Abstract It has been reported that glycogen in Escherichia coli have two structural states, that is, fragility and stability, which alters dynamically. However, molecular mechanisms behind the structural alterations are not fully understood. In this study, we focused on the potential roles of two important glycogen degradation enzymes, glycogen phosphorylase (glgP) and glycogen debranching enzyme (glgX), in glycogen structural alterations. The fine molecular structure of glycogen particles in Escherichia coli and three mutants (ΔglgP, ΔglgX and ΔglgP/ΔglgX) were examined, which showed that glycogen in E. coli ΔglgP and E. coli ΔglgP/ΔglgX were consistently fragile while being consistently stable in E. […]

Abstract There are many commercially available glycogen particles in the market due to their bioactive functions as food additive, drug carrier and natural moisturizer, etc. It would be beneficial to rapidly determine the origins of commercially-available glycogen particles, which could facilitate the establishment of quality control methodology for glycogen-containing products. With its non-destructive, label-free and low-cost features, surface enhanced Raman spectroscopy(SERS) is an attractive technique with high potential to discriminate chemical compounds in a rapid mode. In this study, we applied the combination of SERS technique and machine leaning algorithms on glycogen analysis, which successfully predicted the origins of glycogen […]

Abstract Over the past decades, conventional methods and molecular assays have been developed for the detection of tuberculosis (TB). However, these techniques suffer limitations in the identification of Mycobacterium tuberculosis (Mtb), such as long turnaround time and low detection sensitivity, etc., not even mentioning the difficulty in discriminating antibiotics-resistant Mtb strains that cause great challenges in TB treatment and prevention. Thus, techniques with easy implementation for rapid diagnosis of Mtb infection are in high demand for routine TB diagnosis. Due to the label-free, low-cost and non-invasive features, surface enhanced Raman spectroscopy (SERS) has been extensively investigated for its potential in bacterial pathogen identification. However, at current […]

Content The identification of lysine (symbol Lys or K) succinylation (Ksucc) sites has focused on uncovering the basis for the mechanism and function of lysine succinylation modifications. Traditional experimental methods for Ksucc site localization are usually expensive and time-consuming. Therefore, it is necessary to construct an efficient computational method to predict the presence of Ksucc sites in protein sequences. In this study, we propose a novel and efficient predictor for identifying Ksucc sites based on deep learning algorithms, called Deep_KsuccSite. The predictor employs composition, transformation and distribution (CTD) composition (CTDC), enhanced grouped amino acid composition (EGAAC), amphipathic pseudoamino acid composition […]

Abstract The optical properties of few-layer (FL) GaSe are investigated using thickness- and temperature-dependent Raman scattering and photoluminescence (PL) spectroscopies. The vibrational modes exhibit linear softening with increasing temperature, with temperature coefficient values related to anharmonic phonon-phonon/electron coupling. Micro-PL is used to study the variation of exciton bands and structural features of FL GaSe. The temperature-dependent study from 100 to 380 K shows that the PL red-shifts due to a band gap narrowing, while the intensity decreases attributable to thermally stimulated nonradiative recombination caused by an increase in the electron−phonon interaction. The behavior of free and bound excitons and deep […]

Abstract Molecular mechanisms behind structural alterations between fragile and stable glycogen α particles in liver are not clear yet. In this pilot study, we re-examined the diurnal alterations of glycogen structure from the perspective of liver tissue transcriptome. By comparing the structures of liver glycogen from mice at 12 am, 8 am, 12 pm, and 8 pm (light-on: 6 am; light-off: 6 pm), we re-confirmed that the liver glycogen was fragile at 12 am and 8 am and stable at 12 pm and 8 pm as previously reported. The structural differences of glycogen particles at 12 am and 12 pm […]

Abstract Background The COVID-19 pandemic has caused disruptions to the functioning of societies and their health systems. Prior to the pandemic, health systems in low- and middle-income countries (LMIC) were particularly stretched and vulnerable. The International Society of Global Health (ISoGH) sought to systematically identify priorities for health research that would have the potential to reduce the impact of the COVID-19 pandemic in LMICs. Methods The Child Health and Nutrition Research Initiative (CHNRI) method was used to identify COVID-19-related research priorities. All ISoGH members were invited to participate. Seventy-nine experts in clinical, translational, and population research contributed 192 research questions […]

Objective Epidemiological characteristics of the COVID-19 outbreak in Yangzhou city caused by the highly contagious Delta variant strain of SARS-CoV-2 virus were investigated in this retrospective descriptive study to provide prevention and control guidelines for outbreaks in future. Methods All the epidemiological data used in this study were manually collected from the official website of Yangzhou Municipal Health Committee from July 28 to August 26, 2021 and then were analyzed systematically and statistically in this study. Results A total of 570 COVID-19 cases were reported during the short-term outbreak in Yangzhou City. Ages of infected individuals ranged from 1 to […]

Abstract With its low-cost, label-free and non-destructive features, Raman spectroscopy is becoming an attractive technique with high potential to discriminate the causative agent of bacterial infections and bacterial infections per se. However, it is challenging to achieve consistency and accuracy of Raman spectra from numerous bacterial species and phenotypes, which significantly hinders the practical application of the technique. In this study, we analyzed surfaced enhanced Raman spectra (SERS) through machine learning algorithms in order to discriminate bacterial pathogens quickly and accurately. Two unsupervised machine learning methods, K-means Clustering (K-Means) and Agglomerative Nesting (AGNES) were performed for clustering analysis. In addition, […]

Abstract In this paper, an epidemiological study was performed by focusing on all confirmed patients with COVID-19 in Xuzhou, a prefecture-level city, and a transportation hub with 10.44 million population in the east region of China. The median age of the patients is 42-year-old and 45.57% are male; 25 cases (31.65%) are imported. 23 cases (29.11%) were confirmed between January 26 to 31, 2020 while 56 cases (70.89%) were from February 1 to 16, 2020. Among the ten administrative divisions of Xuzhou city,Suining county (n=31) and Pizhou City (n=15) have the most cases while Tongshan district has none. A representative […]

