Multisample motif discovery and visualization for tandem repeats.

Tandem Repeats (TR) occupy a significant portion of the human genome and are the source of polymorphism due to variations in sizes and motif compositions. Some of these variations have been associated with various neuropathological disorders, highlighting the clinical importance of assessing the motif structure of TRs. Moreover, assessing the TR motif variation can offer valuable insights into evolutionary dynamics and population structure.

Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and .

Tandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization of TRs; however, the underlying bioinformatics perspectives remain challenging. We present and TREAT: is a fast targeted local assembler, cross-compatible across different sequencing platforms.

Nigral Pathology Contributes to Microstructural Integrity of Striatal and Frontal Tracts in Parkinson's Disease.

Background: Motor and cognitive impairment in Parkinson's disease (PD) is associated with dopaminergic dysfunction that stems from substantia nigra (SN) degeneration and concomitant α-synuclein accumulation. Diffusion magnetic resonance imaging (MRI) can detect microstructural alterations of the SN and its tracts to (sub)cortical regions, but their pathological sensitivity is still poorly understood.

Objective: To unravel the pathological substrate(s) underlying microstructural alterations of SN, and its tracts to the dorsal striatum and dorsolateral prefrontal cortex (DLPFC) in PD.

Meningeal inflammation in multiple sclerosis induces phenotypic changes in cortical microglia that differentially associate with neurodegeneration.

Meningeal inflammation strongly associates with demyelination and neuronal loss in the underlying cortex of progressive MS patients, thereby contributing significantly to clinical disability. However, the pathological mechanisms of meningeal inflammation-induced cortical pathology are still largely elusive. By extensive analysis of cortical microglia in post-mortem progressive MS tissue, we identified cortical areas with two MS-specific microglial populations, termed MS1 and MS2 cortex.

Quantitative 3D electromagnetic field determination of 1D nanostructures from single projection.

One-dimensional (1D) nanostructures have been regarded as the most promising building blocks for nanoelectronics and nanocomposite material systems as well as for alternative energy applications. Although they result in confinement of a material, their properties and interactions with other nanostructures are still very much three-dimensional (3D) in nature. In this work, we present a novel method for quantitative determination of the 3D electromagnetic fields in and around 1D nanostructures using a single electron wave phase image, thereby eliminating the cumbersome acquisition of tomographic data.

Development of TEM and SEM high brightness electron guns using cold-field emission from a carbon nanotip.

A newly developed carbon cone nanotip (CCnT) has been used as field emission cathode both in low voltage SEM (30 kV) electron source and high voltage TEM (200 kV) electron source. The results clearly show, for both technologies, an unprecedented stability of the emission and the probe current with almost no decay during 1h, as well as a very small noise (rms less than 0.5%) compared to standard sources which use tungsten tips as emitting cathode.

Pten regulates neuronal soma size: a mouse model of Lhermitte-Duclos disease.

Somatic inactivation of PTEN occurs in different human tumors including glioblastoma, endometrial carcinoma and prostate carcinoma. Germline mutations in PTEN result in a range of phenotypic abnormalities that occur with variable penetrance, including neurological features such as macrocephaly, seizures, ataxia and Lhermitte-Duclos disease (also described as dysplastic gangliocytoma of the cerebellum). Homozygous deletion of Pten causes embryonic lethality in mice.

EWS/FLI alters 5'-splice site selection.

The chimeric gene EWS/FLI is present in at least 85% of Ewing's sarcomas as a result of chromosomal translocations. The resulting fusion protein contains the N terminus of the RNA-binding protein EWS and the ETS DNA-binding domain of the transcription factor FLI-1. Although EWS/FLI binds DNA and activates transcription, both EWS and EWS/FLI also interact with SF1 and U1C, essential components of the splicing machinery.

The splicing factor U1C represses EWS/FLI-mediated transactivation.

EWS is an RNA-binding protein involved in human tumor-specific chromosomal translocations. In approximately 85% of Ewing's sarcomas, such translocations give rise to the chimeric gene EWS/FLI. In the resulting fusion protein, the RNA binding domains from the C terminus of EWS are replaced by the DNA-binding domain of the ETS protein FLI-1.