Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads.

MOTIVATION: The Oxford Nanopore technology has a great potential for the analysis of methylated motifs in genomes, including whole-genome methylome profiling. However, we found that there are no methylation motifs detection algorithms, which would be sensitive enough and return deterministic results. Thus, the MEME suit does not extract all Helicobacter pylori methylation sites de novo even using the iterative approach implemented in the most up-to-date methylation analysis tool Nanodisco. RESULTS: We present Snapper, a new highly sensitive approach, to extract methylation motif sequences based on a greedy motif selection algorithm. Snapper does not require manual control during the enrichment process and has enrichment sensitivity higher than MEME coupled with Tombo or Nanodisco instruments that was demonstrated on H.pylori strain J99 studied earlier by the PacBio technology and on four external datasets representing different bacterial species. We used Snapper to characterize the total methylome of a new H.pylori strain A45. At least four methylation sites that have not been described for H.pylori earlier were revealed. We experimentally confirmed the presence of a new CCAG-specific methyltransferase and inferred a gene encoding a new CCAAK-specific methyltransferase. AVAILABILITY AND IMPLEMENTATION: Snapper is implemented using Python and is freely available as a pip package named "snapper-ont." Also, Snapper and the demo dataset are available in Zenodo (10.5281/zenodo.10117651).

Management of lower urinary tract symptoms in Parkinson's disease in the neurology clinic.

This clinical review aims to evaluate lower urinary tract symptoms (LUTS) in Parkinson's disease (PD) patients and the current treatment options available for these symptoms in a neurology setting. The review also addresses when referral to urology is appropriate. A literature search was conducted using the keywords 'LUTS', 'non-motor symptoms', 'overactive bladder', 'Parkinson's disease' and 'urinary symptoms' using the Medline/Pubmed search engine. Data collected ranged from 2000 to present with emphasis on recent publications. This review was conducted because LUTS in PD has a major impact on quality of life and is associated with early institutionalization. Emphasis is placed on treating overactive bladder with conservative strategies and medical management in the neurology setting. Quality of life can be improved and institutionalization can be delayed with a multimodal approach to bladder care.

A Novel Trial of Mirabegron and Behavioral Modification Including Pelvic Floor Exercise for Overactive Bladder in Parkinson's Disease (MAESTRO).

Overactive bladder (OAB) is experienced by more than half of patients with untreated Parkinson's disease. Treatment of overactive bladder in these patients has included antimuscarinic anticholinergics, raising concerns about the possibility of exacerbating cognitive impairment or constipation. Mirabegron (Myrbetriq), a ß3-receptor agonist, provides relief of OAB without increasing cognitive impairment. While prior studies have examined the effect of mirabegron on OAB in a variety of patient populations, this study is the first controlled, prospective study investigating the effect of mirabegron on overactive bladder in patients with Parkinson's disease. By studying effective treatments for overactive bladder, this trial emphasizes the importance of antimicrobial stewardship so that lower urinary tract symptoms are not treated as lower urinary tract infections with antimicrobials and instead overactive bladder can be treated appropriately with medication. The MAESTRO study compared the effect of adding mirabegron to behavioral modification (including pelvic floor exercises) to behavior modification alone. Results from this novel study show that both the mean absolute change in the volume of micturition (objective measure) and the mean percent change increased significantly between visits two and three in the experimental group using mirabegron. Moreover, improvements in micturition in this study indicate that a larger-scale study of mirabegron with pelvic floor exercises and behavior modification is warranted.

Rare hereditary cause of chronic pancreatitis in a young male: SPINK1 mutation.

Hereditary chronic pancreatitis associated with a mutation in the serine protease inhibitor, Kazal Type-1 (SPINK-1 gene) is extremely rare. The SPINK1 mutation results in trypsinogen activation which predisposes to chronic pancreatitis predominately when combined with CFTR gene mutations. It presents as either chronic or recurrent acute pancreatitis. Symptom control and management of complications is important. Active surveillance with cross-sectional imaging for pancreatic malignancy in individuals with hereditary pancreatitis is advocated due to individuals being high risk. We present an unusual case of a young male who initially presented with renal colic and was incidentally diagnosed with severe chronic pancreatitis on abdominal imaging, with genetic testing confirming a homozygous SPINK1 mutation.