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ObjectiveCerebral amyloidosis and severe tauopathy in the brain are key pathological features of Alzheimer’s disease (AD). Despite a strong influence of the intestinal microbiota on AD, the causal relationship between the gut microbiota and AD pathophysiology is still elusive.DesignUsing a recently developed AD-like pathology with amyloid and neurofibrillary tangles (ADLPAPT) transgenic mouse model of AD, which shows amyloid plaques, neurofibrillary tangles and reactive gliosis in their brains along with memory deficits, we examined the impact of the gut microbiota on AD pathogenesis.ResultsComposition of the gut microbiota in ADLPAPT mice differed from that of healthy wild-type (WT) mice. Besides, ADLPAPT mice showed a loss of epithelial barrier integrity and chronic intestinal and systemic inflammation. Both frequent transfer and transplantation of the faecal microbiota from WT mice into ADLPAPT mice ameliorated the formation of amyloid β plaques and neurofibrillary tangles, glial reactivity and cognitive impairment. Additionally, the faecal microbiota transfer reversed abnormalities in the colonic expression of genes related to intestinal macrophage activity and the circulating blood inflammatory monocytes in the ADLPAPT recipient mice.ConclusionThese results indicate that microbiota-mediated intestinal and systemic immune aberrations contribute to the pathogenesis of AD in ADLPAPT mice, providing new insights into the relationship between the gut (colonic gene expression, gut permeability), blood (blood immune cell population) and brain (pathology) axis and AD (memory deficits). Thus, restoring gut microbial homeostasis may have beneficial effects on AD treatment.

Bacteriophages are central members and potential modulators of the gut microbiome; however, the ecological and evolutionary relationships of gut bacteria and phages are poorly understood. Here we investigated the abundance and diversity of lysogenic bacteria (lysogens) in the bacterial community of C57BL/6J mice by detecting integrated prophages in genomes reconstructed from the metagenome of commensal bacteria. For the activities of lysogens and prophages, we compared the prophage genomes with the metagenome of free phages. The majority of commensal bacteria in different taxa were identified as lysogens. More lysogens were found among Firmicutes and Proteobacteria , than among Bacteroidetes and Actinobacteria . The prophage genomes shared high sequence similarity with the metagenome of free phages, indicating that most lysogens appeared to be active, and that prophages are spontaneously induced as active phages; dietary interventions changed the composition of the induced prophages. By contrast, CRISPR-Cas systems were present in few commensal bacteria, and were rarely active against gut phages. The structure of the bacteria-phage infection networks was “nested-modular”, with modularity emerging across taxonomic scales, indicating that temperate phage features have developed over a long phylogenetic timescale. We concluded that phage generalists contribute to the prevalence of lysogeny in the gut ecosystem.

Although wafer-scale polycrystalline films of insulating hexagonal boron nitride (hBN) can be grown, the grain boundaries can cause both scattering or pinning of charge carriers in adjacent conducting layers that impair device performance. Lee et al. grew wafer-scale single-crystal films of hBN by feeding the precursors into molten gold films on tungsten substrates. The low solubility of boron and nitrogen in gold caused micrometer-scale grains of hBN to form that coalesced into single crystals. These films in turn supported the growth of epitaxial wafer-scale films of graphene and tungsten disulfide. Science , this issue p. 817 Single-crystalline monolayer hexagonal boron nitride films synthesized on a molten gold film served as substrates for growth of graphene and WS 2 . Although polycrystalline hexagonal boron nitride (PC-hBN) has been realized, defects and grain boundaries still cause charge scatterings and trap sites, impeding high-performance electronics. Here, we report a method of synthesizing wafer-scale single-crystalline hBN (SC-hBN) monolayer films by chemical vapor deposition. The limited solubility of boron (B) and nitrogen (N) atoms in liquid gold promotes high diffusion of adatoms on the surface of liquid at high temperature to provoke the circular hBN grains. These further evolve into closely packed unimodal grains by means of self-collimation of B and N edges inherited by electrostatic interaction between grains, eventually forming an SC-hBN film on a wafer scale. This SC-hBN film also allows for the synthesis of wafer-scale graphene/hBN heterostructure and single-crystalline tungsten disulfide.

