Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical ...reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.
Purpose In a time of worldwide physician shortages, the advanced practice providers (APPs) might be a good alternative for physicians as the leaders of a rapid response team. This retrospective ...analysis aimed to establish whether the performance of APP-led rapid response teams is comparable to the performance of rapid response teams led by a medical resident of the ICU. Material and methods In a retrospective single-center cohort study, the electronic medical record of a tertiary hospital was queried during a 12-months period to identify patients who had been visited by our rapid response team. Patient- and process-related outcomes of interventions of rapid response teams led by an APP were compared with those of teams led by a medical resident using various parameters, including the MAELOR tool, which measures the performance of a rapid response team. Results In total, 179 responses of the APP-led teams were analyzed, versus 275 responses of the teams led by a resident. Per APP, twice as many calls were handled than per resident. Interventions of teams led by APPs, and residents did not differ in number of admissions (p = 0.87), mortality (p = 0.8), early warning scores (p = 0.2) or MAELOR tool triggering (p = 0.19). Both groups scored equally on time to admission (p = 0.67) or time until any performed intervention. Conclusion This retrospective analysis showed that the quality of APP-led rapid response teams was similar to the quality of teams led by a resident. These findings need to be confirmed by prospective studies with balanced outcome parameters.
Stroma tissue surrounding cancer cells plays an important role in tumor development and behavior. In colorectal cancer, it has been found that the amount of stroma within the primary tumor is of ...prognostic value. We therefore have evaluated the prognostic value of this tumor–stroma ratio for breast cancer. A cohort of 574 early breast cancer patients, primarily treated with surgery between 1985 and 1994 was analyzed for the tumor–stroma ratio. The percentage of stroma was visually estimated on Haematoxylin-Eosin (H&E) stained histological sections. Patients with more than 50% intra-tumor stroma were quantified as stroma rich and patients with less than 50% as stroma poor. For the total group of patients, stroma-rich tumors had a shorter relapse-free period (RFP) (
P
= 0.001) and overall survival (OS) (
P
= 0.025) compared to stroma-poor tumors. Tumor–stroma ratio was an independent prognostic parameter for the total group of patients (
P
< 0.001) and also in stratified analysis based on systemic treatment. Importantly, in the triple-negative cancer subpopulation, patients with stroma-rich tumors had a 2.92 times higher risk of relapse (
P
= 0.006) compared to those with stroma-poor tumors, independently of other clinico-pathological parameters. Five-year RFP-rates for triple-negative cancer patients with stroma-rich compared to stroma-poor tumors were 56 and 81%, respectively. Tumor–stroma ratio has proven to be an independent prognostic factor for RFP in breast cancer patients and especially in the triple-negative cancer subpopulation. Tumor–stroma ratio could be easily implemented in routine daily pathology diagnostics, as it is simple to determine, reproducible, and performed in quick time.
Bone is a composite material in which collagen fibrils form a scaffold for a highly organized arrangement of uniaxially oriented apatite crystals. In the periodic 67 nm cross-striated pattern of the ...collagen fibril, the less dense 40-nm-long gap zone has been implicated as the place where apatite crystals nucleate from an amorphous phase, and subsequently grow. This process is believed to be directed by highly acidic non-collagenous proteins; however, the role of the collagen matrix during bone apatite mineralization remains unknown. Here, combining nanometre-scale resolution cryogenic transmission electron microscopy and cryogenic electron tomography with molecular modelling, we show that collagen functions in synergy with inhibitors of hydroxyapatite nucleation to actively control mineralization. The positive net charge close to the C-terminal end of the collagen molecules promotes the infiltration of the fibrils with amorphous calcium phosphate (ACP). Furthermore, the clusters of charged amino acids, both in gap and overlap regions, form nucleation sites controlling the conversion of ACP into a parallel array of oriented apatite crystals. We developed a model describing the mechanisms through which the structure, supramolecular assembly and charge distribution of collagen can control mineralization in the presence of inhibitors of hydroxyapatite nucleation.
