Bacterial Genotype, Carrier Risk Factors, and an Antimicrobial Stewardship Approach Relevant to Methicillin-resistant Staphylococcus aureus Prevalence in a Population of Macaques Housed in a Research Facility

Methicillin-resistant Staphylococcus aureus (MRSA) remains a significant problem for human and animal health and can negatively affect the health status of macaques and other nonhuman primates (NHP) in research colonies. However, few publications provide guidance on the prevalence, genotype, or risk factors for macaques with MRSA and even fewer on how to effectively respond to MRSA once identified in a population. After having a clinical case of MRSA in a rhesus macaque, we sought to determine the MRSA carrier prevalence, risk factors, and genotypes of MRSA in a population of research NHPs. Over a 6-wk period in 2015, we collected nasal swabs from 298 NHPs. MRSA was isolated from 28% (n = 83). We then reviewed each macaque's medical record for a variety of variables including animal housing room, sex, age, number of antibiotic courses, number of surgical interventions, and SIV status. Analysis of these data suggests that MRSA carriage is associated with the room location, age of the animal, SIV status, and the number of antibiotic courses. We used multilocus sequence typing and spa typing on a subset of MRSA and MSSA isolates to determine whether the MRSA present in NHPs was comparable with common human strains. Two MRSA sequence types were predominant: ST188 and a novel MRSA genotype, neither of which is a common human isolate in the United States. We subsequently implemented antimicrobial stewardship practices (significantly reducing antimicrobial use) and then resampled the colony in 2018 and found that MRSA carriage had fallen to 9% (26/285). These data suggest that, as in humans, macaques may have a high carrier status of MRSA despite low clinically apparent disease. Implementing strategic antimicrobial stewardship practices resulted in a marked reduction in MRSA carriage in the NHP colony, highlighting the importance of limiting antimicrobial use when possible.

Gene expression profiling of whole blood: A comparative assessment of RNA-stabilizing collection methods

Peripheral Blood gene expression is widely used in the discovery of biomarkers and development of therapeutics. Recently, a spate of commercial blood collection and preservation systems have been introduced with proprietary variations that may differentially impact the transcriptomic profiles. Comparative analysis of these collection platforms will help optimize protocols to detect, identify, and reproducibly validate true biological variance among subjects. In the current study, we tested two recently introduced whole blood collection methods, RNAgard^® and PAXgene^® RNA, in addition to the traditional method of peripheral blood mononuclear cells (PBMCs) separated from whole blood and preserved in Trizol reagent. Study results revealed striking differences in the transcriptomic profiles from the three different methods that imply ex vivo changes in gene expression occurred during the blood collection, preservation, and mRNA extraction processes. When comparing the ability of the three preservation methods to accurately capture individuals’ expression differences, RNAgard^® outperformed PAXgene^® RNA, and both showed better individual separation of transcriptomic profiles than PBMCs. Hence, our study recommends using a single blood collection platform, and strongly cautions against combining methods during the course of a defined study.

Acute and chronic plasma metabolomic and liver transcriptomic stress effects in a mouse model with features of post-traumatic stress disorder

Acute responses to intense stressors can give rise to post-traumatic stress disorder (PTSD). PTSD diagnostic criteria include trauma exposure history and self-reported symptoms. Individuals who meet PTSD diagnostic criteria often meet criteria for additional psychiatric diagnoses. Biomarkers promise to contribute to reliable phenotypes of PTSD and comorbidities by linking biological system alterations to behavioral symptoms. Here we have analyzed unbiased plasma metabolomics and other stress effects in a mouse model with behavioral features of PTSD. In this model, C57BL/6 mice are repeatedly exposed to a trained aggressor mouse (albino SJL) using a modified, resident-intruder, social defeat paradigm. Our recent studies using this model found that aggressor-exposed mice exhibited acute stress effects including changed behaviors, body weight gain, increased body temperature, as well as inflammatory and fibrotic histopathologies and transcriptomic changes of heart tissue. Some of these acute stress effects persisted, reminiscent of PTSD. Here we report elevated proteins in plasma that function in inflammation and responses to oxidative stress and damaged tissue at 24 hrs post-stressor. Additionally at this acute time point, transcriptomic analysis indicated liver inflammation. The unbiased metabolomics analysis showed altered metabolites in plasma at 24 hrs that only partially normalized toward control levels after stress-withdrawal for 1.5 or 4 wks. In particular, gut-derived metabolites were altered at 24 hrs post-stressor and remained altered up to 4 wks after stress-withdrawal. Also at the 4 wk time point, hyperlipidemia and suppressed metabolites of amino acids and carbohydrates in plasma coincided with transcriptomic indicators of altered liver metabolism (activated xenobiotic and lipid metabolism). Collectively, these system-wide sequelae to repeated intense stress suggest that the simultaneous perturbed functioning of multiple organ systems (e.g., brain, heart, intestine and liver) can interact to produce injuries that lead to chronic metabolic changes and disorders that have been associated with PTSD.

