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Background: The occurrence of surgical site infections (SSIs) is associated with increased risk of mortality, development of other infections, and the need for reintervention, posing a significant health burden. The aim of this review was to examine the current data and guidelines around the use of antiseptic povidone‑iodine (PVP-I) for the prevention of SSIs at each stage of surgical intervention. Methods: A literature search for selected key words was performed using PubMed. Additional papers were identified based on author expertise. Results: Scientific evidence demonstrates that PVP-I can be used at every stage of surgical intervention: preoperative, intraoperative, and postoperative. PVP-I is one of the most widely used antiseptics on healthy skin and mucous membranes for preoperative surgical site preparation and is associated with a low SSI rate. For intraoperative irrigation, aqueous PVP-I is the recommended agent and has been demonstrated to decrease SSIs in a range of surgical settings, and for postoperative wound healing, there is a growing body of evidence to support the use of PVP-I. Conclusions: There is a need for more stringent study designs in clinical trials to enable meaningful comparisons between antiseptic agents, particularly for preoperative skin preparation. The use of a single agent (PVP-I) at each stage of surgical intervention could potentially provide advantages, including economic benefits, over agents that can only be used at discrete stages of the surgical procedure. Key message: Evidence supports the use of PVP-I at all stages of surgical intervention, from preoperative measures (including skin preparation, preoperative washing, and nasal decolonization) to intraoperative irrigation, through to postoperative wound management. However, there is a need for more stringent study designs in clinical trials to enable meaningful comparisons between antiseptic agents, particularly for preoperative skin preparation.

Abstract Bacteriophages (phages) are viruses that specifically attack bacteria. Their use as therapeutics, which constitutes a promising alternative to antibiotics, heavily relies on selecting effective lytic phages against the pathogen of interest. Current selection techniques are laborious and do not allow for direct visualization of phage infection dynamics. Here, we present a method that circumvents these limitations. It can be scaled for high-throughput and permits monitoring of the phage infection in real time via a fluorescence signal readout. This is achieved through the use of a membrane-impermeant nucleic acid dye that stains the DNA of damaged or lysed bacteria and new phage progeny. We have tested the method on Pseudomonas aeruginosa and Klebsiella pneumoniae and show that an increase in fluorescence reflects phage-mediated killing. This is confirmed by other techniques including spot tests, colony plating, flow cytometry and metabolic activity measurements. Furthermore, we illustrate how our method may be used to compare the activity of different phages and to screen the susceptibility of clinical isolates to phage. Altogether, we present a fast, reliable way of selecting phages against Gram-negative bacteria, which may be valuable in optimizing the process of selecting phages for therapeutic use.

The jumbo contractile bacteriophage, Kp24, has been isolated from clinical strains of Klebsiella pneumonia. Here, the authors present structural and functional insight into the capsid, tail and tail fibres and how this impacts infectivity.

Glucocorticoids, such as dexamethasone, are used as anti-inflammatory and immunosuppressive drugs, however patients may exhibit resistance or side effects. Here the authors propose that a dexamethasone related neutrophil-specific DNA methylation index can be used as a marker of glucocorticoid exposure and response and as a prognostic factor in brain tumor survival.

Background: Different surgical approaches for total hip arthroplasty (THA) exist, without predisposition when it comes to dislocation risk. The direct anterior approach (DAA) is thought to have reduced risk since soft tissue trauma is minimalized. Therefore, we assessed the dislocation risk for different surgical approaches, and the relative dislocation risk of DAA compared to other approaches. Methods: Six electronic databases were systematically searched for prospective studies reporting dislocation following THA. Proportion meta-analyses were performed to assess the dislocation rate for subgroups of the surgical approach. Meta-analysis for binary outcomes was performed to determine the relative risk of dislocation for the DAA compared to other approaches. Results: Eleven studies with 2025 patients were included (mean age 64.6 years, 44% male, mean follow-up 10.5 months), of which four studies were also used in the risk ratio meta-analysis. Overall dislocation rate was 0.79% (95% CI 0.37–1.69). Subgroup analyses showed that most dislocations occurred in the posterior approaches group (1.38%), however non-significant. Furthermore, the DAA emerged with a non-significant lower risk of dislocation (RR 0.37, 95% CI 0.05–2.46) compared to other surgical approaches. Conclusion: Current literature shows non-significant predisposition for a surgical approach to THA regarding dislocation risk. To what extent patient characteristics influence the risk of dislocation could not be determined. Future research should focus on this, as well as on the influence of a surgeon's experience with a specific approach.

