Serum tumor markers in pediatric osteosarcoma: a summary review

Osteosarcoma is the most common primary high-grade bone tumor in both adolescents and children. Early tumor detection is key to ensuring effective treatment. Serum marker discovery and validation for pediatric osteosarcoma has accelerated in recent years, coincident with an evolving understanding of molecules and their complex interactions, and the compelling need for improved pediatric osteosarcoma outcome measures in clinical trials. This review gives a short overview of serological markers for pediatric osteosarcoma, and highlights advances in pediatric osteosarcoma-related marker research within the past year. Studies in the past year involving serum markers in patients with pediatric osteosarcoma can be assigned to one of four categories, i.e., new approaches and new markers, exploratory studies in specialized disease subsets, large cross-sectional validation studies, and longitudinal studies, with and without an intervention

Phenological shifts of abiotic events, producers and consumers across a continent

Ongoing climate change can shift organism phenology in ways that vary depending on species, habitats and climate factors studied. To probe for large-scale patterns in associated phenological change, we use 70,709 observations from six decades of systematic monitoring across the former Union of Soviet Socialist Republics. Among 110 phenological events related to plants, birds, insects, amphibians and fungi, we find a mosaic of change, defying simple predictions of earlier springs, later autumns and stronger changes at higher latitudes and elevations. Site mean temperature emerged as a strong predictor of local phenology, but the magnitude and direction of change varied with trophic level and the relative timing of an event. Beyond temperature-associated variation, we uncover high variation among both sites and years, with some sites being characterized by disproportionately long seasons and others by short ones. Our findings emphasize concerns regarding ecosystem integrity and highlight the difficulty of predicting climate change outcomes. The authors use systematic monitoring across the former USSR to investigate phenological changes across taxa. The long-term mean temperature of a site emerged as a strong predictor of phenological change, with further imprints of trophic level, event timing, site, year and biotic interactions.Peer reviewe

Escherichia coli isolated from cases of colibacillosis in Russian poultry farms (Perm Krai)

Escherichia coli strains isolated from case of colibacillosis in Russian poultry farms in the region of Perm Krai were analyzed for their sensitivity to main antibiotics and bacteriocins. Sensitivity profiles for 9 antibiotics and 20 bacteriocins were determined with the disc diffusion method and the overlay test, respectively. Further, with the PCR the presence of several bla and integron 1 genes was revealed and the phylogenetic group for each strain determined. Among the 28 studied E. coli strains 85.7% were resistant to at least three antibiotics, 53.6% to five or more drugs, and 10.7% to eight antibiotics. PCR revealed that the bla$_{TEM}$ gene was harbored by 71.4% of strains and the bla$_{CTX-M}$ gene by 53.6% of strains. The class 1 integrons were found in 28.6% of strains. All of the studied strains were insensitive to ten or more bacteriocins. More than 90% of the studied strains were insensitive to pore-forming colicins of group A and B colicins, while 60.7% were insensitive to colicins with DNase and RNase activity. All of the analyzed strains were insensitive to at least two of the tested microcins. Neither the antibiotic resistance profile nor the bacteriocin resistance profile correlated with phylogenetic group of the strains. Thus, the studied strains were shown to possess high levels of multiple resistance to antibiotics and insensitivity to bacteriocins

Maternal genetic features of the Iron Age Tagar population from Southern Siberia (1st millennium BC).

Early nomads in the Eurasian steppes since the beginning of the 1st millennium BC played a key role in the formation of the cultural and genetic landscape of populations of a significant part of Eurasia, from Eastern Europe to Eastern Central Asia. Numerous archaeological cultures associated with early nomads have been discovered throughout the Eurasian steppe belt. The Tagar archaeological culture existed in the Minusinsk basin (Sayan Mountains, Southern Siberia, Russia) in the northeastern periphery of the Eurasian steppe belt from the 8th to 1st century BC during the pre-Scythian, Scythian, and Early Xiongnu-Sarmatian periods. In this study, we evaluated mtDNA diversity in the Tagar population based on representative series (N = 79) belonging to all chronological stages of the culture. The Tagar population had a mixed mtDNA pool dominated by Western Eurasian haplogroups and subgroups (H, HV6, HV*, I, K, T, U2e, U4, U5a, and U*) and, to a lesser degree, Eastern Eurasian haplogroups (A*, A8, C*, C5, D, G2a, and F1b). The Tagar population showed a similar mtDNA pool structure to those of other Iron Age populations representing the "Scythian World." We observed particularly high similarity between the Tagar and Classic Scythians from the North Pontic region. Our results support the assumption that genetic components introduced by Bronze Age migrants from Western Eurasia contributed to the formation of the genetic composition of Scythian period populations in Southern Siberia. Another important component of the Tagar mtDNA pool was autochthonous East Eurasian lineages, some of which (A8 and C4a2a) are potential markers of the westward genetic influence of the eastern populations of the Scythian period. Our results suggest a genetic continuity (at least partial) between the Early, Middle, and Late Tagar populations

