Genomic Characterization of Dairy Associated Leuconostoc Species and Diversity of Leuconostocs in Undefined Mixed Mesophilic Starter Cultures

Undefined mesophilic mixed (DL-type) starter cultures are composed of predominantly Lactococcus lactis subspecies and 1–10% Leuconostoc spp. The composition of the Leuconostoc population in the starter culture ultimately affects the characteristics and the quality of the final product. The scientific basis for the taxonomy of dairy relevant leuconostocs can be traced back 50 years, and no documentation on the genomic diversity of leuconostocs in starter cultures exists. We present data on the Leuconostoc population in five DL-type starter cultures commonly used by the dairy industry. The analyses were performed using traditional cultivation methods, and further augmented by next-generation DNA sequencing methods. Bacterial counts for starter cultures cultivated on two different media, MRS and MPCA, revealed large differences in the relative abundance of leuconostocs. Most of the leuconostocs in two of the starter cultures were unable to grow on MRS, emphasizing the limitations of culture-based methods and the importance of careful media selection or use of culture independent methods. Pan-genomic analysis of 59 Leuconostoc genomes enabled differentiation into twelve robust lineages. The genomic analyses show that the dairy-associated leuconostocs are highly adapted to their environment, characterized by the acquisition of genotype traits, such as the ability to metabolize citrate. In particular, Leuconostoc mesenteroides subsp. cremoris display telltale signs of a degenerative evolution, likely resulting from a long period of growth in milk in association with lactococci. Great differences in the metabolic potential between Leuconostoc species and subspecies were revealed. Using targeted amplicon sequencing, the composition of the Leuconostoc population in the five commercial starter cultures was shown to be significantly different. Three of the cultures were dominated by Ln. mesenteroides subspecies cremoris. Leuconostoc pseudomesenteroides dominated in two of the cultures while Leuconostoc lactis, reported to be a major constituent in fermented dairy products, was only present in low amounts in one of the cultures. This is the first in-depth study of Leuconostoc genomics and diversity in dairy starter cultures. The results and the techniques presented may be of great value for the dairy industry

Peripheral blood cells inform on the presence of breast cancer: A population‐based case–control study

Tumor–host interactions extend beyond the local microenvironment and cancer development largely depends on the ability of malignant cells to hijack and exploit the normal physiological processes of the host. Here, we established that many genes within peripheral blood cells show differential expression when an untreated breast cancer (BC) is present, and harnessed this fact to construct a 50-gene signature that distinguish BC patients from population-based controls. Our results were derived from a series of large datasets within our unique population-based Norwegian Women and Cancer cohort that allowed us to investigate the influence of medications and tumor characteristics on our blood-based test, and were further tested in two external datasets. Our 50-gene signature contained cytostatic signals including the specific suppression of the immune response and medications influencing transcription involved in those processes were identified as confounders. Through analysis of the biological processes differentially expressed in blood, we were able to provide a rationale as to why the systemic response of the host may be a reliable marker of BC, characterized by the underexpression of both immune-specific pathways and “universal” cell programs driven by MYC (i.e., metabolism, growth and cell cycle). In conclusion, gene expression of peripheral blood cells is markedly perturbed by the specific presence of carcinoma in the breast and these changes simultaneously engage a number of systemic cytostatic signals emerging connections with immune escape of BC. WHAT'S NEW? Blood cells are dynamic warehouses of information. In the case of cancer, studies have indicated that blood cells house genetic signatures related to solid tumors. In the present study, genes in peripheral blood cells were found to be differentially expressed in women with untreated breast cancer, enabling the development of a 50-gene signature capable of identifying women with the disease. The gene signature included signals specific to immunosuppression. The association of breast cancer with the underexpression of immune-specific pathways and with MYC-driven “universal” cell programs may explain the systemic response of the host

Peripheral blood cells inform on the presence of breast cancer: A population‐based case–control study