Summary Sensitivity and specificity of the modified Duke criteria for native valve endocarditis are both suboptimal, at approximately 80%. Diagnostic accuracy for intracardiac prosthetic ...material-related infection is even lower. Non-invasive imaging modalities could potentially improve diagnosis of infective endocarditis; however, their diagnostic value is unclear. We did a systematic literature review to critically appraise the evidence for the diagnostic performance of these imaging modalities, according to PRISMA and GRADE criteria. We searched PubMed, Embase, and Cochrane databases. 31 studies were included that presented original data on the performance of electrocardiogram (ECG)-gated multidetector CT angiography (MDCTA), ECG-gated MRI,18 F-fluorodeoxyglucose (18 F-FDG) PET/CT, and leucocyte scintigraphy in diagnosis of native valve endocarditis, intracardiac prosthetic material-related infection, and extracardiac foci in adults. We consistently found positive albeit weak evidence for the diagnostic benefit of18 F-FDG PET/CT and MDCTA. We conclude that additional imaging techniques should be considered if infective endocarditis is suspected. We propose an evidence-based diagnostic work-up for infective endocarditis including these non-invasive techniques.
An important objective of rehabilitation care is to regain adequate balance function to safely ambulate in community. However, in rehabilitation practice, it remains unclear if a stroke survivor ...functionally recovers by restitution or by learning to compensate for the lack of restoration of body function. Aim of this study is to propose and evaluate methods for the objective evaluation of balance during functional walking in stroke survivors.
Stroke survivors performed twice a Timed "Up & Go" (TUG) test. Ground reaction forces and position changes of both feet were measured using instrumented shoes and used to estimate the position of the center of mass (CoM). Balance control and efficiency metrics were defined to evaluate functional walking under variable conditions. Metrics were corrected based on the instantaneous velocity direction of CoM. Intra- and inter-participant variations for different phases of the TUG test were examined. Metrics were related to the Berg balance scale (BBS).
Participants with higher BBS scores show a more efficient walking pattern. Their walking velocity and walking direction is less variable and they are more frequently unstable when walking in a straight line or when turning. Furthermore, the less affected participants are able to move their CoM more towards their affected side.
We developed and demonstrated a method to assess walking balance of stroke survivors. System design and evaluation methods allow balance evaluation during functional walking in daily life. Some presented metrics show correlations with BBS scores. Clear inter- and intra-patient variations in metric values are present that cannot be explained by BBS scores, which supports the additional value of the presented system. Presented methods may be used for objective evaluation of restitution and compensation of walking balance and have a potential application in individual evidence-based therapy.
The hypothalamic neuropeptide oxytocin (OT), which controls childbirth and lactation, receives increasing attention for its effects on social behaviors, but how it reaches central brain regions is ...still unclear. Here we gained by recombinant viruses selective genetic access to hypothalamic OT neurons to study their connectivity and control their activity by optogenetic means. We found axons of hypothalamic OT neurons in the majority of forebrain regions, including the central amygdala (CeA), a structure critically involved in OT-mediated fear suppression. In vitro, exposure to blue light of channelrhodopsin-2-expressing OT axons activated a local GABAergic circuit that inhibited neurons in the output region of the CeA. Remarkably, in vivo, local blue-light-induced endogenous OT release robustly decreased freezing responses in fear-conditioned rats. Our results thus show widespread central projections of hypothalamic OT neurons and demonstrate that OT release from local axonal endings can specifically control region-associated behaviors.
► We constructed a virus to express any protein, e.g., ChR2, only in oxytocin neurons ► Fluorescent oxytocin neurons project simultaneously to the forebrain and pituitary ► Blue-light exposure of oxytocin axons in vitro affects amygdala neuronal activity ► Blue-light amygdala exposure in vivo evokes oxytocin-mediated decreases in fear
To address the role of the hypothalamic oxytocin (OT)-expressing neurons, Knobloch et al. expressed channelrhodopsin-2 in these neurons. OT neurons project to the central amygdala, as well as other forebrain regions, and activation of these neurons induced oxytocin release and freezing responses in fear-conditioned rats.