DISARM (Defense Island System Associated with Restriction Modification) systems can provide bacteria with protection against a wide range of phage. Here, Bravo et al. determine cryo-EM structures of the core DISARM complex that shed light onto phage DNA recognition and activation of this widespread defense system.

Abstract While CRISPR‐Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time‐lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell‐to‐cell variability, which originates from primed CRISPR adaptation. Faster growth and cell division and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cascade binding to the mutated invader DNA, rather than spacer integration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR‐Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.

Abstract Background The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR-Cas biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database. Results By using vast metagenomic sequence databases, we map approximately one-third of more than 200,000 unique CRISPR spacers from a variety of microbes and derive a catalog of more than two hundred unique PAM sequences associated with specific CRISPR-Cas subtypes. These PAMs are further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. We could also deduce CRISPR-Cas subtype-specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (type I-E and type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (types I-A and I-B and type III systems) prefer the coding strand and mRNA. In addition, we find large-scale evidence that both CRISPR-Cas adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA and RNA targeting of invaders, which may be effective at combating mobile genetic invaders. Conclusions This study has broad implications for our understanding of how CRISPR-Cas systems work in a wide range of organisms for which only the genome sequence is known.

Type III CRISPR-Cas systems recognize and cleave target RNAs and produce signalling molecules. Here the authors discover that both processes are governed by a flexible seed region, ultimately resulting in SCOPE, a SARSCoV-2 diagnostic assay with atto-molar sensitivity.

New and rapid antimicrobial susceptibility/resistance testing methods are required for bacteria from positive blood cultures. In this study, a multiplex-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed and validated for the detection of β-lactam, aminoglycoside, and fluoroquinolone resistance mechanisms in blood cultures growing Escherichia coli or Klebsiella pneumoniae complex. Selected targets were the β-lactamases SHV, TEM, OXA-1-like, CTX-M-1-like, CMY-2-like, chromosomal E. coli AmpC (cAmpC), OXA-48-like, NDM, VIM, and KPC; the aminoglycoside-modifying enzymes AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6′)-Ib, ANT(2′′)-I, and APH(3′)-VI; the 16S-RMTases ArmA, RmtB, RmtC, and RmtF; the quinolone resistance mechanisms QnrA, QnrB, AAC(6′)-Ib-cr; the wildtype quinolone resistance determining region of GyrA; and the E. coli porins OmpC and OmpF. The developed assay was evaluated using 100 prospectively collected positive blood cultures, and 148 negative blood culture samples spiked with isolates previously collected from blood cultures or isolates carrying less prevalent resistance mechanisms. The time to result was approximately 3 h. LC-MS/MS results were compared with whole-genome sequencing and antimicrobial susceptibility testing results. Overall, there was a high agreement between LC-MS/MS results and whole-genome sequencing results. In addition, the majority of susceptible and non-susceptible phenotypes were correctly predicted based on LC-MS/MS results. Exceptions were the predictions for ciprofloxacin and amoxicillin/clavulanic acid that matched with the phenotype in 85.9 and 63.7% of the isolates, respectively. Targeted LC-MS/MS based on parallel reaction monitoring can be applied for the rapid and accurate detection of various resistance mechanisms in blood cultures growing E. coli or K. pneumoniae complex.

