Human and animal diet reconstruction studies that rely on tissue chemical signatures aim at providing estimates on the relative intake of potential food groups. However, several sources of ...uncertainty need to be considered when handling data. Bayesian mixing models provide a natural platform to handle diverse sources of uncertainty while allowing the user to contribute with prior expert information. The Bayesian mixing model FRUITS (Food Reconstruction Using Isotopic Transferred Signals) was developed for use in diet reconstruction studies. FRUITS incorporates the capability to account for dietary routing, that is, the contribution of different food fractions (e.g. macronutrients) towards a dietary proxy signal measured in the consumer. FRUITS also provides relatively straightforward means for the introduction of prior information on the relative dietary contributions of food groups or food fractions. This type of prior may originate, for instance, from physiological or metabolic studies. FRUITS performance was tested using simulated data and data from a published controlled animal feeding experiment. The feeding experiment data was selected to exemplify the application of the novel capabilities incorporated into FRUITS but also to illustrate some of the aspects that need to be considered when handling data within diet reconstruction studies. FRUITS accurately predicted dietary intakes, and more precise estimates were obtained for dietary scenarios in which expert prior information was included. FRUITS represents a useful tool to achieve accurate and precise food intake estimates in diet reconstruction studies within different scientific fields (e.g. ecology, forensics, archaeology, and dietary physiology).
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
This study investigates to what extent Bronze Age societies in Northern Italy were permeable accepting and integrating non-local individuals, as well as importing a wide range of raw materials, ...commodities, and ideas from networks spanning continental Europe and the Mediterranean. During the second millennium BC, the communities of Northern Italy engaged in a progressive stabilization of settlements, culminating in the large polities of the end of the Middle/beginning of the Late Bronze Age pivoted around large defended centres (the Terramare). Although a wide range of exotic archaeological materials indicates that the inhabitants of the Po plain increasingly took part in the networks of Continental European and the Eastern Mediterranean, we should not overlook the fact that the dynamics of interaction were also extremely active on local and regional levels. Mobility patterns have been explored for three key-sites, spanning the Early to Late Bronze Age (1900-1100 BC), namely Sant'Eurosia, Casinalbo and Fondo Paviani, through strontium and oxygen isotope analysis on a large sample size (more than 100 individuals). The results, integrated with osteological and archaeological data, document for the first time in this area that movements of people occurred mostly within a territorial radius of 50 km, but also that larger nodes in the settlement system (such as Fondo Paviani) included individuals from more distant areas. This suggests that, from a demographic perspective, the process towards a more complex socio-political system in Bronze Age Northern Italy was triggered by a largely, but not completely, internal process, stemming from the dynamics of intra-polity networks and local/regional power relationships.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most numerous photosynthetic organisms on our planet 1, 2. With a global population size of 3.6 × 1027 3, they are ...responsible for approximately 10% of global primary production 3, 4. Viruses that infect Prochlorococcus and Synechococcus (cyanophages) can be readily isolated from ocean waters 5–7 and frequently outnumber their cyanobacterial hosts 8. Ultimately, cyanophage-induced lysis of infected cells results in the release of fixed carbon into the dissolved organic matter pool 9. What is less well known is the functioning of photosynthesis during the relatively long latent periods of many cyanophages 10, 11. Remarkably, the genomes of many cyanophage isolates contain genes involved in photosynthetic electron transport (PET) 12–18 as well as central carbon metabolism 14, 15, 19, 20, suggesting that cyanophages may play an active role in photosynthesis. However, cyanophage-encoded gene products are hypothesized to maintain or even supplement PET for energy generation while sacrificing wasteful CO2 fixation during infection 17, 18, 20. Yet this paradigm has not been rigorously tested. Here, we measured the ability of viral-infected Synechococcus cells to fix CO2 as well as maintain PET. We compared two cyanophage isolates that share different complements of PET and central carbon metabolism genes. We demonstrate cyanophage-dependent inhibition of CO2 fixation early in the infection cycle. In contrast, PET is maintained throughout infection. Our data suggest a generalized strategy among marine cyanophages to redirect photosynthesis to support phage development, which has important implications for estimates of global primary production.
