Integrative proteomics highlight presynaptic alterations and c-Jun misactivation as convergent pathomechanisms in ALS.

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease mainly affecting upper and lower motoneurons. Several functionally heterogeneous genes have been associated with the familial form of this disorder (fALS), depicting an extremely complex pathogenic landscape. This heterogeneity has limited the identification of an effective therapy, and this bleak prognosis will only improve with a greater understanding of convergent disease mechanisms. Recent evidence from human post-mortem material and diverse model systems has highlighted the synapse as a crucial structure actively involved in disease progression, suggesting that synaptic aberrations might represent a shared pathological feature across the ALS spectrum. To test this hypothesis, we performed the first comprehensive analysis of the synaptic proteome from post-mortem spinal cord and human iPSC-derived motoneurons carrying mutations in the major ALS genes. This integrated approach highlighted perturbations in the molecular machinery controlling vesicle release as a shared pathomechanism in ALS. Mechanistically, phosphoproteomic analysis linked the presynaptic vesicular phenotype to an accumulation of cytotoxic protein aggregates and to the pro-apoptotic activation of the transcription factor c-Jun, providing detailed insights into the shared pathobiochemistry in ALS. Notably, sub-chronic treatment of our iPSC-derived motoneurons with the fatty acid docosahexaenoic acid exerted a neuroprotective effect by efficiently rescuing the alterations revealed by our multidisciplinary approach. Together, this study provides strong evidence for the central and convergent role played by the synaptic microenvironment within the ALS spinal cord and highlights a potential therapeutic target that counteracts degeneration in a heterogeneous cohort of human motoneuron cultures.

Effects of a High-Volume 7-Week Pectoralis Muscle Stretching Training on Muscle Function and Muscle Stiffness.

BACKGROUND: There is evidence that high-volume static stretching training of the lower limbs can increase the range of motion (ROM) while decreasing muscles stiffness. However, to date, there is no evidence on the effects of upper limb stretching training or its effect mechanism. Therefore, this study aimed to investigate the effects of a comprehensive 7-week static stretching training program of the pectoralis major muscle (PMa) on glenohumeral joint ROM, muscle force, and muscle stiffness. METHODS: Thirty-eight healthy, physically active participants (23 male, 15 female) were randomly assigned to either the PMa-static stretching intervention (PMa-SS) group or the control group. The PMa-SS group performed a 7-week intervention comprising three sessions a week for 15 min per session, including three static stretching exercises of the PMa for 5 min each. Before and after the intervention period, shoulder extension ROM, muscle stiffness of the PMa (pars clavicularis), and maximal voluntary isometric contraction (MVIC) peak torque (evaluated at both long (MVIClong) and short (MVICshort) muscle lengths) were investigated on a custom-made testing device at 45° shoulder abduction. RESULTS: In the PMa-SS group, the shoulder extension ROM (+ 6%; p < 0.01; d = 0.92) and the MVIClong (+ 11%; p = 0.01; d = 0.76) increased. However, there were no significant changes in MVICshort or in PMa muscle stiffness in the PMa-SS group. In the control group, no changes occurred in any parameter. CONCLUSION: In addition to the increase in ROM, we also observed an improved MVIC at longer but not shorter muscle lengths. This potentially indicates an increase in fascicle length, and hence a likely increase in sarcomeres in series.

Multiomics and machine-learning identify novel transcriptional and mutational signatures in amyotrophic lateral sclerosis.

Amyotrophic lateral sclerosis is a fatal and incurable neurodegenerative disease that mainly affects the neurons of the motor system. Despite the increasing understanding of its genetic components, their biological meanings are still poorly understood. Indeed, it is still not clear to which extent the pathological features associated with amyotrophic lateral sclerosis are commonly shared by the different genes causally linked to this disorder. To address this point, we combined multiomics analysis covering the transcriptional, epigenetic and mutational aspects of heterogenous human induced pluripotent stem cell-derived C9orf72-, TARDBP-, SOD1- and FUS-mutant motor neurons as well as datasets from patients' biopsies. We identified a common signature, converging towards increased stress and synaptic abnormalities, which reflects a unifying transcriptional program in amyotrophic lateral sclerosis despite the specific profiles due to the underlying pathogenic gene. In addition, whole genome bisulphite sequencing linked the altered gene expression observed in mutant cells to their methylation profile, highlighting deep epigenetic alterations as part of the abnormal transcriptional signatures linked to amyotrophic lateral sclerosis. We then applied multi-layer deep machine-learning to integrate publicly available blood and spinal cord transcriptomes and found a statistically significant correlation between their top predictor gene sets, which were significantly enriched in toll-like receptor signalling. Notably, the overrepresentation of this biological term also correlated with the transcriptional signature identified in mutant human induced pluripotent stem cell-derived motor neurons, highlighting novel insights into amyotrophic lateral sclerosis marker genes in a tissue-independent manner. Finally, using whole genome sequencing in combination with deep learning, we generated the first mutational signature for amyotrophic lateral sclerosis and defined a specific genomic profile for this disease, which is significantly correlated to ageing signatures, hinting at age as a major player in amyotrophic lateral sclerosis. This work describes innovative methodological approaches for the identification of disease signatures through the combination of multiomics analysis and provides novel knowledge on the pathological convergencies defining amyotrophic lateral sclerosis.