Abstract Currently, there exist a variety of glycogen extraction methods, which either damage glycogen spatial structure or only partially extract glycogen, leading to the biased characterization of glycogen fine molecular structure. To understand the dynamic changes of glycogen structures and the versatile functions of glycogen particles in bacteria, it is essential to isolate glycogen with minimal degradation. In this study, a mild glycogen isolation method is demonstrated by using cold-water (CW) precipitation via sugar density gradient ultra-centrifugation (SDGU-CW). The traditional trichloroacetic acid (TCA) method and potassium hydroxide (KOH) method were also performed for comparison. A commonly used lab strain, Escherichia coli BL21(DE3), was used […]

Abstract Many studies shown that neurological diseases are associated with neural mitochondrial dysfunctions and microbiome composition alterations. Since mitochondria emerged from bacterial ancestors during endosymbiosis, mitochondria and bacteria had analogous genomic characteristics, similar bioactive compounds and comparable energy metabolism pathways. Therefore, it is necessary to rationalize the interactions of intestinal microbiota with neural mitochondria. Recent studies have identified neural mitochondrial dysfunction as a critical pathogenic factor for the onset and progress of multiple neurological disorders, in which the nonnegligible role of altered gut flora composition was increasingly noticed. Here, we proposed a new perspective of intestinal microbiota – neural mitochondria […]

Abstract Gut microbiota plays a key role in the pathophysiology of type 2 diabetes mellitus (T2D). Mulberry leaf has a hypoglycemic effect, but the potential mechanism is not fully understood. This study aimed to explore the influences and potential mechanisms of mulberry leaf water extract (MLWE) intervention on mice with T2D induced through a high-fat and high-sucrose diet combined with streptozotocin by the combination of fecal metabolomics and gut microbiota analysis. Results showed that MLWE could decrease fasting blood glucose and body weight while ameliorating lipid profiles, insulin resistance, liver inflammation, and the accumulation of lipid droplets in T2D mice. […]

Abstract Background Obesity is a worldwide problem that resulted from the excessive fat accumulation in adipose tissue, leading to the impairment of individual health. Mulberry leaf is an important traditional Chinese medicine and has been used to alleviate obesity for a long term. However, its underlying molecular mechanisms have not been fully elucidated yet. Purpose In this study, we aimed to investigate the inhibition effects of mulberry leaf water extract (MLWE) on lipid accumulation during the process of differentiation of 3T3-L1 preadipocytes and development of mature adipocytes through the combination of molecular biology assays and metabolomic analysis. Methods The quality consistency and main chemical ingredients of MLWE were analyzed by high performance […]

Objective To identify circulating plasma exosomal transfer RNA-derived fragments (tRFs) as the predictive factors of successful microdissection testicular sperm extraction (micro-TESE) in patients with nonobstructive azoospermia (NOA). Design Case and control prospective study. Setting Academic research laboratory. Patient(s) Twelve patients with NOA with successful sperm retrieval by micro-TESE, 18 patients with NOA with failed sperm retrieval by micro-TESE, and 12 normozoospermic fertile controls. Intervention(s) Blood samples were collected from participants. Main Outcome Measure(s) The abundance of tRFs normalized as counts per million of the total aligned reads with the next-generation sequencing system; candidate tRF levels were validated through quantitative reverse […]

Highlights •Liver fibrosis affects glycogen metabolism.•Liver fibrosis alters the molecular structure of liver glycogen.•Glycogen structure affects its properties.•Liver fibrosis causes a functional deficiency of mitochondria.•Mitochondrial function may affect glycogen molecular structure. Abstract Liver fibrosis (LF) leads to liver failure and short survival. Liver glycogen is a hyperbranched glucose polymer, comprising individual β particles, which can bind together to form aggregated α particles. Glycogen functionality depends on its molecular structure. This study compared the molecular structure of liver glycogen from both LF and healthy rats, and explored underlying mechanisms for observed differences. Glycogen from both groups contained α and β particles; […]

Abstract Liver glycogen is a hyperbranched glucose polymer that is involved in the maintenance of blood sugar levels in animals. The properties of glycogen are influenced by its structure. Hence, a suitable extraction method that isolates representative samples of glycogen is crucial to the study of this macromolecule. Compared to other extraction methods, a method that employs a sucrose density gradient centrifugation step can minimize molecular damage. Based on this method, a recent publication describes how the density of the sucrose solution used during centrifugation was varied (30%, 50%, 72.5%) to find the most suitable concentration to extract glycogen particles […]

Abstract The properties of nanomaterials can be tuned by engineering the size, surface chemistry, and morphology, enabling the design of nanomaterials with desired structures. Following up our previous work on producing spherical exopolysaccharide nanoparticles (EPS-605 NPs), herein we realized the morphology transformation of EPS-605 NPs by the treatments with different solvents. The EPS-605 NPs can be transformed into the filamentous structures in NaOH (0.01 M) and ethanol (50%, v/v). In contrast, sodium dodecyl sulfate (SDS, 0.01 M) or dimethyl sulfoxide solution treatment only reduced the size of EPS-605 NPs without changing their spherical shape. After dialysis against distilled water, the […]

