Neurodegenerative Disease Risk in Carriers of Autosomal Recessive Disease

Genetics has driven significant discoveries in the field of neurodegenerative diseases (NDDs). An emerging theme in neurodegeneration warrants an urgent and comprehensive update: that carrier status of early-onset autosomal recessive (AR) disease, typically considered benign, is associated with an increased risk of a spectrum of late-onset NDDs. Glucosylceramidase beta (GBA1) gene mutations, responsible for the AR lysosomal storage disorder Gaucher disease, are a prominent example of this principle, having been identified as an important genetic risk factor for Parkinson disease. Genetic analyses have revealed further examples, notably GRN, TREM2, EIF2AK3, and several other LSD and mitochondria function genes. In this Review, we discuss the evidence supporting the strikingly distinct allele-dependent clinical phenotypes observed in carriers of such gene mutations and its impact on the wider field of neurodegeneration.

Ultra-Deep DNA Methylation Analysis of X-Linked Genes: GLA and AR as Model Genes

Recessive X-linked disorders may occasionally evolve in clinical manifestations of variable severity also in female carriers. For some of such diseases, the frequency of the symptoms’ appearance during women’s life may be particularly relevant. This phenomenon has been largely attributed to the potential skewness of the X-inactivation process leading to variable phenotypes. Nonetheless, in many cases, no correlation with X-inactivation unbalance was demonstrated. However, methods for analyzing skewness have been mainly limited to Human Androgen Receptor methylation analysis (HUMARA). Recently, the X-inactivation process has been largely revisited, highlighting the heterogeneity existing among loci in the epigenetic state within inactive and, possibly, active X-chromosomes. We reasoned that gene-specific and ultra-deep DNA methylation analyses could greatly help to unravel details of the X-inactivation process and the roles of specific X genes inactivation in disease manifestations. We recently provided evidence that studying DNA methylation at specific autosomic loci at a single-molecule resolution (epiallele distribution analysis) allows one to analyze cell-to-cell methylation differences in a given cell population. We here apply the epiallele analysis at two X-linked loci to investigate whether females show allele-specific epiallelic patterns. Due to the high potential of this approach, the method allows us to obtain clearly distinct allele-specific epiallele profiles.

Ppd-1 Remodels Spike Architecture by Regulating Floral Development in wheat

The determination of spike architecture is critical to grain yield in wheat (Triticum aestivum), yet the underlying mechanisms remain largely unknown. Here, we measured 51 traits associated with spike architecture and floral development in 197 wheat accessions with photoperiod sensitive and insensitive alleles. We included five distinct allele combinations at the Photoperiod-1 (Ppd-1) loci. A systematic dissection of all recorded phenotypes revealed connections between floral development, spike architecture and grain yield. Modifying the durations of spikelet primordia initiation did not necessarily affect spikelet number. In addition, Ppd-1 loci clearly influenced rachis dry weight, pointing to the rachis vascular system as a potential target for higher yield. Ppd-1 displayed opposite effects on the durations of pre and post-anthesis phases. Ppd-1 controlled carpel size, but not anther size. Finally, the photoperiod-insensitive alleles of Ppd-1 triggered floral degeneration. In parallel, we profiled the spike transcriptome at six stages and four positions in three Ppd-1 genotypes which consists of 234 samples. Integrating phenotypic and expression data suggested that loss of function in Ppd-1 loci delayed floral degeneration by regulating autophagy and extended floret development by regulating genes in different families. Therefore, we concluded that Ppd-1 remodels spike architecture by regulating floral development in wheat.

Correlation of Host Range Expansion of Therapeutic Bacteriophage Sb-1 with Allele State at a Hypervariable Repeat Locus

