Programming and reprogramming the brain: a meeting of minds in neural fate

CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome

With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever-increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation, with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use, scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of the obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/#/analyse/cpg.

[Methods to restore fine motor skills in stroke patients]

The review article considers the problem of nonmedical post-stroke rehabilitation, in particular the restoration of fine motor skills in patients in the early period of the disease. A review and analysis of various randomized controlled trials concerning the use of various rehabilitation methods both in monotherapy and in their combined application is carried out, and modern technical devices, with the use of computer technology and biofeedback, are reviewed. Proceeding from the presented literature data and their analysis, there are certain grounds for introducing modern apparatus complexes and robotized devices for fine motor skills restoration in post-stroke patients, especially in the early period, into the multimodal rehabilitation system. However, further research in this direction is needed to achieve a sustained positive result.

Leap Motion Controller Video Game-Based Therapy for Upper Extremity Motor Recovery in Patients with Central Nervous System Diseases. A Systematic Review with Meta-Analysis

Leap Motion Controller (LMC) is a virtual reality device that can be used in the rehabilitation of central nervous system disease (CNSD) motor impairments. This review aimed to evaluate the effect of video game-based therapy with LMC on the recovery of upper extremity (UE) motor function in patients with CNSD. A systematic review with meta-analysis was performed in PubMed Medline, Web of Science, Scopus, CINAHL, and PEDro. We included five randomized controlled trials (RCTs) of patients with CNSD in which LMC was used as experimental therapy compared to conventional therapy (CT) to restore UE motor function. Pooled effects were estimated with Cohen's standardized mean difference (SMD) and its 95% confidence interval (95% CI). At first, in patients with stroke, LMC showed low-quality evidence of a large effect on UE mobility (SMD = 0.96; 95% CI = 0.47, 1.45). In combination with CT, LMC showed very low-quality evidence of a large effect on UE mobility (SMD = 1.34; 95% CI = 0.49, 2.19) and the UE mobility-oriented task (SMD = 1.26; 95% CI = 0.42, 2.10). Second, in patients with non-acute CNSD (cerebral palsy, multiple sclerosis, and Parkinson's disease), LMC showed low-quality evidence of a medium effect on grip strength (GS) (SMD = 0.47; 95% CI = 0.03, 0.90) and on gross motor dexterity (GMD) (SMD = 0.73; 95% CI = 0.28, 1.17) in the most affected UE. In combination with CT, LMC showed very low-quality evidence of a high effect in the most affected UE on GMD (SMD = 0.80; 95% CI = 0.06, 1.15) and fine motor dexterity (FMD) (SMD = 0.82; 95% CI = 0.07, 1.57). In stroke, LMC improved UE mobility and UE mobility-oriented tasks, and in non-acute CNSD, LMC improved the GS and GMD of the most affected UE and FMD when it was used with CT.

Brain Functional Reserve in the Context of Neuroplasticity after Stroke

Stroke is the second cause of death and more importantly first cause of disability in people over 40 years of age. Current therapeutic management of ischemic stroke does not provide fully satisfactory outcomes. Stroke management has significantly changed since the time when there were opened modern stroke units with early motor and speech rehabilitation in hospitals. In recent decades, researchers searched for biomarkers of ischemic stroke and neuroplasticity in order to determine effective diagnostics, prognostic assessment, and therapy. Complex background of events following ischemic episode hinders successful design of effective therapeutic strategies. So far, studies have proven that regeneration after stroke and recovery of lost functions may be assigned to neuronal plasticity understood as ability of brain to reorganize and rebuild as an effect of changed environmental conditions. As many neuronal processes influencing neuroplasticity depend on expression of particular genes and genetic diversity possibly influencing its effectiveness, knowledge on their mechanisms is necessary to understand this process. Epigenetic mechanisms occurring after stroke was briefly discussed in this paper including several mechanisms such as synaptic plasticity; neuro-, glio-, and angiogenesis processes; and growth of axon.

The multipotency-to-commitment transition in Caenorhabditis elegans-implications for reprogramming from cells to organs

In animal embryos, cells transition from a multipotential state, with the capacity to adopt multiple fates, into an irreversible, committed state of differentiation. This multipotency-to-commitment transition (MCT) is evident from experiments in which cell fate is reprogrammed by transcription factors for cell type-specific differentiation, as has been observed extensively in Caenorhabditis elegans. Although factors that direct differentiation into each of the three germ layer types cannot generally reprogram cells after the MCT in this animal, transcription factors for endoderm development are able to do so in multiple differentiated cell types. In one case, these factors can redirect the development of an entire organ in the process of "transorganogenesis". Natural transdifferentiation also occurs in a small number of differentiated cells during normal C. elegans development. We review these reprogramming and transdifferentiation events, highlighting the cellular and developmental contexts in which they occur, and discuss common themes underlying direct cell lineage reprogramming. Although certain aspects may be unique to the model system, growing evidence suggests that some mechanisms are evolutionarily conserved and may shed light on cellular plasticity and disease in humans.