正文 2021年8月8日，课题唐佳伟硕士研究生和熊雪松老师以共同一作在Arabian Journal of Chemistry《阿拉伯化学杂志》（JCR1区，影响因子5.165）发表计算生物学研究论文，阐明桑叶醇提物缓解2型糖尿病的活性物质成分及作用靶点，为桑叶醇提物的商业化开发和应用提供了理论基础。论文的通讯作者为张潇教授和王亮教授，主要合作者包括澳门科技大学刘清华等。目前论文处于接收状态，正式发表后更新论文下载链接。 摘要 糖尿病是一种慢性内分泌代谢紊乱，可导致高血糖。作为最常见的糖尿病类型，2 型糖尿病占所有糖尿病疾病的 90%，其主要特征是胰岛素抵抗。桑叶是常用的中药，许多研究证实桑叶对缓解2型糖尿病的病理状况有积极作用。然而，其抗糖尿病作用和活性成分尚不完全清楚。与费时费力的实验相比，网络药理学为系统研究桑叶中化合物与糖尿病相关基因之间的相互作用提供了一种便捷的方法。尽管对桑叶进行了类似的网络药理学研究，但仅检查了来自公共数据库的化合物或桑叶中的挥发性成分。在这项研究中，我们最初通过液相色谱和质谱联用分析了桑叶乙醇提取物中的生物活性化合物，共产生了 248 种成分。分别从 TCMSP 和 PharmMapper 数据库中共鉴定出 14 种活性成分和 49 种潜在功能化合物，它们对 37 种直接参与 T2DM 发病机制的靶蛋白起作用。山奈酚被证明是最具影响力的活性化合物，而雄激素受体最广泛地受桑叶乙醇提取物中的化合物调节。此外，蛋白质-蛋白质相互作用和靶-通路网络分析表明，就其在不同通路中的功能以及与其他靶蛋白的相互作用而言，AKT1 在 37 种靶蛋白中最为重要。此外，通路分析表明桑叶乙醇提取物通过TNF信号通路、NF-κB信号通路和胰岛素抵抗通路等通路缓解2型糖尿病。综上所述，本研究全面概述了桑叶乙醇提取物的作用机制，其结果可作为进一步实验研究桑叶在治疗2型糖尿病过程中的作用的实践指导。 . 总结 本研究通过 LC-MS 系统地研究了桑叶乙醇提取物中鉴定出的化学成分对 2 型糖尿病治疗的影响。分别从 TCMSP 和 PharmMapper 数据库中共鉴定出 14 种活性成分和 49 种潜在功能化合物，它们对 37 种直接参与 T2DM 发病机制的靶蛋白起作用。山奈酚被证明是最具影响力的活性化合物，而雄激素受体最广泛地受桑叶乙醇提取物中的化合物调节。还通过化合物-目标网络分析确定了潜在的有效成分。蛋白质-蛋白质相互作用和靶-通路网络表明，就其在不同通路中的功能以及与其他靶蛋白的相互作用而言，AKT1 在 37 种靶蛋白中最为重要。此外，通路分析表明桑叶乙醇提取物通过TNF信号通路、NF-κB信号通路、胰岛素抵抗通路等通路缓解2型糖尿病。桑叶乙醇提取物治疗2型糖尿病，从理论上验证了桑叶在分子水平上的作用。此外，根据它们在糖尿病发病机制和治疗中的作用，确定了候选靶蛋白和化合物，用于进一步的实验研究。

摘要 拉曼光谱 (RS) 是一种广泛使用的分析技术，它基于对定义系统中分子振动的检测，可生成包含系统独特且高分辨率指纹的拉曼光谱。然而，法向拉曼散射效应的低强度极大地阻碍了其应用。最近，新出现的表面增强拉曼光谱 (SERS) 技术通过将金和银等金属纳米粒子与样品混合来克服这个问题，与常规 RS 相比，拉曼效应的信号强度大大增强了几个数量级。在临床和研究实验室中，SERS 在适当的机器学习算法的帮助下为快速、灵敏、无标记和无损微生物检测和识别提供了巨​​大的潜力。然而，为特定的细菌种类选择合适的算法仍然具有挑战性，因为在 SERS 分析过程中生成大量数据，并非所有算法都能达到相对较高的准确度。在本研究中，我们分别在 9 种临床重要葡萄球菌属的 117 株葡萄球菌的 2752 个 SERS 光谱上比较了 3 种无监督机器学习方法和 10 种监督机器学习方法，以测试不同机器学习方法对细菌快速分化的能力和准确的预测。根据结果​​，DBSCAN 显示出最佳的聚类能力（Rand 指数 0.9733），而卷积神经网络（CNN）在所有其他监督机器学习方法中名列前茅，成为通过 SERS 光谱预测葡萄球菌种类的最佳模型（ACC 98.21%，AUC 99.93%） .总之，这项研究表明机器学习方法能够区分密切相关的葡萄球菌属物种，因此在临床环境中细菌病原体诊断方面具有巨大的应用潜力。 论文官方网址请点击下方链接： 临床葡萄球菌表面增强拉曼光谱的机器学习算法对比分析Front. Microbiol. | doi: 10.3389/fmicb.2021.696921

Abstract Hepatitis C virus (HCV) is responsible for a variety of human life-threatening diseases, which include liver cirrhosis, chronic hepatitis, fibrosis and hepatocellular carcinoma (HCC) . Computational study of protein-protein interactions between human and HCV could boost the findings of antiviral drugs in HCV therapy and might optimize the treatment procedures for HCV infections. In this analysis, we constructed a prediction model for protein-protein interactions between HCV and human by incorporating the features generated by pseudo amino acid compositions, which were then carried out at two levels: categories and features. In brief, extra-tree was initially used for feature selection while […]

Abstract According to the sit-and-wait hypothesis, long-term environmental survival is positively correlated with increased bacterial pathogenicity because high durability reduces the dependence of transmission on host mobility. Many indirectly transmitted bacterial pathogens, such as Mycobacterium tuberculosis and Burkhoderia pseudomallei, have high durability in the external environment and are highly virulent. It is possible that abiotic stresses may activate certain pathways or the expressions of certain genes, which might contribute to bacterial durability and virulence, synergistically. Therefore, exploring how bacterial phenotypes change in response to environmental stresses is important for understanding their potentials in host infections. In this study, we investigated the effects of […]

由细菌病原体引起的传染病是重要的公共问题。此外，由于抗生素的过度使用，在临床环境中广泛遇到了许多多重耐药的细菌病原体。因此，细菌病原体的快速识别和抗生素耐药性分析可以极大地促进传染病的精确治疗策略。迄今为止，已经开发了许多用于体外诊断的常规和分子方法，无论是手动还是自动化，都已被证明是准确、可靠和省时的。尽管拉曼光谱是地球化学和材料科学等各个领域的成熟技术，但它仍然被认为是传染病研究和诊断的新兴工具。根据目前的研究，现在说拉曼光谱可以为微生物学家和临床医生提供实用指南还为时过早，因为基础研究和临床实施之间仍然存在差距。然而，由于在几个单一步骤中无标记检测和无创识别细菌感染和抗生素耐药性的前景广阔，因此有必要从其优点和缺点方面对该技术进行概述。因此，在这篇综述中，我们回顾了最近在传染病领域的拉曼光谱研究，强调了该技术的应用潜力以及当前阻碍其实际应用的挑战。 总结 拉曼光谱可以提供大量详细的细菌表型信息。尽管大量研究集中于通过遥感快速鉴定细菌种类和抗生素耐药性，但实际情况是该技术尚未在临床环境中得到充分探索。目前，大多数细菌病原体的拉曼光谱基于纯细菌分离物，这严重依赖于培养基培养，而来自实际临床样品的拉曼光谱仍然很少。最近，随着纳米粒子和纳米结构表面的发展，SERS极大地提高了拉曼光谱的信号强度，这极大地有助于更好地区分细菌感染。此外，拉曼光谱由大量复杂化学混合物的光谱组成，需要机器学习方法进行数据处理，如人工智能和深度学习，而不是经典的线性方法。然而，在机器学习辅助分析过程中遇到的问题涉及模型的过拟合或欠拟合，这是由于拉曼光谱的大维度和小样本量问题，尽管有不同的降维方法，如主成分分析用于解决该问题。此外，在招募机器学习方法时，细菌病原体标准RS数据库也是准确及时的实验室诊断的保证。总之，对于细菌分型和抗生素耐药性分析在临床环境中的适用性，迫切需要从真实世界中快速和可靠地自动测量临床样本的拉曼光谱的技术，随着新型拉曼光谱技术、纳米结构材料、计算方法和标准化数据库的快速发展，这将在可预见的未来实现。