•Viruses of abundant marine cyanobacteria shut down CO2 fixation during infection•The strength of the shutdown is dependent on the viral gene content•Viruses encoding genes that actively shut down CO2 fixation are less productive
Puxty et al. show that marine cyanobacterial viruses modify host photosynthesis to maximize energy production but inhibit CO2 fixation. These phototrophs are responsible for ∼10% of global CO2 fixation, and up to 60% of cells are infected at any time. Therefore, this phenomenon has implications for the assessment of primary production of the biosphere.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This research explores oral health indicators and stable carbon and nitrogen isotope data to explore diet, and differences in diet, between people buried in the four different contexts of the St ...Gertrude Church cemetery (15th- 17th centuries AD): the general cemetery, two mass graves, and a collective mass burial pit within the general cemetery. The main aim is to assess whether people buried in the mass graves were rural immigrants, or if they were more likely to be the victims of plague (or another epidemic) who lived in Riga and its suburbs. The data produced (from dental disease assessments and isotope analyses) were compared within, as well as between, the contexts. Most differences emerged when comparing the prevalence rates of dental diseases and other oral health indicators in males and females between the contexts, while isotope analysis revealed more individual, rather than context-specific, differences. The data suggested that the populations buried in the mass graves were different from those buried in the general cemetery, and support the theory that rural immigrants were buried in both mass graves. Significant differences were observed in some aspects of the data between the mass graves, however, possibly indicating that the people buried in them do not represent the same community.
Full text
Available for:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Breastfeeding is known to be a powerful mediator of maternal and childhood health, with impacts throughout the life course. Paleodietary studies of the past 30 years have accordingly taken an ...enduring interest in the health and diet of young children as a potential indicator of population fertility, subsistence, and mortality patterns. While progress has been made in recent decades toward acknowledging the agency of children, many paleodietary reconstructions have failed to incorporate developments in cognate disciplines revealing synergistic dynamics between maternal and offspring biology. Paleodietary interpretation has relied heavily on the “weanling's dilemma,” in which infants are thought to face a bleak choice between loss of immunity or malnutrition. Using a review of immunological and epidemiological evidence for the dynamic and supportive role that breastfeeding plays throughout the complementary feeding period, this article offers context and nuance for understanding past feeding transitions. We suggest that future interpretative frameworks for infant paleodietary and bioarchaeological research should include a broad knowledge base that keeps pace with relevant developments outside of those disciplines.
Full text
Available for:
BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The anaerobic gut pathogen, Clostridioides difficile, forms adherent biofilms that may play an important role in recurrent C. difficile infections. The mechanisms underlying C. difficile community ...formation and inter-bacterial interactions are nevertheless poorly understood. C. difficile produces AI-2, a quorum sensing molecule that modulates biofilm formation across many bacterial species. We found that a strain defective in LuxS, the enzyme that mediates AI-2 production, is defective in biofilm development in vitro. Transcriptomic analyses of biofilms formed by wild type (WT) and luxS mutant (luxS) strains revealed a downregulation of prophage loci in the luxS mutant biofilms compared to the WT. Detection of phages and eDNA within biofilms may suggest that DNA release by phage-mediated cell lysis contributes to C. difficile biofilm formation. In order to understand if LuxS mediates C. difficile crosstalk with other gut species, C. difficile interactions with a common gut bacterium, Bacteroides fragilis, were studied. We demonstrate that C. difficile growth is significantly reduced when co-cultured with B. fragilis in mixed biofilms. Interestingly, the absence of C. difficile LuxS alleviates the B. fragilis-mediated growth inhibition. Dual species RNA-sequencing analyses from single and mixed biofilms revealed differential modulation of distinct metabolic pathways for C. difficile WT, luxS and B. fragilis upon co-culture, indicating that AI-2 may be involved in induction of selective metabolic responses in B. fragilis. Overall, our data suggest that C. difficile LuxS/AI-2 utilises different mechanisms to mediate formation of single and mixed species communities.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of ...the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families
