Biomedical subjects

Mark Stevens

Publications and source records attributed to Mark Stevens.

5 recordsLinked to original sources

PubMed2025

The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.

Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.

Rumen↗

PubMed2006

Production of a full-length infectious GFP-tagged cDNA clone of Beet mild yellowing virus for the study of plant-polerovirus interactions.

The full-length cDNA of Beet mild yellowing virus (Broom's Barn isolate) was sequenced and cloned into the vector pLitmus 29 (pBMYV-BBfl). The sequence of BMYV-BBfl (5721 bases) shared 96% and 98% nucleotide identity with the other complete sequences of BMYV (BMYV-2ITB, France and BMYV-IPP, Germany respectively). Full-length capped RNA transcripts of pBMYV-BBfl were synthesised and found to be biologically active in Arabidopsis thaliana protoplasts following electroporation or PEG inoculation when the protoplasts were subsequently analysed using serological and molecular methods. The BMYV sequence was modified by inserting DNA that encoded the jellyfish green fluorescent protein (GFP) into the P5 gene close to its 3' end. A. thaliana protoplasts electroporated with these RNA transcripts were biologically active and up to 2% of transfected protoplasts showed GFP-specific fluorescence. The exploitation of these cDNA clones for the study of the biology of beet poleroviruses is discussed.

Beta vulgaris↗

PubMed2006

Is the number of documented diabetes process-of-care indicators associated with cardiometabolic risk factor levels, patient satisfaction, or self-rated quality of diabetes care? The Translating Research into Action for Diabetes (TRIAD) study.

OBJECTIVE: Simple process-of-care indicators are commonly recommended to assess and compare quality of diabetes care across health plans. We sought to determine whether variation in the number of simple diabetes processes of care across provider groups is associated with variation in other quality indicators, including cardiometabolic risk factor levels, patient satisfaction with care, or patient-rated quality of care. RESEARCH DESIGN AND METHODS: We used cross-sectional survey and chart audit data for 8,733 patients with diabetes who received care from 68 provider groups nested in 10 health plans that participated in the Translating Research Into Action for Diabetes study. Analyses using hierarchical regression models assessed associations of the mean number of seven simple process measures with each of the following: HbA(1c) (A1C), systolic blood pressure (SBP), HDL and LDL cholesterol levels, patient satisfaction with care, and patient-rated quality of care. RESULTS: After adjusting for case-mix differences across groups and plans, an average of one additional documented process of care for each patient in a group or plan was associated with significantly lower mean LDL cholesterol levels (-4.51 mg/dl [95% CI 1.46-7.58]) but not with A1C, SBP, or HDL cholesterol levels. The number of care processes documented was associated with patient satisfaction measures and self-rated quality of diabetes care. CONCLUSIONS: Variation in the number of simple process-of-care indicators across provider groups or health plans is associated with differences in patient-centered measures of quality, but assessment of the quality of cardiometabolic risk factor control will require more advanced clinical performance indicators.

Aged↗

PubMed2005

Analysis of host response to bacterial infection using error model based gene expression microarray experiments.

A key step in the analysis of microarray data is the selection of genes that are differentially expressed. Ideally, such experiments should be properly replicated in order to infer both technical and biological variability, and the data should be subjected to rigorous hypothesis tests to identify the differentially expressed genes. However, in microarray experiments involving the analysis of very large numbers of biological samples, replication is not always practical. Therefore, there is a need for a method to select differentially expressed genes in a rational way from insufficiently replicated data. In this paper, we describe a simple method that uses bootstrapping to generate an error model from a replicated pilot study that can be used to identify differentially expressed genes in subsequent large-scale studies on the same platform, but in which there may be no replicated arrays. The method builds a stratified error model that includes array-to-array variability, feature-to-feature variability and the dependence of error on signal intensity. We apply this model to the characterization of the host response in a model of bacterial infection of human intestinal epithelial cells. We demonstrate the effectiveness of error model based microarray experiments and propose this as a general strategy for a microarray-based screening of large collections of biological samples.

Bacterial Infections↗

PubMed2004

Rapid review of liquid-based smears as a quality control measure.

The objective of this study was to investigate the effectiveness of a standardized method of rapid review (RR) of monolayer preparations for the identification of abnormalities, the presence of an endocervical component and infectious agents. A total of 200 ThinPrep (Cytyc, Boxborough, MA) slides representing the spectrum of abnormalities commonly encountered in cervical/vaginal cytologic specimens was retrieved from archive. The study set comprised 129 cases within normal limits (WNL); 36 low-grade epithelial abnormalities (LGEA); 28 high-grade epithelial abnormalities (HGEA), including 2 endocervical adenocarcinomas in situ (AIS) and 7 carcinomas. Eighteen false negative (FN) cases were also included for study. Originally missed on initial review, these cases were found to be abnormal on quality control review (17 LGEA; 1 AIS). Commonly encountered infectious agents were represented and included Candida albicans, Trichomonas vaginalis, herpes simplex virus, and Actinomyces. The slides were reviewed using a standardized method of RR (turret technique, for 60 sec) by three experienced screeners masked to the original reference diagnosis. Median sensitivity for LGEA was 70% (range, 67-72%); HGEA, 69% (range, 54-80%); and FN, 65% (range, 56-78%). Specificity remained high, median specificity for LGEA was 95%; HGEA, 97%; and FN, 100%. There was no significant overcalling of any diagnostic category. The chi-square test at P < 0.05 showed no significant difference between RR and full manual rescreen of the ThinPrep smears in this study. While no statistical difference was proven, the sensitivity measurements for all categories of abnormality were moderate due to the high proportion of atypical cases included into the study set. Abnormalities on the monolayer preparations frequently displayed fewer, smaller groups of disaggregated cells with rounded cytoplasmic outlines that were difficult to discern on RR. Interobserver variation was noted. Monolayers with a paucity of diagnostic cells and those displaying subtle nuclear atypia were often overlooked.

False Negative Reactions↗