Monosaccharide composition analysis by 2D quantitative gsHSQCi.

The physicochemical properties and biological activities of polysaccharides depend on their structures. Monosaccharide composition analysis is indispensable for the structural characterization of polysaccharides and is helpful in the quality control of polysaccharide preparation. Here, using a model mixture and tamarind seed polysaccharide as examples, we demonstrated that a quantitative 2D NMR method, gsHSQCi (three gradient-selective Heteronuclear Single Quantum Coherence spectra acquired with incremented repetition times, i = 1, 2, 3) can directly quantify a variety of monosaccharides in solution with adequate precision and accuracy, requiring no derivatization, postprocessing steps and column separation. Both anomeric and non-anomeric signals of monosaccharides can be utilized for content determination. More accurate quantification of fructose in a mixture containing nine monosaccharides is obtained, which is difficult to achieve by quantitative 1D 1HNMR and the common PMP-HPLC method (high-performance liquid chromatography through pre-column derivatization with 1-phenyl-3-methyl-5-pyrazolone) due to the peak overlapping and the poor derivatization efficiency, respectively. The results also revealed that Na[Fe(EDTA)] can serve as a proper relaxation-enhancing agent for saccharide samples to save experimental time. We expect that this approach can be applied as an alternative to analyzing the monosaccharide composition and be helpful in interpreting the structure of polysaccharides.

Lithium tantalate photonic integrated circuits for volume manufacturing.

Electro-optical photonic integrated circuits (PICs) based on lithium niobate (LiNbO3) have demonstrated the vast capabilities of materials with a high Pockels coefficient1,2. They enable linear and high-speed modulators operating at complementary metal-oxide-semiconductor voltage levels3 to be used in applications including data-centre communications4, high-performance computing and photonic accelerators for AI5. However, industrial use of this technology is hindered by the high cost per wafer and the limited wafer size. The high cost results from the lack of existing high-volume applications in other domains of the sort that accelerated the adoption of silicon-on-insulator (SOI) photonics, which was driven by vast investment in microelectronics. Here we report low-loss PICs made of lithium tantalate (LiTaO3), a material that has already been adopted commercially for 5G radiofrequency filters6 and therefore enables scalable manufacturing at low cost, and it has equal, and in some cases superior, properties to LiNbO3. We show that LiTaO3 can be etched to create low-loss (5.6 dB m-1) PICs using a deep ultraviolet (DUV) stepper-based manufacturing process7. We demonstrate a LiTaO3 Mach-Zehnder modulator (MZM) with a half-wave voltage-length product of 1.9 V cm and an electro-optic bandwidth of up to 40 GHz. In comparison with LiNbO3, LiTaO3 exhibits a much lower birefringence, enabling high-density circuits and broadband operation over all telecommunication bands. Moreover, the platform supports the generation of soliton microcombs. Our work paves the way for the scalable manufacture of low-cost and large-volume next-generation electro-optical PICs.

High density lithium niobate photonic integrated circuits.

Photonic integrated circuits have the potential to pervade into multiple applications traditionally limited to bulk optics. Of particular interest for new applications are ferroelectrics such as Lithium Niobate, which exhibit a large Pockels effect, but are difficult to process via dry etching. Here we demonstrate that diamond-like carbon (DLC) is a superior material for the manufacturing of photonic integrated circuits based on ferroelectrics, specifically LiNbO3. Using DLC as a hard mask, we demonstrate the fabrication of deeply etched, tightly confining, low loss waveguides with losses as low as 4 dB/m. In contrast to widely employed ridge waveguides, this approach benefits from a more than one order of magnitude higher area integration density while maintaining efficient electro-optical modulation, low loss, and offering a route for efficient optical fiber interfaces. As a proof of concept, we demonstrate a III-V/LiNbO3 based laser with sub-kHz intrinsic linewidth and tuning rate of 0.7 PHz/s with excellent linearity and CMOS-compatible driving voltage. We also demonstrated a MZM modulator with a 1.73 cm length and a halfwave voltage of 1.94 V.

PhaGAA: an integrated web server platform for phage genome annotation and analysis.

MOTIVATION: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed. RESULTS: Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate the prophage genome at DNA and protein levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists and help advance the phage synthetic biology in basic and application research. AVAILABILITY AND IMPLEMENTATION: PhaGAA is freely available at http://phage.xialab.info/.

Detailed Structural Analysis of the Immunoregulatory Polysaccharides from the Mycobacterium Bovis BCG.

Bacillus Calmette-Guérin polysaccharide and nucleic acid (BCG-PSN), extracted from Mycobacterium bovis, is an immunoregulatory medicine commonly used in clinic. However, the structural characteristics and potential pharmacological efficacy of the polysaccharides from BCG-PSN remain unclear. Herein, two polysaccharides (BCG-1 and BCG-2) were purified and their structures were characterized. Monosaccharide composition analysis combined with methylation analysis and NMR data indicated that BCG-1 and BCG-2 were an α-D-(1→4)-mannan with (1→2)-linked branches, and an α-D-(1→4)-glucan with (1→6)-linked branches, respectively. Herein, the mannan from BCG-PSN was first reported. Bioactivity assays showed that BCG-1 and BCG-2 dose-dependently and potently increased the production of inflammatory mediators (NO, TNF-α, IL-6, IL-1ß, and IL-10), as well as their mRNA expressions in RAW264.7 cells; both have similar or stronger effects compared with BCG-PSN injection. These data suggest that BCG-1 and BCG-2 are very likely the active ingredients of BCG-PSN.

DPProm: A Two-Layer Predictor for Identifying Promoters and Their Types on Phage Genome Using Deep Learning.