Legume nodulation: The host controls the party Ferguson, Brett J.; Mens, Céline; Hastwell, April H. ...
Plant, cell & environment/Plant, cell and environment,
January 2019, Letnik:
42, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Global demand to increase food production and simultaneously reduce synthetic nitrogen fertilizer inputs in agriculture are underpinning the need to intensify the use of legume crops. The symbiotic ...relationship that legume plants establish with nitrogen‐fixing rhizobia bacteria is central to their advantage. This plant–microbe interaction results in newly developed root organs, called nodules, where the rhizobia convert atmospheric nitrogen gas into forms of nitrogen the plant can use. However, the process of developing and maintaining nodules is resource intensive; hence, the plant tightly controls the number of nodules forming. A variety of molecular mechanisms are used to regulate nodule numbers under both favourable and stressful growing conditions, enabling the plant to conserve resources and optimize development in response to a range of circumstances. Using genetic and genomic approaches, many components acting in the regulation of nodulation have now been identified. Discovering and functionally characterizing these components can provide genetic targets and polymorphic markers that aid in the selection of superior legume cultivars and rhizobia strains that benefit agricultural sustainability and food security. This review addresses recent findings in nodulation control, presents detailed models of the molecular mechanisms driving these processes, and identifies gaps in these processes that are not yet fully explained.
Legumes form a beneficial symbiosis with soil bacteria, known as rhizobia, which is signified by the production of nodules on the host plant's roots. The host plant prevents over colonization by rhizobia through various molecular mechanisms that tightly control nodule numbers in response to biotic and abiotic factors. Components of these pathways are key to understanding and optimizing nodulation processes and are the focus of this review.
Asthma is a heterogeneous disease characterized by distinct phenotypes with associated microbial dysbiosis.
Our aim was to identify severe asthma phenotypes based on sputum microbiome profiles and ...assess their stability after 12 to 18 months. A further aim was to evaluate clusters’ robustness after inclusion of an independent cohort of patients with mild-to-moderate asthma.
In this longitudinal multicenter cohort study, sputum samples were collected for microbiome profiling from a subset of the Unbiased Biomarkers in Prediction of Respiratory Disease Outcomes adult patient cohort at baseline and after 12 to 18 months of follow-up. Unsupervised hierarchical clustering was performed by using the Bray-Curtis β-diversity measure of microbial profiles. For internal validation, partitioning around medoids, consensus cluster distribution, bootstrapping, and topological data analysis were applied. Follow-up samples were studied to evaluate within-patient clustering stability in patients with severe asthma. Cluster robustness was evaluated by using an independent cohort of patients with mild-to-moderate asthma.
Data were available for 100 subjects with severe asthma (median age 55 years; 42% males). Two microbiome-driven clusters were identified; they were characterized by differences in asthma onset, smoking status, residential locations, percentage of blood and/or sputum neutrophils and macrophages, lung spirometry results, and concurrent asthma medications (all P values < .05). The cluster 2 patients displayed a commensal-deficient bacterial profile that was associated with worse asthma outcomes than those of the cluster 1 patients. Longitudinal clusters revealed high relative stability after 12 to 18 months in those with severe asthma. Further inclusion of an independent cohort of 24 patients with mild-to-moderate asthma was consistent with the clustering assignments.
Unbiased microbiome-driven clustering revealed 2 distinct robust phenotypes of severe asthma that exhibited relative overtime stability. This suggests that the sputum microbiome may serve as a biomarker for better characterizing asthma phenotypes.
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The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show ...here that chromatin loop size can be increased and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin’s DNA release factor WAPL restricts this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
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•Hi-C analysis demonstrates that chromatin loop size can be increased genome-wide•The duration with which cohesin embraces DNA determines the length of chromatin loops•Haploid genetics reveals that the SCC2/SCC4 complex promotes loop extension•Cohesin limits the compartmentalization of chromatin within the nucleus
Cohesin's dynamic association with DNA determines the length of chromatin loops and allows this complex to correctly structure chromosomes.
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