The effective application of graphene and other 2D materials is strongly dependent on the industrial-scale manufacturing of films and powders of appropriate morphology and quality. Here, we discuss three state-of-the-art mass production techniques, their limitations, and opportunities for future improvement. The industrial application of two-dimensional (2D) materials strongly depends on the large-scale manufacturing of high-quality 2D films and powders. Here, the authors analyze three state-of-the art mass production techniques, discussing the recent progress and remaining challenges for future improvements.

Background Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish. Results We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates ( Firmicutes and Bacteroidetes ). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals). Conclusions Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds. 2jWna3AEmgLMLS436bvUku Video Abstract

Various frameworks and methods, such as quality by design (QbD), real time release test (RTRT), and continuous process verification (CPV), have been introduced to improve drug product quality in the pharmaceutical industry. The methods recognize that an appropriate combination of process controls and predefined material attributes and intermediate quality attributes (IQAs) during processing may provide greater assurance of product quality than end-product testing. The efficient analysis method to monitor the relationship between process and quality should be used. Process analytical technology (PAT) was introduced to analyze IQAs during the process of establishing regulatory specifications and facilitating continuous manufacturing improvement. Although PAT was introduced in the pharmaceutical industry in the early 21st century, new PAT tools have been introduced during the last 20 years. In this review, we present the recent pharmaceutical PAT tools and their application in pharmaceutical unit operations. Based on unit operations, the significant IQAs monitored by PAT are presented to establish a control strategy for CPV and real time release testing (RTRT). In addition, the equipment type used in unit operation, PAT tools, multivariate statistical tools, and mathematical preprocessing are introduced, along with relevant literature. This review suggests that various PAT tools are rapidly advancing, and various IQAs are efficiently and precisely monitored in the pharmaceutical industry. Therefore, PAT could be a fundamental tool for the present QbD and CPV to improve drug product quality.

Background Lung cancer is the leading cause of cancer-related deaths worldwide. The majority of lung cancers are non-small cell lung cancer (NSCLC), accounting for approximately 85% of all lung cancer types. The Cox proportional hazards model (CPH), which is the standard method for survival analysis, has several limitations. The purpose of our study was to improve survival prediction in patients with NSCLC by incorporating prognostic information from F-18 fluorodeoxyglucose positron emission tomography (FDG PET) images into a traditional survival prediction model using clinical data. Results The multimodal deep learning model showed the best performance, with a C-index and mean absolute error of 0.756 and 399 days under a five-fold cross-validation, respectively, followed by ResNet3D for PET (0.749 and 405 days) and CPH for clinical data (0.747 and 583 days). Conclusion The proposed deep learning-based integrative model combining the two modalities improved the survival prediction in patients with NSCLC.

Background Design of valid high-quality primers is essential for qPCR experiments. MRPrimer is a powerful pipeline based on MapReduce that combines both primer design for target sequences and homology tests on off-target sequences. It takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB. Due to the effectiveness of primers designed by MRPrimer in qPCR analysis, it has been widely used for developing many online design tools and building primer databases. However, the computational speed of MRPrimer is too slow to deal with the sizes of sequence DBs growing exponentially and thus must be improved. Results We develop a fast GPU-based pipeline for primer design (GPrimer) that takes the same input and returns the same output with MRPrimer. MRPrimer consists of a total of seven MapReduce steps, among which two steps are very time-consuming. GPrimer significantly improves the speed of those two steps by exploiting the computational power of GPUs. In particular, it designs data structures for coalesced memory access in GPU and workload balancing among GPU threads and copies the data structures between main memory and GPU memory in a streaming fashion. For human RefSeq DB, GPrimer achieves a speedup of 57 times for the entire steps and a speedup of 557 times for the most time-consuming step using a single machine of 4 GPUs, compared with MRPrimer running on a cluster of six machines. Conclusions We propose a GPU-based pipeline for primer design that takes an entire sequence DB as input and returns all feasible and valid primer pairs existing in the DB at once without an additional step using BLAST-like tools. The software is available at https://github.com/qhtjrmin/GPrimer.git .