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.

Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool)

This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternative DNA conformations that differ from the canonical right-handed Watson-Crick double-helix, collectively known as non-B DNA, and on using the associated PolyBrowse, a GBrowse-based genomic browser. The nBMST is a Web-based resource that allows users to submit one or more DNA sequences to search for inverted repeats (cruciform DNA), mirror repeats (triplex DNA), direct/tandem repeats (slipped/hairpin structures), G4 motifs (tetraplex, G-quadruplex DNA), alternating purine-pyrimidine tracts (left-handed Z-DNA), and A-phased repeats (static bending). The nBMST is versatile, simple to use, does not require bioinformatics skills, and can be applied to any type of DNA sequences, including viral and bacterial genomes, up to an aggregate of 20 megabasepairs (Mbp).

The role of methylation in the intrinsic dynamics of B- and Z-DNA

Methylation of cytosine at the 5-carbon position (5 mC) is observed in both prokaryotes and eukaryotes. In humans, DNA methylation at CpG sites plays an important role in gene regulation and has been implicated in development, gene silencing, and cancer. In addition, the CpG dinucleotide is a known hot spot for pathologic mutations genome-wide. CpG tracts may adopt left-handed Z-DNA conformations, which have also been implicated in gene regulation and genomic instability. Methylation facilitates this B-Z transition but the underlying mechanism remains unclear. Herein, four structural models of the dinucleotide d(GC)(5) repeat sequence in B-, methylated B-, Z-, and methylated Z-DNA forms were constructed and an aggregate 100 nanoseconds of molecular dynamics simulations in explicit solvent under physiological conditions was performed for each model. Both unmethylated and methylated B-DNA were found to be more flexible than Z-DNA. However, methylation significantly destabilized the BII, relative to the BI, state through the Gp5mC steps. In addition, methylation decreased the free energy difference between B- and Z-DNA. Comparisons of α/γ backbone torsional angles showed that torsional states changed marginally upon methylation for B-DNA, and Z-DNA. Methylation-induced conformational changes and lower energy differences may contribute to the transition to Z-DNA by methylated, over unmethylated, B-DNA and may be a contributing factor to biological function.

Dysregulation of Semaphorin7A/β1-integrin signaling leads to defective GnRH-1 cell migration, abnormal gonadal development and altered fertility

Reproduction in mammals is dependent on the function of specific neurons that secrete gonadotropin-releasing hormone-1 (GnRH-1). These neurons originate prenatally in the nasal placode and migrate into the forebrain along the olfactory-vomeronasal nerves. Alterations in this migratory process lead to defective GnRH-1 secretion, resulting in heterogeneous genetic disorders such as idiopathic hypogonadotropic hypogonadism (IHH), and other reproductive diseases characterized by the reduction or failure of sexual competence. Combining mouse genetics with in vitro models, we demonstrate that Semaphorin 7A (Sema7A) is essential for the development of the GnRH-1 neuronal system. Loss of Sema7A signaling alters the migration of GnRH-1 neurons, resulting in significantly reduced numbers of these neurons in the adult brain as well as in reduced gonadal size and subfertility. We also show that GnRH-1 cells differentially express the Sema7 receptors β1-integrin and Plexin C1 as a function of their migratory stage, whereas the ligand is robustly expressed along developing olfactory/vomeronasal fibers. Disruption of Sema7A function in vitro inhibits β1-integrin-mediated migration. Analysis of Plexin C1(-/-) mice did not reveal any difference in the migratory process of GnRH-1 neurons, indicating that Sema7A mainly signals through β1-integrin to regulate GnRH-1 cell motility. In conclusion, we have identified Sema7A as a gene implicated in the normal development of the GnRH-1 system in mice and as a genetic marker for the elucidation of some forms of GnRH-1 deficiency in humans.

NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF

Neuronal morphology affects network connectivity, plasticity, and information processing. Uncovering the design principles and functional consequences of dendritic and axonal shape necessitates quantitative analysis and computational modeling of detailed experimental data. Digital reconstructions provide the required neuromorphological descriptions in a parsimonious, comprehensive, and reliable numerical format. NeuroMorpho.Org is the largest web-accessible repository service for digitally reconstructed neurons and one of the integrated resources in the Neuroscience Information Framework (NIF). Here we describe the NeuroMorpho.Org approach as an exemplary experience in designing, creating, populating, and curating a neuroscience digital resource. The simple three-tier architecture of NeuroMorpho.Org (web client, web server, and relational database) encompasses all necessary elements to support a large-scale, integrate-able repository. The data content, while heterogeneous in scientific scope and experimental origin, is unified in format and presentation by an in house standardization protocol. The server application (MRALD) is secure, customizable, and developer-friendly. Centralized processing and expert annotation yields a comprehensive set of metadata that enriches and complements the raw data. The thoroughly tested interface design allows for optimal and effective data search and retrieval. Availability of data in both original and standardized formats ensures compatibility with existing resources and fosters further tool development. Other key functions enable extensive exploration and discovery, including 3D and interactive visualization of branching, frequently measured morphometrics, and reciprocal links to the original PubMed publications. The integration of NeuroMorpho.Org with version-1 of the NIF (NIFv1) provides the opportunity to access morphological data in the context of other relevant resources and diverse subdomains of neuroscience, opening exciting new possibilities in data mining and knowledge discovery. The outcome of such coordination is the rapid and powerful advancement of neuroscience research at both the conceptual and technological level.

A comparative computer simulation of dendritic morphology

Computational modeling of neuronal morphology is a powerful tool for understanding developmental processes and structure-function relationships. We present a multifaceted approach based on stochastic sampling of morphological measures from digital reconstructions of real cells. We examined how dendritic elongation, branching, and taper are controlled by three morphometric determinants: Branch Order, Radius, and Path Distance from the soma. Virtual dendrites were simulated starting from 3,715 neuronal trees reconstructed in 16 different laboratories, including morphological classes as diverse as spinal motoneurons and dentate granule cells. Several emergent morphometrics were used to compare real and virtual trees. Relating model parameters to Branch Order best constrained the number of terminations for most morphological classes, except pyramidal cell apical trees, which were better described by a dependence on Path Distance. In contrast, bifurcation asymmetry was best constrained by Radius for apical, but Path Distance for basal trees. All determinants showed similar performance in capturing total surface area, while surface area asymmetry was best determined by Path Distance. Grouping by other characteristics, such as size, asymmetry, arborizations, or animal species, showed smaller differences than observed between apical and basal, pointing to the biological importance of this separation. Hybrid models using combinations of the determinants confirmed these trends and allowed a detailed characterization of morphological relations. The differential findings between morphological groups suggest different underlying developmental mechanisms. By comparing the effects of several morphometric determinants on the simulation of different neuronal classes, this approach sheds light on possible growth mechanism variations responsible for the observed neuronal diversity.

