Hasil untuk "Microbiology"

D. Sylvia

T. Mino, M. Loosdrecht, J. Heijnen

D. Persing

C. Owens, K. Stoessel

K.R.Aneja

Kalpana Gupta, Thomas M. Hooton, K. G. Naber et al.

G. Pahlow, R. Muck, F. Driehuis et al.

C. Köser, M. Ellington, E. Cartwright et al.

Whole genome sequencing (WGS) promises to be transformative for the practice of clinical microbiology, and the rapidly falling cost and turnaround time mean that this will become a viable technology in diagnostic and reference laboratories in the near future. The objective of this article is to consider at a very practical level where, in the context of a modern diagnostic microbiology laboratory, WGS might be cost-effective compared to current alternatives. We propose that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS, and discuss the technical and infrastructure requirements for this to be implemented.

Arturo Tozzi

Biofilms in human tonsillar crypts show long term persistence with episodic dispersal that current biochemical and microbiological descriptions do not fully explain, particularly with respect to spatial localization. We introduce a biophysical framework in which tonsillar biofilm dynamics arise from the interaction between two mechanical phenomena: a Kosterlitz Thouless type defect nucleation process and a Kelvin Helmholtz type shear driven interfacial instability. Crypt geometry is modeled as a confined, heterogeneous environment that promotes mechanically persistent surface defects generated by growth induced compression. Tangential shear associated with breathing and swallowing selectively amplifies these defects, producing organized surface deformations. Numerical simulations show that only the coexistence of both mechanisms yields localized, propagating, and persistent interface structures, whereas their absence leads to diffuse, unstructured dynamics.

B. Henriques‐Normark, E. Tuomanen

B. Wilson, M. Ho

Jan Albrecht, Lara S. Dautzenberg, Manfred Opper et al.

Variability of motility behavior in populations of microbiological agents is a ubiquitous phenomenon even in the case of genetically identical cells. Accordingly, passive objects introduced into such biological systems and driven by them will also exhibit heterogeneous motion patterns. Here, we study a biohybrid system of passive beads driven by active ameboid cells and use a likelihood approach to estimate the heterogeneity of the bead dynamics from their discretely sampled trajectories. We showcase how this approach can deal with information-scarce situations and provides natural uncertainty bounds for heterogeneity estimates. Using these advantages we particularly uncover that the heterogeneity in the system is time-dependent.

Laura Gough, Rommel Miranda, Matthew Hemm et al.

ABSTRACT The Diffusion of Innovations (DOI) model can be used to explore how faculty prioritize learning about and adopting new pedagogical approaches. Here, we use the DOI framework to contextualize biology faculty perceptions of a professional development (PD) program designed to help them create a full semester course-based undergraduate research experience (CURE) class at a large, public comprehensive university. PD sessions included exploring self-reflexive identity while fostering inclusive classroom spaces through understanding and interrupting implicit bias and microaggressions. This qualitative study sought to determine 11 biology faculty members’ beliefs about the influence of their year-long PD on their CURE development and teaching practices. Findings suggest that faculty were motivated to teach CUREs for a variety of reasons. A common incentive was integrating research into a CURE to bring their passion into their classroom and to engage more students in research. This may be particularly important at institutions where faculty have a heavy teaching load. Faculty also reported modifying their teaching in their CUREs and other courses to be more inclusive and equitable. The importance of peer interactions in the PD was emphasized repeatedly as faculty learned from experts, the literature, and faculty who had already developed a CURE. Our results illustrate that a community of practice structure can enhance the learning aspect of the community, helping faculty consider their implementation of inclusive, equitable, and high-impact practices as an ongoing educational process for themselves and emphasizing the importance of reflection and iteration in a DOI framework.

Jana K. Dickter, Yuqi Zhao, Vishwas Parekh et al.

