Histone variants in archaea - An undiscovered country.

Exchanging core histones in the nucleosome for paralogous variants can have important functional ramifications. Many of these variants, and their physiological roles, have been characterized in exquisite detail in model eukaryotes, including humans. In comparison, our knowledge of histone biology in archaea remains rudimentary. This is true in particular for our knowledge of histone variants. Many archaea encode several histone genes that differ in sequence, but do these paralogs make distinct, adaptive contributions to genome organization and regulation in a manner comparable to eukaryotes? Below, we review what we know about histone variants in archaea at the level of structure, regulation, and evolution. In all areas, our knowledge pales when compared to the wealth of insight that has been gathered for eukaryotes. Recent findings, however, provide tantalizing glimpses into a rich and largely undiscovered country that is at times familiar and eukaryote-like and at times strange and uniquely archaeal. We sketch a preliminary roadmap for further exploration of this country; an undertaking that may ultimately shed light not only on chromatin biology in archaea but also on the origin of histone-based chromatin in eukaryotes

Non-random inversion landscapes in prokaryotic genomes are shaped by heterogeneous selection pressures

Inversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1,651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased toward (symmetric) inversions around the origin–terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus–Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favoring symmetric rearrangements in archaea with a single origin of replication. Within clades, we find strong but clade-specific relationships between symmetric inversion bias and different features of adaptive genome architecture, including the distance of essential genes to the origin of replication and the preferential localization of genes on the leading strand. We suggest that heterogeneous selection pressures have converged to produce similar patterns of structural genome evolution across prokaryotes

Organic acid toxicity, tolerance, and production in Escherichia coli biorefining applications

Organic acids are valuable platform chemicals for future biorefining applications. Such applications involve the conversion of low-cost renewable resources to platform sugars, which are then converted to platform chemicals by fermentation and further derivatized to large-volume chemicals through conventional catalytic routes. Organic acids are toxic to many of the microorganisms, such as Escherichia coli, proposed to serve as biorefining platform hosts at concentrations well below what is required for economical production. The toxicity is two-fold including not only pH based growth inhibition but also anion-specific effects on metabolism that also affect growth. E. coli maintain viability at very low pH through several different tolerance mechanisms including but not limited to the use of decarboxylation reactions that consume protons, ion transporters that remove protons, increased expression of known stress genes, and changing membrane composition. The focus of this mini-review is on organic acid toxicity and associated tolerance mechanisms as well as several examples of successful organic acid production processes for E. coli

Deep conservation of histone variants in Thermococcales archaea

Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA accessibility is the replacement of histones in the nucleosome with paralogous variants. Histones are also present in archaea but whether and how histone variants contribute to the generation of different physiologically relevant chromatin states in these organisms remains largely unknown. Conservation of paralogs with distinct properties can provide prima facie evidence for defined functional roles. We recently revealed deep conservation of histone paralogs with different properties in the Methanobacteriales, but little is known experimentally about these histones. In contrast, the two histones of the model archaeon Thermococcus kodakarensis, HTkA and HTkB, have been examined in some depth, both in vitro and in vivo. HTkA and HTkB exhibit distinct DNA-binding behaviours and elicit unique transcriptional responses when deleted. Here, we consider the evolution of HTkA/B and their orthologs across the order Thermococcales. We find histones with signature HTkA- and HTkB-like properties to be present in almost all Thermococcales genomes. Phylogenetic analysis indicates the presence of one HTkA- and one HTkB-like histone in the ancestor of Thermococcales and long-term maintenance of these two paralogs throughout Thermococcales diversification. Our results support the notion that archaea and eukaryotes have convergently evolved histone variants that carry out distinct adaptive functions. Intriguingly, we also detect more highly diverged histone-fold proteins, related to those found in some bacteria, in several Thermococcales genomes. The functions of these bacteria-type histones remain unknown, but structural modelling suggests that they can form heterodimers with HTkA/B-like histones

Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates

It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes. The repertoire of naturally occurring cytosine modifications, however, extends beyond 5-methylcytosine to include its oxidation derivatives, notably 5-hydroxymethylcytosine. The effects of these modifications on sequence evolution are unknown. Here, we combine base-resolution maps of methyl- and hydroxymethylcytosine in human and mouse with population genomic, divergence and somatic mutation data to show that hydroxymethylated and methylated cytosines show distinct patterns of variation and evolution. Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors. Controlling for multiple potential confounders, we find derived C to G SNPs to be 1.43-fold (1.22-fold) more common at hydroxymethylated sites compared to methylated sites in human (mouse). Increased C to G rates are evident across diverse functional and sequence contexts and, in cancer genomes, correlate with the expression of Tet enzymes and specific components of the mismatch repair pathway (MSH2, MSH6, and MBD4). Based on these and other observations we suggest that hydroxymethylation is associated with a distinct mutational burden and that the mismatch repair pathway is implicated in causing elevated transversion rates at hydroxymethylated cytosines

Racial Disparities in Breast Cancer Survival: The Mediating Effects of Macro-Social Context and Social Network Factors

ABSTRACT This study attempts to clarify the associations between macro-social and social network factors and continuing racial disparities in breast cancer survival. The study improves on prior methodologies by using a neighborhood disadvantage measure that assesses both economic and social disadvantage and an ego-network measurement tool that assesses key social network characteristics. Our population-based sample included 786 breast cancer patients (nHWhite=388; nHBlack=398) diagnosed during 2005-2008 in Chicago, IL. The data included census-derived macro-social context, self-reported social network, self-reported demographic and medically abstracted health measures. Mortality data from the National Death Index (NDI) were used to determine 5-year survival. Based on our findings, neighborhood concentrated disadvantage was negatively associated with survival among nHBlack and nHWhite breast cancer patients. In unadjusted models, social network size, network density, practical support, and financial support were positively associated with 5-year survival. However, in adjusted models only practical support was associated with 5-year survival. Our findings suggest that the association between network size and breast cancer survival is sensitive to scaling of the network measure, which helps to explain inconsistencies in past findings. Social networks of nHWhites and nHBlacks differed in size, social support dimensions, network density, and geographic proximity. Among social factors, residence in disadvantaged neighborhoods and unmet practical support explained some of the racial disparity in survival. Differences in late stage diagnosis and comorbidities between nHWhites and nHBlacks also explained some of the racial disparity in survival. Our findings highlight the relevance of social factors, both macro and inter-personal in the racial disparity in breast cancer survival. Findings suggest that reduced survival of nHBlack women is in part due to low social network resources and residence in socially and economically deprived neighborhoods. Our findings indicate that, to improve survival among breast cancer patients, policies need to focus on continued improvement of access to care and reduction of racially patterned social and economic hardship. Additionally, our findings support the need for health care providers to assess social support resources of breast cancer patients at the time of diagnosis

Social Support Needs of Minority Breast Cancer Patients: Significance of Racial Homogeneity and Kin Composition of Social Networks

Social support from family and friends assists breast cancer patients navigate a life crisis, but more needs to be understood about specific social network characteristics that can benefit breast cancer patients. To address this need, the primary aim of this study was to identify social network factors that facilitate or reduce social support. Given racially patterned gaps in social support among breast cancer patients, a secondary goal was to identify network characteristics that are linked to gaps in support. We examined these research questions using data from a sample of 915 breast cancer patients (NHWhite=373; NHBlack=377; Hispanic=165) and 4,021 of their network members. To improve on prior research, we collected detailed social network data using a personal-network measurement tool and assessed needed and received support on five support components. Study findings identified specific network characteristics that facilitate these social support components. Network size was associated with increased practical, informational, emotional, and spiritual support. Network density was associated with increased practical support. Racial homogeneity in networks were associated with reduced informational support while a higher number of daughters in support networks was associated with increased emotional support. Compared to NHWhite patients, NHBlack patients were more likely to experience inadequate practical and financial support. Additionally, compared to NHWhite patients, Hispanic patients were more likely to experience inadequate informational and emotional support. The study found that network density, racial homogeneity, and gender composition of NHWhite, NHBlack and Hispanic social networks contributed to the racially patterned disparities in social support. Findings in this study could inform interventions aimed at increasing social support through greater mobilization of existing network ties as well as policy-driven, formal community building initiatives aimed at replicating benefits of naturally occurring networks