Neurons in the brain have a variety of complex arbor shapes that help determine both their interconnectivity and functional roles. Molecular biology is beginning to uncover important details on the development of these tree-like structures, but how and why vastly different shapes arise is still largely unknown. We developed a novel set of computer models of branching in which measurements of real nerve cell structures digitally traced from microscopic imaging are resampled to create virtual trees. The different rules that the models use to create the most similar virtual trees to the real data support specific hypotheses regarding development. Surprisingly, the arborizations that differed most in the optimal rules were found on opposite sides of the same type of neuron, namely apical and basal trees of pyramidal cells. The details of the rules suggest that pyramidal cell trees may respond in unique and complex ways to their external environment. By better understanding how these trees are formed in the brain, we can learn more about their normal function and why they are often malformed in neurological diseases.

Local diameter fully constrains dendritic size in basal but not apical trees of CA1 pyramidal neurons

Computational modeling of dendritic morphology is a powerful tool for quantitatively describing complex geometrical relationships, uncovering principles of dendritic development, and synthesizing virtual neurons to systematically investigate cellular biophysics and network dynamics. A feature common to many morphological models is a dependence of the branching probability on local diameter. Previous models of this type have been able to recreate a wide variety of dendritic morphologies. However, these diameter-dependent models have so far failed to properly constrain branching when applied to hippocampal CA1 pyramidal cells, leading to explosive growth. Here we present a simple modification of this basic approach, in which all parameter sampling, not just bifurcation probability, depends on branch diameter. This added constraint prevents explosive growth in both apical and basal trees of simulated CA1 neurons, yielding arborizations with average numbers and patterns of bifurcations extremely close to those observed in real cells. However, simulated apical trees are much more varied in size than the corresponding real dendrites. We show that, in this model, the excessive variability of simulated trees is a direct consequence of the natural variability of diameter changes at and between bifurcations observed in apical, but not basal, dendrites. Conversely, some aspects of branch distribution were better matched by virtual apical trees than by virtual basal trees. Dendritic morphometrics related to spatial position, such as path distance from the soma or branch order, may be necessary to fully constrain CA1 apical tree size and basal branching pattern.

A Cross-Platform Freeware Tool for Digital Reconstruction of Neuronal Arborizations From Image Stacks

Digital reconstruction of neuronal arborizations is an important step in the quantitative investigation of cellular neuroanatomy. In this process, neurites imaged by microscopy are semi-manually traced through the use of specialized computer software and represented as binary trees of branching cylinders (or truncated cones). Such form of the reconstruction files is efficient and parsimonious, and allows extensive morphometric analysis as well as the implementation of biophysical models of electrophysiology. Here, we describe Neuron_ Morpho, a plugin for the popular Java application ImageJ that mediates the digital reconstruction of neurons from image stacks. Both the executable and code of Neuron_ Morpho are freely distributed (www.maths. soton.ac.uk/staff/D'Alessandro/morpho or www.krasnow.gmu.edu/L-Neuron), and are compatible with all major computer platforms (including Windows, Mac, and Linux). We tested Neuron_Morpho by reconstructing two neurons from each of the two preparations representing different brain areas (hippocampus and cerebellum), neuritic type (pyramidal cell dendrites and olivar axonal projection terminals), and labeling method (rapid Golgi impregnation and anterograde dextran amine), and quantitatively comparing the resulting morphologies to those of the same cells reconstructed with the standard commercial system, Neurolucida. None of the numerous morphometric measures that were analyzed displayed any significant or systematic difference between the two reconstructing systems.

Cervicofacial Actinomyces viscosus infection in a Brazilian fila: a case report and literature review

A five-month-old, male Brazilian fila presented with a three-day history of a focal swelling in the left superior palpebra and a focal, subcutaneous swelling over the dorsal cervical region. Both lesions initially responded to warm compresses and a two-week course of oral amoxicillin-clavulanic acid therapy. The eyelid swelling recurred after discontinuation of the oral antibiotic therapy. The lesion was progressive and was refractory to trimethoprim-sulfadiazine therapy. Culture and sensitivity performed from a surgical biopsy sample of the eyelid mass identified Actinomyces viscosus and other bacterial genera. A combination of surgical debulkment, Penrose drain placement, and a one-month course of oral oxacillin therapy has resulted in clinical regression of the lesion at a six-month postoperative evaluation.