Differences in spatial versus temporal reaction norms for spring and autumn phenological events

For species to stay temporally tuned to their environment, they use cues such as the accumulation of degree-days. The relationships between the timing of a phenological event in a population and its environmental cue can be described by a population-level reaction norm. Variation in reaction norms along environmental gradients may either intensify the environmental effects on timing (cogradient variation) or attenuate the effects (countergradient variation). To resolve spatial and seasonal variation in species' response, we use a unique dataset of 91 taxa and 178 phenological events observed across a network of 472 monitoring sites, spread across the nations of the former Soviet Union. We show that compared to local rates of advancement of phenological events with the advancement of temperature-related cues (i.e., variation within site over years), spatial variation in reaction norms tend to accentuate responses in spring (cogradient variation) and attenuate them in autumn (countergradient variation). As a result, among-population variation in the timing of events is greater in spring and less in autumn than if all populations followed the same reaction norm regardless of location. Despite such signs of local adaptation, overall phenotypic plasticity was not sufficient for phenological events to keep exact pace with their cues-the earlier the year, the more did the timing of the phenological event lag behind the timing of the cue. Overall, these patterns suggest that differences in the spatial versus temporal reaction norms will affect species' response to climate change in opposite ways in spring and autumn

Содержание нейроспецифических пептидов, маркеров нейромессенджера и нейрорецептора в сыворотке крови детей с вариативными сенсорными расстройствами, легкими когнитивными нарушениями и другой нейропатологией

