Method for reproducible automated bacterial cell culture and measurement.

Microbial cell culture is one of the most commonly performed protocols for synthetic biology, and laboratories are increasingly using 96-well plates and laboratory automation systems for cell culture. Here, we describe a method for reproducible microbial culture using laboratory automation systems, including automated liquid handling, automated plate sealing and de-sealing, automated incubation and measurement of growing cultures. We discuss the key considerations that, in our experience, are important for reproducibility and present statistical analyses of data from 150 automated microbial growth experiments performed over 27 months using our automated method.

Interpretable modeling of genotype-phenotype landscapes with state-of-the-art predictive power.

Large-scale measurements linking genetic background to biological function have driven a need for models that can incorporate these data for reliable predictions and insight into the underlying biophysical system. Recent modeling efforts, however, prioritize predictive accuracy at the expense of model interpretability. Here, we present LANTERN (landscape interpretable nonparametric model, https://github.

Predicted coronavirus Nsp5 protease cleavage sites in the human proteome.

Background: The coronavirus nonstructural protein 5 (Nsp5) is a cysteine protease required for processing the viral polyprotein and is therefore crucial for viral replication. Nsp5 from several coronaviruses have also been found to cleave host proteins, disrupting molecular pathways involved in innate immunity. Nsp5 from the recently emerged SARS-CoV-2 virus interacts with and can cleave human proteins, which may be relevant to the pathogenesis of COVID-19.

Measurements drive progress in directed evolution for precise engineering of biological systems.

Precise engineering of biological systems requires quantitative, high-throughput measurements, exemplified by progress in directed evolution. New approaches allow high-throughput measurements of phenotypes and their corresponding genotypes. When integrated into directed evolution, these quantitative approaches enable the precise engineering of biological function.

The genotype-phenotype landscape of an allosteric protein.

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli, LacI.

[The Guideline "Sedation for Gastrointestinal Endoscopy"].

The guideline "Sedation for gastrointestinal endoscopy" (AWMF-register-no. 021/014) was published initially in 2008. Because of new and developing evidence, the guideline was updated in 2015.

A Bayesian non-parametric mixed-effects model of microbial growth curves.

Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety. Traditional parametric growth curve models capture the population growth behavior through a set of summarizing parameters.

Synergistic Impacts of Organic Acids and pH on Growth of : A Comparison of Parametric and Bayesian Non-parametric Methods to Model Growth.

Different weak organic acids have significant potential as topical treatments for wounds infected by opportunistic pathogens that are recalcitrant to standard treatments. These acids have long been used as bacteriostatic compounds in the food industry, and in some cases are already being used in the clinic. The effects of different organic acids vary with pH, concentration, and the specific organic acid used, but no studies to date on any opportunistic pathogens have examined the detailed interactions between these key variables in a controlled and systematic way.

Additives used to reduce perioperative opioid consumption 1: Alpha2-agonists.

Because of their significant side effects, especially in obese patients, the routine perioperative use of opioids has been questioned recently. Alpha-agonists are drugs with a considerable analgesic potency with the potential to reduce opioid consumption. Alpha-agonists bind to alpha-adrenergic receptors in the CNS and peripherally.

Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks.

Archaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of transcription factor proteins and their target genes. Recent developments in genetics, genomics, and computational methods used with archaeal model organisms have enabled the mapping and prediction of global GRN structures.

A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea.

Iron is required for key metabolic processes but is toxic in excess. This circumstance forces organisms across the tree of life to tightly regulate iron homeostasis. In hypersaline lakes dominated by archaeal species, iron levels are extremely low and subject to environmental change; however, mechanisms regulating iron homeostasis in archaea remain unclear.

Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis.

Gene regulatory networks (GRNs) are critical for dynamic transcriptional responses to environmental stress. However, the mechanisms by which GRN regulation adjusts physiology to enable stress survival remain unclear. Here we investigate the functions of transcription factors (TFs) within the global GRN of the stress-tolerant archaeal microorganism .

Effect of Xenon Anesthesia Compared to Sevoflurane and Total Intravenous Anesthesia for Coronary Artery Bypass Graft Surgery on Postoperative Cardiac Troponin Release: An International, Multicenter, Phase 3, Single-blinded, Randomized Noninferiority Trial.

Background: Ischemic myocardial damage accompanying coronary artery bypass graft surgery remains a clinical challenge. We investigated whether xenon anesthesia could limit myocardial damage in coronary artery bypass graft surgery patients, as has been reported for animal ischemia models.

Methods: In 17 university hospitals in France, Germany, Italy, and The Netherlands, low-risk elective, on-pump coronary artery bypass graft surgery patients were randomized to receive xenon, sevoflurane, or propofol-based total intravenous anesthesia for anesthesia maintenance.

Neuron-Specific Enolase Predicts Poor Outcome After Cardiac Arrest and Targeted Temperature Management: A Multicenter Study on 1,053 Patients.

Objective: Outcome prediction after cardiac arrest is important to decide on continuation or withdrawal of intensive care. Neuron-specific enolase is an easily available, observer-independent prognostic biomarker. Recent studies have yielded conflicting results on its prognostic value after targeted temperature management.

Detecting differential growth of microbial populations with Gaussian process regression.

Microbial growth curves are used to study differential effects of media, genetics, and stress on microbial population growth. Consequently, many modeling frameworks exist to capture microbial population growth measurements. However, current models are designed to quantify growth under conditions for which growth has a specific functional form.

Evidence and consensus based guideline for the management of delirium, analgesia, and sedation in intensive care medicine. Revision 2015 (DAS-Guideline 2015) - short version.

In 2010, under the guidance of the DGAI (German Society of Anaesthesiology and Intensive Care Medicine) and DIVI (German Interdisciplinary Association for Intensive Care and Emergency Medicine), twelve German medical societies published the "Evidence- and Consensus-based Guidelines on the Management of Analgesia, Sedation and Delirium in Intensive Care". Since then, several new studies and publications have considerably increased the body of evidence, including the new recommendations from the American College of Critical Care Medicine (ACCM) in conjunction with Society of Critical Care Medicine (SCCM) and American Society of Health-System Pharmacists (ASHP) from 2013. For this update, a major restructuring and extension of the guidelines were needed in order to cover new aspects of treatment, such as sleep and anxiety management.