Abstract Background: Mulberry leaf as a traditional Chinese medicine is able to treat obesity, diabetes, and dyslipidemia. It is well known that diabetes leads to intestinal microbiota dysbiosis. It is also recently discovered that liver glycogen structure is impaired in diabetic animals. Since mulberry leaves are able to improve the diabetic conditions through reducing blood glucose level, it would be interesting to investigate whether they have any positive effects on intestinal microbiota and liver glycogen structure. Methods: In this study, we first determined the bioactive components of ethanol extract of mulberry leaves via high-performance liquid chromatography (HPLC) and liquid chromatography/mass spectrometry (LC/MS). […]

Abstract Background The coronavirus disease 2019 (COVID-19) is spreading rapidly across countries and has infected tens of millions of people all over the world. So far, the pandemic is ongoing globally, and the situation is still worsening Methods In this retrospective, single-center cohort analysis, we included 25 adult inpatients with laboratory confirmed COVID-19 disease from the affiliated hospital of Xuzhou Medical University (Xuzhou, China). Epidemiological characterizations, clinical findings, and medical treatments were all reported. In addition, laboratory markers were investigated in terms of course of treatment. Results Epidemiological features and clinical findings were present for all 25 patients. Laboratory markers […]

Abstract Liver glycogen is a branched glucose polymer that functions as a blood-sugar buffer in animals. Previous studies have shown that glycogen’s molecular structure affects its properties. This makes it important to develop a technique that extracts and purifies a representative sample of glycogen. Here we aim to optimize the sucrose density gradient centrifugation method for preserving glycogen’s molecular structure by varying the density of the sucrose solution. The preservation of glycogen’s structure involves: 1) minimizing molecular damage and 2) obtaining a structurally representative sample of glycogen. The addition of a 10-minute boiling step was also tested as a means […]

Abstract Diurnal alteration of glycogen molecular structure has been identified in healthy mice. Recently, both fragile (disintegration in dimethyl sulfoxide) and stable (not disintegrating in DMSO) glycogen particles were found in Escherichia coli. However, how glycogen structure changes dynamically in E. coli is not clear. The question examined here is whether fragile, stable glycogen α particles occur in bacteria, following a similar pattern as in mice. In this study, we examine the dynamic changes of glycogen molecular structure over 24-h in E. coli BL21(DE3), using transmission electron microscopy, size exclusion chromatography and fluorophore-assisted carbohydrate electrophoresis at representative time points. It was found that glycogen structure […]

Abstract Glycogen is a highly-branched polysaccharide that is widely distributed across the three life domains. It has versatile functions in physiological activities such as energy reserve, osmotic regulation, blood glucose homeostasis, and pH maintenance. Recent research also confirms that glycogen plays important roles in longevity and cognition. Intrinsically, glycogen function is determined by its structure that has been intensively studied for many years. The recent association of glycogen α-particle fragility with diabetic conditions further strengthens the importance of glycogen structure in its function. By using improved glycogen extraction procedures and a series of advanced analytical techniques, the fine molecular structure […]

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张潇教授团队在SCI期刊BMC Genomics 发表机器学习预测蛋白质修饰靶点研究论文 2020年11月，医学信息与工程学院张潇教授团队在SCI期刊BMC Genomics发表研究论文Mal-Prec: computational prediction of protein Malonylation sites via machine learning based feature integration，针对蛋白质序列的丙二酰化预测这一问题，提出基于机器学习算法的新型解决方案。BMC Genomics是JCR1区，中科院2区SCI杂志，影响因子3.594，主要关注基因组学、功能基因组学、表观基因组学、蛋白质组学和转录组学等方面新方法和新技术的研究工作。论文通讯作者为张潇教授和刘莘教授，第一作者为智能医学工程教研室刘莘教授和王亮教授，主要合作者包括徐州医科大学产业管理办公室主任胡俊峰教授，以及徐州医科大学访问学者、美国杜兰大学终身教授李剑博士。 蛋白质酰基化修饰是一类特别的蛋白质翻译后修饰，其修饰基团的供体是代谢途径的中间产物。除乙酰化修饰外，近年还鉴定出了一系列新型的酰基化修饰，包括丙酰化、丁酰化、琥珀酰化、豆蔻酰化、和丙二酰化等，但这些新型酰基化修饰对蛋白质结构与功能的调控作用尚不清楚，其与重大疾病的发生发展是否具有相关性是亟待解决的问题。 论文官方网址请点击下方链接： https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07166-w

Abstract Background Clonorchis sinensis, a fluke dwelling in the intrahepatic bile ducts causes clonorchiasis, which affect about 15 million people wide-distributed in eastern Asia. During C. sinensis infection, worm-host interaction results in activation of patterns recognition receptors (PRRs) such as Toll-like receptors (TLRs) and further triggers immune responses, which determines the outcome of the infection. However, the mechanisms by which pathogen-associated molecules patterns from C. sinensis interact with TLRs were poorly understood. In the present study, we assumed that the molecules from C. sinensis may regulate host immune responses via TLR2 signaling pathway. Methodology/Principal findings In the present study, we have identified a ~34 kDa CsHscB from C. sinensis which physically bound […]

