The new base excision repair pathway in mammals mediated by tyrosyl-DNA-phosphodiesterase 1

Human tyrosyl-DNA phosphodiesterase 1 (Tdp1) hydrolyzesthe phosphodiester bond at a DNA 3' end linked to a tyrosyl moiety and has been implicated in the repair of Topoisomerase I (TopI )-DNA covalent complexes. Tdp1 can also hydrolyze other 3' end DNA alterations including 3' phosphoglycolate and 3' abasic (AP) sites, and exhibits the 3' nucleosidase activity indicating that it may function as a general 3' end-processing DNA repair enzyme. Recently we have shown a new Tdp1 activity generating DNA strand break with the 3' phosphate termini from the AP site. AP sites are formed spontaneously and are inevitable intermediates during base excision repair of DNA base damages. AP sites are both mutagenic and cytotoxic, and key enzymes for their removal are AP endonucleases. However, AP endonuclease independent repair, initiated by DNA glycosylases performing beta, delta-elimination cleavage of the AP sites, has been described in mammalian cells. Here, we describe another AP endonuclease independent repair pathway for removal of AP sites that is initiated by tyrosyl phosphodiesterase Tdp1. We propose that repair is completed by the action of a polynucleotide kinase, a DNA polymerase and finally a DNA ligase to seal the gap Keywords: base excision repair, AP site, tyrosyl-DNA phosphodiesterase 1.Тирозил-ДНК-фосфодіестераза 1 (Tdp1) людини гідролізує 3'-фосфотирозильні зв’язки, які утворюються in vivo в результаті приєднання до ДНК-топоізомерази I (TopI). Tdp1 людини також здатна видаляти з 3'-кінця ДНК інші модифікувальні групи, включаючи 3'-фосфогліколати і залишки дезоксирибози, тобто функціонувати як 3'-фосфодіестераза і фермент репарації. Недавно ми показали, що Tdp1 людини притаманна ще одна активність – вона може гідролізувати апуринові/апіримідинові (АР) сайти всередині ланцюга ДНК з утворенням 3'-кінцевого фосфату. АР-сайти – це одне з найчастіше виникаючих пошкоджень ДНК. Ключовим ферментом, який розщеплює АР-сайти, є апуринова/апіримідинова ендонуклеаза 1 (АРЕ1). Проте в клітинах ссавців існує шлях репарації, незалежний від АРЕ1, у якому беруть участь ДНК-глікозилази. У даній роботі описано ще один АРЕ1-незалежний шлях репарації АР-сайтів за участі Tdp1. До повного циклу репарації залучені полінуклеотидкіназа/фосфатаза, яка має 3'-фосфатазну активність, ДНК-полімераза та ДНК-лігаза. Ключові слова: ексцизійна репарація основ, АР-сайт, тирозил-ДНК-фосфодіестераза 1.Тирозил-ДНК-фосфодиэстераза 1 (Tdp1) человека гидролизует 3'- фосфотирозильные связи, образующиеся in vivo в результате присоединения к ДНК-топоизомеразе I (TopI). Tdp1 человека также способна удалять с 3'-конца ДНК другие модифицирующие группы, включая 3'-фосфогликолаты и остатки дезоксирибозы, т. е. функционировать как 3'-фосфодиэстераза и фермент репарации. Недавно мы показали, что Tdp1 человека обладает еще одной активностью – она может гидролизовать апуриновые/апиримидиновые (АР) сайты внутри цепи ДНК с образованием 3'концевого фосфата. АР-сайты – это одно из наиболее часто возникающих повреждений в ДНК. Ключевым ферментом, расщепляющим АР-сайты, является апуриновая/апиримидиновая эндонуклеаза 1 (АРЕ1). Однако в клетках млекопитающих существует путь репарации, независимый от АРЕ1, с участием ДНК-гликозилаз. В данной работе описан еще один АРЕ1-независимый путь репарации АР-сайтов с участием Tdp1. В полный цикл репарации вовлечены полинуклеотидкиназа/фосфатаза, обладающая 3'-фосфатазной активностью, ДНК-полимераза и ДНК-лигаза. Ключевые слова: эксцизионная репарация оснований, АР-сайт, тирозил-ДНК-фосфодиэстераза 1

Снижение сывороточного уровня морфогенетического белка Klotho у больных хронической болезнью почек: клиническое значение