With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of data makes it possible to establish computational models for promoter identification with robustness. In this work, we introduce DPProm, a two-layer model composed of DPProm-1L and DPProm-2L, to predict promoters and their types for phages. On the first layer, as a dual-channel deep neural network ensemble method fusing multi-view features (sequence feature and handcrafted feature), the model DPProm-1L is proposed to identify whether a DNA sequence is a promoter or non-promoter. The sequence feature is extracted with convolutional neural network (CNN). And the handcrafted feature is the combination of free energy, GC content, cumulative skew, and Z curve features. On the second layer, DPProm-2L based on CNN is trained to predict the promoters' types (host or phage). For the realization of prediction on the whole genomes, the model DPProm, combines with a novel sequence data processing workflow, which contains sliding window and merging sequences modules. Experimental results show that DPProm outperforms the state-of-the-art methods, and decreases the false positive rate effectively on whole genome prediction. Furthermore, we provide a user-friendly web at http://bioinfo.ahu.edu.cn/DPProm. We expect that DPProm can serve as a useful tool for identification of promoters and their types.

The structures of two glucomannans from Bletilla formosana and their protective effect on inflammation via inhibiting NF-κB pathway.

Bletilla formosana is a traditional Chinese herbal medicine and is widely consumed as foods and medicines in China. However, the chemical structure and bioactivity of its polysaccharides remain unknown. Herein, two new polysaccharides, BFP60 and BFP80, with molecular weights of 3.99 kDa and 10.07 kDa, respectively, were isolated and purified from dried tuber of B. formosana. Structural analysis suggested that BFP60 and BFP80 may have backbone consisted of →4)-ß-d-Man-(1→,→4)-ß-d-Glc-(1→,→4)-2-O-acetyl-ß-d-Man-(1→, and →4)-3-O-acetyl-ß-d-Man-(1→. Inflammation assay in LPS-induced RAW264.7 cells showed that the productions of NO and pro-inflammatory cytokines including IL-6, IL-1ß, TNF-α, and IFN-γ were significantly reduced, and the expression of iNOS, COX-2, and target proteins in the NF-κB pathway were suppressed after BFP60 and BFP80 pretreatment. These findings indicated that this novel polysaccharide had significant inflammatory protective effects in vitro.

Machine learning for percolation utilizing auxiliary Ising variables.

Machine learning for phase transition has received intensive research interest in recent years. However, its application in percolation still remains challenging. We propose an auxiliary Ising mapping method for the machine learning study of the standard percolation as well as a variety of statistical mechanical systems in correlated percolation representation. We demonstrate that unsupervised machine learning is able to accurately locate the percolation threshold, independent of the spatial dimension of system or the type of phase transition, which can be first-order or continuous. Moreover, we show that, by neural network machine learning, auxiliary Ising configurations for different universalities can be classified with a high confidence level. Our results indicate that the auxiliary Ising mapping method, despite its simplicity, can advance the application of machine learning in statistical and condensed-matter physics.

Structures of fructan and galactan from Polygonatum cyrtonema and their utilization by probiotic bacteria.

Polygonatum cyrtonema is a known tonic herb in Chinese Materia Medica, extensively consumed in China, but the structure and activity of its polysaccharide components remain to be clarified. Herein, two new polysaccharides (a fructan and a galactan) were purified from the dried and the processed P. cyrtonema rhizome, respectively. Structural analysis suggested that the fructan consisted of a (2 â†’ 6) linked ß-d-Fruf residues backbone with an internal α-d-Glcp residue and two (2 â†’ 1) linked ß-d-Fruf residues branches, and that the galactan was a (1 â†’ 4)-ß-d-galactan branched with a single ß-d-galactose at C-6 at about every nine residues in its main chain. The bioactive assay showed that the fructan and the galactan remarkably promoted growth of Bifidobacterium and Lactobacillus strains, indicating that they possess prebiotic activity. These findings may help expand the application of the polysaccharides from the tonic herb P. cyrtonema as functional ingredients in food products.

Huangyusang decoction for Type 2 diabetes: A protocol for systematic review and meta analysis.

BACKGROUND: Diabetes is a chronic metabolic disease characterized by elevated blood glucose levels due to insulin resistance and ß-cell dysfunction. In China, Huangyusang decoction (HYS) has been widely used to treat Type 2 diabetes. However, there is no systematic review found. In order to evaluate the efficacy and safety of HYS in the treatment of Type 2 diabetes, we need to conduct a meta-analysis and systematic evaluation. METHODS: We will enroll the randomized controlled trials (RCTs) evaluating the effectiveness and safety of HYS in the treatment of Type 2 diabetes. Data come mainly from 4 Chinese databases (CNKI, Wanfang, CBM, and VIP Database) and 4 English databases (PubMed, Embase, Cochrane Library, and Web of science). The enrollment of RCTs is from the starting date of database establishment till January 30, 2021. Fasting blood glucose is considered as the main indicator of the dyslipidemia, while the body mass index, glycated hemoglobin, fasting insulin, triglycerides, and cholesterol are regarded as the secondary indicators. There are safety indicators including liver enzyme and kidney function. The work such as selection of literature, data collection, quality evaluation of included literature, and assessment of publication bias will be conducted by 2 independent researchers. Meta-analysis will be performed by RevMan 5.0 software. RESULTS: This study will provide high-quality evidence for the effectiveness and safety of HYS in the treatment of type 2 diabetes. CONCLUSION: The results of the study will help us determine whether HYS can effectively treat type 2 diabetes. ETHICS AND DISSEMINATION: This study does not require ethical approval. We will disseminate our findings by publishing results in a peer-reviewed journal. OSF REGISTRATION NUMBER: DOI 10.17605/OSF.IO/AXBRV.