Abstract Isoliquiritigenin (ILG) and isoliquiritin (ILQ), two kinds of major flavonoids in licorice, are biological active substances with antioxidant, anti-inflammatory, and tumor-suppressive effects. However, their in vivo metabolites, possible material basis of this two licorice chalcones for the treatment of diseases, have not been studied completely. To determine the metabolism of ILG and ILQ, after oral administration of 100 mg/kg/day of these compounds for consecutive 8 days, the metabolites of these two licorice chalcones in mice plasma, urine, feces, and bile were determined using liquid chromatography coupled with quadrupole/time-of-flight mass spectrometry in this study. The structures of those metabolites were tentatively identified […]

Abstract Glycogen is a highly branched polysaccharide that is widely present in all life domains. It has been identified in many bacterial species and functions as an important energy storage compound. In addition, it plays important roles in bacterial transmission, pathogenicity, and environmental viability. There are five essential enzymes (coding genes) directly involved in bacterial glycogen metabolism, which forms a single operon glgBXCAP with a suboperonic promoter in glgC gene in Escherichia coli. Currently, there is no comparative study of how the disruptions of the five glycogen metabolism genes influence bacterial phenotypes, such as growth rate, biofilm formation, and environmental survival, etc. In this study, […]

Abstract Shigellosis is a highly infectious disease that is mainly transmitted via fecal-oral contact of the bacteria Shigella. Four species have been identified in Shigella genus, among which Shigella flexneri is used to be the most prevalent species globally and commonly isolated from developing countries. However, it is being replaced by Shigella sonnei that is currently the main causative agent for dysentery pandemic in many emerging industrialized countries such as Asia and the Middle East. For a better understanding of S. sonnei virulence and antibiotic resistance, we sequenced 12 clinical S. sonnei strains with varied antibiotic-resistance profiles collected from four cities in Jiangsu Province, China. Phylogenomic analysis clustered antibiotic-sensitive and resistant S. […]

Abstract Continuing efforts have been made to produce functional exopolysaccharides (EPSs) using cheap substrates for valuable applications. Cheese whey is a lactose-rich byproduct of cheese-producing industries. In this research, a one-step bioprocess for the bioconversion of cheese whey to a hetero-exopolysaccharide using a ropy EPS producing strain Lactobacillus plantarum JNULCC001 with high β-galactosidase activity was performed. The prepared hetero-exopolysaccharide is named EPS-001 and composed of galactose, glucose, mannose, and arabinose with several functional groups, including carboxyl, hydroxyl, and amide groups, endowing its thermo-stable and highly negatively charged properties. The rheological analysis of the fermented whey indicates its high viscous and shear thinning […]

Abstract Archaea are a group of primary life forms on Earth and could thrive in many unique environments. Their successful colonization of extreme niches requires corresponding adaptations at proteogenomic level in order to maintain stable cellular structures and active physiological functions. Although some studies have already investigated the extremophilic lifestyles of archaeal species based on genomic features and protein structures, there is a lack of comparative proteogenomic analysis in a large scale. In this study, we explored 686 high-quality archaeal genomes (proteomes) sourced from the Pathosystems Resource Integration Center (PATRIC) database. General patterns of genomic features such as genome size, […]

Abstract 我们报We report epidemiologic, laboratory, and clinical findings for 7 patients with 2019 novel coronavirus disease in a 2-family cluster. Our study confirms asymptomatic and human-to-human transmission through close contacts in familial and hospital settings. These findings might also serve as a practical reference for clinical diagnosis and medical treatment. Conclusion In summary, our epidemiologic study demonstrates asymptomatic and human-to-human transmission of SARS-CoV-2 infection through close contacts in both familial and hospital settings. In addition, the laboratory test results, together with course of medical therapies described, can provide a practical reference for COVID-19 diagnosis and treatment. Please click the link […]

Abstract 肝糖原是一种高度支化的葡萄糖聚合物，对血糖稳态很重要。 它包括由β粒子连接而成的α粒子； 分子结构昼夜变化。 在糖尿病肝脏中，α粒子很脆弱，在二甲基亚砜等离液剂中很容易分裂成β粒子。 我们在这里使用大小排阻色谱来研究禁Liver glycogen, a highly branched glucose polymer, is important for blood sugar homeostasis. It comprises α particles which are made of linked β particles; the molecular structure changes diurnally. In diabetic liver, the α particles are fragile, easily breaking apart into β particles in chaotropic agents such as dimethyl sulfoxide. We here use size-exclusion chromatography to study how fasting changes liver-glycogen structure in vivo for mice in which type-2 diabetes had previously been induced. Diabetic glycogen degraded enzymatically more quickly in the fasted animals than did glycogen without fasting, with fewer α particles, which however were still […]

Abstract Glycogen, a glucose homopolymer with many glucose chains, is the primary blood-sugar reservoir in many organisms. It comprises β particles (∼20 nm) which can bind together to form large α particles with a rosette morphology. When dimethyl sulfoxide (DMSO) is added to glycogen from diabetic livers, α particles break apart to β particles (‘fragility’), possibly due to H-bond disruption; this is not seen in healthy livers. Glycogen α and β particles, and α-particle fragility, are observed in mammals and bacteria, and are examined here in the worm Caenorhabditis elegans, with glycogen from two C. elegans strains, cultured in normal and high-glucose conditions. There […]

As of March 13, 2020, the ongoing pandemic of COVID-19 worldwide has caused more than 130,000 infections and the death toll near 5,000. A study of 72,314 Chinese patient records revealed that most cases (80.9%) had mild symptoms while the elderly and people with comorbid conditions such as hypertension and diabetes are at higher risk of severe disease (1). So far, more than 60,000 patients have recovered from COVID-19 pneumoniae and are discharged home based on the Novel Coronavirus Infection Diagnosis and Treatment Plan released by the China National Health Commission (CNHC). The discharge standards include: (I) body temperature back […]

Abstract Ethnopharmacological relevance Licorice is an ancient food and medicinal plant. Liquiritigenin and liquiritin, two kinds of major flavonoes in licorice, are effective substances used as antioxidant, anti-inflammatory and tumor-suppressive food, cosmetics or medicines. However, their in vivo metabolites have not been fully explored. Aim of study To clarify the metabolism of liquiritigenin and liquiritin in mice. Materials and methods In this study, we developed a liquid chromatography coupled with quadrupole/time-of-flight mass spectrometry approach to determine the metabolites in mice plasma, bile, urine and feces after oral administration of liquiritigenin or liquiritin. The structures of those metabolites were tentatively identified according to […]

