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Multiple sclerosis is a chronic inflammatory, demyelinating disease, although it has been suggested that in the progressive late phase, inflammatory lesion activity declines. We recently showed in the Netherlands Brain Bank multiple sclerosis-autopsy cohort considerable ongoing inflammatory lesion activity also at the end stage of the disease, based on microglia/macrophage activity. We have now studied the role of T cells in this ongoing inflammatory lesion activity in chronic multiple sclerosis autopsy cases. We quantified T cells and perivascular T-cell cuffing at a standardized location in the medulla oblongata in 146 multiple sclerosis, 20 neurodegenerative control and 20 non-neurological control brain donors. In addition, we quantified CD3+, CD4+, and CD8+ T cells in 140 subcortical white matter lesions. The location of CD8+ T cells in either the perivascular space or the brain parenchyma was determined using CD8/laminin staining and confocal imaging. Finally, we analysed CD8+ T cells, isolated from fresh autopsy tissues from subcortical multiple sclerosis white matter lesions (n = 8), multiple sclerosis normal-appearing white matter (n = 7), and control white matter (n = 10), by flow cytometry. In normal-appearing white matter, the number of T cells was increased compared to control white matter. In active and mixed active/inactive lesions, the number of T cells was further augmented compared to normal-appearing white matter. Active and mixed active/inactive lesions were enriched for both CD4+ and CD8+ T cells, the latter being more abundant in all lesion types. Perivascular clustering of T cells in the medulla oblongata was only found in cases with a progressive disease course and correlated with a higher percentage of mixed active/inactive lesions and a higher lesion load compared to cases without perivascular clusters in the medulla oblongata. In all white matter samples, CD8+ T cells were located mostly in the perivascular space, whereas in mixed active/inactive lesions, 16.3% of the CD8+ T cells were encountered in the brain parenchyma. CD8+ T cells from mixed active/inactive lesions showed a tissue-resident memory phenotype with expression of CD69, CD103, CD44, CD49a, and PD-1 and absence of S1P1. They upregulated markers for homing (CXCR6), reactivation (Ki-67), and cytotoxicity (GPR56), yet lacked the cytolytic enzyme granzyme B. These data show that in chronic progressive multiple sclerosis cases, inflammatory lesion activity and demyelinated lesion load is associated with an increased number of T cells clustering in the perivascular space. Inflammatory active multiple sclerosis lesions are populated by CD8+ tissue-resident memory T cells, which show signs of reactivation and infiltration of the brain parenchyma.

The regeneration-associated gene (RAG) expression program is activated in injured peripheral neurons after axotomy and enables long-distance axon re-growth. Over 1000 genes are regulated, and many transcription factors are upregulated or activated as part of this response. However, a detailed picture of how RAG expression is regulated is lacking. In particular, the transcriptional targets and specific functions of the various transcription factors are unclear. Jun was the first-regeneration-associated transcription factor identified and the first shown to be functionally important. Here we fully define the role of Jun in the RAG expression program in regenerating facial motor neurons. At 1, 4 and 14 days after axotomy, Jun upregulates 11, 23 and 44% of the RAG program, respectively. Jun functions relevant to regeneration include cytoskeleton production, metabolic functions and cell activation, and the downregulation of neurotransmission machinery. In silico analysis of promoter regions of Jun targets identifies stronger over-representation of AP1-like sites than CRE-like sites, although CRE sites were also over-represented in regions flanking AP1 sites. Strikingly, in motor neurons lacking Jun, an alternative SRF-dependent gene expression program is initiated after axotomy. The promoters of these newly expressed genes exhibit over-representation of CRE sites in regions near to SRF target sites. This alternative gene expression program includes plasticity-associated transcription factors and leads to an aberrant early increase in synapse density on motor neurons. Jun thus has the important function in the early phase after axotomy of pushing the injured neuron away from a plasticity response and towards a regenerative phenotype.

A human neuroma-in continuity (NIC), formed following a peripheral nerve lesion, impedes functional recovery. The molecular mechanisms that underlie the formation of a NIC are poorly understood. Here we show that the expression of multiple genes of the Wnt family, including Wnt5a, is changed in NIC tissue from patients that underwent reconstructive surgery. The role of Wnt ligands in NIC pathology and nerve regeneration is of interest because Wnt ligands are implicated in tissue regeneration, fibrosis, axon repulsion and guidance. The observations in NIC prompted us to investigate the expression of Wnt ligands in the injured rat sciatic nerve and in the dorsal root ganglia (DRG). In the injured nerve, four gene clusters were identified with temporal expression profiles corresponding to particular phases of the regeneration process. In the DRG up- and down regulation of certain Wnt receptors suggests that nerve injury has an impact on the responsiveness of injured sensory neurons to Wnt ligands in the nerve. Immunohistochemistry showed that Schwann cells in the NIC and in the injured nerve are the source of Wnt5a, whereas the Wnt5a receptor Ryk is expressed by axons traversing the NIC. Taken together, these observations suggest a central role for Wnt signalling in peripheral nerve regeneration.

In the originally published version of this manuscript, there were errors in the details and enumeration for authors' affiliations.

Over the last few decades several common single nucleotide polymorphisms (SNPs) have been identified that correlate with clinical outcome in multiple sclerosis (MS), but the pathogenic mechanisms underlying the clinical effects of these SNPs are unknown. This is in part due to the difficulty in the functional translation of genotype into disease-relevant mechanisms. Building on our recent work showing the association of clinical disease course with post-mortem MS lesion characteristics, we hypothesized that SNPs that correlate with clinical disease course would also correlate with specific MS lesion characteristics in autopsy tissue. To test this hypothesis 179 MS brain donors from the Netherlands Brain Bank MS autopsy cohort were genotyped for 102 SNPs, selected based on their reported associations with clinical outcome or their associations with genes that show differential gene expression in MS lesions. Three SNPs linked to MS clinical severity showed a significant association between the genotype and either the proportion of active lesions (rs2234978/FAS and rs11957313/KCNIP1) or the proportion of mixed active/inactive lesions (rs8056098/CLEC16A). Three SNPs linked to MS pathology-associated genes showed a significant association with either proportion of active lesions (rs3130253/MOG), incidence of cortical grey matter lesions (rs1064395/NCAN) or the proportion of remyelinated lesions (rs5742909/CTLA4). In addition, rs2234978/FAS T-allele carriers showed increased FAS gene expression levels in perivascular T cells and perilesional oligodendrocytes, cell types that have been implicated in MS lesion formation. Thus, by combining pathological characterization of MS brain autopsy tissue with genetics, we now start to translate genotypes linked to clinical outcomes in MS into mechanisms involved in MS lesion pathogenesis. This article is protected by copyright. All rights reserved.