The locus coeruleus (LC) plays a central role in regulating human cognition, arousal, and autonomic states. Efforts to characterize the LC's function in humans using functional magnetic resonance imaging have been hampered by its small size and location near a large source of noise, the fourth ventricle. We tested whether the ability to characterize LC function is improved by employing neuromelanin-T1 weighted images (nmT1) for LC localization and multi-echo functional magnetic resonance imaging (ME-fMRI) for estimating intrinsic functional connectivity (iFC). Analyses indicated that, relative to a probabilistic atlas, utilizing nmT1 images to individually localize the LC increases the specificity of seed time series and clusters in the iFC maps. When combined with independent components analysis (ME-ICA), ME-fMRI data provided significant improvements in the temporal signal to noise ratio and DVARS relative to denoised single echo data (1E-fMRI). The effects of acquiring nmT1 images and ME-fMRI data did not appear to only reflect increases in power: iFC maps for each approach overlapped only moderately. This is consistent with findings that ME-fMRI offers substantial advantages over 1E-fMRI acquisition and denoising. It also suggests that individually identifying LC with nmT1 scans is likely to reduce the influence of other nearby brainstem regions on estimates of LC function.

Single-particle tracking PALM (sptPALM) provides quantitative information in vivo if the protein of interest remains in a single diffusional state during track acquisition. Here the authors develop a custom-built sptPALM microscope and a Monte-Carlo based diffusion distribution analysis to study dynamic DNA-dCas9 interactions in live bacteria.

In-situ resource utilization (ISRU) is increasingly acknowledged as an essential requirement for the construction of sustainable extra-terrestrial colonies. Even with decreasing launch costs, the ultimate goal of establishing colonies must be the usage of resources found at the destination of interest. Typical approaches towards ISRU are often constrained by the mass and energy requirements of transporting processing machineries, such as rovers and massive reactors, and the vast amount of consumables needed. Application of self-reproducing bacteria for the extraction of resources is a promising approach to reduce these pitfalls. In this work, the bacterium Shewanella oneidensis was used to reduce three different types of Lunar and Martian regolith simulants, allowing for the magnetic extraction of iron-rich materials. The combination of bacterial treatment and magnetic extraction resulted in a 5.8-times higher quantity of iron and 43.6% higher iron concentration compared to solely magnetic extraction. The materials were 3D printed into cylinders and the mechanical properties were tested, resulting in a 400% improvement in compressive strength in the bacterially treated samples. This work demonstrates a proof of concept for the on-demand production of construction and replacement parts in space exploration.

Background: Modeling and simulation is increasingly used to study pediatric pharmacokinetics, but clinical implementation of age-appropriate doses lags behind. Therefore, we aimed to develop model-informed doses using published pharmacokinetic data and a decision framework to adjust dosing guidelines based on these doses, using piperacillin and amikacin in critically ill children as proof of concept.Methods: Piperacillin and amikacin pharmacokinetic models in critically ill children were extracted from literature. Concentration-time profiles were simulated for various dosing regimens for a virtual PICU patient dataset, including the current DPF dose and doses proposed in the studied publications. Probability of target attainment (PTA) was compared between the different dosing regimens. Next, updated dosing recommendations for the DPF were proposed, and evaluated using a new framework based on PK study quality and benefit-risk analysis of clinical implementation.Results: Three studies for piperacillin (critically ill children) and one for amikacin (critically ill pediatric burn patients) were included. Simulated concentration-time profiles were performed for a virtual dataset of 307 critically ill pediatric patients, age range 0.1–17.9 y. PTA for unbound piperacillin trough concentrations >16 mg/L was >90% only for continuous infusion regimens of 400 mg/kg/day vs. 9.7% for the current DPF dose (80 mg/kg/6 h, 30 min infusion). Amikacin PTA was >90% with 20 mg/kg/d, higher than the PTA of the DPF dose of 15 mg/kg/d (63.5%). Using our new decision framework, altered DPF doses were proposed for piperacillin (better PTA with loading dose plus continuous infusion), but not for amikacin (studied and target population were not comparable and risk for toxicity with higher dose).Conclusions: We show the feasibility to develop model-informed dosing guidelines for clinical implementation using existing pharmacokinetic data. This approach could complement literature and consensus-based dosing guidelines for off-label drugs in the absence of stronger evidence to support pediatricians in daily practice.

