ecosystem-fabrication-ecofab-protocols-for-construction-laboratory

Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A ...

the-causal-effects-plasma-metabolites-on-achilles-tendon-injury

The Causal Effects of Plasma Metabolites on Achilles Tendon Injury: A Mendelian Randomization Study

To investigate the causal effects of plasma metabolites on the progression and recovery of Achilles tendon injury (ATI), Mendelian randomization (MR) was ...

Lawrence Berkeley National Laboratory

Department of Energy

Ningxia medical university

Cost-effective hydrolysis of biomass into sugars for biofuel production requires high-performance low-cost glycoside hydrolase (GH) cocktails that are active under demanding process conditions. Improving the performance of GH cocktails depends on knowledge of many critical parameters, including individual enzyme stabilities, optimal reaction conditions, kinetics, and specificity of reaction. With this information, rate- and/or yield-limiting reactions can be potentially improved through substitution, synergistic complementation, or protein engineering. Given the wide range of substrates and methods used for GH characterization, it is difficult to compare results across a myriad of approaches to identify high performance and synergistic combinations of enzymes. Here, we describe a platform for systematic screening of GH activities using automatic biomass handling, bioconjugate chemistry, robotic liquid handling, and nanostructure-initiator mass spectrometry (NIMS). Twelve well-characterized substrates spanning the types of glycosidic linkages found in plant cell walls are included in the experimental workflow. To test the application of this platform and substrate panel, we studied the reactivity of three engineered cellulases and their synergy of combination across a range of reaction conditions and enzyme concentrations. We anticipate that large-scale screening using the standardized platform and substrates will generate critical datasets to enable direct comparison of enzyme activities for cocktail design.

Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS.

Nanostructure-initiator mass spectrometry (NIMS) is a matrix-free desorption/ionization technique with high sensitivity for small molecules. Surface preparation has relied on hydrofluoric acid (HF) electrochemical etching which is undesirable given the significant safety controls required in this specialized process. In this study, we examine a conventional and widely used process for producing black silicon based on sulfur hexafluoride/oxygen (SF6/O2) inductively coupled plasma (ICP) etching at cryogenic temperatures and we find it to be suitable for NIMS. A systematic study varying parameters in the plasma etching process was performed to understand the relationship of black silicon morphology and its sensitivity as a NIMS substrate. The results suggest that a combination of higher silicon temperature and oxygen flow rate gives rise to the formation of black silicon with fine pillar structures, whose aspect ratio are ∼ 8.7 and depth are <1 μm resulting in higher NIMS sensitivity which is attributed to surface restructuring caused by their low melting point upon laser irradiation. Interestingly, we find selectivity of these black silicon substrates to different analytes depending on the etching parameters. Though, the sensitivity of the dry etching process is lower than the traditional "wet" electrochemical etching process, it is suitable for many applications and is prepared using conventional equipment without the use of HF.

Application of Black Silicon for Nanostructure-Initiator Mass Spectrometry.

Biological assays often require expensive reagents and tedious manipulations. These shortcomings can be overcome using digitally operated microfluidic devices that require reduced sample volumes to automate assays. One particular challenge is integrating bioassays with mass spectrometry based analysis. Towards this goal we have developed μNIMS, a highly sensitive and high throughput technique that integrates droplet microfluidics with nanostructure-initiator mass spectrometry (NIMS). Enzyme reactions are carried out in droplets that can be arrayed on discrete NIMS elements at defined time intervals for subsequent mass spectrometry analysis, enabling time resolved enzyme activity assay. We apply the μNIMS platform for kinetic characterization of a glycoside hydrolase enzyme (CelE-CMB3A), a chimeric enzyme capable of deconstructing plant hemicellulose into monosaccharides for subsequent conversion to biofuel. This study reveals NIMS nanostructures can be fabricated into arrays for microfluidic droplet deposition, NIMS is compatible with droplet and digital microfluidics, and can be used on-chip to assay glycoside hydrolase enzyme in vitro.

On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening.

The illegal use of melamine in powdered baby formula resulted in a widespread outbreak of melamine-associated pediatric urolithiasis and kidney damage in China in 2008. We conducted this study because more needs to be known about the long-term effects of melamine-associated urolithiasis and kidney damage.

Assessment of chronic renal injury from melamine-associated pediatric urolithiasis: an eighteen-month prospective cohort study.

Non-alcoholic fatty liver disease (NAFLD) is a global health problem with high geographic heterogeneity. We aimed to investigate regional-specific concomitant rate of NAFLD and quantitative relationship between liver fat content (LFC) and glucose metabolism parameters in representative clinical populations from six provinces/municipalities of China.