The neuron‐intrinsic response to axonal injury differs markedly between neurons of the peripheral and central nervous system. Following a peripheral lesion, a robust axonal growth program is initiated, whereas neurons of the central nervous system do not mount an effective regenerative response. Increasing the neuron‐intrinsic regenerative response would therefore be one way to promote axonal regeneration in the injured central nervous system. The large‐diameter sensory neurons located in the dorsal root ganglia are pseudo‐unipolar neurons that project one axon branch into the spinal cord, and, via the dorsal column to the brain stem, and a peripheral process to the muscles and skin. Dorsal root ganglion neurons are ideally suited to study the neuron‐intrinsic injury response because they exhibit a successful growth response following peripheral axotomy, while they fail to do so after a lesion of the central branch in the dorsal column. The dorsal column injury model allows the neuron‐intrinsic regeneration response to be studied in the context of a spinal cord injury. Here we will discuss the advantages and disadvantages of this model. We describe the surgical methods used to implement a lesion of the ascending fibers, the anatomy of the sensory afferent pathways and anatomical, electrophysiological, and behavioral techniques to quantify regeneration and functional recovery. Subsequently we review the results of experimental interventions in the dorsal column lesion model, with an emphasis on the molecular mechanisms that govern the neuron‐intrinsic injury response and manipulations of these after central axotomy. Finally, we highlight a number of recent advances that will have an impact on the design of future studies in this spinal cord injury model, including the continued development of adeno‐associated viral vectors likely to improve the genetic manipulation of dorsal root ganglion neurons and the use of tissue clearing techniques enabling 3D reconstruction of regenerating axon tracts. © 2018 The Authors. Developmental Neurobiology Published by Wiley Periodicals, Inc. Develop Neurobiol 00: 000–000, 2018

Altered levels of steroids have been reported in the brain, cerebral spinal fluid and plasma of patients with mood disorders. Neuroimaging studies have reported both functional and structural alterations in mood disorders, for instance in the anterior cingulate cortex (ACC) and dorsolateral prefrontal cortex (DLPFC). In order to determine whether the endogenous production of steroids is altered in the ACC and DLPFC of patients with major depressive disorder (MDD) or bipolar disorder (BPD), quantitative real‐time PCR was performed to detect mRNA expression level of key enzymes in the steroid biosynthetic pathways. In MDD, a significant decrease in mRNA level of cytochrome P450 17A1 (CYP17A1, synthesizing C19 ketosteroids) in the ACC and a significant increase in mRNA levels of hydroxysteroid sulfotransferase 2A1 [SULT2A1, catalyzing the sulfate conjugation of dehydroepiandrosterone (DHEA)] were observed in the DLPFC, suggesting alterations in DHEA and its sulfate metabolite DHEAS levels. Decreased intensity and distribution of CYP17A1 immunohistochemical staining was found in the ACC of MDD patients. Interestingly, there was a significant positive correlation between the mRNA levels of CYP17A1 and tyrosine‐related kinase B (TrkB) full length isoform. In a unique post‐mortem human brain slice culture paradigm, BDNF mRNA expression was found to be significantly increased following incubation with DHEA. Together, these data indicate a close relationship between DHEA and BDNF‐TrkB pathways in depression. Furthermore, in the DLPFC, higher mRNA levels of 11β‐hydroxysteroid dehydrogenase‐1 (HSD11B1, reducing cortisone to the active hormone cortisol) and steroidogenic acute regulatory protein (STAR, facilitating the shuttle of cholesterol through the intermembrane space) were found in the MDD patients and BPD patients, respectively. In conclusion, this study suggests the presence of a disturbance in the endogenous synthesis of DHEA and DHEAS in mood disorders, which has a close relationship with BDNF‐TrkB signaling.

Altered levels of steroids have been reported in the brain, cerebral spinal fluid and plasma of patients with mood disorders. Neuroimaging studies have reported both functional and structural alterations in mood disorders, for instance in the anterior cingulate cortex (ACC) and dorsolateral prefrontal cortex (DLPFC). In order to determine whether the endogenous production of steroids is altered in the ACC and DLPFC of patients with major depressive disorder (MDD) or bipolar disorder (BPD), quantitative real-time PCR was performed to detect mRNA expression level of key enzymes in the steroid biosynthetic pathways. In MDD, a significant decrease in mRNA level of cytochrome P450 17A1 (CYP17A1, synthesizing C19 ketosteroids) in the ACC and a significant increase in mRNA levels of hydroxysteroid sulfotransferase 2A1 [SULT2A1, catalyzing the sulfate conjugation of dehydroepiandrosterone (DHEA)] were observed in the DLPFC, suggesting alterations in DHEA and its sulfate metabolite DHEAS levels. Decreased intensity and distribution of CYP17A1 immunohistochemical staining was found in the ACC of MDD patients. Interestingly, there was a significant positive correlation between the mRNA levels of CYP17A1 and tyrosine-related kinase B (TrkB) full length isoform. In a unique post-mortem human brain slice culture paradigm, BDNF mRNA expression was found to be significantly increased following incubation with DHEA. Together, these data indicate a close relationship between DHEA and BDNF-TrkB pathways in depression. Furthermore, in the DLPFC, higher mRNA levels of 11β-hydroxysteroid dehydrogenase-1 (HSD11B1, reducing cortisone to the active hormone cortisol) and steroidogenic acute regulatory protein (STAR, facilitating the shuttle of cholesterol through the intermembrane space) were found in the MDD patients and BPD patients, respectively. In conclusion, this study suggests the presence of a disturbance in the endogenous synthesis of DHEA and DHEAS in mood disorders, which has a close relationship with BDNF-TrkB signaling.