Predictors of successful discontinuation of antipsychotics and antidepressants.

BACKGROUND: To offer support for patients who decide to discontinue antipsychotic and antidepressant medication, identifying which potentially modifiable factors correlate with discontinuation success is crucial. Here, we analyzed the predictive value of the professional support received, circumstances prior to discontinuation, a strategy of discontinuation, and use of functional and non-functional coping strategies during discontinuation on self-reported discontinuation success and on objective discontinuation. METHODS: Patients who had attempted discontinuing antipsychotics (AP) and/or antidepressants (AD) during the past 5 years (n = 316) completed an online survey including questions on subjective and objective discontinuation success, sociodemographic, clinical and medication-related factors, and scales to assess the putative predictors. RESULTS: A regression model with all significant predictors explained 20-30% of the variance in discontinuation success for AD and 30-40% for AP. After controlling for baseline sociodemographic, clinical and medication-related factors, the most consistent predictor of subjective discontinuation success was self-care behavior, in particular mindfulness, relaxation and making use of supportive relationships. Other predictors depended on the type of medication: For AD, good alliance with the prescribing physician predicted higher subjective success whereas gradual tapering per se was associated with lower subjective success and a lower chance of full discontinuation. In those tapering off AP, leaving time to adjust between dose reductions was associated with higher subjective success and fewer negative effects. CONCLUSIONS: The findings can inform evidence-based clinical guidelines and interventions aiming to support patients during discontinuation. Further studies powered to take interactions between variables into account are needed to improve the prediction of successful discontinuation.

Aging-Dependent Altered Transcriptional Programs Underlie Activity Impairments in Human C9orf72-Mutant Motor Neurons.

Amyotrophic Lateral Sclerosis (ALS) is an incurable neurodegenerative disease characterized by dysfunction and loss of upper and lower motor neurons (MN). Despite several studies identifying drastic alterations affecting synaptic composition and functionality in different experimental models, the specific contribution of impaired activity to the neurodegenerative processes observed in ALS-related MN remains controversial. In particular, contrasting lines of evidence have shown both hyper- as well as hypoexcitability as driving pathomechanisms characterizing this specific neuronal population. In this study, we combined high definition multielectrode array (HD-MEA) techniques with transcriptomic analysis to longitudinally monitor and untangle the activity-dependent alterations arising in human C9orf72-mutant MN. We found a time-dependent reduction of neuronal activity in ALSC9orf72 cultures occurring as synaptic contacts undergo maturation and matched by a significant loss of mutant MN upon aging. Notably, ALS-related neurons displayed reduced network synchronicity most pronounced at later stages of culture, suggesting synaptic imbalance. In concordance with the HD-MEA data, transcriptomic analysis revealed an early up-regulation of synaptic terms in ALSC9orf72 MN, whose expression was decreased in aged cultures. In addition, treatment of older mutant cells with Apamin, a K+ channel blocker previously shown to be neuroprotective in ALS, rescued the time-dependent loss of firing properties observed in ALSC9orf72 MN as well as the expression of maturity-related synaptic genes. All in all, this study broadens the understanding of how impaired synaptic activity contributes to MN degeneration in ALS by correlating electrophysiological alterations to aging-dependent transcriptional programs.

Synaptic disruption and CREB-regulated transcription are restored by K+ channel blockers in ALS.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease, which is still missing effective therapeutic strategies. Although manipulation of neuronal excitability has been tested in murine and human ALS models, it is still under debate whether neuronal activity might represent a valid target for efficient therapies. In this study, we exploited a combination of transcriptomics, proteomics, optogenetics and pharmacological approaches to investigate the activity-related pathological features of iPSC-derived C9orf72-mutant motoneurons (MN). We found that human ALSC9orf72 MN are characterized by accumulation of aberrant aggresomes, reduced expression of synaptic genes, loss of synaptic contacts and a dynamic "malactivation" of the transcription factor CREB. A similar phenotype was also found in TBK1-mutant MN and upon overexpression of poly(GA) aggregates in primary neurons, indicating a strong convergence of pathological phenotypes on synaptic dysregulation. Notably, these alterations, along with neuronal survival, could be rescued by treating ALS-related neurons with the K+ channel blockers Apamin and XE991, which, respectively, target the SK and the Kv7 channels. Thus, our study shows that restoring the activity-dependent transcriptional programme and synaptic composition exerts a neuroprotective effect on ALS disease progression.