Colon-targeted oral nanoparticles (NPs) have emerged as an ideal, safe, and effective therapy for ulcerative colitis (UC) owing to their ability to selectively accumulate in inflamed colonic mucosa. Cyclosporine A (CSA), an immunosuppressive agent, has long been used as rescue therapy in severe steroid-refractory UC. In this study, we developed CSA-loaded dual-functional polymeric NPs composed of Eudragit FS30D as a pH-sensitive polymer for targeted delivery to the inflamed colon, and poly(lactic-co-glycolic acid) (PLGA) as a sustained-release polymer. CSA-loaded Eudragit FS30D nanoparticles (ENPs), PLGA nanoparticles (PNPs), and Eudragit FS30D/PLGA nanoparticles (E/PNPs) were prepared using the oil-in-water emulsion method. Scanning electron microscope images and zeta size data showed successful preparation of CSA-loaded NPs. PNPs exhibited a burst drug release of >60% at pH 1.2 (stomach pH) in 0.5 h, which can lead to unwanted systemic absorption and side effects. ENPs effectively inhibited the burst drug release at pH 1.2 and 6.8 (proximal small intestine pH); however, nearly 100% of the CSA in ENPs was released rapidly at pH 7.4 (ileum-colon pH) owing to complete NP dissolution. In contrast to single-functional PNPs and ENPs, the dual-functional E/PNPs minimized burst drug release (only 18%) at pH 1.2 and 6.8, and generated a sustained release at pH 7.4 thereafter. Importantly, in distribution studies in the gastrointestinal tracts of mice, E/PNPs significantly improved CSA distribution to the colon compared with PNPs or ENPs. In a mouse model of colitis, E/PNP treatment improved weight loss and colon length, and decreased rectal bleeding, spleen weight, histological scoring, myeloperoxidase activity, macrophage infiltration, and expression of proinflammatory cytokines compared with PNPs or ENPs. Overall, this work confirms the benefits of CSA-loaded E/PNPs for efficiently delivering CSA to the colon, suggesting their potential for UC therapy.

Background 1,3-propanediol (1,3-PDO) is the most widely studied value-added product that can be produced by feeding glycerol to bacteria, including Lactobacillus sp. However, previous research reported that L . reuteri only produced small amounts and had low productivity of 1,3-PDO. It is urgent to develop procedures that improve the production and productivity of 1,3-PDO. Results We identified a novel L . reuteri CH53 isolate that efficiently converted glycerol into 1,3-PDO, and performed batch co-fermentation with glycerol and glucose to evaluate its production of 1,3-PDO and other products. We optimized the fermentation conditions and nitrogen sources to increase the productivity. Fed-batch fermentation using corn steep liquor (CSL) as a replacement for beef extract led to 1,3-PDO production (68.32 ± 0.84 g/L) and productivity (1.27 ± 0.02 g/L/h) at optimized conditions (unaerated and 100 rpm). When CSL was used as an alternative nitrogen source, the activity of the vitamin B12-dependent glycerol dehydratase ( dhaB ) and 1,3-propanediol oxidoreductase ( dhaT ) increased. Also, the productivity and yield of 1,3-PDO increased as well. These results showed the highest productivity in Lactobacillus species. In addition, hurdle to 1,3-PDO production in this strain were identified via analysis of the half-maximal inhibitory concentration for growth (IC50) of numerous substrates and metabolites. Conclusions We used CSL as a low-cost nitrogen source to replace beef extract for 1,3-PDO production in L. reuteri CH53. These cells efficiently utilized crude glycerol and CSL to produce 1,3-PDO. This strain has great promise for the production of 1,3-PDO because it is generally recognized as safe (GRAS) and non-pathogenic. Also, this strain has high productivity and high conversion yield.