The Lrp Family of Transcription Regulators in Archaea

Archaea possess a eukaryotic-type basal transcription apparatus that is regulated by bacteria-like transcription regulators. A universal and abundant family of transcription regulators are the bacterial/archaeal Lrp-like regulators. The Lrp family is one of the best studied regulator families in archaea, illustrated by investigations of proteins from the archaeal model organisms: Sulfolobus, Pyrococcus, Methanocaldococcus, and Halobacterium. These regulators are extremely versatile in their DNA-binding properties, response to effector molecules, and molecular regulatory mechanisms. Besides being involved in the regulation of the amino acid metabolism, they also regulate central metabolic processes. It appears that these regulatory proteins are also involved in large regulatory networks, because of hierarchical regulations and the possible combinatorial use of different Lrp-like proteins. Here, we discuss the recent developments in our understanding of this important class of regulators

Analysis of the DNA-binding sequence specificity of the archaeal transcriptional regulator Ss-LrpB from Sulfolobus solfataricus by systematic mutagenesis and high resolution contact probing

To determine the sequence specificity of dimeric Ss-LrpB, a high resolution contact map was constructed and a saturation mutagenesis conducted on one half of the palindromic consensus box. Premodification binding interference indicates that Ss-LrpB establishes most of its tightest contacts with a single strand of two major groove segments and interacts with the minor groove at the center of the box. The requirement for bending is reflected in the preference for an A+T rich center and confirmed with C·G and C·I substitutions. The saturation mutagenesis indicates that major groove contacts with C·G at position 5 and its symmetrical counterpart are most critical for the specificity and strength of the interaction. Conservation at the remaining positions improved the binding. Hydrogen bonding to the O(6) and N(7) acceptor atoms of the G(5′) residue play a major role in complex formation. Unlike many other DNA-binding proteins Ss-LrpB does not establish hydrophobic interactions with the methyls of thymine residues. The binding energies determined from the saturation mutagenesis were used to construct a sequence logo, which pin-points the overwhelming importance of C·G at position 5. The knowledge of the DNA-binding specificity will constitute a precious tool for the search of new physiologically relevant binding sites for Ss-LrpB in the genome

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

The DNA-binding domains of S. acidocaldarius BarR and S. solfataricus Ss-LrpB might share a common ancestor. (PDF 198 kb

Situational judgment tests: A review of recent research

Purpose - The purpose of this paper is to give an empirically-based review of the strengths and weaknesses of situational judgment tests (SJTs). Design/methodology/approach - The features, history, and development of SJTs are discussed. Next, a computerized search (from 1990-2007) is conducted to retrieve empirical studies related to SJTs. The effectiveness of SJTs is discussed in terms of reliability, criterion-related validity, incremental validity, construct-related validity, utility, adverse impact, applicant perceptions, fakability, and susceptibility to practice and coaching effects. Findings - Strengths of SJTs are that they show criterion-related validity and incremental validity above cognitive ability and personality tests. SJTs have also less adverse impact towards minorities (especially if the cognitive loading of the SJT is low). Furthermore, applicant reactions towards SJTs are positive and SJTs enable to test large applicant groups at once (through the Internet). In terms of weaknesses, SJTs might be prone to faking, practice, and coaching effects. There is also debate about what constructs are measured by SJTs. Research limitations/implications - Five avenues for future research are discussed: construct-related validity of SJTs, utility of SJTs vis-a-vis other predictors, impact of SJT features on validity and adverse impact, examination of alternative stimulus and response formats, and cross-cultural transportability of SJTs. Practical implications - Practitioners receive evidence-based information about the features, development, and strengths and weaknesses of SJTs. Originality/value - Apart from the USA, SJTs have not made strong inroads in selection practice in Europe and other parts of the world. This evidence-based paper might highlight the value of SJTs

Wearables measuring electrodermal activity to assess perceived stress in care:A scoping review

Background:Chronic stress responses can lead to physical and behavioural health problems, often experienced and observed in the care of people with intellectual disabilities or people with dementia. Electrodermal activity (EDA) is a bio-signal for stress, which can be measured by wearables and thereby support stress management. However, the how, when and to what extent patients and healthcare providers can benefit is unclear. This study aims to create an overview of available wearables enabling the detection of perceived stress by using EDA.Methods:Following the PRISMA-SCR protocol for scoping reviews, four databases were included in the search of peer-reviewed studies published between 2012 and 2022, reporting detection of EDA in relation to self-reported stress or stress-related behaviours. Type of wearable, bodily location, research population, context, stressor type and the reported relationship between EDA and perceived stress were extracted.Results:Of the 74 included studies, the majority included healthy subjects in laboratory situations. Field studies and studies using machine learning (ML) to predict stress have increased in the last years. EDA is most often measured on the wrist, with offline data processing. Studies predicting perceived stress or stress-related behaviour using EDA features, reported accuracies between 42% and 100% with an average of 82.6%. Of these studies, the majority used ML.Conclusion:Wearable EDA sensors are promising in detecting perceived stress. Field studies with relevant populations in a health or care context are lacking. Future studies should focus on the application of EDA-measuring wearables in real-life situations to support stress management

DNA‐Interacting characteristics of the archaeal Rudiviral protein SIRV2_Gp1

Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod‐shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix‐turn‐helix motif and was therefore hypothesized to bind DNA. The DNA‐binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N‐terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.Publisher PDFPeer reviewe

Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen

Pantoea agglomerans is a Gram-negative facultative anaerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-alpha, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-alpha, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-alpha, IL-6 and NO involved solely activation of the NF-kappa B, IL-10 secretion was largely dependent on NF-kappa B and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic host

Bayesian evidence synthesis in case of multi-cohort datasets:An illustration by multi-informant differences in self-control

Abstract The trend toward large-scale collaborative studies gives rise to the challenge of combining data from different sources efficiently. Here, we demonstrate how Bayesian evidence synthesis can be used to quantify and compare support for competing hypotheses and to aggregate this support over studies. We applied this method to study the ordering of multi-informant scores on the ASEBA Self Control Scale (ASCS), employing a multi-cohort design with data from four Dutch cohorts. Self-control reports were collected from mothers, fathers, teachers and children themselves. The available set of reporters differed between cohorts, so in each cohort varying components of the overarching hypotheses were evaluated. We found consistent support for the partial hypothesis that parents reported more self-control problems than teachers. Furthermore, the aggregated results indicate most support for the combined hypothesis that children report most problem behaviors, followed by their mothers and fathers, and that teachers report the fewest problems. However, there was considerable inconsistency across cohorts regarding the rank order of children’s reports. This article illustrates Bayesian evidence synthesis as a method when some of the cohorts only have data to evaluate a partial hypothesis. With Bayesian evidence synthesis, these cohorts can still contribute to the aggregated results

Gender Specific Brood Cells in the Solitary Bee Colletes halophilus (Hymenoptera; Colletidae)

We studied the reproductive behaviour of the solitary bee Colletes halophilus based on the variation in cell size, larval food amount and larval sex in relation to the sexual size dimorphism in this bee. Brood cells with female larvae are larger and contain more larval food than cells with males. Occasionally males are reared in female-sized cells. We conclude that a female C. halophilus in principal anticipates the sex of her offspring at the moment brood cell construction is started. Additionally a female is able to ‘change her mind’ about the sex of her offspring during a single brood cell cycle. We present a model that can predict the sex of the larvae in an early stage of development