animals, the population with quality water, for which hygienic assessment of water of infectious safety for human and animal health is carried out. Full supply of livestock enterprises with good quality water is one of the main prerequisites for successful production of quality and safe livestock products. The goal of the work. In connection with this, the purpose of our research was to investigate the sanitary and microbiological parameters of the drinking water of livestock farms. Sanitary and microbiological studies of drinking water sources for animals were conducted. It was found that in the studied samples, the number of bacteria of the group of Escherichia coli (BGKP) in 1 liter of water (coli-index) ranges from 200 to 140 000 and more. Of all the samples tested for this indicator, only 39.4% of the reservoirs met the normative indicator. Water samples from artesian wells in 12.3% of cases did not meet the sanitary and hygienic requirements for the amount of BGKP. When carrying out sanitary-microbiological analysis of samples of water from various elements of water supply systems with respect to conditionally pathogenic microflora, it was found that the samples that were collected from the wafers had the highest degree of microbial contamination. The total number of microorganisms was 107 CFU/cm3, and the coli index exceeded 240 thousand units. Examining the water samples found that 40% of the samples had an increased amount of enterobacteria. From the samples tested, 100 cultures of conditionally pathogenic microflora were isolated, including E. faecalis – 32%, E. coli – 23%, E. cloacae – 9%, E. faecium – 11% and K. pneumoniae – 4%, of which 59.3 respectively: 30.4; 33.3; 54.5 and 75% had hemolytic properties. E. faecalis showed resistance to erythromycin, cefuroxime, benzylpenicillin, ampicillin, tetracycline, vancomycin; E. faecium – to vancomycin, ciprofloxacin, tetracycline; representatives of the family Enterobacteriacea (E. coli, K. pneumoniae, E. cloacae) – mainly to amoxicillin, streptomycin, levomycetin.У статті наведені дані щодо дослідження санітарно-мікробіологічних показників питної води тваринницьких ферм. Критеріями санітарно-гігієнічної оцінки води з мікробіологічного погляду є загальна кількість мікрофлори і наявність або відсутність у ній кишкової палички, визначення патогенних мікроорганізмів, у тому числі сальмонел, що характеризують її придатність до споживання тваринами. Основною метою санітарно-мікробіологічного дослідження є забезпечення тварин якісною водою, для чого проводиться гігієнічне оцінювання води щодо інфекційної безпеки для здоров’я людей і тварин. Повне забезпечення тваринницьких підприємств доброякісною водою в достатній кількості – одна з основних передумов успішного виробництва якісної та безпечної продукції тваринництва. В зв’язку з цим метою наших досліджень було дослідження санітарно-мікробіологічних показників питної води тваринницьких ферм. Було проведено санітарно-мікробіологічні дослідження джерел питної води для тварин. При цьому встановлено, що у досліджуваних пробах кількість бактерій групи кишкової палички (БГКП) в 1 л води (колі-індекс) коливається від 200 до 140 000 та більше. Зі всіх досліджених проб за даним показником нормативному показнику відповідало тільки 39,4% водоймищ. Проби води із артезіанських свердловин в 12,3% випадків не відповідали санітарно-гігієнічним вимогам за кількістю БГКП. При проведенні санітарно-мікробіологічного аналізу проб води з різних елементів систем водопостачання щодо умовно-патогенної мікрофлори встановили, що найвищий ступінь мікробної контамінації мали проби, які було відібрано з напувалок. Загальна кількість мікроорганізмів склала 107 КУО/см3, а колі-індекс перевищував 240 тис. одиниць. Дослідивши проби води, встановили, що 40% зразків мали підвищену кількість ентеробактерій. Із підданих дослідженню проб води виділили 100 культур умовно-патогенної мікрофлори, в тому числі Е. faecalis – 32%, Е. coli – 23%, Е. cloacae – 9%, Е. faecium – 11% і К. pneumoniae – 4%, із них відповідно 59,3; 30,4; 33,3; 54,5 і 75% були притаманні гемолітичні властивості. Е. faecalis виявили стійкість до еритроміцину, цефуроксиму, бензилпеніциліну, ампіциліну, тетрацикліну, ванкоміцину; Е. faecium – до ванкоміцину, ципрофлоксацину, тетрацикліну; представники родини Enterobacteriacea (Е. coli, К. pneumoniae, E. cloacae) – переважно до амоксициліну, стрептоміцину, левоміцетину