Description Genome Plasticity in Health and Disease provides a fully up-to-date overview on genome plasticity and its role in human physiology and disease. Following an introduction to the field, a diverse range of chapters cover genomic and epigenomic analysis and the use of model organisms and genomic databases in studies. Specific molecular and biochemical mechanisms of genome plasticity are examined, including somatic variants, De Novo variants, founder variations, isolated populations dynamics, copy-number variations, mobile elements, DNA methylation, histone modifications, transcription factors, non-coding RNAs, telomere dynamics and RNA editing. Later chapters explore disease relevance for cancer, as well as cardiovascular, neuropsychiatric, […]

Abstract We aimed to examine whether golgi protein GOLPH3 could affect the secretion of glioma cell-derived exosomes. The exosomes were extracted by ultra-centrifugation from the supernatant of U251 and U87 cell cultures and identified by transmission electron microscopy (TEM), Malvern analyzer, and western blot. The quantity of exosomes was examined by measuring the total protein levels and the number of multiple vesicle bodies (MVBs), the source of exosomes. The exosome miRNAs were analyzed by high-throughput sequencing followed by GO and KEGG analysis, and validated by qRT-PCR. GOLPH3 could not affect the total protein levels of exosomes and the number of […]

Abstract In Caenorhabditis elegans, the binding of Piwi protein to a non-coding RNA form, called piRNA, has been found to be important to both reproductive and aging processes. As the biosynthesis of piRNA is modulated by mitochondrial function, it is likely that the interaction between mitochondrial function and piRNA expression plays an unknown, yet important, role in reproductive and aging processes because both processes are known to be affected by declines in mitochondrial quality and activity. While the relationship between reproduction and longevity is not characterized in full, the optimality theory of aging and the disposable soma theory suggest that a […]

Abstract The low success rates in the treatment of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant TB (XDR-TB), which account for 55% and 34% respectively, led the WHO to conclude that MDR/XDR-TB is a serious public health crisis. However, the virulence of MDR/XDR-Mycobacterium Tuberculosis(Mtb) has not been analyzed in details, which could provide a specific guidance for the control and prevention. In this review, we discuss different aspects of MDR/XDR-Mtb virulence and its relationship to fitness cost by probing the following questions: (1) what mediates the virulence of MDR/XDR-Mtb? (What is the relationship between fitness and virulence of Mtb? (2) Is it possible […]

Abstract Recently, mitochondrial-nuclear interaction in aging has been widely studied. However, the nuclear genome controlled by natural mitochondrial variations that influence aging has not been comprehensively understood so far. We hypothesized that mitochondrial polymorphisms could play critical roles in the aging process, probably by regulation of the whole-transcriptome expression. Our results showed that mitochondria polymorphisms not only decreased the mitochondrial mass but also miRNA, lncRNA, mRNA, circRNA and metabolite profiles. Furthermore, most genes that are associated with mitochondria show age-related expression features (P = 3.58E-35). We also constructed a differentially expressed circRNA-lncRNA-miRNA-mRNA regulatory network and a ceRNA network affected by […]

Abstract Glycogen, a highly-branched glucose polymer, functions as a sugar reservoir in many organs and tissues. Liver glycogen comprises small β particles which can bind to form into large agglomerates (α particles) which readily degrade to β particles in diabetic livers. Muscle glycogen has only β particles, optimal for quick energy release. Healthy kidney contains negligible glycogen, but there is an abnormally high accumulation in diabetic kidneys. We here compare the molecular structure of glycogen in diabetic kidneys with that in liver and muscle, using a diabetic rat model. This involved exploring extraction techniques to minimize glycogen degradation. Using size […]

Abstract Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length gc in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent […]

Abstract The increasing prevalence of hyperuricemia has been recognized as an emerging public health concern in both developed and developing countries. Hyperuricemia is a metabolic condition characterized by an elevated serum uric acid, and associated with renal damage, diabetes, autoimmune disorders, and cardiovascular diseases. Although human genetic variation has been recognized as a factor, posttranslational cellular processes and glycan biomarkers have not been studied extensively for susceptibility to hyperuricemia. We evaluated whether immunoglobulin (Ig)G N-glycans play a role in hyperuricemia in the general population. This cross-sectional study enrolled 635 participants (208 men and 427 women), ages ≥18 years, from a community-based […]

Abstract Glycogen is a homogenous and multi-disperse polysaccharide that is present in many clinically significant bacteria, such as Escherichia coli, Vibrio cholera and Mycobacterium tuberculosis. Its structure and metabolism have been linked with environmental viability, intracellular growth, pathogenicity and transmission capacity. However, due to the harsh extraction conditions and also the inconsistent methods for structure characterisation, understanding of bacterial glycogen structure and its association with bacterial metabolism and physiology has been hindered. Here we gave a concise overview of bacterial glycogen structure with a focus on its recently discovered higher level organisation, α particle. Standardised procedures for glycogen extraction and structure detection are also […]

Abstract The aim of this study was to explore the feasibility of using different 3D printed internal geometries as tablet formulations to obtain controlled release profiles. In order to obtain controllable release profiles, three types of tablet models (Cylinder, Horn and Reversed Horn) with controlled structures were designed. The cylinder model shows a constant release profile and can keep the drug concentration within a certain range. The horn model exhibits an increasing release profile, which is suitable for the patients who have the drug resistance in the course of medication. The reversed horn model has a decreasing release profile that […]

Abstract Diabetic nephropathy (DN) is one of the most serious microvascular complications and the leading causes of death in diabetes mellitus (DM). To find biomarkers for prognosing the occurrence and development of DN has significant clinical value for its prevention, diagnosis, and treatment. In this study, a non-targeted cell metabolomics–based ultra-performance liquid chromatography coupled with quadrupole time of flight mass spectrometry and gas chromatography coupled with mass spectrometry was developed and performed the dynamic metabolic profiles of rat renal cells including renal tubular epithelial cells (NRK-52E) and glomerular mesangial cells (HBZY-1) in response to high glucose at time points of […]