The last decade has witnessed a remarkable increase in our ability to measure genetic information. Advancements of sequencing technologies are challenging the existing methods of data storage and analysis. While methods to cope with the data deluge are progressing, many biologists have lagged behind due to the fast pace of computational advancements and tools available to address their scientific questions. Future generations of biologists must be more computationally aware and capable. This means they should be trained to give them the computational skills to keep pace with technological developments. Here, we propose a model that bridges experimental and bioinformatics concepts using the Oxford Nanopore Technologies (ONT) sequencing platform. We provide both a guide to begin to empower the new generation of educators, scientists, and students in performing long-read assembly of bacterial and bacteriophage genomes and a standalone virtual machine containing all the required software and learning materials for the course.

الملخص: أهداف البحث: البالغون ذوو الإعاقة معرضون لخطورة عالية لسوء التغذية مقارنة بنظرائهم من غير المعوقين، بسبب مشاكل التغذية والظروف الطبية المرتبطة بحالاتهم. قمنا بتقييم انتشار سوء التغذية لمجموعة من السيدات النزيلات في مركز إعادة تأهيل، وتم التحقق من صعوبات التغذية، والمشاكل الطبية ذات الصلة بالتغذية. طرق البحث: هذه الدراسة استخدمت نسختين للتقييم الغذائي المصغر- النموذج القصير (MNA-SF) لفحص سوء التغذية؛ التقييم الغذائي المصغر- النموذج القصير الأول المصغر لتقييم التغذية (MNA-SF1) عن مؤشر كتلة الجسم والنموذج القصير الثاني المصغر لتقييم التغذية (MNA-SF2) كطريقة بديلة بقياس محيط الساق. تم جمع البيانات من ٥٣ سيدة تعاني من إعاقات ذهنية وبدنية في دراسة مستعرضة لنزيلات مركز إعادة التأهيل بالكويت. النتائج: من بين جميع المشاركات، تبين أن ٦٣.٥٪ يعانين من زيادة الوزن أو السمنة، بينما تعاني ١١.٥٪ من نقص الوزن. باستخدام النموذج القصير الأول المصغر لتقييم التغذية وجد أن ٥٧.٧٪ في خطر الإصابة بسوء التغذية بينما ١١.٥٪ يعانين من سوء التغذية. تم التعرف على مزيد من المرضى المعرضين لخطر سوء التغذية أو في الواقع يعانين من سوء التغذية باستخدام النموذج القصير الثاني المصغر لتقييم التغذية (٥٩.٦٪ و٢٣.١٪، على التوالي). من مشاكل التغذية التي ذُكرت صعوبة الحفاظ على وضعية الجلوس، والإمساك بالطعام على الصحن، ووضع الطعام في الفم، والبلع. وزاد وجود العدوى الأمر سوءا للإنذار بسوء التغذية بغض النظر عن حالة أوزانهن. الاستنتاجات: تشير نتائج الدراسة بأن النموذج القصير الثاني المصغر لتقييم التغذية أكثر فعالية للتعرف على سوء التغذية. ويمكن للسمنة أن تحجب تحديد مرضى سوء التغذية إذا اعتمد الطبيب فقط على استخدام النموذج القصير الأول المصغر لتقييم التغذية الذي يعتمد على مؤشر كتلة الجسم. Abstract: Objectives: Adults with disabilities are at a higher risk of malnutrition than are their non-disabled counterparts owing to feeding problems and associated medical conditions. We evaluated the prevalence of malnutrition in a group of institutionalized women and investigated any feeding difficulties and nutrition-related medical problems. Methods: This study used two versions of the Mini Nutritional Assessment-Short Form (MNA-SF) to screen malnutrition: the MNA-SF1 which uses the body mass index, and the MNA-SF2 which uses the calf circumference. Data were collected from 53 women with intellectual and physical disabilities in a cross-sectional survey of residents of the Kuwait Rehabilitation Centre. Results: Of all participants, 63.5% were found to be overweight or obese, while 11.5% were underweight. Using the MNA-SF1, 57.7% were found to be at risk of malnourishment while 11.5% were malnourished. More patients were identified to be at risk of malnutrition or to be actually malnourished using the MNA-SF2 (59.6% and 23.1%, respectively). Reported feeding problems included difficulties in maintaining a sitting position, manipulating food on a plate, conveying food to the mouth, and in swallowing. The presence of infections worsened the prognoses of malnourished women regardless of their weight status. Conclusions: Our findings suggest that MNA-SF2 is a more sensitive tool for identifying malnourishment than MNA-SF1. Obesity can obscure the identification of malnourished patients if clinicians rely solely on the MNA-SF1, which uses the body mass index. الكلمات المفتاحية: البالغين ذوي الإعاقة, مؤشر كتلة الجسم, العادات الغذائية, المجتمع الكويتي, السمنة, الحالة الغذائية, Keywords: Adults with disabilities, Body mass index, Dietary habits, Kuwaiti society, Nutritional status, Obesity