ABSTRACT Staphylococci are frequent agents of health care-associated infections and include methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to first-line antibiotic treatments. Bacteriophage (phage) therapy is a promising alternative antibacterial option to treat MRSA infections. S. aureus-specific phage Sb-1 has been widely used in Georgia to treat a variety of human S. aureus infections. Sb-1 has a broad host range within S. aureus, including MRSA strains, and its host range can be further expanded by adaptation to previously resistant clinical isolates. The susceptibilities of a panel of 25 genetically diverse clinical MRSA isolates to Sb-1 phage were tested, and the phage had lytic activity against 23 strains (92%). The adapted phage stock (designated Sb-1A) was tested in comparison with the parental phage (designated Sb-1P). Sb-1P had lytic activity against 78/90 strains (87%) in an expanded panel of diverse global S. aureus isolates, while eight additional strains in this panel were susceptible to Sb-1A (lytic against 86/90 strains [96%]). The Sb-1A stock was shown to be a mixed population of phage clones, including approximately 4% expanded host range mutants, designated Sb-1M. In an effort to better understand the genetic basis for this host range expansion, we sequenced the complete genomes of the parental Sb-1P and two Sb-1M mutants. Comparative genomic analysis revealed a hypervariable complex repeat structure in the Sb-1 genome that had a distinct allele that correlated with the host range expansion. This hypervariable region was previously uncharacterized in Twort-like phages and represents a novel putative host range determinant. IMPORTANCE Because of limited therapeutic options, infections caused by methicillin-resistant Staphylococcus aureus represent a serious problem in both civilian and military health care settings. Phages have potential as alternative antibacterial agents that can be used in combination with antibiotic drugs. For decades, phage Sb-1 has been used in former Soviet Union countries for antistaphylococcal treatment in humans. The therapeutic spectrum of activity of Sb-1 can be increased by selecting mutants of the phage with expanded host ranges. In this work, the host range of phage Sb-1 was expanded in the laboratory, and a hypervariable region in its genome was identified with a distinct allele state that correlated with this host range expansion. These results provide a genetic basis for better understanding the mechanisms of phage host range expansion.

Molecular Epidemiology of Streptococcus equi subsp. zooepidemicus Isolated from Thoroughbred Horses Using Multi Locus Sequence Typing (MLST) in Korea

Background:Multi Locus Sequence Typing (MLST) is a new global molecular typing method used for analyzing the DNA polymorphisms in bacteria. In this study, using MLST, we analyzed the sequence profiles ofStreptococcus (S.) zooepidemicusisolates from the Jeju and Jangsu provinces in South Korea.Objective:This study characterized the molecular epidemiology ofS. zooepidemicusinfection in Thoroughbred horses using MLST with an aim to control and prevent bacterial endometritis in mares.Methods:A total of 79S. zooepidemicusisolates were included in this study. Sequencing of the 7 loci for the MLST analysis was performed as described in the MLST website manual (http://pubmlst.org/szooepidemicus/) with some modifications. For each locus, every unique sequence was assigned a distinct allele number, and each Sequence Type (ST) was defined by a series of 7 integers (the allelic profile) corresponding to the alleles at the 7 loci (arcC,nrdE,proS,spi,tdk,tpi, andyqiL)using the MLST module in the Main Workbench.Results:Among the 79 isolates, 73 different MLST patterns were identified, each corresponding to 1-3 strains. The genetic relationships between the 79 isolates are presented in a dendrogram, and they diverged by up to 11% homology. At 11% homology, three MLST groups, M1, M2, and M3, were identified, and at 26% homology, five subgroups, L1-L5, were observed.We observed various MLST patterns in the strains isolated from Jeju and Jangsu. In addition, by estimating the epidemiological relationships among the strains isolated from Jangsu in 2007 and Jeju in 2009, which had similar MLST patterns, we determined that some strains from Jangsu may have been transported to Jeju.Conclusion:MLST can be used as a framework for determining the epidemiological relationships that form the genetic basis of host and infection site selection.

A Novel Involvement of the PurG and PurI Proteins in Thiamine Synthesis Via the Alternative Pyrimidine Biosynthetic (APB) Pathway in Salmonella typhimurium

Thiamine is thought to be synthesized by two alternative pathways, one involving the first four enzymes of the purine pathway and a second that can function independently of the purine pathway. Insertion mutations in purG and purl prevent thiamine synthesis through the alternative pyrimidine biosynthetic (APB) pathway under aerobic but not anaerobic growth conditions. In contrast, point mutations in purG and purl caused one of three distinct phenotypes: Pur− Apb−, Pur− Apb+, or Pur+ Apb−. Analysis of these three mutant classes demonstrated two genetically separable functions for PurG and PurI in thiamine synthesis. In addition to their known enzymatic role in de novo purine synthesis, we propose that PurG and PurI play a novel, possibly nonenzymatic role in the APB pathway. Suppression analysis of Pur− Apb− mutants identified two new genetic loci involved in the APB pathway, apbB and apbD. We show here that mutations in apbB and apbD cause distinct, allele-specific suppression of the thiamine requirement of purG and purl mutants. Our results suggest that PurG and PurI and one or more components of the APB pathway may function as a complex needed for aerobic function of the APB pathway.