Mapping Nucleosome Location Using FS-Seq.

The organization of nucleosomes in eukaryotic chromatin is thought to play a critical role in the regulation of the biological function of the chromatin. Because of this potential role in regulation, a number of techniques have been developed, which combine chromatin fragmentation around nucleosomes with next-generation sequencing to map the location of nucleosomes in chromatin. In this section, a procedure using a kit from New England Biolabs (NEB NEXT Ultra II FS DNA library prep Kit) to fragment chromatin in preparation for next-generation sequencing is described and compared to other available procedures for mapping nucleosome location.

Early in an SV40 infection, histone modifications correlate with the presence or absence of RNAPII and direction of transcription.

Since epigenetic regulation seemed likely to be involved in SV40 early transcription following infection, we have analyzed the organization of nucleosomes carrying histone modifications (acetyl-H3, acetyl-H4, H3K9me1, H3K9me3, H3K4me1, H3K4me3, H3K27me3, H4K20me1) at 30 min and 2 h post infection in SV40 minichromosomes prepared in the absence or presence of the transcription inhibitor dichloro-1-beta-d-ribofuranosyl benzimidazole. The former condition was used to determine how SV40 chromatin structure changed during early transcription, and the latter was used to determine the role of active transcription. The location of RNAPII was used as a marker to identify where histone modifications were most likely to be involved in regulation.

Differential SP1 interactions in SV40 chromatin from virions and minichromosomes.

SP1 binding in SV40 chromatin in vitro and in vivo was characterized in order to better understand its role during the initiation of early transcription. We observed that chromatin from disrupted virions, but not minichromosomes, was efficiently bound by HIS-tagged SP1 in vitro, while the opposite was true for the presence of endogenous SP1 introduced in vivo. Using ChIP-Seq to compare the location of SP1 to nucleosomes carrying modified histones, we found that SP1 could occupy its whole binding site in virion chromatin but only the early side of its binding site in most of the minichromosomes carrying modified histones due to the presence of overlapping nucleosomes.

Comparing a new method for mapping nucleosomes in simian virus 40 chromatin to standard procedures.

The location of nucleosomes in chromatin significantly impacts many biological processes including DNA replication, repair, and gene expression. A number of techniques have been developed for mapping nucleosome locations in chromatin including MN-Seq (micrococcal nuclease digestion followed by next-generation sequencing), ATAC-Seq (Assay for Transposase-Accessible Chromatin followed by next-generation sequencing), and ChIP-Seq (chromatin immunoprecipitation and fragmentation followed by next-generation sequencing). All of these techniques have been successfully used, but each with its own limitations.

Color discrimination errors associate with axial motor impairments in Parkinson's disease.

Background: Visual function deficits are more common in imbalance-predominant compared to tremor-predominant PD suggesting a pathophysiological role of impaired visual functions in axial motor impairments.

Objective: To investigate the relationship between changes in color discrimination and motor impairments in PD while accounting for cognitive or other confounder factors.

Methods: PD subjects (n=49, age 66.

Mentally stimulating activities associate with better cognitive performance in Parkinson disease.

Subjects at risk of dementia benefit from participation in mentally stimulating activities, but no prior studies have investigated similar associations in Parkinson disease (PD). The aim of this study was to investigate the relationship between times spent engaging in mentally stimulating activities and cognitive functions in PD while accounting for the degree of primary neurodegenerations. PD patients (N = 41, 33 males; age 68.

Motor Speech Apraxia in a 70-Year-Old Man with Left Dorsolateral Frontal Arachnoid Cyst: A [F]FDG PET-CT Study.

Motor speech apraxia is a speech disorder of impaired syllable sequencing which, when seen with advancing age, is suggestive of a neurodegenerative process affecting cortical structures in the left frontal lobe. Arachnoid cysts can be associated with neurologic symptoms due to compression of underlying brain structures though indications for surgical intervention are unclear. We present the case of a 70-year-old man who presented with a two-year history of speech changes along with decreased initiation and talkativeness, shorter utterances, and dysnomia.

Prevalence of impaired odor identification in Parkinson disease with imaging evidence of nigrostriatal denervation.

There is wide variability in the reported prevalence rates of abnormal smell in Parkinson disease (PD). This study assessed the prevalence of abnormal smell, using the University of Pennsylvania Smell Identification Test (UPSIT), in 183 patients with PD with confirmed PET imaging evidence of nigrostriatal denervation. Impaired olfaction in this sample was nearly universal (97.