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  1. Article: Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing

    Carter, Michelle Qiu / Laniohan, Nicole / Lo, Chien-Chi / Chain, Patrick S G

    Microorganisms

    2022  Volume 10, Issue 5

    Abstract: Shiga toxin- ... ...

    Abstract Shiga toxin-producing
    Language English
    Publishing date 2022-04-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10050866
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  2. Article ; Online: Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

    Michelle Qiu Carter / Nicole Laniohan / Chien-Chi Lo / Patrick S. G. Chain

    Microorganisms, Vol 10, Iss 866, p

    2022  Volume 866

    Abstract: Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to ... ...

    Abstract Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.
    Keywords Shiga toxin-producing Escherichia coli (STEC) ; pangenome ; pathogenicity islands ; virulence genes ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Genomic and Phenotypic Characterization of Shiga Toxin-Producing

    Carter, Michelle Qiu / Quiñones, Beatriz / He, Xiaohua / Pham, Antares / Carychao, Diana / Cooley, Michael B / Lo, Chien-Chi / Chain, Patrick S G / Lindsey, Rebecca L / Bono, James L

    Microorganisms

    2023  Volume 11, Issue 11

    Abstract: Escherichia ... ...

    Abstract Escherichia albertii
    Language English
    Publishing date 2023-11-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11112803
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  4. Article: Advances and Challenges in Metatranscriptomic Analysis.

    Shakya, Migun / Lo, Chien-Chi / Chain, Patrick S G

    Frontiers in genetics

    2019  Volume 10, Page(s) 904

    Abstract: Sequencing-based analyses of microbiomes have traditionally focused on addressing the question of community membership and profiling taxonomic abundance through amplicon sequencing of 16 rRNA genes. More recently, shotgun metagenomics, which involves the ...

    Abstract Sequencing-based analyses of microbiomes have traditionally focused on addressing the question of community membership and profiling taxonomic abundance through amplicon sequencing of 16 rRNA genes. More recently, shotgun metagenomics, which involves the random sequencing of all genomic content of a microbiome, has dominated this arena due to advancements in sequencing technology throughput and capability to profile genes as well as microbiome membership. While these methods have revealed a great number of insights into a wide variety of microbiomes, both of these approaches only describe the presence of organisms or genes, and not whether they are active members of the microbiome. To obtain deeper insights into how a microbial community responds over time to their changing environmental conditions, microbiome scientists are beginning to employ large-scale metatranscriptomics approaches. Here, we present a comprehensive review on computational metatranscriptomics approaches to study microbial community transcriptomes. We review the major advancements in this burgeoning field, compare strengths and weaknesses to other microbiome analysis methods, list available tools and workflows, and describe use cases and limitations of this method. We envision that this field will continue to grow exponentially, as will the scope of projects (e.g. longitudinal studies of community transcriptional responses to perturbations over time) and the resulting data. This review will provide a list of options for computational analysis of these data and will highlight areas in need of development.
    Language English
    Publishing date 2019-09-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2019.00904
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  5. Article ; Online: Relationship Between Change in Participation and Later Mental Health Problems in Children.

    Lo, Oi Ying Heidi / Wong, Yi Man / Kwok, Nga Ting / Ma, Pui-Sze / Chien, Chi-Wen

    OTJR : occupation, participation and health

    2024  , Page(s) 15394492231216663

    Abstract: Background: Participation in everyday activities is beneficial for mental health. However, little is known about the extent to which changes in children's participation are associated with later mental health.: Objectives: To investigate the ... ...

    Abstract Background: Participation in everyday activities is beneficial for mental health. However, little is known about the extent to which changes in children's participation are associated with later mental health.
    Objectives: To investigate the association between changes in the frequency and involvement in home, school, and community activities and subsequent mental health problems in children.
    Results: After controlling for demographic factors, hierarchical regression analysis revealed that reductions in children's involvement in home and community activities were significantly associated with elevated levels of externalizing and internalizing problems. Furthermore, an increase in children's involvement in school activities showed significant relationships with better mental health outcomes.
    Conclusion: These findings inform participation-based interventions for occupational therapists aimed at mitigating children's future mental health problems.
    Language English
    Publishing date 2024-01-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2081243-7
    ISSN 1938-2383 ; 1539-4492 ; 0276-1599
    ISSN (online) 1938-2383
    ISSN 1539-4492 ; 0276-1599
    DOI 10.1177/15394492231216663
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  6. Article ; Online: Comparison between one-jaw and two-jaw designs in virtual surgery planning for patients with class III malocclusion.