A rating scale to inform successful discontinuation of antipsychotics and antidepressants.

Practitioners lack guidance on how to support discontinuation of psychotropic medication. An understanding of what constitutes discontinuation success that encompasses the patients' perspective could advance knowledge in this clinically relevant area. Here, we report the development and validation of a scale to assess subjective discontinuation success. Participants who attempted discontinuing antidepressants and/or antipsychotics during the past 5 years (n = 396) completed a questionnaire on subjective discontinuation success (Discontinuation Success Scale, DSS) developed in consultation with people with lived experience of discontinuation. Construct validity was tested by exploratory and confirmatory factor analysis. Criterion validity was tested by assessing DSS-scores' associations with objective success (i.e., full cessation, reduced dose) in combination with scoring above a predefined criterion on the Well-Being Index. Factor analyses yielded a three-dimensional scale reflecting subjective discontinuation success, positive effects, and negative effects of discontinuation. A 24-item DSS demonstrated sufficient model fit for the participants discontinuing antidepressants or antipsychotics, respectively. Significant associations with objective success and well-being were found. Participants who had achieved full cessation and scored high on well-being reached the highest DSS scores. The DSS is a viable tool for future research aimed at identifying predictors of discontinuation success in order to inform recommendations related to discontinuation.

Draft Genome Sequences of Five Historical Bacillus anthracis Strains.

Bacillus anthracis is the causative agent of anthrax, a disease of livestock, wildlife, and humans. Here, we present the draft genome sequences of five historical B. anthracis strains that were preserved as lyophilates in glass vials for decades.

Enzymatic Activity of HPGD in Treg Cells Suppresses Tconv Cells to Maintain Adipose Tissue Homeostasis and Prevent Metabolic Dysfunction.

Regulatory T cells (Treg cells) are important for preventing autoimmunity and maintaining tissue homeostasis, but whether Treg cells can adopt tissue- or immune-context-specific suppressive mechanisms is unclear. Here, we found that the enzyme hydroxyprostaglandin dehydrogenase (HPGD), which catabolizes prostaglandin E2 (PGE2) into the metabolite 15-keto PGE2, was highly expressed in Treg cells, particularly those in visceral adipose tissue (VAT). Nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ)-induced HPGD expression in VAT Treg cells, and consequential Treg-cell-mediated generation of 15-keto PGE2 suppressed conventional T cell activation and proliferation. Conditional deletion of Hpgd in mouse Treg cells resulted in the accumulation of functionally impaired Treg cells specifically in VAT, causing local inflammation and systemic insulin resistance. Consistent with this mechanism, humans with type 2 diabetes showed decreased HPGD expression in Treg cells. These data indicate that HPGD-mediated suppression is a tissue- and context-dependent suppressive mechanism used by Treg cells to maintain adipose tissue homeostasis.

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.

The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.

BLAST-based validation of metagenomic sequence assignments.

When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by "first-pass" classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.

Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens.

High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.

Benefits of Individualized Feedback in Internet-Based Interventions for Depression: A Randomized Controlled Trial.

BACKGROUND: Even though there is an increasing number of studies on the efficacy of Internet-based interventions (IBI) for depression, experimental trials on the benefits of added guidance by clinicians are scarce and inconsistent. This study compared the efficacy of semistandardized feedback provided by psychologists with fully standardized feedback in IBI. METHODS: Participants with mild-to-moderate depression (n = 1,089, 66% female) from the client pool of a health insurance company participated in a cognitive-behavioral IBI targeting depression over 6 weeks. Individuals were randomized to weekly semistandardized e-mail feedback from psychologists (individual counseling; IC) or to automated, standardized feedback where a psychologist could be contacted on demand (CoD). The contents and tasks were identical across conditions. The primary outcome was depression; secondary outcomes included anxiety, rumination, and well-being. Outcomes were assessed before and after the intervention and 3, 6, and 12 months later. Changes in outcomes were evaluated using latent change score modeling. RESULTS: Both interventions yielded large pre-post effects on depression (Beck Depression Inventory-II: dIC = 1.53, dCoD = 1.37; Patient Health Questionnaire-9: dIC = 1.20, dCoD = 1.04), as well as significant improvements of all other outcome measures. The effects remained significant after 3, 6, and 12 months. The groups differed with regard to attrition (IC: 17.3%, CoD: 25.8%, p = 0.001). Between-group effects were statistically nonsignificant across outcomes and measurement occasions. CONCLUSION: Adding semistandardized guidance in IBI for depression did not prove to be more effective than fully standardized feedback on primary and secondary outcomes, but it had positive effects on attrition.