Methods The present study aimed to identify patterns and processes in acquisition of oral bacteria and to characterize the microbiota of different dentition states and habitats. Mucosal, salivary, supragingival, and subgingival biofilm samples were collected from orally and systemically healthy children and mother-child dyads in predentate, primary, mixed, and permanent dentitions. 16S rRNA gene sequences were compared to the Human Oral Microbiome Database (HOMD). Functional potential was inferred using PICRUSt. Results Unweighted and weighted UniFrac distances were significantly smaller between each mother-predentate dyad than infant-unrelated female dyads. Predentate children shared a median of 85% of species-level operational taxonomic units (s-OTUs) and 100% of core s-OTUs with their mothers. Maternal smoking, but not gender, mode of delivery, feeding habits, or type of food discriminated between predentate microbial profiles. The primary dentition demonstrated expanded community membership, structure, and function when compared to the predentate stage, as well as significantly lower similarity between mother-child dyads. The primary dentition also included 85% of predentate core s-OTUs. Subsequent dentitions exhibited over 90% similarity to the primary dentition in phylogenetic and functional structure. Species from the predentate mucosa as well as new microbial assemblages were identified in the primary supragingival and subgingival microbiomes. All individuals shared 65% of species between supragingival and subgingival habitats; however, the salivary microbiome exhibited less than 35% similarity to either habitat. Conclusions Within the limitations of a cross-sectional study design, we identified two definitive stages in oral bacterial colonization: an early predentate imprinting and a second wave with the eruption of primary teeth. Bacterial acquisition in the oral microbiome is influenced by the maternal microbiome. Personalization begins with the eruption of primary teeth; however, this is limited to phylogeny; functionally, individuals exhibit few differences, suggesting that microbial assembly may follow a defined schematic that is driven by the functional requirements of the ecosystem. This early microbiome forms the foundation upon which newer communities develop as more colonization niches emerge, and expansion of biodiversity is attributable to both introduction of new species and increase in abundance of predentate organisms. Electronic supplementary material The online version of this article (10.1186/s40168-018-0443-2) contains supplementary material, which is available to authorized users.

Background Alterations in peripheral sex hormones may play an important role in sex differences in terms of stress responses and mood disorders. It is not yet known whether and how stress-related brain systems and brain sex steroid levels fluctuate in relation to changes in peripheral sex hormone levels, or whether the different sexes show different patterns. We aimed to investigate systematically, in male and female rats, the effect of decreased circulating sex hormone levels following gonadectomy on acute and chronic stress responses, manifested as changes in plasma and hypothalamic sex steroids and hypothalamic stress-related molecules. Method Experiment (Exp)-1: Rats (14 males, 14 females) were gonadectomized or sham-operated (intact); Exp-2: gonadectomized and intact rats (28 males, 28 females) were exposed to acute foot shock or no stressor; and Exp-3: gonadectomized and intact rats (32 males, 32 females) were exposed to chronic unpredictable mild stress (CUMS) or no stressor. For all rats, plasma and hypothalamic testosterone (T), estradiol (E2), and the expression of stress-related molecules were determined, including corticotropin-releasing hormone, vasopressin, oxytocin, aromatase, and the receptors for estrogens, androgens, glucocorticoids, and mineralocorticoids. Results Surprisingly, no significant correlation was observed in terms of plasma sex hormones, brain sex steroids, and hypothalamic stress-related molecule mRNAs (p > 0.113) in intact or gonadectomized, male or female, rats. Male and female rats, either intact or gonadectomized and exposed to acute or chronic stress, showed different patterns of stress-related molecule changes. Conclusion Diminished peripheral sex hormone levels lead to different peripheral and central patterns of change in the stress response systems in male and female rats. This has implications for the choice of models for the study of the different types of mood disorders which also show sex differences.

Adeno-associated viral vectors have numerous applications in neuroscience, including the study of gene function in health and disease, targeting of light-sensitive proteins to anatomically distinct sets of neurons to manipulate neuronal activity (optogenetics), and the delivery of fluorescent protein to study anatomical connectivity in the brain. Moreover several phase I/II clinical trials for gene therapy of eye and brain diseases with adeno-associated viral vectors have shown that these vectors are well tolerated by human patients. In this chapter we describe a detailed protocol for the small scale production of recombinant adeno-associated viral vectors. This protocol can be executed by investigators with experience in cell culture and molecular biological techniques in any well-equipped molecular neurobiology laboratory. With this protocol we typically obtain research batches of 100-200 μL that range in titer from 5 × 10

Adeno-associated viral vectors have numerous applications in neuroscience, including the study of gene function in health and disease, targeting of light-sensitive proteins to anatomically distinct sets of neurons to manipulate neuronal activity (optogenetics), and the delivery of fluorescent protein to study anatomical connectivity in the brain. Moreover several phase I/II clinical trials for gene therapy of eye and brain diseases with adeno-associated viral vectors have shown that these vectors are well tolerated by human patients. In this chapter we describe a detailed protocol for the small scale production of recombinant adeno-associated viral vectors. This protocol can be executed by investigators with experience in cell culture and molecular biological techniques in any well-equipped molecular neurobiology laboratory. With this protocol we typically obtain research batches of 100-200 μL that range in titer from 5 × 1012 to 2 × 1013 genomic copies/mL.

Background Guidelines regarding the impact and value of prophylaxis or maintenance therapy in equine gastric ulcer syndrome (EGUS) are not well-established or defined. The merits and the magnitude of effects of prophylaxis for spontaneous or recurrent squamous gastric ulceration in horses in training are uncertain. Objectives To pool data from randomised controlled trials (RCTs) to eliminate reporting bias and evaluate the efficacy of prophylactic omeprazole in the prevention of EGUS in training horses, and secondarily to compare prophylactic dosages of omeprazole. Study design Meta-analysis. Methods This meta-analysis was conducted according to the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A systematic literature search identified RCTs comparing omeprazole prophylaxis with sham in prevention of EGUS. Data were analysed using the Mantel-Haenszel test method to calculate risk ratio (RR) or mean difference (MD) with 95% confidence intervals (CIs). Primary outcome was efficacy of prophylaxis. Secondary outcome was endoscopic severity of ulceration. The influence of study characteristics on the outcomes was examined by subgroup analyses. Results In preventing gastric ulcer occurrence, omeprazole prophylaxis was superior to sham in training horses (7 trials, 566 horses, RR 0.28, 95% CI 0.18-0.43; 23.4% in omeprazole prophylaxis vs. 77.2% in sham; high quality evidence). Prevalence of ulceration was 75.3 and 87.2% in the sham arms of the 1 mg/kg and 2 mg/kg omeprazole groups, respectively. Severity scores were significantly lower for omeprazole vs. sham (mean difference [MD] -1.05; 95% CI -1.35 to -0.69). Subgroup analyses comparing prophylactic omeprazole dosages resulted in a mean difference of -0.94 and -1.60 for the 1 and 2 mg/kg groups, respectively. Main limitations Studies showed heterogeneity with regard to prophylactic dose. Conclusions Omeprazole prophylaxis in active training horses significantly reduces gastric ulceration compared with no prophylaxis (sham) with the absolute effect of 566 fewer ulcers per 1000 horses treated.