ABSTRACT We investigated the presence of viral DNA and RNA in cutaneous squamous cell carcinoma (cSCC) tumor and normal tissues from nine individuals with a history of hematopoietic stem cell transplantation (HCT). Microbiome quantification through DNA and RNA sequencing (RNA-seq) revealed the presence of 18 viruses in both tumor and normal tissues. DNA sequencing (DNA-seq) identified Torque teno virus, Saimiriine herpesvirus 1, Merkel cell polyomavirus, Human parvovirus B19, Human gammaherpesvirus-4, Human herpesvirus-6, and others. RNA-seq revealed additional viruses such as Tobamovirus, Pinus nigra virus, Orthohepadnavirus, Human papillomavirus-5, Human herpesvirus-7, Human gammaherpesvirus-4, Gammaretrovirus, and others. Notably, DNA-seq indicated that tumor samples exhibited low levels of Escherichia virus in three out of nine subjects and elevated levels of Human gammaherpesvirus-4 in one subject, while normal samples frequently contained Gammaretrovirus and occasionally Escherichia virus. A comparative analysis using both DNA- and RNA-seq captured three common viruses: Abelson murine leukemia virus, Murine type C retrovirus, and Human gammaherpesvirus-4. These findings were corroborated by an independent data set, supporting the reliability of the viral detection methods utilized. The study provides insights into the viral landscape in post-HCT patients, emphasizing the need for comprehensive viral monitoring in this vulnerable population.IMPORTANCEThis study is important because it explores the potential role of viruses in the development of cSCC in individuals who have undergone allogeneic HCT. cSCC is common in this population, particularly in those with chronic graft-versus-host disease on long-term immunosuppression. By using advanced metagenomic and metatranscriptomic next-generation sequencing, we aimed to identify viral pathogens present in tumor and adjacent normal tissue. The results could lead to targeted preventive or therapeutic interventions for these high-risk people, potentially improving their outcomes and management of cSCC.

Saritha Kodikara, Kim-Anh Lê Cao

Abstract Background The microbiome is a complex ecosystem of interdependent taxa that has traditionally been studied through cross-sectional studies. However, longitudinal microbiome studies are becoming increasingly popular. These studies enable researchers to infer taxa associations towards the understanding of coexistence, competition, and collaboration between microbes across time. Traditional metrics for association analysis, such as correlation, are limited due to the data characteristics of microbiome data (sparse, compositional, multivariate). Several network inference methods have been proposed, but have been largely unexplored in a longitudinal setting. Results We introduce LUPINE (LongitUdinal modelling with Partial least squares regression for NEtwork inference), a novel approach that leverages on conditional independence and low-dimensional data representation. This method is specifically designed to handle scenarios with small sample sizes and small number of time points. LUPINE is the first method of its kind to infer microbial networks across time, while considering information from all past time points and is thus able to capture dynamic microbial interactions that evolve over time. We validate LUPINE and its variant, LUPINE_single (for single time point analysis) in simulated data and four case studies, where we highlight LUPINE’s ability to identify relevant taxa in each study context, across different experimental designs (mouse and human studies, with or without interventions, and short or long time courses). To detect changes in the networks across time and groups or in response to external disturbances, we used different metrics to compare the inferred networks. Conclusions LUPINE is a simple yet innovative network inference methodology that is suitable for, but not limited to, analysing longitudinal microbiome data. The R code and data are publicly available for readers interested in applying these new methods to their studies. Video Abstract

Dandan Zhu, Guo Chen, Guo Chen et al.

IntroductionSchistosomiasis japonica, a zoonotic parasitic disease, induces complex immune regulation during infection. The inflammatory responses and immunosuppressive mechanisms co-exist to maintain immune homeostasis in schistosomiasis. B7-H4 is a critical immune checkpoint molecule that modulates T cell activation and exerts immunosuppressive effects. Our previous investigations revealed that B7-H4 mRNA expression was elevated in mice infected with Schistosoma japonicum, with interleukin-10 (IL-10) demonstrating regulatory capacity to enhance B7-H4 expression in RAW264.7 macrophages. In this study, we further explore the mechanism underlying IL-10-mediated B7-H4 upregulation.MethodsWestern blot was performed to detect B7-H4 expression levels, both in mice infected with Schistosoma japonicum and in RAW264.7 cells stimulated with IL-10. RT-qPCR was performed to screen microRNAs (miR-140 et al.) in RAW264.7 cells stimulated with IL-10. Then dual-luciferase reporter assay was performed to confirm that miR-140 can directly bind to the 3’UTR of B7-H4. miR-140 promoter activity in RAW264.7 cells was also detected via dual-luciferase reporter assays. In addition, ChIP was performed to confirm the binding of transcription factors and miR-140 promoter.ResultsNotably, miR-140 was decreased in IL-10-treated microphages, accompanied by B7-H4 expression was upregulated. miR-140 can directly bind to the 3’UTR of B7-H4 and then inhibit the expression of B7-H4 in RAW264.7 cells. Meanwhile, miR-140 mimics can also attenuate IL-10-induced B7-H4 expression in RAW264.7 cells. Then we found that IL-10 may inhibit miR-140 promoter activity in RAW264.7 cells through transcription factors that binding to the - 576/- 94 bp region of the miR-140 promoter. Results by Western blot and ChIP further indicated that IL-10 could downregulate miR-140 promoter activity in a STAT5 dependence manner. After the sequence of STAT5 binding site within the - 456/- 446 bp region of the miR-140 promoter was mutated, IL-10 failed to suppress the activity produced by mutant miR-140 promoter.DiscussionIn summary, IL-10 can inhibit miR-140 through STAT5, thereby upregulating the expression of B7-H4 in RAW264.7 cells. This study may suggest a new mechanism underlying IL-10-mediated B7-H4 upregulation in macrophages.