Ефективність комплексних дезінфікуючих заходів в умовах птахогосподарства

The key to successful work of a modern poultry industry and the safety of its products for consumers is high-quality disinfection. Modern disinfectants used in poultry farms are different in composition, concentration of active substances, means of application and other properties. Most of them are represented by imported products. Their replacement in the domestic market with effective, safe and economical drugs is extremely relevant. It should be highly effective means, possessing a wide spectrum of virilicidal, bactericidal, sporocidal and fungicidal action. The goal of the work. The purpose of our research was to evaluate the effectiveness of the complex disinfection in the production conditions of the Bi-Dez and DezSan products. Materials and methods of research. Production testing of the disinfection of poultry facilities and equipment using the Bi-dez and DezSan schemes was carried out at one of the poultry farms of the Sumy region. At the first stage, the water supply system was treated by filling the piping line with a 0.1% solution of Bi-dez with an exposure of 1 hour. At the second stage, moisture was disinfected with 0.8% solution DezSan from the rate of 0.2–0.3 liters of solution per 1 m2, exposure time – 2–3 hours. Then, in the room, the fine dispersed aerosol of this biocide was sprayed into a 10% solution (1 liter of preparation per 9 liters of water) – aerosol disinfection by fogging at a rate of 5 ml of solution per 1 m3 of space, exposure time – at least 3 hours. Results of research and discussion. Evaluating the effectiveness of disinfection of the water supply system with the Bi-dez compound, found that the total microbial contamination of the water before treatment was 235 CFU/ml. In addition to other bacteria, it was isolated from the intestinal bacillus. After the rehabilitation, the microbial water pollution decreased to 4 CFU/ml. Sanitary-indicative microorganisms (E. coli, salmonella and staphylococci) were not detected in the system faults. The total amount of microorganisms in the air after disinfection with the drug DezSan decreased by 2.6 times (12 thousand mc/m3) compared with the baseline bacterial background (29 thousand mc/m3), and the intestinal rod after treatment from the selected in the poultry house air samples were not allocated. Conclusions and prospects for further research. Reducing the microbial background and the death of opportunistic microorganisms in the premises and the system of drinking poultry farms contribute to the veterinary well-being of poultry farms. In the future, it is planned to conduct a study of the drug DezSan, identified it irritating, skin-resorptive, cumulative and other properties.В статті наведені дані щодо проведення комплексу дезінфікуючих заходів в птахівничому господарстві за використання вітчизняних препаратів Бі-дез і ДезСан. Сучасні дезінфектанти, що використовуються на птахофабриках, різні за складом, концентрацією діючих речовин, засобів застосування та іншими властивостями. Більшість з них представлено імпортними продуктами. Їх заміщення на вітчизняному ринку ефективними, безпечними і економічними препаратами вкрай актуально. Це повинні бути високоефективні засоби, що володіють широким спектром віруліцидної, бактерицидної, спороцидної і фунгіцидної дії. Виробничі випробування дезінфекції приміщень пташника та обладнання з використанням схеми Бі-дез та ДезСан провели на одній з птахофабрик Сумської області. Препарат Бі-дез був застосований для знезараження води в системі напування птиці, препарат ДезСан – у вигляді аерозолю для знезараження повітря та поверхонь пташинка. Звільнені від птиці приміщення, призначені для її підлогового утримання, дезінфікували в декілька етапів. На першому етапі обробили систему водопостачання за допомогою наповнення лінії напування 0,1% розчином Бі-дез з експозицією 1 год. На другому етапі провели вологу дезінфекцію 0,8% – розчином ДезСан із розрахунку 0,2–0,3 л розчину на 1 м2, час експозиції – 2–3 години. Потім розпиляли в приміщенні дрібнодисперсний аерозоль цього біоциду 10% розчин (1 л препарату на 9 л води) – аерозольна дезінфекція шляхом туманоутворення з розрахунку 5 мл розчину на 1 м3 приміщення, час експозиції – мінімум 3 години. Обидва препарати показали високу ефективність знезараження, що було виявлено при контролі за санітарно-показовою мікрофлорою. Оцінюючи ефективність дезінфекції системи водопостачання препаратом Бі-дез встановили, що загальна мікробна забрудненість води до обробки складала 235 КУО/мл. Крім інших бактерій з неї виділяли кишкову паличку. Після санації мікробна забрудненість води знизилися до 4 КУО/мл. Санітарно-показових мікроорганізмів (кишкової палички, сальмонел і стафілококів) в змивах системи не виявили. Загальна кількість мікроорганізмів у повітрі після проведення дезінфекції препаратом ДезСан знизилась в 2,6 раза (12 тис. м.к/м3) порівняно з вихідним бактеріальним фоном (29 тис. м.к/м3), а кишкової палички після обробки з відібраних в пташнику проб повітря не виділили