Multiple sclerosis (MS) is a highly heterogeneous disease with large inter-individual differences in disease course. MS lesion pathology shows considerable heterogeneity in localization, cellular content and degree of demyelination between patients. In this study, we investigated pathological correlates of disease course in MS using the autopsy cohort of the Netherlands Brain Bank (NBB), containing 182 MS brain donors. Using a standardized autopsy procedure including systematic dissection from standard locations, 3188 tissue blocks containing 7562 MS lesions were dissected. Unbiased measurements of lesion load were made using the tissue from standard locations. Lesion demyelinating and innate inflammatory activity were visualized by immunohistochemistry for proteolipid protein and human leukocyte antigen. Lesions were classified into active, mixed active/inactive (also known as chronic active), inactive or remyelinated, while microglia/macrophage morphology was classified as ramified, amoeboid or foamy. The severity score was calculated from the time from first symptoms to EDSS-6. Lesion type prevalence and microglia/macrophage morphology were analyzed in relation to clinical course, disease severity, lesion load and sex, and in relation to each other. This analysis shows for the first time that (1) in progressive MS, with a mean disease duration of 28.6 ± 13.3 years (mean ± SD), there is substantial inflammatory lesion activity at time to death. 57% of all lesions were either active or mixed active/inactive and 78% of all patients had a mixed active/inactive lesion present; (2) patients that had a more severe disease course show a higher proportion of mixed active/inactive lesions (p = 6e-06) and a higher lesion load (p = 2e-04) at the time of death, (3) patients with a progressive disease course show a higher lesion load (p = 0.001), and a lower proportion of remyelinated lesions (p = 0.03) compared to patients with a relapsing disease course, (4) males have a higher incidence of cortical grey matter lesions (p = 0.027) and a higher proportion of mixed active/inactive lesions compared to females across the whole cohort (p = 0.007). We confirm that there is a higher proportion of mixed active/inactive lesions (p = 0.006) in progressive MS compared to relapsing disease. Identification of mixed active/inactive lesions on MRI is necessary to determine whether they can be used as a prognostic tool in living MS patients.

Dysbiotic oral bacterial communities have a critical role in the etiology and progression of periodontal diseases. The goal of this study was to investigate the extent to which smoking increases risk for disease by influencing the composition of the subgingival microbiome in states of clinical health. Subgingival plaque samples were collected from 200 systemically and periodontally healthy smokers and nonsmokers. 16S pyrotag sequencing was preformed generating 1 623 713 classifiable sequences, which were compared with a curated version of the Greengenes database using the quantitative insights into microbial ecology pipeline. The subgingival microbial profiles of smokers and never-smokers were different at all taxonomic levels, and principal coordinate analysis revealed distinct clustering of the microbial communities based on smoking status. Smokers demonstrated a highly diverse, pathogen-rich, commensal-poor, anaerobic microbiome that is more closely aligned with a disease-associated community in clinically healthy individuals, suggesting that it creates an at-risk-for-harm environment that is primed for a future ecological catastrophe.

Adeno-associated viral (AAV) vectors based on serotype 5 are an efficient means to target dorsal root ganglia (DRG) to study gene function in the primary sensory neurons of the peripheral nervous system. In this study, we have developed a compact AAV dual promoter vector composed of the cytomegalovirus (CMV) and chicken beta-actin (CAG) promoters in a back-to-back configuration with a shared enhancer, and show efficient expression of two proteins simultaneously in DRG neurons. We demonstrate how this is useful for experiments on axonal regeneration, by co-expressing a gene of interest and an axonal marker. Using a farnesylated form of eGFP, which is actively transported along axons, we show superior long-distance labelling of axons of DRG neurons compared with normal eGFP. Additionally, we have efficiently transduced lumbar DRG neurons by injecting the AAV dual promoter vector into the dorsal intrathecal space, which is a less invasive delivery method. In summary, we have developed an AAV dual promoter vector designed for simultaneous expression of a gene of interest and a fluorescent protein to label long-distance axonal projections, which allows specific quantification of axons from transduced neurons after injury.

Nail-wire targets (20 μm diameter copper wires with 80 μm hemispherical head) were used to investigate energy transport by relativistic fast electrons generated in intense laser-plasma interactions. The targets were irradiated using the 300 J, 1 ps, and 2 × 1020 W · cm-2 Vulcan laser at the Rutherford Appleton Laboratory. A spherically bent crystal imager, a highly ordered pyrolytic graphite spectrometer, and single photon counting charge-coupled device gave absolute Cu Kα measurements. Results show a concentration of energy deposition in the head and an approximately exponential fall-off along the wire with about 60 μm 1/e decay length due to resistive inhibition. The coupling efficiency to the wire was 3.3 ± 1.7% with an average hot electron temperature of 620 ± 125 keV. Extreme ultraviolet images (68 and 256 eV) indicate additional heating of a thin surface layer of the wire. Modeling using the hybrid E-PLAS code has been compared with the experimental data, showing evidence of resistive heating, magnetic trapping, and surface transport. © 2009 American Institute of Physics.