Involvement of catecholaminergic neurons in motor innervation of striated muscle in the mouse esophagus.

Enteric co-innervation is a peculiar innervation pattern of striated esophageal musculature. Both anatomical and functional data on enteric co-innervation related to various transmitters have been collected in different species, although its function remains enigmatic. However, it is unclear whether catecholaminergic components are involved in such a co-innervation. Thus, we examined to identify catecholaminergic neuronal elements and clarify their relationship to other innervation components in the esophagus, using immunohistochemistry with antibodies against tyrosine hydroxylase (TH), vesicular acetylcholine transporter (VAChT), choline acetyltransferase (ChAT) and protein gene product 9.5 (PGP 9.5), α-bungarotoxin (α-BT) and PCR with primers for amplification of cDNA encoding TH and dopamine-ß-hydroxylase (DBH). TH-positive nerve fibers were abundant throughout the myenteric plexus and localized on about 14% of α-BT-labelled motor endplates differing from VAChT-positive vagal nerve terminals. TH-positive perikarya represented a subpopulation of only about 2.8% of all PGP 9.5-positive myenteric neurons. Analysis of mRNA showed both TH and DBH transcripts in the mouse esophagus. As ChAT-positive neurons in the compact formation of the nucleus ambiguus were negative for TH, the TH-positive nerve varicosities on motor endplates are presumably of enteric origin, although a sympathetic origin cannot be excluded. In the medulla oblongata, the cholinergic ambiguus neurons were densely supplied with TH-positive varicosities. Thus, catecholamines may modulate vagal motor innervation of esophageal-striated muscles not only at the peripheral level via enteric co-innervation but also at the central level via projections to the nucleus ambiguus. As Parkinson's disease, with a loss of central dopaminergic neurons, also affects the enteric nervous system and dysphagia is prevalent in patients with this disease, investigation of intrinsic catecholamines in the esophagus may be worthwhile to understand such a symptom.

TALEN-mediated genome engineering to generate targeted mice.

Genetic mouse models are critical for biomedical research to understand gene function and pathophysiology. In the last years, the generation of genetic mouse models has been revolutionized by the emergence of transcription activator-like effector nucleases (TALENs). TALENs are programmable, sequence-specific DNA-binding proteins fused to a non-specific endonuclease domain used as powerful tools for site-specific induction of DNA double-strand breaks. These result in disruption of the gene product of the targeted locus by mutations induced during repair by error-prone non-homologous end-joining. Alternatively, these DNA double-strand breaks can be exploited to integrate a user-defined sequence by homologous recombination if an appropriate repair plasmid is provided. In this review, we highlight the major technological improvements for genome editing in murine oocytes which have been achieved using TALENs, discuss current limitations of the technology, suggest strategies to broadly apply TALENs, and describe possible future directions to facilitate gene editing in murine oocytes.

Toward High-Efficiency Solution-Processed Planar Heterojunction Sb2S3 Solar Cells.

Low-cost hybrid solar cells have made tremendous steps forward during the past decade owing to the implementation of extremely thin inorganic coatings as absorber layers, typically in combination with organic hole transporters. Using only extremely thin films of these absorbers reduces the requirement of single crystalline high-quality materials and paves the way for low-cost solution processing compatible with roll-to-roll fabrication processes. To date, the most efficient absorber material, except for the recently introduced organic-inorganic lead halide perovskites, has been Sb2S3, which can be implemented in hybrid photovoltaics using a simple chemical bath deposition. Current high-efficiency Sb2S3 devices utilize absorber coatings on nanostructured TiO2 electrodes in combination with polymeric hole transporters. This geometry has so far been the state of the art, even though flat junction devices would be conceptually simpler with the additional potential of higher open circuit voltages due to reduced charge carrier recombination. Besides, the role of the hole transporter is not completely clarified yet. In particular, additional photocurrent contribution from the polymers has not been directly shown, which points toward detrimental parasitic light absorption in the polymers. This study presents a fine-tuned chemical bath deposition method that allows fabricating solution-processed low-cost flat junction Sb2S3 solar cells with the highest open circuit voltage reported so far for chemical bath devices and efficiencies exceeding 4%. Characterization of back-illuminated solar cells in combination with transfer matrix-based simulations further allows to address the issue of absorption losses in the hole transport material and outline a pathway toward more efficient future devices.