Three-dimensional imaging of intracochlear tissue by scanning laser optical tomography (SLOT)

The presented study focuses on the application of scanning laser optical tomography (SLOT) for non-destructive visualization of anatomical structures inside the human cochlea ex vivo. SLOT is a laser-based highly efficient microscopy technique, which allows for tomographic imaging of the internal structure of transparent large-scale specimens (up to 1 cm3). Thus, in the field of otology this technique is best convenient for an ex vivo study of the inner ear anatomy. For this purpose, the preparation before imaging comprises mechanically assisted decalcification, dehydration as well as optical clearing of the cochlea samples. Here, we demonstrate results of SLOT visualizing hard and soft tissue structures of the human cochlea with an optical resolution in the micrometer range using absorption and autofluorescence as contrast mechanisms. Furthermore, we compare our results with the method of X-ray micro tomography (micro-CT, μCT) as clinical gold standard which is based only on absorption. In general, SLOT can provide the advantage of covering all contrast mechanisms known from other light microscopy techniques, such as fluorescence or scattering. For this reason, a protocol for antibody staining has been developed, which additionally enables selective mapping of cellular structures within the cochlea. Thus, we present results of SLOT imaging rodent cochleae showing specific anatomical structures such as hair cells and neurofilament via fluorescence. In conclusion, the presented study has shown that SLOT is an ideally suited tool in the field of otology for in toto visualization of the inner ear microstructure. © 2016 SPIE

Expiratory Muscle Strength Training for Therapy of Pharyngeal Dysphagia in Parkinson's Disease

Background Pharyngeal dysphagia in Parkinson's disease (PD) is a common and clinically relevant symptom associated with poor nutrition intake, reduced quality of life, and aspiration pneumonia. Despite this, effective behavioral treatment approaches are rare. Objective The objective of this study was to verify if 4 week of expiratory muscle strength training can improve pharyngeal dysphagia in the short and long term and is able to induce neuroplastic changes in cortical swallowing processing. Methods In this double-blind, randomized, controlled trial, 50 patients with hypokinetic pharyngeal dysphagia, as confirmed by flexible endoscopic evaluation of swallowing, performed a 4-week expiratory muscle strength training. Twenty-five participants used a calibrated (“active”) device, 25 used a sham handheld device. Swallowing function was evaluated directly before and after the training period, as well as after a period of 3 month using flexible endoscopic evaluation of swallowing. Swallowing-related cortical activation was measured in 22 participants (active:sham; 11:11) using whole-head magnetencephalography. Results The active group showed significant improvement in the flexible endoscopic evaluation of swallowing–based dysphagia score after 4 weeks and after 3 months, whereas in the sham group no significant changes from baseline were observed. Especially, clear reduction in pharyngeal residues was found. Regarding the cortical swallowing network before and after training, no statistically significant differences were found by magnetencephalography examination. Conclusions Four-week expiratory muscle strength training significantly reduces overall dysphagia severity in PD patients, with a sustained effect after 3 months compared with sham training. This was mainly achieved by improving swallowing efficiency. The treatment effect is probably caused by peripheral mechanisms, as no changes in the cortical swallowing network were identified. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Societ

Does negative auto-regulation increase gene duplicability?

BACKGROUND: A prerequisite for a duplication to spread through and persist in a given population is retaining expression of both gene copies. Yet changing a gene's dosage is frequently detrimental to fitness. Consequently, dosage-sensitive genes are less likely to duplicate. However, in cases where the level of gene product is controlled, via negative feedback, by its own abundance, an increase in gene copy number can in principle be decoupled from an increase in protein while both copies remain expressed. Using data from the transcriptional networks of E. coli and S. cerevisiae, we test the hypothesis that genes under negative auto-regulation show enhanced duplicability. RESULTS: Controlling for several known correlates of duplicability, we find no statistically significant support in either E. coli or S. cerevisiae that transcription factors under negative auto-regulation hold a duplicability advantage over transcription factors with no auto-regulation. CONCLUSION: Based on the analysis of transcriptional networks in E. coli and S. cerevisiae, there is no evidence that negative auto-regulation has contributed, on a genome-wide scale, to the variability in gene family sizes in these species