Regional difference in the susceptibility of non-alcoholic fatty liver disease in China.

 subsp.  (SDSD) is one of the most prevalent pathogens causing bovine mastitis worldwide. However, there is a lack of comprehensive information regarding genetic diversity, complete profiles of virulence factors (VFs), and antimicrobial resistance (AMR) genes for SDSD associated with bovine mastitis in China. In this study, a total of 674 milk samples, including samples from 509 clinical and 165 subclinical mastitis cases, were collected from 17 herds in 7 provinces in China from November 2016 to June 2019. All SDSD isolates were included in phylogenetic analysis based on 16S rRNA and multi-locus sequence typing (MLST). In addition, whole genome sequencing was performed on 12 representative SDSD isolates to screen for VFs and AMR genes and to define pan-, core and accessory genomes. The prevalence of SDSD from mastitis milk samples was 7.57% (51/674). According to phylogenetic analysis based on 16S rRNA, 51 SDSD isolates were divided into 4 clusters, whereas based on MLST, 51 SDSD isolates were identified as 11 sequence types, including 6 registered STs and 5 novel STs (ST521, ST523, ST526, ST527, ST529) that belonged to 2 distinct clonal complexes (CCs) and 4 singletons. Based on WGS information, 108 VFs genes in 12 isolates were determined in 11 categories. In addition, 23 AMR genes were identified in 11 categories. Pan-, core and accessory genomes were composed of 2,663, 1,633 and 699 genes, respectively. These results provided a comprehensive profiles of SDSD virulence and resistance genes as well as phylogenetic relationships among mastitis associated SDSD in North China.

Comparative Genomic Analysis of  Isolated From Bovine Mastitis in China.

Selective serotonin reuptake inhibitors (SSRIs) are the first-line pharmacotherapy for obsessive-compulsive disorder (OCD), but a large proportion of patients do not achieve remission after an adequate SSRI trial. To the best of our knowledge, there have been no well-powered randomized controlled trials (RCTs) of sequenced pharmacotherapy using pragmatic research designs. China provides a unique context for undertaking such a trial that will recruit the largest treatment-naïve participants and systematically compare the efficacy of different sequenced pharmacotherapy.

Protocol for a Pragmatic Trial of Pharmacotherapy Options Following Unsatisfactory Initial Treatment in OCD (PROCEED).

Although autophagy can eliminate some intracellular pathogens, others, e.g., , Salmonella, , can evade it. The phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) pathway, a key regulator of autophagy, is involved in initiation and promotion of a range of pathological diseases. As the effects of  on the autophagic pathway are not well documented, our objective was to elucidate the effects of  infection on the PI3K-Akt-mTOR cellular autophagic pathway in bovine mammary epithelial cells (bMECs). Ultrastructure of bMECs infected with  was assessed with transmission electron microscopy, co-localization of LC3 puncta with  was confirmed by laser confocal microscopy, and autophagy-related indicators were quantified with Western blotting and RT-PCR. In -infected bMECs, intracellular  was encapsulated by membrane-like structures, the expression level of LC3-II and Beclin1 protein decreased at the middle stage of infection, degradation of SQSTM1/P62 was blocked, autophagy of bMECs was inhibited, and PI3K-Akt-mTOR protein was activated by phosphorylation. Furthermore, the tumor suppressor PTEN can inhibit the PI3K-Akt signaling pathway through dephosphorylation of phosphatidylinositol 3,4,5-trisphosphate and may be important for cellular resistance to infection. In the present study, the number of intracellular  was inversely related to the change in the level of autophagy markers (e.g., LC3-II, SQSTM1/P62) within host cells induced by the low knockdown of Akt or PTEN. We concluded that -infected bMECs alleviated cellular autophagy through a PI3K-Akt-mTOR pathway, and that PTEN acted as a protective gene regulating autophagy, a key step in controlling infection.

 inhibits autophagy in bovine mammary epithelial cells  a PTEN/PI3K-Akt-mTOR-dependent pathway.

To compare the effect of three different surgical methods on rabbit Achilles tendon rupture.

Comparison of the Effects of Open Surgery and Minimally Invasive Surgery on the Achilles Tendon Rupture Healing Based on Angiogenesis.

Kidney disease is manifested in a wide variety of phenotypes, many of which have an important hereditary component. To delineate the genotypic and phenotypic spectrum of pediatric nephropathy, a multicenter registration system is being implemented based on the Chinese Children Genetic Kidney Disease Database (CCGKDD). In this study, all the patients with kidney and urological diseases were recruited from 2014 to 2020. Genetic analysis was conducted using exome sequencing for families with multiple affected individuals with nephropathy or clinical suspicion of a genetic kidney disease owing to early-onset or extrarenal features. The genetic diagnosis was confirmed in 883 of 2256 (39.1%) patients from 23 provinces in China. Phenotypic profiles showed that the primary diagnosis included steroid-resistant nephrotic syndrome (SRNS, 23.5%), glomerulonephritis (GN, 32.2%), congenital anomalies of the kidney and urinary tract (CAKUT, 21.2%), cystic renal disease (3.9%), renal calcinosis/stone (3.6%), tubulopathy (9.7%), and chronic kidney disease of unknown etiology (CKDu, 5.8%). The pathogenic variants of 105 monogenetic disorders were identified. Ten distinct genomic disorders were identified as pathogenic copy number variants (CNVs) in 11 patients. The diagnostic yield differed by subgroups, and was highest in those with cystic renal disease (66.3%), followed by tubulopathy (58.4%), GN (57.7%), CKDu (43.5%), SRNS (29.2%), renal calcinosis /stone (29.3%) and CAKUT (8.6%). Reverse phenotyping permitted correct identification in 40 cases with clinical reassessment and unexpected genetic conditions. We present the results of the largest cohort of children with kidney disease in China where diagnostic exome sequencing was performed. Our data demonstrate the utility of family-based exome sequencing, and indicate that the combined analysis of genotype and phenotype based on the national patient registry is pivotal to the genetic diagnosis of kidney disease.

Genetic Architecture of Childhood Kidney and Urological Diseases in China.

With the fast pace of modern life, people have less time for meals, but few studies have examined the association between the habit of fast eating and metabolic diseases.

Association between fast eating speed and metabolic dysfunction-associated steatotic liver disease: a multicenter cross-sectional study and meta-analysis.

Irregular eating patterns, such as skipping breakfast and late dinner consumption, have been linked to adverse metabolic profiles. However, the impact of these behaviors or their combined effect on metabolic dysfunction-associated steatotic liver disease (MASLD) remains unclear.

The role of irregular eating behaviors in metabolic dysfunction-associated steatotic liver disease: evidence from a multicenter cross-sectional study in China.

Bovine mastitis, especially subclinical mastitis (SCM), with minimal clinical signs, is detrimental due to its resistance to treatment, recurrence, and substantial economic impact on global dairy industry. The modified form of Huangqi Shengmai Yin (HSY), classical traditional herbal medicine renowned for its effects in antimicrobial and circulatory-enhancing and thus beneficial for subclinical mastitis, has been developed for treatment attempt of SCM, yet its therapeutic effect and mechanism remains unclear. This study aims to investigate the therapeutic effects of mHSY on SCM in cows, and elucidate its potential therapeutic mechanism.

Modified Huangqi Shengmai Yin enhances ruminal microbiome and metabolites activity in dairy cows with subclinical mastitis.

Bovine mastitis, mainly caused by contagious pathogens like , , and , environmental pathogens such as , , , and a more opportunistic pathogen like , severely threatens dairy production. These mastitis pathogens rely on their respective virulence characteristics to exert different inflammation of the mammary gland. Meanwhile, antimicrobials remain the primary treatment for bovine mastitis, but growing resistance often causes failure. Therapeutic approaches targeting the virulence factors utilized by these mastitis-causing pathogens are expected to become effective alternatives to antimicrobial therapy in dairy farming. Therefore, the objective of this review is to investigate the prevalence and pathogenic roles of virulence genes in mastitis pathogens, with an extensive exploration of the emerging vaccination approaches targeting the virulence factors for safeguarding dairy animal health.

ArticleTotal : 2	Year
Publication title Cited by 60	2018
Publication title	2026

Article	Year
Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Frontiers in bioengineering and biotechnology\| PubMed ID: 26528471	2015
Application of Black Silicon for Nanostructure-Initiator Mass Spectrometry. Analytical chemistry\| PubMed ID: 26741735	2016
On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening. Lab on a chip\| PubMed ID: 27957569	2017
Assessment of chronic renal injury from melamine-associated pediatric urolithiasis: an eighteen-month prospective cohort study. Annals of Saudi medicine\| PubMed ID: 27478910	2016
Regional difference in the susceptibility of non-alcoholic fatty liver disease in China. BMJ open diabetes research & care\| PubMed ID: 32522731	2020
Comparative Genomic Analysis of Isolated From Bovine Mastitis in China. Frontiers in microbiology\| PubMed ID: 34745056	2021
Protocol for a Pragmatic Trial of Pharmacotherapy Options Following Unsatisfactory Initial Treatment in OCD (PROCEED). Frontiers in psychiatry\| PubMed ID: 35651818	2022
inhibits autophagy in bovine mammary epithelial cells a PTEN/PI3K-Akt-mTOR-dependent pathway. Frontiers in microbiology\| PubMed ID: 35958147	2022
Comparison of the Effects of Open Surgery and Minimally Invasive Surgery on the Achilles Tendon Rupture Healing Based on Angiogenesis. Computational intelligence and neuroscience\| PubMed ID: 36093506	2022
Genetic Architecture of Childhood Kidney and Urological Diseases in China. Phenomics (Cham, Switzerland)\| PubMed ID: 36939782	2021
Association between fast eating speed and metabolic dysfunction-associated steatotic liver disease: a multicenter cross-sectional study and meta-analysis. Nutrition & diabetes\| PubMed ID: 39143072	2024
The role of irregular eating behaviors in metabolic dysfunction-associated steatotic liver disease: evidence from a multicenter cross-sectional study in China. Journal of translational medicine\| PubMed ID: 40753232	2025
Modified Huangqi Shengmai Yin enhances ruminal microbiome and metabolites activity in dairy cows with subclinical mastitis. Frontiers in veterinary science\| PubMed ID: 40860916	2025
Virulence factors of bovine mastitis pathogens: distribution, pathogenesis, and emerging vaccines targeting virulence factors: a literature review. Frontiers in veterinary science\| PubMed ID: 41684720	2025

Jian Gao

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