A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component

Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants. One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions

Первый опыт применения машинной холодовой оксигенированной перфузии почечного трансплантата от доноров с расширенными критериями

Objective: to evaluate the safety and efficacy of hypothermic oxygenated machine perfusion (HOPE) for kidney grafts obtained from expanded criteria donors (ECD).Materials and methods. From June 2018 to June 2021, 200 surgeries involving kidney transplants from deceased donors were performed at Botkin City Clinical Hospital. Of these, 123 were men (61.5%) and 77 were women (38.5%). The mean age was 47.62 ± 11.69 (20–73) years. In 102 cases, kidney grafts were procured from ECD. In 92 recipients (90.2%) of kidney transplants from an expanded criteria donor, static cold storage done according to the standard technique was used to preserve the organ; these patients constituted observation group 1. In 10 recipients (9.8%), hypothermic oxygenated perfusion was used in addition to static cold preservation; these patients formed observation group 2.Results. No 30-day mortality was recorded in both observation groups. The mean static cold storage time in group 1 patients was 612.33 ± 178.88 (133–1180) minutes. Overall incidence of delayed graft function was 26.5% (53/200). Incidence of delayed graft function was 19.3% (19/98) for organs from standard donors using static cold storage and 35.8% (33/92) for ECD organs. Twenty-five patients (12.5%) had postoperative complications. Postoperative complications with delayed graft function were diagnosed in 12 patients, which was 22.6% (12/53), with immediate function in 13 patients, which was 8.8% (13/147). Mean cold storage time in group 2 patients was 319.11 ± 110.24 (311–525) minutes. Mean HOPE time was 202.34 ± 21.48 (150–210) minutes. Delayed graft function was recorded in 1 group 2 patient (10%). No complications, including perfusion-related one, were recorded in this group.Conclusion. The unique technique used at Botkin City Clinical Hospital for HOPE in kidney transplant is safe. It provides a low risk of delayed graft function for ECD kidneys.Цель: оценить безопасность и эффективность машинной холодовой оксигенированной перфузии почечных трансплантатов от доноров с расширенными критериями.Материалы и методы. С июня 2018 года по июнь 2021 года в хирургической клинике Боткинской больницы выполнено 200 трансплантаций почки от посмертного донора. Из них 123 – мужчинам (61,5%) и 77 – женщинам (38,5%). Средний возраст составил 47,62 ± 11,69 (20–73) года. В 102 случаях почечный трансплантат был изъят у донора с расширенными критериями. У 92 реципиентов (90,2%) почечного трансплантата от донора с расширенными критериями для сохранения органа использовалась статическая холодовая консервация по стандартной методике, эти пациенты составили I группу наблюдения. У 10 реципиентов (9,8%) выполнялась постхолодовая машинная оксигенированная перфузия, эти пациенты составили II группу наблюдения.Результаты. В обеих группах наблюдения не зафиксировано 30-дневной летальности. Среднее время статической холодовой консервации у пациентов первой группы составило 612,33 ± 178,88 (133–1180) минуты. Общая частота отсроченной функции почечного трансплантата составила 26,5% (53/200). При использовании органа от стандартного донора с применением статической холодовой консервации частота развития отсроченной функции трансплантата составила 19,3% (19/98), от донора с расширенными критериями – 35,8% (33/92). Послеоперационные осложнения зафиксированы у 25 пациентов (12,5%). Послеоперационные осложнения при развитии отсроченной функции трансплантата диагностированы у 12 больных, что составило 22,6% (12/53), с немедленной функцией – у 13 больных, что составило 8,8% (13/147). Среднее время холодовой консервации у пациентов II группы составило 319,11 ± 110,24 (311–525) минуты. Среднее время машинной холодовой оксигенированной перфузии – 202,34 ± 21,48 (150–210) минуты. У 1 пациента (10%) II группы наблюдения зафиксирована отсроченная функция трансплантата. Осложнений, в том числе связанных с перфузией, в этой группе больных не зафиксировано.Заключение. Оригинальная методика Боткинской больницы по машинной холодовой оксигенированной перфузии почечного трансплантата безопасна. Ее проведение ассоциируется с низким риском развития отсроченной функции почечного трансплантата от доноров с расширенными критериями

Хэнтей-Даурская складчатая система Монголо-Охотского пояса (магматизм, седиментогенез, геодинамика)