Background. The role of recently discovered neurospecific peptides in the pathogenesis of acute and progressive neurologic disorders, their neuroprotective features, and possibilities to use them as markers for the course and prognosis of certain diseases have been actively studied in recent decades. However, neurospecific peptides are almost not studied in chronic residual diseases. In our study we measured the levels of neurospecific peptides and some other markers to achieve understanding of general neurophysiological trends in congenital and acquired chronic non-progressive brain pathology with reference to the selection of relevant groups — study objects. Objective. The aim of the study is to study patterns of neurospecific peptides, neurotransmitters and neuroreceptor markers distribution in the serum of children with various pathogenetic variants of chronic neuropathology. Methods. The study included children from 3 to 16 years old with different pathologies. The sample was divided into groups by pathology type: no sensory and neurological disorders, congenital sensory deficit due to mutation of genes expressed and not expressed in the brain, early acquired sensory deficit of multifactorial nature, congenital mild and severe organic disorders of central nervous system (CNS) in residual stage without baseline sensory deficit, acquired functional CNS disorders without baseline organic defect and sensory deficit. The following laboratory data (neurophysiological components) was studied: nerve growth factor, brain-derived neurotropic factor, neurotrophin-3, neurotrophin-4, neuregulin-1-beta-1, beta-secretase, sirtuin-1, synaptophysin, neuronal nitric oxide synthase, and anti-NR2 glutamate receptor antibodies. The parameters of cognitive activity, sense of vision, sense of smell, and acoustic sense were also evaluated. Results. The study included 274 participants. Neuropeptides and markers have shown a variable degree and range in the group spectrum of differences from normal levels. The most variable in the examined sample was NO-synthase, as well as levels of both neurotrophins, beta-secretase, and glutamate receptor marker. All visual deficits were associated with increased NO-synthase levels (p < 0.001). Neuroplasticity peptides (beta-secretase, neurotrophin-3 and 4) have been activated in all pathological conditions. Nerve growth factor and brain-derived neurotropic factor were specifically activated in mild organic CNS lesions (mild cognitive impairments), while neuregulin — in congenital genetically determined visual deficits. There was no specific activation of neuropeptides and NO-synthase level tended to decrease in cases of severe CNS lesions. Conclusion. The study results suggest that all types of early visual impairment are associated with increased physiological neuronal activity, and non-organic neurological functional disorders — mainly with increased physiological synaptic activity. General neuroplasticity processes were activated in all cases of visual deficits but more specific. However, more specific and well-studied processes were activated in mild organic CNS lesions, and neuroplasticity processes did not activate adequately in severe organic CNS lesions probably due to the limited neuronal and synaptic resources.Обоснование. В последние десятилетия активно исследуются вклад недавно открытых нейроспецифических пептидов в патогенез ряда острых и прогрессирующих заболеваний нервной системы, их нейропротективные свойства и возможности их использования для маркирования течения и прогноза некоторых заболеваний. При этом нейроспецифические пептиды почти не изучаются при хронических резидуальных состояниях. В нашем исследовании мы использовали определение уровней нейроспецифических пептидов и некоторых других маркеров для достижения понимания генеральных нейрофизиологических тенденций при врожденной и приобретенной хронической непрогрессирующей патологии мозга на основании подбора соответствующих групп — объектов исследования. Цель исследования — изучить закономерности распределения комплекса нейроспецифических пептидов, маркеров нейромессенджера и нейрорецептора в сыворотке крови детей с различными патогенетическими вариантами хронической нейропатологии. Методы. В исследование были включены дети с различной патологией в возрасте от 3 до 16 лет. Выборка была поделена на группы по типу патологии: отсутствие сенсорных и неврологических нарушений, врожденный сенсорный дефицит вследствие мутации генов, экспрессируемых и не экспрессируемых в мозге, рано приобретенный сенсорный дефицит полиэтиологической природы, врожденные легкие и тяжелые органические нарушения функций центральной нервной системы (ЦНС) в резидуальной стадии без исходного сенсорного дефицита, приобретенные функциональные расстройства ЦНС без исходного органического дефекта и сенсорного дефицита. В батарею измеряемых лабораторно в крови нейрофизиологических компонентов включили фактор роста нервов, нейротрофический фактор мозга, нейротрофин-3, нейротрофин-4, нейрегулин-1-бета-1, бета-секретазу, сиртуин-1, синаптофизин, нейрональную синтазу оксида азота и антитела к глутаматному рецептору NR2. Также оценивались параметры когнитивной деятельности, зрения, обоняния и слухового восприятия. Результаты. В исследование включены 274 участника. Установлено, что нейропептиды и маркеры показали вариативную степень и широту по групповому спектру отличий от нормы. Наиболее изменчивой в обследуемой выборке показала себя NO-синтаза, также часто различались уровни обоих нейротрофинов, бета-секретазы и маркера рецептора глутамата. При любых дефицитах зрения с большой достоверностью был повышен уровень NO-синтазы (р < 0,001). При всех патологических состояниях активировались пептиды нейропластичности — бета-секретаза, нейротрофины-3 и -4. При легких органических поражениях ЦНС (легкие когнитивные нарушения) специфично активировались фактор роста нервов и мозговой нейротрофический фактор, а при врожденных генетически детерминированных зрительных дефицитах специфично активировался нейрегулин. При тяжелых поражениях ЦНС специфической активации нейропептидов не определялось, а уровень NO-синтазы демонстрировал тенденцию к снижению по сравнению с нормой. Заключение. Результаты исследования позволяют предположить, что при всех типах раннего слабовидения происходит повышенная напряженность физиологической нейрональной деятельности, а при неорганических неврологических функциональных расстройствах — преимущественно повышение физиологической синаптической активности. При всех дефицитах зрения активированы процессы общей нейропластичности, но более специфические и изученные из них активируются при легких органических поражениях ЦНС, при тяжелых же органических поражениях ЦНС процессы нейропластичности недостаточно активны, вероятно, вследствие ограниченности нейрональных и синаптических ресурсов

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective

Population genomics of post-glacial western Eurasia

Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations

Population genomics of post-glacial western Eurasia

Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations