Multiplex Base-Editing Enables Combinatorial Epigenetic Regulation for Genome Mining of Fungal Natural Products.

Genome mining of cryptic natural products (NPs) remains challenging, especially in filamentous fungi, owing to their complex genetic regulation. Increasing evidence indicates that several epigenetic modifications often act cooperatively to control fungal gene transcription, yet the ability to predictably manipulate multiple genes simultaneously is still largely limited. Here, we developed a multiplex base-editing (MBE) platform that significantly improves the capability and throughput of fungal genome manipulation, leading to the simultaneous inactivation of up to eight genes using a single transformation. We then employed MBE to inactivate three negative epigenetic regulators combinatorially in Aspergillus nidulans, enabling the activation of eight cryptic gene clusters compared to the wild-type strains. A group of novel NPs harboring unique cichorine and polyamine hybrid chemical scaffolds were identified, which were not reported previously. We envision that our scalable and efficient MBE platform can be readily applied in other filamentous fungi for the genome mining of novel NPs, providing a powerful approach for the exploitation of fungal chemical diversity.

Effectiveness and safety of switching to teriflunomide in older patients with relapsing multiple sclerosis: A real-world retrospective multicenter analysis.

BACKGROUND: The prevalence of multiple sclerosis (MS) in older people is increasing due to population aging and availability of effective disease-modifying therapies (DMTs). Treating older people with MS is complicated by age-related and MS-related comorbidities, immunologic effects of prior DMTs, and immunosenescence. Teriflunomide is a once-daily oral immunomodulator that has demonstrated efficacy and acceptable safety in clinical trials of adults with relapsing forms of MS (RMS). However, there are limited clinical trial and real-world data regarding teriflunomide use in people with MS aged >55 years. We analyzed real-world data to assess the effectiveness and safety of teriflunomide in older people with RMS who had switched to this agent from other DMTs. METHODS: People with RMS (relapsing remitting and active secondary progressive MS) aged ≥55 years who had switched from other DMTs to teriflunomide (7 mg or 14 mg) for ≥1 year were identified retrospectively by chart review at four sites in the United States. Data were extracted from medical records from 1 year pre-index to 2 years post-index (index defined as the teriflunomide start date). Assessments of effectiveness included annualized relapse rate (ARR), Expanded Disability Status Scale (EDSS) score, and magnetic resonance imaging (MRI) outcomes. Assessments of safety included lymphocyte counts, infections, and malignancies. We examined the effectiveness outcomes and lymphocyte counts within sub-groups defined by age (55-64, ≥65 years), sex, MS type, and prior route of DMT administration (oral, injectable, infusible). RESULTS: In total, 182 patients with RMS aged ≥55 years who switched from other DMTs to teriflunomide were identified (mean [SD] age: 62.5 [5.4] years). Mean ARR decreased from the start of teriflunomide treatment (mean [SD]: 0.43 [0.61]) to year 1 post-index (0.13 [0.65]) and year 2 post-index (0.05 [0.28]). Mean EDSS score remained unchanged from index (mean [SD]: 4.5 [1.8]) to 1 year post-treatment (4.5 [1.8]) and increased slightly at 2 years post-treatment (4.7 [1.7]). MRI scans from index and years 1 and 2 post-index compared with scans from the previous year indicated that most patients had stable or improved MRI outcomes at index (87.7%) and remained stable or improved at years 1 (96.0%) and 2 (93.6%). Lymphopenia decreased at years 1 (21.4%) and 2 post-index (14.8%, compared to index (23.5%). By 1 year post-index, fewer patients had grade 3 or 4 lymphopenia, and at 2 years post-index, there were no patients with grade 3 or 4 lymphopenia. Infection incidence was low (n = 40, 22.0%) and none were related to teriflunomide. The decreases in lymphopenia were driven by decreases among people who switched from a prior oral DMT; there were no notable differences in lymphopenia across the other sub-groups examined. ARR, EDSS score, and MRI outcomes across all sub-groups were similar to the results of the overall population. CONCLUSION: Our multicenter, longitudinal, retrospective study demonstrated that patients with RMS aged 55 or older switching to teriflunomide from other DMTs had significantly improved ARR, stable disability, and stable or improved MRI over up to 2 years' follow up. Safety results were acceptable with fewer patients exhibiting lymphopenia at years 1 and 2 post-index.

Preliminary Study of a Modular MR-Compatible Robot for Image-Guided Insertion of Multiple Needles.

Percutaneous needle-based interventions such as transperineal prostate brachytherapy require the accurate placement of multiple needles to treat cancerous lesions within the target organ. To guide needle placement, magnetic resonance imaging (MRI) offers excellent visualization of the target lesion without the need for ionizing radiation. To date, multi-needle insertion relies on a grid template, which limits the ability to steer individual needles. This work describes an MR-compatible robot designed for the sequential insertion of multiple non-parallel needles under MR guidance. The 6-DOF system is designed with an articulated arm to extend the reach of the robot. This strategy presents a novel approach enabling the robot to maneuver around existing needles while minimizing the footprint of the robot. Forward kinematics as well as optimization-based inverse kinematics are presented. The impact of the robot on image quality was tested for four sequences (T1w-TSE, T2w-TSE, THRIVE and EPI) on a 3T Philips Achieva system. Quantification of the signal-to-noise ratio showed a 46% signal loss in a gelatin phantom when the system was powered on but no further adverse effects when the robot was moving. Joint level testing showed a maximum error of 2.10 ± 0.72°s for revolute joints and 0.31 ± 0.60 mm for prismatic joints. The theoretical workspace spans the proposed clinical target surface of 10 x 10 cm. Lastly, the feasibility of multi-needle insertion was demonstrated with four needles inserted under real-time MR-guidance with no visible loss in image quality.

Reducing distracted pedestrian behavior using Bluetooth beacon technology: A crossover trial.

BACKGROUND: The number of fatal pedestrian injuries in the United States has steadily increased over the past decade. Multiple factors likely contribute to this trend, but the growth of pedestrians distracted by mobile devices is widely hypothesized to play a major role. Existing strategies to reduce distracted pedestrian behavior are few and mostly ineffective. The present study evaluated StreetBit, a mostly-passive primary prevention program to reduce distracted pedestrian behavior by alerting distracted pedestrians directly on their smartphone when they approach an intersection, reminding them to attend to traffic as they crossed. METHODS: 385 individuals who regularly crossed a target street corner at an urban university downloaded StreetBit on their phones and participated in a crossover design study whereby the app was inactive for 3 weeks (baseline behavior phase), actively provided alerts for 3 weeks (intervention phase), and then was inactive again for 4 weeks (post-intervention phase). User distraction while crossing the intersection was collected electronically for a total of 34,923 street-crossing events throughout the 10-week study. RESULTS: In crude (unadjusted) models, participant distraction was similar across all phases of the research; this result was maintained after adjusting for potential covariates as well as after conducting a sensitivity analysis limited to data from only week 3 of each study intervention phase. In a model stratified by phone/warning type and baseline distraction rates, Android phone users who received a warning that blocked the full screen and had a high baseline distraction rate (≥75% distracted crossings) had a 64% decreased odds of distraction during the alert phase (OR 0.36, 95% CI 0.25-0.51) and a 52% decreased odds of distraction during the post-intervention phase (OR 0.48, 95% CI 0.25-0.94). Users reported positive impressions about the StreetBit app in a post-intervention survey. DISCUSSION: StreetBit, an innovative app designed to prevent distracted pedestrian behavior through a mostly-passive primary prevention strategy relying on intrusive reminders, proved effective among smartphone users who received a warning blocking the full screen and who were frequently distracted at baseline, but not among other users. The results appear to reflect the confluence of two influencing factors. First, due to software development limitations, visually-distracted Android users received a highly intrusive app warning that blocked their smartphone screen whereas iOS users received a less intrusive banner notification blocking a small upper portion of the screen. Second, most users were curious to see if the app was functioning properly, creating artificially-inflated estimates of distraction as users purposefully watched their phones when crossing. Thus, our results indicate promise for StreetBit as an effective intervention and warrant continued software development and empirical testing.

A human scFv antibody that targets and neutralizes high molecular weight pathogenic amyloid-ß oligomers.

Brain accumulation of soluble oligomers of the amyloid-ß peptide (AßOs) is increasingly considered a key early event in the pathogenesis of Alzheimer's disease (AD). A variety of AßO species have been identified, both in vitro and in vivo, ranging from dimers to 24mers and higher order oligomers. However, there is no consensus in the literature regarding which AßO species are most germane to AD pathogenesis. Antibodies capable of specifically recognizing defined subpopulations of AßOs would be a valuable asset in the identification, isolation, and characterization of AD-relevant AßO species. Here, we report the characterization of a human single chain antibody fragment (scFv) denoted NUsc1, one of a number of scFvs we have identified that stringently distinguish AßOs from both monomeric and fibrillar Aß. NUsc1 readily detected AßOs previously bound to dendrites in cultured hippocampal neurons. In addition, NUsc1 blocked AßO binding and reduced AßO-induced neuronal oxidative stress and tau hyperphosphorylation in cultured neurons. NUsc1 further distinguished brain extracts from AD-transgenic mice from wild type (WT) mice, and detected endogenous AßOs in fixed AD brain tissue and AD brain extracts. Biochemical analyses indicated that NUsc1 targets a subpopulation of AßOs with apparent molecular mass greater than 50 kDa. Results indicate that NUsc1 targets a particular AßO species relevant to AD pathogenesis, and suggest that NUsc1 may constitute an effective tool for AD diagnostics and therapeutics.

In vivo treatment with the NF-κB inhibitor ursodeoxycholic acid (UDCA) improves tension development in the isolated mdx costal diaphragm.

INTRODUCTION: Previous experiments have indicated that in vivo administration of ursodeoxycholic acid (UDCA) inhibits nuclear NF-κB activation and has beneficial effects on the structure and function of dystrophic (mdx) muscle. We examined the effect of UDCA on tension development in dystrophic muscle. METHODS: Isometric tension development was examined in costal diaphragms that were freshly isolated from vehicle and UDCA treated mdx mice. Percent recovery scores were obtained by directly comparing these measurements to those obtained from age-matched nondystrophic mice. RESULTS: Vehicle treated mdx mice exhibited significantly reduced optimal muscle lengths (lo ) and specific twitch and tetanic tensions compared with age-matched nondystrophic mice. UDCA treated preparations exhibited significantly improved tension development with a 33% recovery score. CONCLUSIONS: Because UDCA is used in treating certain clinical disorders, these results provide a rationale for human clinical trials using this and related drugs for treatment of Duchenne and related muscular dystrophies.

SIFTER search: a web server for accurate phylogeny-based protein function prediction.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

Elucidating molecular mass and shape of a neurotoxic Aß oligomer.

Alzheimer's disease (AD), the most prevalent type of dementia, has been associated with the accumulation of amyloid ß oligomers (AßOs) in the central nervous system. AßOs vary widely in size, ranging from dimers to larger than 100 kDa. Evidence indicates that not all oligomers are toxic, and there is yet no consensus on the size of the actual toxic oligomer. Here we used NU4, a conformation-dependent anti-AßO monoclonal antibody, to investigate size and shape of a toxic AßO assembly. By using size-exclusion chromatography and immuno-based detection, we isolated an AßO-NU4 complex amenable for biochemical and morphological studies. The apparent molecular mass of the NU4-targeted oligomer was 80 kDa. Atomic force microscopy imaging of the AßO-NU4 complex showed a size distribution centered at 5.37 nm, an increment of 1.5 nm compared to the size of AßOs (3.85 nm). This increment was compatible with the size of NU4 (1.3 nm), suggesting a 1:1 oligomer to NU4 ratio. NU4-reactive oligomers extracted from AD human brain concentrated in a molecular mass range similar to that found for in vitro prepared oligomers, supporting the relevance of the species herein studied. These results represent an important step toward understanding the connection between AßO size and toxicity.

Effect of dietary glutamine on tumor glutathione levels and apoptosis-related proteins in DMBA-induced breast cancer of rats.

Glutamine (GLN) is a non-essential amino acid that is present in nearly every biochemical pathway and is the major intraorgan nitrogen carrier. GLN via glutamate, is one of the precursors for the synthesis of glutathione (GSH), the major endogenous antioxidant in mammalian cells, which protects them from oxidative injury and cell death. Cancer cells have higher GSH levels than the surrounding normal cells, which attributes to a higher rate of cell proliferation and resistance to chemotherapy. Therefore, selective tumor depletion of GSH presents a promising strategy in cancer treatment. Experimental studies have associated decreased GSH levels with inhibition of proliferation and stimulation of apoptosis. Previous results of our laboratory have provided evidence that dietary GLN diminished tumor development in implantable as well as 7,12-dimethylbenz[a]anthracene (DMBA)-induced breast cancer and elevated GSH in the host tissues. In this study we examined the effects of GLN on GSH levels in DMBA-induced mammary tumors and correlated the results with protein and mRNA expression of apoptosis-related proteins Bcl-2, Bax and caspase-3 in tumor cells. The results have shown that GLN supplementation caused a significant decrease in the tumor GSH levels and the ratio GSH/oxidized GSH (GSSG), accompanied by up-regulation of Bax and caspase-3, and down-regulation of Bcl-2. These findings suggest that dietary GLN supplementation suppresses mammary carcinogenesis by activation of apoptosis in tumor cells and this probably is a result of GSH down-regulation.