Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single-cell level.

Drafting gene regulatory networks (GRNs) requires embryological knowledge pertaining to the cell type families, information on the regulatory genes, causal data from gene knockdown experiments and validations of the identified interactions by cis-regulatory analysis. We use multi-omics involving next-generation sequencing to obtain the necessary information for drafting the Strongylocentrotus purpuratus (Sp) posterior gut GRN. Here, we present an update to the GRN using: (1) a single-cell RNA-sequencing-derived cell atlas highlighting the 2 day-post-fertilization (dpf) sea urchin gastrula cell type families, as well as the genes expressed at the single-cell level; (2) a set of putative cis-regulatory modules and transcription factor-binding sites obtained from chromatin accessibility ATAC-seq data; and (3) interactions directionality obtained from differential bulk RNA sequencing following knockdown of the transcription factor Sp-Pdx1, a key regulator of gut patterning in sea urchins.

Nanometer flat blazed x-ray gratings using ion beam figure correction.

With the development of nanometer accuracy stitching interferometry, ion beam figuring (IBF) of x-ray mirrors can now be achieved with unprecedented performance. However, the process of producing x-ray diffraction gratings on these surfaces may degrade the figure quality due to process errors introduced during the ruling of the grating grooves. To address this challenge, we have investigated the post-production correction of gratings using IBF, where stitching interferometry is used to provide in-process feedback.

Advanced low blaze angle x-ray gratings via nanoimprint replication and plasma etch.

We developed a new method of making ultra-low blaze angle diffraction gratings for x-ray applications. The method is based on reduction of the blaze angle of a master grating by nanoimprint replication followed by a plasma etch. A master blazed grating with a relatively large blaze angle is fabricated by anisotropic wet etching of a Si single crystal substrate.

Single-Cell Transcriptomic Analysis Reveals the Molecular Profile of Go-Opsin Photoreceptor Cells in Sea Urchin Larvae.

The ability to perceive and respond to light stimuli is fundamental not only for spatial vision but also to many other light-mediated interactions with the environment. In animals, light perception is performed by specific cells known as photoreceptors and, at molecular level, by a group of GPCRs known as opsins. Sea urchin larvae possess a group of photoreceptor cells (PRCs) deploying a Go-Opsin (Opsin3.

Active DNA demethylation of developmental -regulatory regions predates vertebrate origins.

DNA methylation [5-methylcytosine (5mC)] is a repressive gene-regulatory mark required for vertebrate embryogenesis. Genomic 5mC is tightly regulated through the action of DNA methyltransferases, which deposit 5mC, and ten-eleven translocation (TET) enzymes, which participate in its active removal through the formation of 5-hydroxymethylcytosine (5hmC). TET enzymes are essential for mammalian gastrulation and activation of vertebrate developmental enhancers; however, to date, a clear picture of 5hmC function, abundance, and genomic distribution in nonvertebrate lineages is lacking.

An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes.

Transcription factors are crucial drivers of cellular differentiation during animal development and often share ancient evolutionary origins. The T-box transcription factor Brachyury plays a pivotal role as an early mesoderm determinant and neural repressor in vertebrates; yet, the ancestral function and key evolutionary transitions of the role of this transcription factor remain obscure. Here, we present a genome-wide target-gene screen using chromatin immunoprecipitation sequencing in the sea anemone Nematostella vectensis, an early branching non-bilaterian, and the sea urchin Strongylocentrotus purpuratus, a representative of the sister lineage of chordates.

6000 lines/mm blazed grating for a high-resolution x-ray spectrometer.

We have designed and fabricated a high groove density blazed grating for a Resonant Inelastic X-ray Scattering spectrometer for the new Qerlin beamline at the Advanced Light Source (ALS) synchrotron facility. The gratings were fabricated using a set of nanofabrication techniques including e-beam lithography, nanoimprint, plasma etch, and anisotropic wet etching. Two gratings with groove density of 6000 lines/mm and 3000 lines/mm and optimized for operation in the 1 and 2 negative diffraction order respectively were fabricated and tested.

A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin .

Molecular research on the evolution of extraocular photoreception has drawn attention to photosensitive animals lacking proper eye organs. Outside of vertebrates, little is known about this type of sensory system in any other deuterostome. In this study, we investigate such an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin .

Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota.

Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column.

Single-cell RNA sequencing of the larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome.

Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. Here, we use single-cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva, representing an important developmental transition from non-feeding to feeding larva. We identify 21 distinct cell clusters, representing cells of the digestive, skeletal, immune, and nervous systems.

Highly efficient ultra-low blaze angle multilayer grating.

We have developed an advanced process for blaze angle reduction of x-ray gratings for the soft, tender, and EUV spectral ranges. The process is based on planarization of an anisotropically etched Si blazed grating followed by a chemically selective plasma etch. This provides a way to adjust the blaze angle to any lower value with high accuracy.

ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos.

Cis-regulatory elements (CREs) and transcription factors (TFs) associated with them determine temporal and spatial domains of gene expression. Therefore, identification of these CREs and TFs is crucial to elucidating transcriptional programs across taxa. With chromatin accessibility facilitating transcription factor access to DNA, the identification of regions of open chromatin sheds light both on the function of the regulatory elements and their evolution, thus allowing the recognition of potential CREs.

Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol'shie Khruslomeny at the White Sea Coast.

Microbiological, molecular ecological, biogeochemical, and isotope geochemical research was carried out at the polar Lake Bol'shie Khruslomeny at the coast of the Kandalaksha Bay, White Sea in March and September 2017. The uppermost mixolimnion was oxic, with low salinity (3-5%). The lower chemocline layer was brown-green colored, with very high content of particulate organic matter (up to 11.