Tumor–host interactions extend beyond the local microenvironment and cancer development largely depends on the ability of malignant cells to hijack and exploit the normal physiological processes of the host. Here, we established that many genes within peripheral blood cells show differential expression when an untreated breast cancer (BC) is present, and harnessed this fact to construct a 50-gene signature that distinguish BC patients from population-based controls. Our results were derived from a series of large datasets within our unique population-based Norwegian Women and Cancer cohort that allowed us to investigate the influence of medications and tumor characteristics on our blood-based test, and were further tested in two external datasets. Our 50-gene signature contained cytostatic signals including the specific suppression of the immune response and medications influencing transcription involved in those processes were identified as confounders. Through analysis of the biological processes differentially expressed in blood, we were able to provide a rationale as to why the systemic response of the host may be a reliable marker of BC, characterized by the underexpression of both immune-specific pathways and “universal” cell programs driven by MYC (i.e., metabolism, growth and cell cycle). In conclusion, gene expression of peripheral blood cells is markedly perturbed by the specific presence of carcinoma in the breast and these changes simultaneously engage a number of systemic cytostatic signals emerging connections with immune escape of BC

Peripheral blood cells inform on the presence of breast cancer: A population‐based case–control study

Tumor–host interactions extend beyond the local microenvironment and cancer development largely depends on the ability of malignant cells to hijack and exploit the normal physiological processes of the host. Here, we established that many genes within peripheral blood cells show differential expression when an untreated breast cancer (BC) is present, and harnessed this fact to construct a 50-gene signature that distinguish BC patients from population-based controls. Our results were derived from a series of large datasets within our unique population-based Norwegian Women and Cancer cohort that allowed us to investigate the influence of medications and tumor characteristics on our blood-based test, and were further tested in two external datasets. Our 50-gene signature contained cytostatic signals including the specific suppression of the immune response and medications influencing transcription involved in those processes were identified as confounders. Through analysis of the biological processes differentially expressed in blood, we were able to provide a rationale as to why the systemic response of the host may be a reliable marker of BC, characterized by the underexpression of both immune-specific pathways and “universal” cell programs driven by MYC (i.e., metabolism, growth and cell cycle). In conclusion, gene expression of peripheral blood cells is markedly perturbed by the specific presence of carcinoma in the breast and these changes simultaneously engage a number of systemic cytostatic signals emerging connections with immune escape of BC

Retrieval and re-evaluation of previously diagnosed chronic hepatitis C infections lost to medical follow-up in the Netherlands

ObjectivesMany individuals previously diagnosed with chronic hepatitis C virus (HCV) infection are likely to be lost to medical follow-up and, therefore, remain untreated despite new highly effective drug treatment, direct acting antivirals. We aim to identify and retrieve these chronic HCV-infected individuals to re-evaluate them and offer treatment.MethodsPossible chronic HCV infections were identified from test results of the medical microbiological laboratory, notifications to the public health service, and the hospital registries over the past 15 years were checked in South Limburg, the Netherlands. Individuals were contacted based on the physician-patient relationship of the gastroenterologist or microbiologist (retrieval). Individuals were informed about the new treatment options, offered an HCV-RNA test, and if still positive, referred to the gastroenterologist for treatment (re-evaluation).ResultsIn total, 689 individuals with a positive anti-HCV test in the past were identified, 308 (45%) were eligible for retrieval, 90 (29%) of them were retrieved, 34 (38%) of those retrieved were re-evaluated, 19 (56%) of those tested were HCV-RNA positive, and 12 (63%) of these individuals were offered treatment.ConclusionDuring every step of the retrieval chain, many patients were lost. Nevertheless, with substantial effort, we were able to identify, retrieve, and positively re-evaluate a limited number of individuals with a possible chronic HCV infection who were lost to medical follow-up (19 patients). With this case-finding approach, we were able to prevent potential severe complications in these patients and contribute to a small step in the eradication of HCV in the Netherlands.</p