The regenerative ability of CNS axons decreases with age however this ability remains largely intact in PNS axons throughout adulthood. These differences are likely to correspond with age-related silencing of proteins necessary for axon growth and elongation. In previous studies, it has been shown that reintroduction of the alpha9 integrin subunit (tenascin-C receptor, ?9) that is downregulated in adult CNS can improve neurite outgrowth and sensory axon regeneration after a dorsal rhizotomy or a dorsal column crush spinal cord lesion. In the current study, we demonstrate that virally-expressed integrins (?9, ?6, or ?1 integrin) in the adult rat sensorimotor cortex and adult red nucleus are excluded from axons following neuronal transduction. Attempts to stimulate transport by inclusion of a cervical spinal injury and thus an upregulation of extracellular matrix molecules at the lesion site, or co-transduction with its binding partner, ?1 integrin, did not induce integrin localization within axons. In contrast, virally-expressed ?9 integrin in developing rat cortex (postnatal day 5 or 10) demonstrated clear localization of integrins in cortical axons revealed by the presence of integrin in the axons of the corpus callosum and internal capsule as well as in the neuronal cell body. Furthermore, examination of dorsal root ganglia neurons and retinal ganglion cells demonstrated integrin localization both within peripheral nerve as well as dorsal root axons and within optic nerve axons, respectively. Together, our results suggest a differential ability for in vivo axonal transport of transmembrane proteins dependent on neuronal age and subtype.Significance Statement: Most CNS neurons have an intrinsically low ability to regenerate their axons. This study has asked whether the transport into axons of integrins, the receptors that mediate growth through extracellular matrix, might reveal reasons for the poor regenerative ability of CNS axons. Tagged integrins were expressed in sensory, retinal ganglion cell, cortical and red nucleus neurons. The integrins were transported down the axons of sensory and retinal ganglion cell axons, but not down the axons of adult cortical or red nucleus neurons. However, during the postnatal period of corticospinal axon growth, cortical neurons admitted integrins into their axons. The findings suggest that exclusion of integrins and other receptors from CNS axons may be a cause for their poor regenerative ability.

The 16S rRNA gene is widely used for taxonomic profiling of microbial ecosystems; and recent advances in sequencing chemistry have allowed extremely large numbers of sequences to be generated from minimal amounts of biological samples. Analysis speed and resolution of data to species-level taxa are two important factors in large-scale explorations of complex microbiomes using 16S sequencing. We present here new software, Phylogenetic Tools for Analysis of Species-level Taxa (PhyloToAST), that completely integrates with the QIIME pipeline to improve analysis speed, reduce primer bias (requiring two sequencing primers), enhance species-level analysis and add new visualization tools. The code is free and open source and can be accessed at http://phylotoast.org.

The dorsal column lesion model of spinal cord injury targets sensory fibres which originate from the dorsal root ganglia and ascend in the dorsal funiculus. It has the advantages that fibres can be specifically traced from the sciatic nerve, verifiably complete lesions can be performed of the labelled fibres, and it can be used to study sprouting in the central nervous system from the conditioning lesion effect. However, functional deficits from this type of lesion are mild, making assessment of experimental treatment-induced functional recovery difficult. Here, five functional tests were compared for their sensitivity to functional deficits, and hence their suitability to reliably measure recovery of function after dorsal column injury. We assessed the tape removal test, the rope crossing test, CatWalk gait analysis, and the horizontal ladder, and introduce a new test, the inclined rolling ladder. Animals with dorsal column injuries at C4 or T7 level were compared to sham-operated animals for a duration of eight weeks. As well as comparing groups at individual timepoints we also compared the longitudinal data over the whole time course with linear mixed models (LMMs), and for tests where steps are scored as success/error, using generalized LMMs for binomial data. Although, generally, function recovered to sham levels within 2-6 weeks, in most tests we were able to detect significant deficits with whole time-course comparisons. On the horizontal ladder deficits were detected until 5-6 weeks. With the new inclined rolling ladder functional deficits were somewhat more consistent over the testing period and appeared to last for 6-7 weeks. Of the CatWalk parameters base of support was sensitive to cervical and thoracic lesions while hind-paw print-width was affected by cervical lesion only. The inclined rolling ladder test in combination with the horizontal ladder and the CatWalk may prove useful to monitor functional recovery after experimental treatment in this lesion model.

Although it is established that peri-implantitis is a bacterially induced disease, little is known about the bacterial profile of peri-implant communities in health and disease. The purpose of the present investigation was to examine the microbial signatures of the peri-implant microbiome in health and disease.Subgingival and submucosal plaque samples were collected from forty subjects with periodontitis, peri-implantitis, periodontal and peri-implant health and analysed using 16S pyrosequencing.Peri-implant biofilms demonstrated significantly lower diversity than subgingival biofilms in both health and disease, however, several species, including previously unsuspected and unknown organisms, were unique to this niche. The predominant species in peri-implant communities belonged to the genera Butyrivibrio, Campylobacter, Eubacterium, Prevotella, Selenomonas, Streptococcus, Actinomyces, Leptotrichia, Propionibacterium, Peptococcus, Lactococcus and Treponema. Peri-implant disease was associated with lower levels of Prevotella and Leptotrichia and higher levels of Actinomyces, Peptococcus, Campylobacter, non-mutans Streptococcus, Butyrivibrio and Streptococcus mutans than healthy implants. These communities also demonstrated lower levels of Prevotella, non-mutans Streptococcus, Lactobacillus, Selenomonas, Leptotrichia, Actinomyces and higher levels of Peptococcus, Mycoplasma, Eubacterium, Campylobacter, Butyrivibrio, S. mutans and Treponema when compared to periodontitis-associated biofilms.The peri-implant microbiome differs significantly from the periodontal community in both health and disease. Peri-implantitis is a microbially heterogeneous infection with predominantly gram-negative species, and is less complex than periodontitis.

For many experiments in the study of the peripheral nervous system, it would be useful to genetically manipulate primary sensory neurons. We have compared vectors based on adeno-associated virus (AAV) serotypes 1, 2, 3, 4, 5, 6, and 8, and lentivirus (LV), all expressing green fluorescent protein (GFP), for efficiency of transduction of sensory neurons, expression level, cellular tropism, and persistence of transgene expression following direct injection into the dorsal root ganglia (DRG), using histological quantification and qPCR. Two weeks after injection, AAV1, AAV5, and AAV6 had transduced the most neurons. The time course of GFP expression from these three vectors was studied from 1 to 12 weeks after injection. AAV5 was the most effective serotype overall, followed by AAV1. Both these serotypes showed increasing neuronal transduction rates at later time points, with some injections of AAV5 yielding over 90% of DRG neurons GFP(+) at 12 weeks. AAV6 performed well initially, but transduction rates declined dramatically between 4 and 12 weeks. AAV1 and AAV5 both transduced large-diameter neurons, IB4(+) neurons, and CGRP(+) neurons. In conclusion, AAV5 is a highly effective gene therapy vector for primary sensory neurons following direct injection into the DRG.