Structure of clathrin coat with bound Hsc70 and auxilin: mechanism of Hsc70-facilitated disassembly

The chaperone Hsc70 drives the clathrin assembly–disassembly cycle forward by stimulating dissociation of a clathrin lattice. A J-domain containing co-chaperone, auxilin, associates with a freshly budded clathrin-coated vesicle, or with an in vitro assembled clathrin coat, and recruits Hsc70 to its specific heavy-chain-binding site. We have determined by electron cryomicroscopy (cryoEM), at about 11 Å resolution, the structure of a clathrin coat (in the D6-barrel form) with specifically bound Hsc70 and auxilin. The Hsc70 binds a previously analysed site near the C-terminus of the heavy chain, with a stoichiometry of about one per three-fold vertex. Its binding is accompanied by a distortion of the clathrin lattice, detected by a change in the axial ratio of the D6 barrel. We propose that when Hsc70, recruited to a position close to its target by the auxilin J-domain, splits ATP, it clamps firmly onto its heavy-chain site and locks in place a transient fluctuation. Accumulation of the local strain thus imposed at multiple vertices can then lead to disassembly

Clathrin Is Spindle-Associated but Not Essential for Mitosis

Clathrin is a multimeric protein involved in vesicle coat assembly. Recently clathrin distribution was reported to change during the cell cycle and was found to associate with the mitotic spindle. Here we test whether the recruitment of clathrin to the spindle is indicative of a critical functional contribution to mitosis.Previously a chicken pre-B lymphoma cell line (DKO-R) was developed in which the endogenous clathrin heavy chain alleles were replaced with the human clathrin heavy chain under the control of a tetracycline-regulatable promoter. Receptor-mediated and fluid-phase endocytosis were significantly inhibited in this line following clathrin knockout, and we used this to explore the significance of clathrin heavy chain expression for cell cycle progression. We confirmed using confocal microscopy that clathrin colocalised with tubulin at mitotic spindles. Using a propidium iodide flow cytometric assay we found no statistical difference in the cell cycle distribution of the knockout cells versus the wild-type. Additionally, we showed that the ploidy and the recovery kinetics following cell cycle arrest with nocodazole were unchanged by repressing clathrin heavy chain expression.We conclude that the association of clathrin with the mitotic spindle and the contribution of clathrin to endocytosis are evolutionarily conserved. However we find that the contribution of clathrin to mitosis is less robust and dependent on cellular context. In other cell-lines silencing RNA has been used by others to knockdown clathrin expression resulting in an increase in the mitotic index of the cells. We show an effect on the G2/M phase population of clathrin knockdown in HEK293 cells but show that repressing clathrin expression in the DKO-R cell-line has no effect on the size of this population. Consequently this work highlights the need for a more detailed molecular understanding of the recruitment and function of clathrin at the spindle, since the localisation but not the impact of clathrin on mitosis appears to be robust in plants, mammalian and chicken B-cells

Distinct Dynamics of Endocytic Clathrin-Coated Pits and Coated Plaques

Here we classify endocytic structures at the adherent (bottom) surface of many cells in culture into shorter-lived coated pits and longer-lived coated plaques which internalize by different mechanisms

The Compartmentalized Bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum Have Membrane Coat-Like Proteins

Compartmentalized bacteria have proteins that are structurally related to eukaryotic membrane coats, and one of these proteins localizes at the membrane of vesicles formed inside bacterial cells