    Hattori, Yoshitsugu / Pai, Betty Chien-Jung / Lo, Chi-Chin / Chou, Pang-Yun / Lo, Lun-Jou

    Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery

    2024  

    Abstract: Orthognathic surgery is highly effective for treating maxillomandibular discrepancies in patients with class III malocclusion. However, whether one- or two-jaw surgery should be selected remains controversial. Our study aimed to evaluate quantitative ... ...

    Abstract Orthognathic surgery is highly effective for treating maxillomandibular discrepancies in patients with class III malocclusion. However, whether one- or two-jaw surgery should be selected remains controversial. Our study aimed to evaluate quantitative differences between one-jaw and two-jaw surgical designs. In total, 100 consecutive patients with skeletal class III malocclusion who underwent orthognathic surgery with preoperative three-dimensional simulation between August 2016 and November 2021 were recruited. Based on the same final occlusal setup, a two-jaw surgery design and two types of one-jaw design were created. In total, 400 image sets, including preoperative images and three types of surgical simulation, were measured and compared. The one-jaw mandibular setback design led to improvement in most cephalometric measurements and facial symmetry. Although the one-jaw maxillary advancement design improved the ANB angle and facial convexity, it induced maxillary protrusion and reduced facial symmetry. Compared with the other designs, the two-jaw design provided significantly closer cephalometric measurements to the normative values, better symmetry, and less occlusal cant. Overall, the two-jaw design provided a quantitatively better facial appearance in terms of symmetry, proportion, and profile. Although an optimal surgical design necessitates thorough preoperative evaluation and a shared decision-making process, two-jaw surgery can be considered for improving overall facial esthetics and harmony.
    Language English
    Publishing date 2024-02-16
    Publishing country Scotland
    Document type Journal Article
    ZDB-ID 91267-0
    ISSN 1878-4119 ; 1010-5182 ; 0301-0503
    ISSN (online) 1878-4119
    ISSN 1010-5182 ; 0301-0503
    DOI 10.1016/j.jcms.2024.02.023
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 882: Show issues Location:
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  7. Article ; Online: The Gut Microbiome and Alcoholic Liver Disease

    Erick S. LeBrun / Meghali Nighot / Viszwapriya Dharmaprakash / Anand Kumar / Chien-Chi Lo / Patrick S. G. Chain / Thomas Y. Ma

    Life, Vol 11, Iss 7, p

    Ethanol Consumption Drives Consistent and Reproducible Alteration in Gut Microbiota in Mice

    2021  Volume 7

    Abstract: Phenotypic health effects, both positive and negative, have been well studied in association with the consumption of alcohol in humans as well as several other mammals including mice. Many studies have also associated these same health effects and ... ...

    Abstract Phenotypic health effects, both positive and negative, have been well studied in association with the consumption of alcohol in humans as well as several other mammals including mice. Many studies have also associated these same health effects and phenotypes to specific members of gut microbiome communities. Here we utilized a chronic plus binge ethanol feed model (Gao-binge model) to explore microbiome community changes across three independent experiments performed in mice. We found significant and reproducible differences in microbiome community assemblies between ethanol-treated mice and control mice on the same diet absent of ethanol. We also identified significant differences in gut microbiota occurring temporally with ethanol treatment. Peak shift in communities was observed 4 days after the start of daily alcohol consumption. We quantitatively identified many of the bacterial genera indicative of these ethanol-induced shifts including 20 significant genera when comparing ethanol treatments with controls and 14 significant genera based on temporal investigation. Including overlap of treatment with temporal shifts, we identified 25 specific genera of interest in ethanol treatment microbiome shifts. Shifts coincide with observed presentation of fatty deposits in the liver tissue, i.e., Alcoholic Liver Disease-associated phenotype. The evidence presented herein, derived from three independent experiments, points to the existence of a common, reproducible, and characterizable “mouse ethanol gut microbiome”.
    Keywords gut microbiome ; microbial ecology ; indicator species ; bacterial communities ; mouse model ; alcohol effects ; Science ; Q
    Subject code 590
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California

    Carter, Michelle Qiu / Quiñones, Beatriz / He, Xiaohua / Pham, Antares / Carychao, Diana / Cooley, Michael B. / Lo, Chien-Chi / Chain, Patrick S. G. / Lindsey, Rebecca L. / Bono, James L.

    Microorganisms. 2023 Nov. 18, v. 11, no. 11 p.2803-

    2023  

    Abstract: Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains ...