Neuroma formation after peripheral nerve injury is detrimental to functional recovery and is therefore a significant clinical problem. The molecular basis for this phenomenon is not fully understood. Here, we show that the expression of the chemorepulsive protein semaphorin 3A (sema3A), but not semaphorin 3F, is increased in human neuroma tissue that has formed in severe obstetric brachial plexus lesions. Sema3A is produced by fibroblasts in the epineurial space and appears to be secreted into the extracellular matrix. It surrounds fascicles, minifascicles, or single axons, suggesting a role in fasciculation and inhibition of neurite outgrowth. Lentiviral vector-mediated knock-down of Neuropilin 1, the receptor for sema3A, leads to increased neurite outgrowth of F11 cells cultured on neuroma tissue, but not of F11 cells cultured on normal nerve tissue. These findings demonstrate the putative inhibitory role of sema3A in human neuroma tissue. Our observations are the first demonstration of the expression of sema3A in human neural scar tissue and support a role for this protein in the inhibition of axonal regeneration in injured human peripheral nerves. These findings contribute to the understanding of the outgrowth inhibitory properties of neuroma tissue.

The existence of symbiotic relationships between bacteria in different ecosystems and their host niches have long been known to science. The human body also hosts vast numbers of bacteria in several habitats. Emerging evidence from the gastro-intestinal tract, genito-urinary tract and respiratory indicates that there are several health benefits to hosting a complex and diverse microbial community i. Bacteria colonize the oral cavity within a few minutes after birth and form stable communities . Our knowledge of the oral microbiome has expanded exponentially with development of novel exploratory methods that allow us to examine diversity, structure, function and topography without the need to cultivate the individual components of the biofilm. The purpose of this perspective, therefore, is to examine the strength of current evidence supporting a role for the oral microbiome in maintaining oral health. While several lines of evidence are emerging to suggest that indigenous oral microbiota may have a role in immune education and preventing pathogen expansion, much more work is needed to definitively establish whether oral bacteria do indeed contribute to sustaining oral health, and if so, the mechanisms underlying this role.

It is known that several oral infections have a strong ethnic predilection. Evidence is emerging that periodontitis, the sixth most prevalent disease in the world, has a definite ethnic distributio...

Peripheral nerve injury results in the activation of a number of transcription factors (TFs) in injured neurons, some of which may be key regulators of the regeneration-associated gene (RAG) programme. Among known RAG TFs, ATF3, Smad1, STAT3 and c-Jun have all been linked to successful axonal regeneration and have known functional and physical interactions. We hypothesised that TF expression would promote regeneration of the central axon branch of DRG neurons in the absence of a peripheral nerve lesion and that simultaneous overexpression of multiple RAG TFs would lead to greater effects than delivery of a single TF. Using adeno-associated viral vectors, we overexpressed either the combination of ATF3, Smad1, STAT3 and c-Jun with farnesylated GFP (fGFP), ATF3 only with fGFP, or fGFP only, in DRG neurons and assessed axonal regeneration after dorsal root transection or dorsal column injury and functional improvement after dorsal root injury. ATF3 alone and the combination of TFs promoted faster regeneration in the injured dorsal root. Surprisingly, however, the combination did not perform better than ATF3 alone. Neither treatment was able to induce functional improvement on sensory tests after dorsal root injury or promote regeneration in a dorsal column injury model. The lack of synergistic effects among these factors indicates that while they do increase the speed of axon growth, there may be functional redundancy between these TFs. Because axon growth is considerably less than that seen after a conditioning lesion, it appears these TFs do not induce the full regeneration programme.

The reticulate phylogeny of the Triticeae is demonstrated by extensive conflict among diploid gene trees, and by the presence of numerous allopolyploid combinations. Elymus is a geographically widespread allopolyploid genus which includes multiple distinct genomic combinations. By definition, all Elymus species include at least one set of Pseudoroegneria genomes, but these may be combined with genomes from one or more of several other Triticeae genera. Because allopolyploids represent a confluence of divergent evolutionary lineages, molecular phylogenetic analyses of allopolyploid species often include nuclear gene sequences, which potentially represent all of the distinct lineages that coexist within an individual plant. Here, we present data from two nuclear genes, s-amylase and starch synthase, in an attempt to characterize differences between cytogenetically distinct StStYY, StStHH, and StStStStHH species, and between the North American and Eurasian tetraploid species. Patterns of diversity among species also shed light on possible introgression following polyploidization.

Tumor necrosis factor (TNF)- α, a cytokine present in inflammed lungs, is known to mediate some of the adverse effects of ozone and inhaled particles. The authors evaluated transgenic mice with constitutive pulmonary expression of TNF- αunder transcriptional regulation of the surfactant protein-C promoter as an animal model of biological susceptibility to air pollutants. To simulate a repeated, episodic exposure to air pollutants, wild-type and TNF mice inhaled air or a mixture of ozone (0.4 ppm) and urban particles (EHC-93, 4.8 mg/m3) for 4 h, once per week, for 12 consecutive weeks and were sacrificed 20 h after last exposure. TNF mice exhibited chronic lung inflammation with septal thickening, alveolar enlargement, and elevated protein and cellularity in bronchoalveolar lavage fluid (genotype main effect, p L-DOPA after exposure to the air pollutants (Genotype × Exposure factor interaction, p = .014). Serum creatine kinase-MM isoform increased in TNF mice exposed to pollutants (Genotype × Exposure factor interaction, p = .043). The marked pollutant-related nitration in the lungs of the TNF mice reveals basic differences in free radical generation and scavenging in the inflamed lungs in response to pollutants. Furthermore, elevation of circulating creatine kinase-MM isoform specifically in TNF mice exposed to pollutants suggests systemic adverse impacts from lung inflamma-tory mediators, possibly on muscles and the cardiovascular system.