The geostructural, petrological, geochemical, geochronological and biostratigraphic studies were conducted in the Hentei-Dauria fold system of the Mongolia-Okhotsk orogenic belt. This Paleozoic system is composed mainly of three heterochronous rock associations related to the onset and development of oceanic basins and active margins in the conjugation zone of the Siberian continent and the Mongolia-Okhotsk ocean. This region developed in three stages: (1) Late Caledonian (Ordovician – Early Silurian), (2) Early Hercynian (Late Silurian – Devonian), and (3) Late Hercynian (Carboniferous–Permian). In the Late Caledonian, oceanic seafloor spreading was initiated, deep-sea siliceous deposits were formed, basaltic and andesitic pillow lavas were erupted, and layered and cumulative gabbros, gabbro-dolerite dykes and subduction zones with island-arc magmatism were formed. After a short quiescence period, new zones of spreading and subduction occurred at the active margins of the Mongolia-Okhotsk ocean in the Early Hercynian. In the Late Hercynian, large back-arc sedimentary basins, accretionary prisms and connecting intraplate magmatic complexes were formed in all structures of the Hentei-Dauria fold system. As a result of our studies, we propose a comprehensive model showing the geodynamic development of the Hentei-Dauria fold system that occurred in the area of the Mongolia-Okhotsk Ocean and its margins.В результате проведенных структурно-геологических, петролого-геохимических, геохронологических и биостратиграфических исследований установлено, что палеозойская Хэнтей-Даурская складчатая система Монголо-Охотского орогенного пояса сложена главным образом тремя разновозрастными ассоциациями пород, связанными с заложением и развитием океанических бассейнов и активных окраин в зоне сопряженного взаимодействия Сибирского континента и Монголо-Охотского океана в течение трех этапов: 1) позднекаледонского (ордовикско-раннесилурийского), во время которого произошло заложение океанического спредингового бассейна и формирование глубоководных кремнистых отложений, излияние пиллоу-лав базальтов и андезибазальтов, образование расслоенных и кумулятивных габбро, даек габбро-долеритов, а также зон субдукции с островодужным магматизмом, 2) раннегерцинского (позднесилурийско-девонского), когда после небольшого перерыва вновь произошло заложение новых зон спрединга и субдукции на активных окраинах Монголо-Охотского океана, и 3) позднегерцинского (каменноугольно-пермского), завершившегося образованием крупных задуговых осадочных бассейнов, формированием аккреционных призм и сшивающих внутриплитных магматических комплексов во всех структурах Хэнтей-Даурской складчатой системы. На основе полученных данных разработана комплексная модель геодинамического развития Хэнтей-Даурской складчатой системы, сформированной на месте Монголо-Охотского океана и его окраин.

Комплексный подход к профилактике развития отсроченной функции почечного трансплантата

Objective: to determine the efficacy and safety of an integrated strategy aimed at preventing delayed renal graft function (DGF).Materials and methods. From June 2018 to December 2022, 478 deceased-donor kidney transplants were performed at Botkin Hospital, Moscow. The patients were divided into two groups: Group I consisted of 128 patients who did not use the integrated strategy; Group II included 67 patients in whom the DGF prevention strategy was used at the perioperative stage. The integrated strategy involved the use of hypothermic oxygenated machine perfusion (HOPE) using expanded criteria donors, the use of a second warm ischemia (SWI) elimination device, personalized initial calcineurin inhibitor (CI) dosing, and use of alprostadil for high vascular resistance in renal graft arteries.Results. DGF occurred in 5 of 44 patients (11.4%) that used the integrated strategy, and in 13 of 44 patients (29.5%) in the control group. The differences were statistically significant (p = 0.034), there was a medium strength relationship between the traits (V = 0.225). The use of the integrated DGF prevention approach reduced the chances of developing DGF by a factor of 0.3 (95% CI: 0.1–0.95). The risk of DGF in the integrated strategy group was 61.3% of the risk of DGF in the non-strategy group, thus the relative risk (RR) is 1.63 (95% CI: 1.1–2.4). Median duration of graft function normalization was statistically significantly lower in group II: 5 (IQR: 3–9) versus 15 (IQR: 7–19) days (p = 0.012). Mean length of hospital stay was 19.1 ± 4.2 (95% CI: 14.5–26.1) bed-days in group I and 13.9 ± 3.4 (95% CI: 9.3–17.2) bed-days in group II. Differences in this indicator were also statistically significant (p = 0.043).Conclusion. The set of DGF prevention measures, developed at Botkin Hospital, evidence-based and implemented in clinical practice, can reduce the burden of modifiable risk factors of this complication significantly, thereby improving treatment outcomes for kidney transplant recipients considerably.Цель: определить эффективность и безопасность применения комплексного подхода к профилактике развития отсроченной функции почечного трансплантата.Материалы и методы. С июня 2018-го по декабрь 2022 года в Городской клинической больнице имени С.П. Боткина выполнено 478 трансплантаций почки от посмертного донора. В зависимости от применения комплексного подхода больные были разделены на две группы: I группу составили 128 больных, кому не применялся комплексный подход; во II группу наблюдения были включены 67 больных, кому на периоперационном этапе применялся комплексный подход к профилактике развития отсроченной функции почечного трансплантата. Комплексный подход заключался в применении машинной оксигенированной холодовой перфузии при использовании доноров с расширенными критериями, применении устройства для элиминации вторичной тепловой ишемии, персонализированном подходе к назначению стартовой дозы ингибитора кальциневрина, применении алпростадила при высоком сосудистом сопротивлении в артериях почечного трансплантата.Результаты. Отсроченная функция почечного трансплантата при использовании комплексного подхода к ее профилактике развилась в 5 из 44 наблюдений (11,4%), в контрольной группе – у 13 из 44 пациентов (29,5%). Различия были статистически значимыми (р = 0,034), и между признаками была отмечена связь средней силы (V = 0,225). Использование комплексного профилактического подхода уменьшало шансы развития ОФПТ в 0,3 раза (95% ДИ: 0,1–0,95). Риск ОФПТ при использовании комплексного подхода составил 61,3% от риска развития отсроченной функции при отсутствии ее профилактики, таким образом, ОР = 1,63 (95% ДИ: 1,1–2,4). Медиана длительности нормализации функции трансплантата была статистически значимо ниже во II группе: 5 (IQR: 3–9) против 15 (IQR: 7–19) суток (р = 0,012). Средняя длительность госпитализации в I группе составила 19,1 ± 4,2 (95% ДИ: 14,5–26,1) койко-дня, во II – 13,9 ± 3,4 (95% ДИ: 9,3–17,2) койко-дня. Различия по данному показателю были также статистически значимыми (р = 0,043).Заключение. Разработанный в Боткинской больнице научно-обоснованный и внедренный в клиническую практику комплекс профилактических мер отсроченной функции почечного трансплантата позволяет существенно снизить бремя модифицируемых факторов риска данного осложнения и тем самым значимо улучшить результаты лечения реципиентов почечного трансплантата