    Abstract Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains isolated from wild birds in a major agricultural region in California. Shiga toxin genes stx2f were present in all avian strains. Pangenome analyses of 20 complete genomes revealed a total of 11,249 genes, of which nearly 80% were accessory genes. Both core gene-based phylogenetic and accessory gene-based relatedness analyses consistently grouped the three stx2f-positive clinical strains with the five avian strains carrying ST7971. Among the three Stx2f-converting prophage integration sites identified, ssrA was the most common one. Besides the locus of enterocyte effacement
    Keywords Escherichia albertii ; Shiga toxin ; birds ; food pathogens ; genomics ; loci ; lysogeny ; pathogenesis ; pathogenicity ; pathogenicity islands ; phenotype ; phylogeny ; risk ; type III secretion system ; California
    Language English
    Dates of publication 2023-1118
    Publishing place MDPI AG
    Document type Article ; Online
    Note Resource is Open Access
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11112803
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: A suggested mortality benefit with integrated health care versus conventional home health care in Taiwan.

    Ho, Shao-Chang / Hsieh, Chi-Jeng / Lo, Lun-Chien / Lin, Jaung-Geng

    Home health care services quarterly

    2023  Volume 43, Issue 1, Page(s) 1–17

    Abstract: In Taiwan, the Integrated Home Care (IHC) project was introduced for medically compromised patients living at home receiving Home Health Care (HHC) in 2016. The focus of the project was on organizing care teams and managing care for patients. The aim of ... ...

    Abstract In Taiwan, the Integrated Home Care (IHC) project was introduced for medically compromised patients living at home receiving Home Health Care (HHC) in 2016. The focus of the project was on organizing care teams and managing care for patients. The aim of this study was to investigate the benefits and impacts of IHC in Taiwan. The primary outcome measure was the mortality rate of patients who received IHC versus those who did not receive IHC (non-IHC). The secondary outcomes were medical utilization and expenditure. The results showed that IHC was associated with a statistically significant reduction in mortality compared to non-IHC for home-dwelling patients over 90-, 180-, and 365-days periods. Additionally, IHC users were less likely to be hospitalized and had shorter hospitalization times compared to non-IHC users. Furthermore, IHC was found to reduce medical expenditure compared to non-IHC.
    MeSH term(s) Humans ; Taiwan ; Hospitalization ; Home Care Services ; Delivery of Health Care ; Health Expenditures
    Language English
    Publishing date 2023-04-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 604604-6
    ISSN 1545-0856 ; 0162-1424
    ISSN (online) 1545-0856
    ISSN 0162-1424
    DOI 10.1080/01621424.2023.2195810
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    Zs.B 2455: Show issues Location:
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  10. Article ; Online: Precise Genomic Riboregulator Control of Metabolic Flux in Microbial Systems.

    Pandey, Naresh / Davison, Steffi A / Krishnamurthy, Malathy / Trettel, Daniel S / Lo, Chien-Chi / Starkenburg, Shawn / Wozniak, Katherine L / Kern, Theresa L / Reardon, Sean D / Unkefer, Clifford J / Hennelly, Scott P / Dale, Taraka

    ACS synthetic biology

    2022  Volume 11, Issue 10, Page(s) 3216–3227

    Abstract: Engineered microbes can be used for producing value-added chemicals from renewable feedstocks, relieving the dependency on nonrenewable resources such as petroleum. These microbes often are composed of synthetic metabolic pathways; however, one major ... ...

    Abstract Engineered microbes can be used for producing value-added chemicals from renewable feedstocks, relieving the dependency on nonrenewable resources such as petroleum. These microbes often are composed of synthetic metabolic pathways; however, one major problem in establishing a synthetic pathway is the challenge of precisely controlling competing metabolic routes, some of which could be crucial for fitness and survival. While traditional gene deletion and/or coarse overexpression approaches do not provide precise regulation,
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli/metabolism ; Phosphoenolpyruvate/metabolism ; Pseudomonas putida/genetics ; Pseudomonas putida/metabolism ; Metabolic Engineering ; Pyruvic Acid/metabolism ; Genomics ; RNA/metabolism ; Petroleum/metabolism
    Chemical Substances Phosphoenolpyruvate (73-89-2) ; Pyruvic Acid (8558G7RUTR) ; RNA (63231-63-0) ; Petroleum
    Language English
    Publishing date 2022-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.1c00638
    Database MEDical Literature Analysis and Retrieval System OnLINE

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