Objective: to determine the role of serum Klotho (s-Klotho) protein levels changes in patients with different stages of chronic kidney disease (CKD).Methods: The study involved 130 patients with CKD stages 1–5D (mean age ― 41±6.7 years). Serum levels of parathyroid hormone (PTH), calcium, phosphorus and s-Klotho protein (ELISA method) at baseline and after 1 year of follow-up were examined in all the patients so as the blood pressure (BP), including central (aortic), pulse wave velocity ― with the help of «Sphygmоcor» (Australia), echocardiography, radiography of the abdominal aorta in a lateral projection were also performed.Results: when comparing the s-Klotho levels in patients with different CKD stages, it was found that the level change associated with the reduction of glomerular filtration rate (GFR) ahead of phosphorus and PTH increase in serum, stared at 3A CKD, whereas hyperphosphatemia and PTH increase started at 4–5 CKD stages. According to ROC analysis, decreasing of s-Klotho levels below 387 pg/ml was indicated a calcification risk of abdominal aorta increased with an 80% sensitivity and 75% specificity. In addition, a strong negative relationship of low s-Klotho levels and heart remodeling was found. When comparing the patients with hypertension who were receiving antihypertensive monotherapy, the highest serum levels of Klotho protein were observed in those of them whose target blood pressure level was achieved primarily through Angiotensin II Receptors Blockers (ARB), compared to those who was administered another drug group (p0.01) or has not reached the target blood pressure level (p=0,008).Conclusion: The change of serum Klotho levels (decrease) in CKD progression is associated with the degree (increase) of cardiovascular calcification and remodeling (the development of left ventricular hypertrophy, and cardiomyopathy) and it can be seen as an early independent marker of the cardiovascular system lesions in CKD. Our preliminary data of the effect of blood pressure correction on s-Klotho levels may indicate the possibility of drug maintaining serum Klotho levels and it requires further research.Цель исследования: определить значение изменения сывороточного уровня белка Klotho (s-Klotho) у пациентов с хронической болезнью почек (ХБП) 1–5D стадий.Методы. Обследованы 130 больных ХБП 1–5D стадий (67 мужчин и 63 женщины; средний возраст 41±6,7 года). Причинами ХБП у обследованных больных были хронический гломерулонефрит ― у 30, тубулоинтерстициальный нефрит (лекарственной, подагрической этиологии) ― у 23, поликистоз почек ― у 22, гипертензивный нефросклероз ― у 28, сахарный диабет 2-го типа ― у 27. У всех больных исходно и через 1 год наблюдения исследованы сывороточные уровни паратиреоидного гормона (ПТГ), кальция, фосфора, белка s-Klotho (методика ELISA). Всем пациентам измеряли уровень артериального давления (АД), в том числе центрального (аортального), скорость пульсовой волны с помощью аппарата SphygmоCor (Австралия); выполняли эхокардиографию, рентгенографию брюшной аорты в боковой проекции.Результаты. При сравнении уровня s-Klotho у больных с разными стадиями ХБП оказалось, что по мере снижения скорости клубочковой фильтрации (СКФ) его изменение в сыворотке начинается уже с 3А стадии ХБП и опережает повышение уровня фосфора и ПТГ, которые отмечены с 4–5-й стадии ХБП. Согласно ROC-анализу, значение s-Klotho ниже 387 пг/мл с чувствительностью 80% и специфичностью 75% свидетельствовало об увеличении риска кальцификации aбдоминальной аорты. Кроме того, выявлена cтатистически значимая отрицательная взаимосвязь низкого уровня s-Klotho c ремоделированием сердца (развитие гипертрофии левого желудочка и кардиомиопатии). При сравнении пациентов с артериальной гипертензией, которые получали антигипертензивную монотерапию, наиболее высокий уровень белка s-Klotho отмечен у пациентов, у которых целевой уровень АД был достигнут преимущественно с помощью блокаторов рецепторов к ангиотензину II, по сравнению с теми, кто использовал другие группы препаратов (р0,01) или не достиг целевого уровня АД (p=0,008).Заключение. Изменение сывороточного уровня Klotho (снижение) по мере прогрессирования ХБП ассоциировано с увеличением степени ремоделирования сердца и кальцификации сердца и сосудов и может рассматриваться в качестве раннего самостоятельного маркера поражения сердечно-сосудистой системы при ХБП. Полученные нами предварительные данные о влиянии коррекции АД на уровень s-Klotho свидетельствуют о возможности медикаментозного поддержания сывороточного уровня s-Klotho и требуют дальнейших исследований

Diffusive dynamics and jamming in ensembles of robots with variable friction

In the present paper, we experimentally study the diffusive dynamics in ensembles of self-propelled and self-rotating bristle-bots. Considering the dependence of the system dynamics on the packing density of robots as well as on the friction between individual robots, we show that the friction slightly affects the diffusive dynamics but leads to a significant change in the jamming transition corresponding to the formation of rigid clusters of robots

Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings

Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice

Virtual Ontogeny of Cortical Growth Preceding Mental Illness

Background: Morphology of the human cerebral cortex differs across psychiatric disorders, with neurobiology and developmental origins mostly undetermined. Deviations in the tangential growth of the cerebral cortex during pre/perinatal periods may be reflected in individual variations in cortical surface area later in life. Methods: Interregional profiles of group differences in surface area between cases and controls were generated using T1-weighted magnetic resonance imaging from 27,359 individuals including those with attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depressive disorder, schizophrenia, and high general psychopathology (through the Child Behavior Checklist). Similarity of interregional profiles of group differences in surface area and prenatal cell-specific gene expression was assessed. Results: Across the 11 cortical regions, group differences in cortical area for attention-deficit/hyperactivity disorder, schizophrenia, and Child Behavior Checklist were dominant in multimodal association cortices. The same interregional profiles were also associated with interregional profiles of (prenatal) gene expression specific to proliferative cells, namely radial glia and intermediate progenitor cells (greater expression, larger difference), as well as differentiated cells, namely excitatory neurons and endothelial and mural cells (greater expression, smaller difference). Finally, these cell types were implicated in known pre/perinatal risk factors for psychosis. Genes coexpressed with radial glia were enriched with genes implicated in congenital abnormalities, birth weight, hypoxia, and starvation. Genes coexpressed with endothelial and mural genes were enriched with genes associated with maternal hypertension and preterm birth. Conclusions: Our findings support a neurodevelopmental model of vulnerability to mental illness whereby prenatal risk factors acting through cell-specific processes lead to deviations from typical brain development during pregnancy

Reproducibility in the absence of selective reporting : An illustration from large-scale brain asymmetry research

Altres ajuts: Max Planck Society (Germany).The problem of poor reproducibility of scientific findings has received much attention over recent years, in a variety of fields including psychology and neuroscience. The problem has been partly attributed to publication bias and unwanted practices such as p-hacking. Low statistical power in individual studies is also understood to be an important factor. In a recent multisite collaborative study, we mapped brain anatomical left-right asymmetries for regional measures of surface area and cortical thickness, in 99 MRI datasets from around the world, for a total of over 17,000 participants. In the present study, we revisited these hemispheric effects from the perspective of reproducibility. Within each dataset, we considered that an effect had been reproduced when it matched the meta-analytic effect from the 98 other datasets, in terms of effect direction and significance threshold. In this sense, the results within each dataset were viewed as coming from separate studies in an "ideal publishing environment," that is, free from selective reporting and p hacking. We found an average reproducibility rate of 63.2% (SD = 22.9%, min = 22.2%, max = 97.0%). As expected, reproducibility was higher for larger effects and in larger datasets. Reproducibility was not obviously related to the age of participants, scanner field strength, FreeSurfer software version, cortical regional measurement reliability, or regional size. These findings constitute an empirical illustration of reproducibility in the absence of publication bias or p hacking, when assessing realistic biological effects in heterogeneous neuroscience data, and given typically-used sample sizes

Subcortical volumes across the lifespan: data from 18,605 healthy individuals aged 3-90 years

Age has a major effect on brain volume. However, the normative studies available are constrained by small sample sizes, restricted age coverage and significant methodological variability. These limitations introduce inconsistencies and may obscure or distort the lifespan trajectories of brain morphometry. In response, we capitalized on the resources of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Consortium to examine age-related trajectories inferred from cross-sectional measures of the ventricles, the basal ganglia (caudate, putamen, pallidum, and nucleus accumbens), the thalamus, hippocampus and amygdala using magnetic resonance imaging data obtained from 18,605 individuals aged 3-90 years. All subcortical structure volumes were at their maximum value early in life. The volume of the basal ganglia showed a monotonic negative association with age thereafter; there was no significant association between age and the volumes of the thalamus, amygdala and the hippocampus (with some degree of decline in thalamus) until the sixth decade of life after which they also showed a steep negative association with age. The lateral ventricles showed continuous enlargement throughout the lifespan. Age was positively associated with inter-individual variability in the hippocampus and amygdala and the lateral ventricles. These results were robust to potential confounders and could be used to examine the functional significance of deviations from typical age-related morphometric patterns.Education and Child Studie

Methodical questions on assasment of risk associated with behavioral factors’ impact on population health

The study offers an algorithm and methods for semi-quantitative assessment of health risk associated with impact of behavioral factors that have scarce data for quantitative parametrization of the “factor – response” relation. Some of these factors include, first of all, irresponsible medical and hygienic behavior, violations of work and rest, sleep and wakefulness schedule. It was shown that the semi-quantitative risk assessment assumes the development of private mark scales for each estimated behavioral factor, as well as a choice of an integration way of scores, a choice of a way for establishing the negative effects’ severity, formation of risk matrix. For example, the factor "irresponsible health behavior" demonstrates the method of the mark characteristics of the risk taking potential of separate risk components to be used in calculating of the individual and integrated indexes of health deterioration probability. The following components have been taken into account: a) timeliness of visiting a doctor, b) the practice of preventive examinations, c) compliance (commitment to the treatment appointed by a doctor), d) reception of medicines without appointment of the doctor, e) the request for the recommendation of medicines and methods of treatment to someone, except the doctor. The study offers a logical scheme of the behavioral risk factor analysis at the individual level for using on a stage of the exposure evaluation. It was shown that the tools used for exposure characterization must assume the possibility for assessment of the typicality and stability of behavioral patterns realized by individuals or a group. It is recommended to apply the matrix for semi-quantitative assessment of health risks associated with the activity of behavioral factors. The matrix combines two types of descriptors that both characterize a semi – quantitative probability assessment and assess the adverse effect severity