Abstract Shigellosis is the major cause of dysentery globally. It is mainly attributed to two Shigella species, Shigella sonnei and Shigella flexneri, which leads to approximately 165 million infections and 1.1 million deaths each year. Rapid increase and widening of spectrum in antibiotics resistance make Shigella hard to be adequately controlled through existing prevention and treatment measures. It has also been observed that enhanced virulence and advent of antibiotic resistance (AR) could arise almost simultaneously. However, genetic linkages between the two factors are missing or largely ignored, which hinders experimental verification of the relationship. In this study, we sequenced 15 clinically isolated S. flexneri strains. Genome assembly, annotation and […]

Abstract Glycogen, a randomly branched glucose polymer, provides energy storage in organisms. It forms small β particles which in animals bind to form composite α particles, which give better glucose release. Simulations imply β particle size is controlled only by activities and sizes of glycogen biosynthetic enzymes and sizes of polymer chains. Thus, storing more glucose requires forming more β particles, which are expected to sometimes form α particles. No α particles have been reported in bacteria, but the extraction techniques might have caused degradation. Using milder glycogen extraction techniques on Escherichia coli, transmission electron microscopy and size-exclusion chromatography showed […]

Abstract Previous bioinformatics studies have linked gain or loss of energy reserves with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the theoretical distribution patterns of energy reserves across bacterial species could provide a shortcut route to look into bacterial lifestyle and physiology. So far, five major energy reserves have been identified in bacteria due to their capacity to support bacterial persistence under nutrient deprivation conditions. These include polyphosphate (polyP), glycogen, wax ester (WE), triacylglycerol (TAG), and polyhydroxyalkanoates (PHAs). Although the enzymes related with metabolism of energy reserves are well […]

Abstract Sodium valproate is the most commonly used antiepileptic drug that patients need to keep taking over a long period of time or on a permanent basis. Its blood concentration should be accurately detected to avoid toxicity or side-effects, especially for children and the aged. Dried blood spot (DBS) sampling from finger prick is a minimally invasive and patient-friendly procedure for blood collection. However, there are few studies about rapid detection of sodium valproate in DBS samples in current literatures. In this work, we developed an ink auxiliary headspace gas chromatography mass spectrometry (GC–MS) strategy for direct detection of sodium […]

Abstract Background:Proteins may have none, single, double, or multiple domains, while a single domain may appear in multiple proteins. Their distribution patterns may have impacts on bacterial physi-ology and lifestyle. Objective:This study aims to understand how domains are distributed and duplicated in bacterial prote-omes, in order to better understand bacterial physiology and lifestyles. Methods:In this study, we used 16712 Hidden Markov Models to screen 944 bacterial reference prote-omes versus a threshold E-value<0.001. The number of non-redundant domains and duplication rates of redundant domains for each species were calculated. The unique domains, if any, were also identified for each species. In […]

Abstract Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of […]

Abstract In bacteria, glycogen plays important roles in carbon and energy storage. Its structure has recently been linked with bacterial environmental durability. Among the essential genes for bacterial glycogen metabolism, the glgB-encoded branching enzyme GBE plays an essential role in forming α-1,6-glycosidic branching points, and determines the unique branching patterns in glycogen. Previously, evolutionary analysis of a small sets of GBEs based on their N-terminal domain organization revealed that two types of GBEs might exist: (1) Type 1 GBE with both N1 and N2 (also known as CBM48) domains and (2) Type 2 GBE with only the N2 domain. In this […]

内容简介 芳香疗法的核心是植物精油。精油源自植物的次级代谢产物，是植物中醇类、醛类、酸类、酚类、丙酮类以及萜烯类等化学物质的浓缩，具有多种生物活性。《精油的科学》中所说的精油是指纯天然的植物提取物，而非人工合成的香精。大量的临床案例和实验研究证实，芳香疗法在**消炎、缓解压力、心理干预以及改善精神障碍等方面具有良好效果。该书从芳香感知的原理到现代精油贸易，从传统的蒸馏法到先进的超临界二氧化碳提取都有涉及。此外，《精油的科学》从生活和临床两方面入手，用数据和实例说话，深入浅出地介绍了精油的各方面功能。最后，简要介绍了一些具有特色的精油品种以及精油在香水工业中的应用。 前言/序言 美国国立卫生研究院下属的癌症研究所把芳香疗法定义为使用植物精油提升身体、精神和情感健康的一种辅助医疗方式。芳香，植物在人类社会中已有数千年的使用历史，其药用价值在印度、埃及和中国等古老文明中均有记载。东方人通常直接使用芳香或药用植物治疗疾病，而植物精油的提取和使用则起源于欧洲，到中世纪时期臻于成熟。法国化学家雷内·盖特弗塞在研究了不同精油对疾病功效的基础上，于20世纪初建立了芳香疗法的基本体系。到20世纪末期，芳香疗法被正式纳入辅助和替代疗法的范畴，逐渐被西方社会接受和认可。相关数据表明有约38%的成年美国人曾经寻求辅助和替代疗法缓解压力、焦虑以及疼痛等症状，市场份额高达339亿美元。鉴于该领域的旺盛需求，美国国立卫生研究院于1998年成立了辅助和整合健康研究院，每年投入约1亿美元的经费专门从事替代医学方面的研究，大力促进了芳香疗法在科学框架内的发展，提升了其在公共领域的认知度。 目前，芳香疗法主要通过香薰、口服及按摩三种途径实现精油和人体的相互作用。在这三种作用方式中，香薰法最有效也最为常见。香薰精油通过嗅觉系统实现与人体相互作用，从而达到缓解心理和精神障碍的功效。嗅觉是人类最重要的感官感受之一。鼻孑无法辨识气味就像耳朵听不到声音或是眼睛看不见东西一样，会对我们的生活和健康造成严重影响。在人类进化史上，嗅觉扮演了举足轻重的角色。西班牙自然科学博物馆的研究人员于2011年发现人类祖先嗅觉敏感度的提升不仅增强了部落成员的辨识能力，还有效提升了群体间的相互协作意识，使得人类祖先在早期激烈的进化竞争中超越尼安德人，成就了现代人类文明的繁荣昌盛。人类对气味的感知主要归因于嗅神经系统和鼻三叉神经系统的相互作用，而起决定作用的则是位于大脑内部的嗅球。嗅球是由上万个嗅细胞的神经纤维缠集在一起形成的球状体，可以快速识别精油中的复杂成分并形成对气味的综合认识，最后将信息转化为神经信号传导至海马体和杏仁核区域。因此嗅觉和记忆之间有着极其亲密的联系，并会对人的情感产生一定影响。 芳香疗法的核心是植物精油。精油源自植物的次级代谢产物，是植物中醇类、醛类、酸类、酚类、丙酮类以及萜烯类等化学物质的浓缩，具有多种生物活性。本书中所说的精油是指纯天然的植物提取物，而非人工合成的香精。大量的临床案例和实验研究证实，芳香疗法在杀菌消炎、缓解压力、心理干预以及改善精神障碍等方面具有良好效果。本书共分九个部分八十五小节，从芳香感知的原理到现代精油贸易，从传统的蒸馏法到先进的超临界二氧化碳提取都有涉及。此外，本书从生活和临床两方面人手，用数据和实例说话，深入浅出地介绍了精油的各方面功能。最后，简要介绍了一些具有特色的精油品种以及精油在香水工业中的应用。本书力求在科普性和趣味性之间寻求平衡，让读者在获取知识的同时，不会觉得内容过于枯燥乏味。本书各章节间既相互独立，也存在一定联系，读者朋友们可以根据个人喜好选择相应篇章阅读。 书籍购买请点击下方链接： https://item.jd.com/12549402.html