Prokaryotic CRISPR-Cas systems provide adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, Staals et al. analyse millions of such events in a native CRISPR-Cas system, showing that newly acquired spacers provoke additional rounds of spacer acquisition.

The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.

This study compares different methods to extract soil moisture information through the assimilation of Soil Moisture Active Passive (SMAP) observations. Neural network (NN) and physically-based SMAP soil moisture retrievals were assimilated into the National Aeronautics and Space Administration (NASA) Catchment model over the contiguous United States for April 2015 to March 2017. By construction, the NN retrievals are consistent with the global climatology of the Catchment model soil moisture. Assimilating the NN retrievals without further bias correction improved the surface and root zone correlations against in situ measurements from 14 SMAP core validation sites (CVS) by 0.12 and 0.16, respectively, over the model-only skill, and reduced the surface and root zone unbiased root-mean-square error (ubRMSE) by 0.005 m 3 m − 3 and 0.001 m 3 m − 3 , respectively. The assimilation reduced the average absolute surface bias against the CVS measurements by 0.009 m 3 m − 3 , but increased the root zone bias by 0.014 m 3 m − 3 . Assimilating the NN retrievals after a localized bias correction yielded slightly lower surface correlation and ubRMSE improvements, but generally the skill differences were small. The assimilation of the physically-based SMAP Level-2 passive soil moisture retrievals using a global bias correction yielded similar skill improvements, as did the direct assimilation of locally bias-corrected SMAP brightness temperatures within the SMAP Level-4 soil moisture algorithm. The results show that global bias correction methods may be able to extract more independent information from SMAP observations compared to local bias correction methods, but without accurate quality control and observation error characterization they are also more vulnerable to adverse effects from retrieval errors related to uncertainties in the retrieval inputs and algorithm. Furthermore, the results show that using global bias correction approaches without a simultaneous re-calibration of the land model processes can lead to skill degradation in other land surface variables.

BACKGROUND: Neuroplasticity drives recovery of walking after a lesion of the descending tract. Intramuscular coherence analysis provides a way to quantify corticomotor drive during a functional task, like walking and changes in coherence serve as a marker for neuroplasticity. Although intramuscular coherence analysis is already applied and rapidly growing in interest, the reproducibility of variables derived from coherence is largely unknown. The purpose of this study was to determine the test-retest reliability and agreement of intramuscular coherence variables obtained during walking in healthy subjects. METHODOLOGY/PRINCIPAL FINDINGS: Ten healthy participants walked on a treadmill at a slow and normal speed in three sessions. Area of coherence and peak coherence were derived from the intramuscular coherence spectra calculated using rectified and non-rectified M. tibialis anterior Electromyography (EMG). Reliability, defined as the ability of a measurement to differentiate between subjects and established by the intra-class correlation coefficient, was on the limit of good for area of coherence and peak coherence when derived from rectified EMG during slow walking. Yet, the agreement, defined as the degree to which repeated measures are identical, was low as the measurement error was relatively large. The smallest change to exceed the measurement error between two repeated measures was 66% of the average value. For normal walking and/or other EMG-processing settings, not rectifying the EMG and/or high-pass filtering with a high cutoff frequency (100 Hz) the reliability was only moderate to poor and the agreement was considerably lower. CONCLUSIONS/SIGNIFICANCE: Only for specific conditions and EMG-processing settings, the derived coherence variables can be considered to be reliable measures. However, large changes (>66%) are needed to indicate a real difference. So, although intramuscular coherence is an easy to use and a sufficiently reliable tool to quantify intervention-induced neuroplasticity, the large effects needed to reveal a real change limit its practical use.

Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called CRISPRs (clustered regularly interspaced short palindromic repeat), into which invader DNA fragments are incorporated. CRISPR transcripts are processed into small RNAs that guide CRISPR-associated (Cas) proteins to invading nucleic acids by complementary base pairing. However, to avoid autoimmunity it is essential that these RNA-guides exclusively target invading DNA and not complementary DNA sequences (i.e., self-sequences) located in the host's own CRISPR locus. Previous work on the Type III-A CRISPR system from Staphylococcus epidermidis has demonstrated that a portion of the CRISPR RNA-guide sequence is involved in self versus non-self discrimination. This self-avoidance mechanism relies on sensing base pairing between the RNA-guide and sequences flanking the target DNA. To determine if the RNA-guide participates in self versus non-self discrimination in the Type I-E system from Escherichia coli we altered base pairing potential between the RNA-guide and the flanks of DNA targets. Here we demonstrate that Type I-E systems discriminate self from non-self through a base pairing-independent mechanism that strictly relies on the recognition of four unchangeable PAM sequences. In addition, this work reveals that the first base pair between the guide RNA and the PAM nucleotide immediately flanking the target sequence can be disrupted without affecting the interference phenotype. Remarkably, this indicates that base pairing at this position is not involved in foreign DNA recognition. Results in this paper reveal that the Type I-E mechanism of avoiding self sequences and preventing autoimmunity is fundamentally different from that employed by Type III-A systems. We propose the exclusive targeting of PAM-flanked sequences to be termed a target versus non-target discrimination mechanism.

Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.

BackgroundCRISPR/Cas is a widespread adaptive immune system in prokaryotes. This system integrates short stretches of DNA derived from invading nucleic acids into genomic CRISPR loci, which function as memory of previously encountered invaders. In Escherichia coli, transcripts of these loci are cleaved into small RNAs and utilized by the Cascade complex to bind invader DNA, which is then likely degraded by Cas3 during CRISPR interference.ResultsWe describe how a CRISPR-activated E. coli K12 is cured from a high copy number plasmid under non-selective conditions in a CRISPR-mediated way. Cured clones integrated at least one up to five anti-plasmid spacers in genomic CRISPR loci. New spacers are integrated directly downstream of the leader sequence. The spacers are non-randomly selected to target protospacers with an AAG protospacer adjacent motif, which is located directly upstream of the protospacer. A co-occurrence of PAM deviations and CRISPR repeat mutations was observed, indicating that one nucleotide from the PAM is incorporated as the last nucleotide of the repeat during integration of a new spacer. When multiple spacers were integrated in a single clone, all spacer targeted the same strand of the plasmid, implying that CRISPR interference caused by the first integrated spacer directs subsequent spacer acquisition events in a strand specific manner.ConclusionsThe E. coli Type I-E CRISPR/Cas system provides resistance against bacteriophage infection, but also enables removal of residing plasmids. We established that there is a positive feedback loop between active spacers in a cluster--in our case the first acquired spacer--and spacers acquired thereafter, possibly through the use of specific DNA degradation products of the CRISPR interference machinery by the CRISPR adaptation machinery. This loop enables a rapid expansion of the spacer repertoire against an actively present DNA element that is already targeted, amplifying the CRISPR interference effect.

A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified.

Assessing individual responses to glucocorticoid drug therapies that compromise immune status and affect survival outcomes in neuro-oncology is a great challenge. Here we introduce a blood-based neutrophil dexamethasone methylation index (NDMI) that provides a measure of the epigenetic response of subjects to dexamethasone. This marker outperforms conventional approaches based on leukocyte composition as a marker of glucocorticoid response. The NDMI is associated with low CD4 T cells and the accumulation of monocytic myeloid-derived suppressor cells and also serves as prognostic factor in glioma survival. In a non-glioma population, the NDMI increases with a history of prednisone use. Therefore, it may also be informative in other conditions where glucocorticoids are employed. We conclude that DNA methylation remodeling within the peripheral immune compartment is a rich source of clinically relevant markers of glucocorticoid response.