Podoviridae
,
Siphoviridae
, and
Myoviridae
as well as the order
Caudovirales
were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
Full text
Available for:
EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The Anderson phage typing scheme has been successfully used worldwide for epidemiological surveillance of Salmonella enterica serovar Typhimurium. Although the scheme is being replaced by whole ...genome sequence subtyping methods, it can provide a valuable model system for study of phage-host interaction. The phage typing scheme distinguishes more than 300 definitive types of Salmonella Typhimurium based on their patterns of lysis to a unique collection of 30 specific Salmonella phages. In this study, we sequenced the genomes of 28 Anderson typing phages of Salmonella Typhimurium to begin to characterize the genetic determinants that are responsible for the differences in these phage type profiles. Genomic analysis of typing phages reveals that Anderson phages can be classified into three different groups, the P22-like, ES18-like and SETP3-like clusters. Most Anderson phages are short tailed P22-like viruses (genus Lederbergvirus); but phages STMP8 and STMP18 are very closely related to the lambdoid long tailed phage ES18, and phages STMP12 and STMP13 are related to the long noncontractile tailed, virulent phage SETP3. Most of these typing phages have complex genome relationships, but interestingly, two phage pairs STMP5 and STMP16 as well as STMP12 and STMP13 differ by a single nucleotide. The former affects a P22-like protein involved in DNA passage through the periplasm during its injection, and the latter affects a gene whose function is unknown. Using the Anderson phage typing scheme would provide insights into phage biology and the development of phage therapy for the treatment of antibiotic resistant bacterial infections.
Full text
Available for:
IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Bacterioplankton plays an essential role in aquatic ecosystems, and cyanobacteria are an influential part of the microbiome in many water bodies. In freshwaters used for recreational activities or ...drinking water, toxic cyanobacteria cause concerns due to the risk of intoxication with cyanotoxins, such as microcystins. In this study, we aimed to unmask relationships between toxicity, cyanobacterial community composition, and environmental factors. At the same time, we assessed the correlation of a genetic marker with microcystin concentration and aimed to identify the main microcystin producer. We used Illumina MiSeq sequencing to study the bacterioplankton in two recreational lakes in South Germany. We quantified a microcystin biosynthesis gene (
) using qPCR and linked this information with microcystin concentration to assess toxicity. Microcystin biosynthesis gene (
)-clone libraries were used to determine the origin of microcystin biosynthesis genes. Bloom toxicity did not alter the bacterial community composition, which was highly dynamic at the lowest taxonomic level for some phyla such as Cyanobacteria. At the OTU level, we found distinctly different degrees of temporal variation between major bacteria phyla. Cyanobacteria and Bacteroidetes showed drastic temporal changes in their community compositions, while the composition of Actinobacteria remained rather stable in both lakes. The bacterial community composition of Alpha- and Beta-proteobacteria remained stable over time in Lake Klostersee, but it showed temporal variations in Lake Bergknappweiher. The presence of potential microcystin degraders and potential algicidal bacteria amongst prevalent Bacteroidetes and Alphaproteobacteria implied a role of those co-occurring heterotrophic bacteria in cyanobacterial bloom dynamics. Comparison of both lakes studied revealed a large shared microbiome, which was shaped toward the lake specific community composition by environmental factors. Microcystin variants detected were microcystin-LR, -RR, and -YR. The maximum microcystin concentrations measured was 6.7 μg/L, a value still acceptable for recreational waters but not drinking water. Microcystin concentration correlated positively with total phosphorus and
copy number. We identified low abundant
sp. as the only microcystin producer in both lakes. Therefore, risk assessment efforts need to take into account the fact that non-dominant species may cause toxicity of the blooms observed.
PDF