Abstract Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification […]

Abstract Glycogen plays important roles in bacteria. Its structure and storage capability have received more attention recently because of the potential correlations with environmental durability and pathogenicity. However, the low level of intracellular glycogen makes extraction and structure characterization difficult, inhibiting functional studies. Bacteria grown in regular media such as lysogeny broth and tryptic soy broth do no accumulate large amounts of glycogen. Comparative analyses of bacterial media reported in literature for glycogen-related studies revealed that there was no consistency in the recipes reported. Escherichia coli DH5α is a convenient model organism for gene manipulation studies with respect to glycogen. […]

Abstact Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain […]

Abstact The objective of this study was to fabricate a tablet with a convex drug release profile. A circumscribed sphere with a regular tetrahedron (pyramid) cavity shell model was created by a computer-aided design (CAD) program and printed by a 3D printer. Paracetamol (APAP) mixed with polyvinyl alcohol (PVA) gel was filled into the cavity. The tablets were obtained through drying. The release profile was obtained by detecting the APAP concentration in phosphate buffer solution through ultraviolet absorption spectrophotometry. Along with the decrement of tablet diameter, drug exposure area gradually increases the release rate of the drug. The results indicate […]

Abstract As one of the basic research methods of bioinformatics, DNA motif finding is of great significance to the study of mechanisms for regulating gene expression and the discovery of biological functional sites. However, because of the high sensitivity of DNA data, the privacy disclosure of these data during motif finding has become a bottleneck in the field of gene research. Meanwhile, traditional privacy protection data mining methods cannot deal with DNA sequences directly, and the existing private motif finding methods usually decrease the utility of the results. To solve these problems, we propose a high-utility motif finding algorithm based […]

摘要 这一耐人寻味的坐等假说预测，细菌在外部环境中的耐久性与它们的毒力呈正相关。自从1987年首次提出这一假说以来，该假说在细菌毒力领域的有效性一直引发争论。作为媒介传播与毒力权衡的特例，媒介现在被环境寿命取代，在过去的30年里，只有零星的研究表明环境耐久性可能与毒力有关。然而，自从Walther和Ewald(2004)的综述发表以来，目前还没有对这些工作的系统研究，也没有对静坐等待假说的流行病学分析进行更新。在这篇文章中，我们将实验证据、流行病学数据和理论分析放在一起来支持静观其变假说。根据毒力(+/-)和耐久性(+/-)表型得失的流行病学资料，我们将细菌分为四类，即静待病原菌(++)、媒介传播病原菌(+-)、专性胞内细菌(–)和自由生活细菌(-+)。之后，由于高通量测序技术的快速发展，我们借助生物信息学技术深入研究了丰富的细菌蛋白质组数据，从分子水平上对这两个因素进行了研究。使用来自Gene Ontology和UniProt数据库的耐久性相关基因序列和从毒力因子数据库收集的毒力因子，通过HMMER软件包批量搜索相应的20个细菌蛋白质组以寻找同源序列。统计分析只确定了8个具有静坐等待潜力的非媒介传播细菌的死亡率和生存时间之间的适度的，并且在统计上没有显著的相关性。同时，通过组间比较，寄主死亡率较高的细菌在外部环境中的耐久性明显更强。生物信息学分析结果与流行病学数据吻合较好，即具有坐等潜势的非媒介传播病原菌的毒力基因和耐久性基因数量高于其他细菌群。然而，由于细菌样本量相对较小，实验数据不规范，这些结论受到了限制。

Abstract Aspiration of bile into the cystic fibrosis (CF) lung has emerged as a prognostic factor for reduced microbial lung biodiversity and the establishment of often fatal, chronic pathogen infections. Staphylococcus aureus is one of the earliest pathogens detected in the lungs of children with CF, and once established as a chronic infection, strategies for its eradication become limited. Several lung pathogens are stimulated to produce biofilms in vitro in the presence of bile. In this study, we further investigated the effects of bile on S. aureus biofilm formation. Most clinical S. aureus strains and the laboratory strain RN4220 were stimulated to form biofilms with sub-inhibitory concentrations of […]

Abstact Background:Glycogen average chain length (ACL) has been linked with bacterial durability, but this was on the basis of observations across different species. We therefore wished to investigate the relationship between bacterial durability and glycogen ACL by varying glycogen average chain length in a single species. It has been shown that progressive shortening of the N-terminus of glycogen branching enzyme (GBE) leads to a lengthening of oligosaccharide inter-α-1,6-glycosidic chain lengths, so we sought to harness this to create a set of Escherichia coli DH5α strains with a range of glycogen average chain lengths, and assess these strains for durability related attributes, such […]

Abstract Glycogen is conventionally viewed as an energy reserve that can be rapidly mobilized for ATP production in higher organisms. However, several studies have noted that glycogen with short average chain length in some bacteria is degraded very slowly. In addition, slow utilization of glycogen is correlated with bacterial viability, that is, the slower the glycogen breakdown rate, the longer the bacterial survival time in the external environment under starvation conditions. We call that a durable energy storage mechanism (DESM). In this review, evidence from microbiology, biochemistry, and molecular biology will be assembled to support the hypothesis of glycogen as […]