Using ATAC-seq and RNA-seq to increase resolution in GRN connectivity.

Echinoderms have some of the most complete reconstructed developmental gene regulatory networks (GRN) of any embryo, accounting for the formation of most embryo tissues and organs. Yet, many nodes (genes and regulators) and their regulatory interactions are still to be uncovered. Traditionally, knockdown/knockout experiments are performed to determine regulator-gene interactions, which are individually validated by cis-regulatory analysis.

Do Corticosteroids Still Have a Place in the Treatment of Chronic Pain?

Corticosteroids have played a standard role in the multimodal pain management in the treatment of chronic spinal pain (cervical and lumbar) and osteoarthritis pain over the past three decades. In this review we discuss different types of injectable steroids that are mainly used for injection into the epidural space (for the treatment of radicular back and neck pain), and as intra-articular injections for different types of osteoarthritis related pain conditions. Furthermore, we discuss different approaches taken for epidural corticosteroid injections and spinal surgical rates when injections fail to resolve painful conditions, as well as the possibility of using local anesthetics alone for neuraxial injections, instead of in combination with corticosteroids.

[Possibilities of retention of work capacity in patients with Parkinson's disease].

Aim: To study the efficacy of replacement of the single daily dose of two-component levodopa by three-component levodopa in work capable patients with Parkinson's disease with motor fluctuations during the most active working hours.

Material And Methods: The study included 157 patients from 19 Russian centers specialized in extrapyramidal pathology. The period of highest working activity was analyzed in all patients.

Ultra-low blaze angle gratings for synchrotron and free electron laser applications.

We have developed a method for the manufacture of x-ray diffraction gratings with arbitrarily small blaze angles. These gratings are made by a process in which a high blaze angle grating made by anisotropic etching of Si (111) is subjected to planarization and reactive ion etching. Differential etching of the planarization medium and silicon ensures reduction of the blaze angle.

Electrophysiology of the rhythmic defecation program in nematode Heterorhabditis megidis.

The nervous system controls most rhythmic behaviors, with a remarkable exception. In Caenorhabditis elegans periodic defecation rhythm does not appear to involve the nervous system. Such oscillations are studied in detail with genetic and molecular biology tools.

Large area nanoimprint enables ultra-precise x-ray diffraction gratings.

A process for fabrication of ultra-precise diffraction gratings for high resolution x-ray spectroscopy was developed. A grating pattern with constant or variable line spacing (VLS) is recorded on a quartz plate by use of e-beam lithography with nanometer scale accuracy of the groove placement. The pattern is transferred to a massive grating blank by large area nanoimprint followed by dry or/and wet etching for groove shaping.

Lacrimal Gland Repair Using Progenitor Cells.

In humans, the lacrimal gland (LG) is the primary contributor to the aqueous layer of the tear film. Production of tears in insufficient quantity or of inadequate quality may lead to aqueous-deficiency dry eye (ADDE). Currently there is no cure for ADDE.

The NuMask® is as Effective as the Face Mask in Achieving Maximal Preoxygentation.

Background: Preoxygenation before anesthetic induction is a widely accepted maneuver to increase oxygen reserves and delay desaturation during apnea. There is limited data regarding the use of the NuMask® in the perioperative setting, and no data as to its efficacy in achieving maximal preoxygenation. We hypothesize that the NuMask® may be a useful alternative to the face mask in achieving maximal preoxygenation.

Refraction effects in soft x-ray multilayer blazed gratings.

A 2500 lines/mm Multilayer Blazed Grating (MBG) optimized for the soft x-ray wavelength range was fabricated and tested. The grating coated with a W/BC multilayer demonstrated a record diffraction efficiency in the 2nd blazed diffraction order in the energy range from 500 to 1200 eV. Detailed investigation of the diffraction properties of the grating demonstrated that the diffraction efficiency of high groove density MBGs is not limited by the normal shadowing effects that limits grazing incidence x-ray grating performance.

[Results of comprehensive management of patients with chronic lower limb ischaemia using gene-engineering technologies of angiogenesis stimulation (Part 2)].

Presented herein are the results of clinical use of gene engineering methods of stimulating angiogenesis in patients with lower limb chronic ischaemia. An open prospective controlled clinical study included a total of 160 patients with lower limb chronic ischaemia. Gene engineering technologies of angiogenesis stimulation were used both as an independent method of treatment in comprehensive conservative therapy (80 patients) and as comprehensive treatment in combination with revascularizing operations (80 patients).

[Results of comprehensive management of patients with chronic lower limb ischaemia using gene-engineering technologies of angiogenesis stimulation (Part 1)].

Presented herein are the results of clinical use of gene engineering methods of stimulating angiogenesis in patients with chronic lower limb ischaemia. An open prospective controlled clinical study included a total of 160 patients with chronic lower limb ischaemia. Gene engineering technologies of angiogenesis stimulation were used both as an independent method of treatment in comprehensive conservative therapy (80 patients) and as comprehensive treatment in combination with revascularizing operations (80 patients).

[Genetic engineering technologies of stimulating angiogenesis as an innovation trend in angiology and vascular surgery].

Presented herein is a review of the principles, fundamental concepts, and possibilities of genetic engineering technologies of stimulating angiogenesis for treatment of patients with lower limb chronic ischaemia. This is followed by a detailed discussion of the structure and results of Russian and foreign studies on this direction, also considering the causes of differences of their results. Outlined is a circle of clinical situations in relation to which these technologies may be regarded as most promising.