Amal Jayawardena, Andrew Hung, Greg Qiao et al.

Multidrug resistance (MDR) to conventional antibiotics is one of the most urgent global health threats, necessitating the development of effective and biocompatible antimicrobial agents that are less inclined to provoke resistance. Structurally Nanoengineered Antimicrobial Peptide Polymers (SNAPPs) are a novel and promising class of such alternatives. These star-shaped polymers are made of a dendritic core with multiple arms made of co-peptides with varying amino acid sequences. Through a comprehensive set of in vivo experiments, we (Nature Microbiology, 1, 16162, 2016) showed that SNAPPs with arms made of random blocks of lysine (K) and valine (V) residues exhibit sub-micron M efficacy against Gram-negative and Gram-positive bacteria tested. Cryo-TEM images suggested pore formation by SNAPP with random block co-peptide arms as one of their mode of actions. However, the molecular mechanisms responsible for this mode of action of SNAPP were not fully understood. To address this gap, we employed atomistic molecular dynamics simulation technique to investigate the influence of three different sequences of amino acids, namely 1) alternating block KKV 2) random block and 3) di-block motifs on secondary structure of their arms and SNAPP's overall configuration as well as their interactions with lipid bilayer. We, for the first time identified a step-by-step mechanism through which alternating block and random SNAPPs interact with lipid bilayer and leads to pore formation, hence cell death. These insights provide a strong foundation for further optimization of the chemical structure of SNAPPs for maximum performance against MDR bacteria, therefore offering a promising avenue for addressing antibiotic resistance and development of effective antibacterial agents.

Jens‐Peter Barnekow Lillesø, Davide Barsotti, James Kalema et al.

Abstract Forest and landscape restoration are increasingly popular nature‐based solutions to mitigate climate change and safeguard biodiversity. Restoration planning and monitoring implies that a reference ecosystem has been defined to which the restored site can be compared, but how to best select such reference? We tested three different potential natural vegetation (PNV) maps of the same areas in Kenya and Uganda for their utility as ecological references with independent data that were not used when those maps were made. These independent datasets included presence observations of woody species from 76 sites in forest reserves in Kenya and Uganda, and classification of surveyed species into a system that included “forest‐only” and “nonforest‐only” ecological types. Our tests show that (1) the three vegetation maps largely agree on the environmental envelopes/ranges within which forests occur. (2) There are large differences in how well the maps predict the presence of forest‐only species. (3) Two maps, based on empirical observations (V4A and White), predict forest types well, whereas the third, based on climate envelopes only (NS), performs poorly. (4) A large area in Uganda is potentially in one of two alternative stable states. We conclude that it is possible to evaluate the utility of PNV maps at a more detailed scale than the level of biome and ecoregion. This indicates that it is possible to map PNV at scales required for reference for restoration and management of forest vegetation. We recommend that empirically based maps of potential natural vegetation are used in restoration planning (biome and PNV maps based on climate envelopes alone may be unreliable tools) as a baseline model for predicting the distribution of reference ecosystems under current and future conditions. It could conveniently be done by deconstructing the existing biome maps, supported by rapid botanical surveys.