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death’ (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death’ (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death

Inhibition of cathepsin B by caspase-3 inhibitors blocks programmed cell death in <i>Arabidopsis</i>

Programmed cell death (PCD) is used by plants for development and survival to biotic and abiotic stresses. The role of caspases in PCD is well established in animal cells. Over the past 15 years, the importance of caspase-3-like enzymatic activity for plant PCD completion has been widely documented despite the absence of caspase orthologues. In particular, caspase-3 inhibitors blocked nearly all plant PCD tested. Here, we affinity-purified a plant caspase-3-like activity using a biotin-labelled caspase-3 inhibitor and identified Arabidopsis thaliana cathepsin B3 (AtCathB3) by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Consistent with this, recombinant AtCathB3 was found to have caspase-3-like activity and to be inhibited by caspase-3 inhibitors. AtCathepsin B triple-mutant lines showed reduced caspase-3-like enzymatic activity and reduced labelling with activity-based caspase-3 probes. Importantly, AtCathepsin B triple mutants showed a strong reduction in the PCD induced by ultraviolet (UV), oxidative stress (H2O2, methyl viologen) or endoplasmic reticulum stress. Our observations contribute to explain why caspase-3 inhibitors inhibit plant PCD and provide new tools to further plant PCD research. The fact that cathepsin B does regulate PCD in both animal and plant cells suggests that this protease may be part of an ancestral PCD pathway pre-existing the plant/animal divergence that needs further characterisation

Pair Correlations in a Bidisperse Ferrofluid in an External Magnetic Field:Theory and Computer Simulations

The pair distribution function g(r) for a ferrofluid modeled by a bidisperse system of dipolar hard spheres is calculated. The influence of an external uniform magnetic field and polydispersity on g(r) and the related structure factor is studied. The calculation is performed by diagrammatic expansion methods within the thermodynamic perturbation theory in terms of the particle number density and the interparticle dipole–dipole interaction strength. Analytical expressions are provided for the pair distribution function to within the first order in number density and the second order in dipole–dipole interaction strength. The constructed theory is compared with the results of computer (Monte Carlo) simulations to determine the range of its validity. The scattering structure factor is determined using the Fourier transform of the pair correlation func-tion g(r) – 1. The influence of the granulometric composition and magnetic field strength on the height and position of the first peak of the structure factor that is most amenable to an experimental study is analyzed. The data obtained can serve as a basis for interpreting the experimental small[1]angle neutron scattering results and determining the regularities in the behavior of the structure factor, its dependence on the fractional com-position of a ferrofluid, interparticle correlations, and external magnetic field. © Pleiades Publishing, Inc., 2014

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field