Melengestrol acetate (MGA) contraceptives are widely used in zoo felids to regulate fertility and may have deleterious effects on endometrial health. To determine whether MGA exposure was associated with endometrial disease, the genital tracts of 212 zoo felids (99 MGA treated and 113 control) representing 23 species were evaluated. Adenomatous and cystic hyperplasia were prevalent in both MGA-treated (85%) and control (61%) groups, and the risk of developing these lesions increased with age. Treatment with MGA further increased the risk of developing advanced hyperplasia regardless of dose, and treatment for >72 months significantly elevated that risk, whereas parous animals had a lower risk. Endometrial polyps, fibrosis, adenomyosis, and hydrometra occurred in both MGA-treated and control animals. MGA treatment was associated with an increased risk of hydrometra and mineralization but not of adenomyosis, polyps, or fibrosis after adjusting for advanced hyperplasia. Acute or chronic endometritis were associated with advanced hyperplasia but not with MGA treatment. These results indicate that proliferative and inflammatory endometrial lesions are common spontaneous diseases in zoo cats, and MGA contraceptives increase the risk of some diseases. The association of MGA with endometrial lesions that could impair fertility should be considered when using this contraceptive in genetically valuable felids.

Oral infections have a strong ethnic predilection; suggesting that ethnicity is a critical determinant of oral microbial colonization. Dental plaque and saliva samples from 192 subjects belonging to four major ethnicities in the United States were analyzed using terminal restriction fragment length polymorphism (t-RFLP) and 16S pyrosequencing. Ethnicity-specific clustering of microbial communities was apparent in saliva and subgingival biofilms, and a machine-learning classifier was capable of identifying an individual’s ethnicity from subgingival microbial signatures. The classifier identified African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity. The data demonstrates a significant association between ethnic affiliation and the composition of the oral microbiome; to the extent that these microbial signatures appear to be capable of discriminating between ethnicities.

Using the implicit/hybrid Eulerian simulation code ePLAS1,2, we study the effects of viscous modeling choices on the predicted implosive behavior of ICF targets as employed on the NIF. Results from traditional artificial viscosity and real viscosity are compared in both planar and 2D cylindrical geometry. We examine the implosion of spherical and slightly ellipsoidal DT shells containing dense DT gas in ∼20 – 50 micron “voids.” Before implosion the shells have been shock compressed to ∼102 to 103 g/cm3 densities, and 0.3 to 1.2 keV temperatures. Effects from real viscosity are largely independent of density, but can work to smear shocks over some 20 microns when the ion temperature approaches 1.0 keV. Artificial viscosity sets shocks of all strength to ∼3 × the local cell widths.

The authors would like to supply additional information in relation to the study. The characteristics of the sample population included in the study are outlined in the table supplied. The methods pertaining to this are as follows: Informed consent and inclusion into study: Each subject who qualified for the study was explained the purpose and procedures of the research and written informed consent obtained. Questionnaires were used to assess demographics, oral hygiene and diet. Oral hygiene habits were assessed by frequency of brushing, flossing, smoking history and visits to the dentist, while food habits were assessed by routine exposures to one of the four diet patterns: (i) Standard American (diet rich in red meat, bologna, sausages, hotdogs and similar foods, refined grains (for example, bread), pasta and similar dishes, and desserts). (ii) Hispanic and Latino (diet rich in rice, beans, corn (as flour, e.g. tortilla, or fresh), avocado, olives, fruits, sweet breads, red meats), (iii) Asian (diet rich in rice, noodles, millet, fresh and salted vegetables, seafood, poultry, eggs, legumes) or (iv) not fitting into any of the above categories. The legend for Figure 1 should be revised to read as below: Figure 1 Non-metric multidimensional scaling (NMDS) of t-RFLP peak areas.

Laser-based experiments have shown that Rayleigh–Taylor (RT) growth in thin, perturbed copper foils leads to a phase dominated by narrow spikes between thin bubbles. These experiments were well modeled and diagnosed until this “ spike” phase, but not into this spike phase. Experiments were designed, modeled, and performed on the OMEGA laser [T. R. Boehly, D. L. Brown, R. S. Craxton et al., Opt. Commun. 133, 495 (1997)] to study the late-time spike phase. To simulate the conditions and evolution of late time RT, a copper target was fabricated consisting of a series of thin ridges (spikes in cross section) 150 μm apart on a thin flat copper backing. The target was placed on the side of a scale-1.2 hohlraum with the ridges pointing into the hohlraum, which was heated to 190 eV. Side-on radiography imaged the evolution of the ridges and flat copper backing into the typical RT bubble and spike structure including the “ mushroom-like feet” on the tips of the spikes. RAGE computer models [R. M. Baltrusaitis, M. ...

The Rayleigh–Taylor instability of radiatively driven thin copper foils is studied under pure ablation, as well as with beryllium buffers to provide additional pressure drive, in support of the target design for Inertial Confinement Fusion. Modeling was done with the RAGE adaptive mesh refinement code [R. M. Baltrusaitis, M. L. Gittings, R. P. Weaver, R. F. Benjamin, and J. M. Budzinski, Phys. Fluids 8, 2471 (1996)] of experiments done on the OMEGA [T. R. Boehly, D. L. Brown, R. S. Craxton et al., Opt. Commun. 133, 495 (1997)] laser. The copper foils were typically 11.5 μm thick with 0.45 μm amplitude and 45 μm wavelength cosine surface perturbations. The beryllium layer was 5 μm thick. The drive was a “PS26”-like [J. D. Lindl, Phys. Plasmas 2, 3933 (1995)] laser pulse delivering peak 160–185 eV radiation temperatures. Good agreement between experiment and simulation has been obtained out to 4.5 ns. Mechanisms for late time agreement are discussed.

A preformed plasma simulating the corona of a fast ignitor target has been probed with 527 nm and 1054 nm lasers exceeding the critical power for ponderomotive electron cavitation. For both colors, the f number of the probe beam is increased as it propagates through the plasma. Transmission of the diffraction-limited beams is higher for the green than for the 1 μm case.

A structurally intact and competent lower esophageal sphincter in the experimental model shortens and becomes incompetent during gastric distention. The aim of this study was to evaluate postprandial reflux as an indirect measure of this volume-induced sphincter shortening and incompetency. Reflux (pH4) in the 2-hour period following a meal was retrospectively analyzed from the 24-hour esophageal pH recordings of 94 healthy volunteers and 609 symptomatic patients. Forty-six percent of patients had pathologic postprandial reflux (95th percentile of normal). The prevalence was lower in patients with a structurally intact compared to a defective lower esophageal sphincter (32% vs. 58%; P0.001). Pathologic postprandial reflux was greater in patients with abnormal compared to normal findings on 24-hour pH study (76% vs. 21%; P0.001). Patients with a normal 24-hour pH study and postprandial reflux had shorter sphincter lengths (2.33 vs. 2.82 cm; P0.001) and lower pressures (10.78 vs. 14.24 mm Hg; P0.005). A hiatal hernia increased the prevalence of postprandial reflux (P0.001) in all patients (67% vs. 38%) and in the subgroup with a structurally intact sphincter (75% vs. 27%, P0.001). Postprandial reflux is a dynamic indicator of sphincter competency, and increases as the structural sphincter characteristics deteriorate and is augmented by a hiatal hernia.