Interactions between the tumor and the blood systemic response of breast cancer patients

<div><p>Although systemic immunity is critical to the process of tumor rejection, cancer research has largely focused on immune cells in the tumor microenvironment. To understand molecular changes in the patient systemic response (SR) to the presence of BC, we profiled RNA in blood and matched tumor from 173 patients. We designed a system (MIxT, Matched Interactions Across Tissues) to systematically explore and link molecular processes expressed in each tissue. MIxT confirmed that processes active in the patient SR are especially relevant to BC immunogenicity. The nature of interactions across tissues (i.e. which biological processes are associated and their patterns of expression) varies highly with tumor subtype. For example, aspects of the immune SR are underexpressed proportionally to the level of expression of defined molecular processes specific to basal tumors. The catalog of subtype-specific interactions across tissues from BC patients provides promising new ways to tackle or monitor the disease by exploiting the patient SR.</p></div

Bishops, priests and penance in late Saxon England

This article examines the textual and manuscript evidence for the practice of penance in late Saxon England. It also examines the significance for pastoral care of the linguistic evidence for specialized vernacular terms for penance: 'scrift' for 'confessor', 'dædbote' and compounds of 'hreow' for 'penance' and 'remorse'. The linguistic and textual evidence suggests that penance was a regular part of lay piety. The manuscript evidence, on the other hand, supports recent contentions that penitentials were used by bishops and should be linked to canon law. However, the manuscript evidence cannot be properly understood unless the scant survival rate of humble priestly handbooks is taken into account. Moreover, bishops in this period were deeply involved in furthering pastoral care and their interests and concerns should not be divorced from a pastoral and local context. In conclusion, the article will argue that penitential practices were firmly rooted in the Anglo-Saxon church's ministry for the laity

Gene co-expression networks, modules and associations with clinicopathological attributes of BC patients.

<p>(A) Network visualization using the edge-weighted spring embedded layout from Cytoscape (v3.2.1) including the top gene connections (topological overlap > 0.1) in tumor. Each node (gene) is color-coded by the module to which it belongs, Keywords representing top pathway enrichments (biological processes) are indicated for each module. (B) Network visualization including the top gene connections in the patient SR. The legend follows Fig 2A. (C) Associations between tumor modules and clinicopathological attributes of patients. Associations were estimated using Pearson correlation (Student’s p) or ANOVA. Shading is proportional to -log₁₀(fdr) of the associations (fdr <i>≤</i> 0.15). HER2S: HER2 score; LUMS: luminal score; MKS: Mitotic kinase gene expression score; hrt: hormone replacement therapy (D) Associations between SR modules and clinicopathological attributes of patients. The legend follows Fig 2C.</p

Individual characteristics and SR markers of BC subtypes.

<p>(A) Collection of biospecimen from BC patients and controls. (B) Individual characteristics of BC patients and controls. (C) Parallel plot displaying the repartition of BC patients across RNA-based subtyping schemes. (D) Sparse hierarchical clustering of BC patients based on genes expressed in tumor (upper) and the patient SR (lower). Clinicopathological and subtypes attributes are presented below the dendrogram. (E) Significant gene markers of subtypes in SR (false discovery rate, fdr <i>≤</i> 0.2). Blue and red shade correspond to under- and over- expression of the marker in a given subtype vs the others, respectively. Shading is proportional to the level of significance of the gene marker.</p

Subtype-Specific Matched Interactions across Tissue (ssMIxT).

<p>(A) Schematic of ssMIxT analysis (B) Significant associations between modules in SR and tumor from BC patients by subtype (MIxT statistic, p-value < 0.005). SR and tumor modules with top pathway enrichment keywords are presented in rows and columns, respectively. Subtype(s) in which the significant associations are found are indicated in the table. Blue and red borders correspond to negative and positive correlations between ranksums, respectively. Findings discussed in the text are highlighted in orange.</p