A multifluid implicit plasma simulation code has been used to study the transport of hot electrons generated by an intense $(\ensuremath{\ge}3\ifmmode\times\else\texttimes\fi{}{10}^{18}\phantom{\rule{0ex}{0ex}}\mathrm{W}/\mathrm{cm}{}^{2})$ short-pulse 1.06 \ensuremath{\mu}m laser into plasma targets over a broad range of densities $[(0.35--200){n}_{\mathrm{crit}}]$, as arising in the Fast Ignitor approach to inertial confinement fusion. The most intense (16--250 MG) magnetic fields generated in this interaction are traced to the ponderomotive push on background electrons, and tardy electron shielding. These fields can focus the heated electrons toward the axis of the beam, while impeding the direct return flow of background electrons.

Recent experiments have shown that low density foam layers can significantly mitigate the perturbing effects of beam nonuniformities affecting the acceleration of thin shells. This problem is studied parametrically with two-dimensional LASNEX [G. B. Zimmerman and W. L. Kruer, Comments Plasma Phys. Controlled Fusion 2, 51 (1975)]. Foam-buffered targets are employed, consisting typically of 250 A of gold, and 50 μm of 50 mg/cm3 C10H8O4 foam attached to a 10 μm foil. In simulation these were characteristically exposed to 1.2 ns, flat-topped green light pulses at 1.4×1014 W/cm2 intensity, bearing 30 μm lateral perturbations of up to 60% variation in intensity. Without the buffer layers the foils were severely disrupted by 1 ns. With buffering only minimal distortion was manifest at 3 ns. The smoothing is shown to derive principally from the high thermal conductivity of the heated foam. The simulation results imply that (1) the foam thickness should exceed the disturbance wavelength; (2) intensities exceeding ...

In an experiment relevant to the fast ignitor fusion concept, a preformed plasma simulating the corona of a fusion target has been probed with laser intensities exceeding 1018 W/cm2. It is seen that the f number of the probe beam is increased as it propagates through the target plasma—a channeling of the power. The transmission and backscatter of the probe beam have been examined, and the analysis suggests anomalous absorption of laser light in shorter scale length plasmas.

Creation of a low density, high temperature plasma buffer between the absorption and ablation layers of a directly driven inertial confinement fusion implosion capsule has been proposed as a means to reduce “early time” imprint from laser nonuniformities. This thermal smoothing blanket might be created from a low density foam layer wrapped around the deuterium–tritium filled microballoon. Preliminary spherical implosion tests of this concept using a polystyrene foam layer surrounding a glass microballoon were performed at the Nova laser [Rev. Sci. Instrum. 57, 2101 (1986)], using a 527 nm drive wavelength. Comparison of capsule yield and imploded core symmetry showed promising improvements in overall target performance, relative to one-dimensional undegraded hydrodynamic simulations, when the foam-buffer layer was present.

Peripheral nerve injury in humans often leads to incomplete functional recovery. In this review we discuss the potential for gene therapy to be used as a strategy alongside surgical repair techniques for the study of peripheral nerve regeneration in rodent models and with a view to its eventual use for the promotion of successful regeneration in the clinic. Gene therapy can be defined as the introduction of a foreign, therapeutic gene into living cells in order to treat a disease. The first attempts to express a foreign gene in peripheral neurons date back more than 25 years. The vectors used at that time were imperfect-mainly because they contained viral genes that were expressed in the target cells and elicited an immunological response. Fortunately significant progress has been made: today adeno-associated viral vectors can be produced completely free of viral genes and Phase I and II clinical studies have shown that these vectors are well tolerated. The technology for gene delivery has reached a state of readiness for clinical translation in many fields of neurology, including peripheral nerve repair. The current range of potential therapeutic genes for the repair of the traumatized peripheral nerve has also grown over the years and now includes neurotrophic factors with specificities for various subtypes of peripheral neurons, cell adhesion and extracellular matrix molecules and transcription factors. This review for this Festschrift, published to celebrate the 70th birthday of Willem Hendrik Gispen, contains many "footprints" from the time the senior author (JV) worked with Willem Hendrik, first as a student intern, then as a Ph.D. student (1983-1987) and later as a postdoctoral fellow (1989-1993). The preface of this article highlights personal memories of a time that will never come back.

A new method is presented to model the intermediate regime between collisionless and Coulomb collision dominated plasmas in particle-in-cell codes. Collisional processes between particles of different species are treated through the concept of a grid-based “collision field,” which can be particularly efficient for multi-dimensional applications. In this method, particles are scattered using a force which is determined from the moments of the distribution functions accumulated on the grid. The form of the force is such to reproduce the multi-fluid transport equations through the second (energy) moment. Collisions between particles of the same species require a separate treatment. For this, a Monte Carlo-like scattering method based on the Langevin equation is used. The details of both methods are presented, and their implementation in a new hybrid (particle ion, massless fluid electron) algorithm is described. Aspects of the collision model are illustrated through several one- and two-dimensional test problems as well as examples involving laser produced colliding plasmas.

We propose, and computationally evaluate a new approach to high voltage plasma opening switches. The generator current is engineered to pass through a series of switch plasma modules, each providing a separate emission gap. The resistance from the sum of these gaps is in parallel with the load. Thus, modular plasma gaps can be added to encourage optimal energy transfer to a high impedance load. >

Summary form only given. A final pulse of hot electrons can induce preheat and shock ignition[su1} under direct drive, as recently demonstrated2 with the implicit/hybrid code ePLAS3,4. The ePLAS model follows a laser generated hot electron component (fluid or particles) through background plasma of cold fluid electrons and ions. It allows for variations in the hot electron spectrum and directivity, and can suggest tuning options to optimize implosion timing and symmetry for shock Ignition.