Characterizing criticality of proteins by systems dynamics: <Emphasis Type="Italic">Escherichia coli</Emphasis> central carbon metabolism as a working example

Background

Systems biology calls for studying system-level properties of genes and proteins rather than their individual chemical/biological properties, regarding the bio-molecules as system components. By characterizing how critical the components are to the system and classifying them accordingly, we can study the underlying complex mechanisms, facilitating researches in drug target selection, metabolic engineering, complex disease, etc. Up to date, most studies aiming at this goal are confined to the topology-based or flux-analysis approaches. However, proteins have tertiary structures and specific functions, especially in metabolic systems. Thus topological properties such as connectivity, path length, etc., are not good surrogates for protein properties. Also, the manner of individual sensitivity analysis in most flux-analysis approaches cannot reveal the simultaneous impacts on collateral components as well as the overall impact on the system, thus lacking in system-level perspective.

Results

In the present work, we developed a method to directly assess protein system-level properties based on system dynamics and in silico knockouts, regarding to the conceptual term "criticality". Applying the method to E. coli central carbon metabolic system, we found that multiple enzymes including phosphoglycerate kinase, enolase, transketolase-b, etc., had critical roles in the system in terms of both system states and dynamical stability. In contrast, another set of enzymes including glucose-6-phosphate isomerise, pyruvate kinase, phosphoglucomutase, etc., exerted very little influences when deleted. The finding is consistent with experimental characterization of metabolic essentiality and other studies on E. coli gene essentiality and functions. We also found that enzymes could affect distant metabolites or enzymes even greater than a close neighbour and asymmetry in system-level properties of enzymes catalyzing alternative pathways could give rise to local flux compensation.

Conclusions

Our method creates a different angle for evaluating protein criticality to a biological system from the conventional methodologies. Moreover, the method leads to consistent results with experimental references, showing its efficiency in studying protein system-level properties. Besides working on metabolic systems, the application of the method can be extended to other kinds of bio-systems to reveal the constitutive/functional properties of system building blocks.

     

Cardiac Autonomic Nervous System Activation and Metabolic Profile in Young Children: The ABCD Study

Background

In adults, increased sympathetic and decreased parasympathetic nervous system activity are associated with a less favorable metabolic profile. Whether this is already determined at early age is unknown. Therefore, we aimed to assess the association between autonomic nervous system activation and metabolic profile and its components in children at age of 5–6 years.

Methods

Cross-sectional data from an apparently healthy population (within the ABCD study) were collected at age 5–6 years in 1540 children. Heart rate (HR), respiratory sinus arrhythmia (RSA; parasympathetic activity) and pre-ejection period (PEP; sympathetic activity) were assessed during rest. Metabolic components were waist-height ratio (WHtR), systolic blood pressure (SBP), fasting triglycerides, glucose and HDL-cholesterol. Individual components, as well as a cumulative metabolic score, were analyzed.

Results

In analysis adjusted for child’s physical activity, sleep, anxiety score and other potential confounders, increased HR and decreased RSA were associated with higher WHtR (P< 0.01), higher SBP (p<0.001) and a higher cumulative metabolic score (HR: p < 0.001; RSA: p < 0.01). Lower PEP was only associated with higher SBP (p <0.05). Of all children, 5.6% had 3 or more (out of 5) adverse metabolic components; only higher HR was associated with this risk (per 10 bpm increase: OR = 1.56; p < 0.001).

Conclusions

This study shows that decreased parasympathetic activity is associated with central adiposity and higher SBP, indicative of increased metabolic risk, already at age 5–6 years.     

Assessing variability in root traits of wild Lupinus angustifolius germplasm: basis for modelling root system structure

Background and aims

Intra-specific variation in root system architecture and consequent efficiency of resource capture by major crops has received recent attention. The aim of this study was to assess variability in a number of root traits among wild genotypes of narrow-leafed lupin (Lupinus angustifolius L.), to provide a basis for modelling of root structure.

Methods

A subset of 111 genotypes of L. angustifolius was selected from a large germplasm pool based on similarity matrices calculated using Diversity Array Technology markers. Plants were grown for 6?weeks in the established semi-hydroponic phenotyping systems to measure the fine-scale features of the root systems.

Results

Root morphology of wild L. angustifolius was primarily dominated by the taproot and first-order branches, with the presence of densely or sparsely distributed second-order branches in the late growth stage. Large variation in most root traits was identified among the tested genotypes. Total root length, branch length and branch number in the entire root system and in the upper roots were the most varied traits (coefficient of variation CV >0.50). Over 94% of the root system architectural variation determined from the principal components analysis was captured by six components (eigenvalue >1). Five relatively homogeneous groups of genotypes with distinguished patterns of root architecture were separated by k-means clustering analysis.

Conclusions

Variability in the fine-scale features of root systems such as branching behaviour and taproot growth rates provides a basis for modelling root system structure, which is a promising path for selecting desirable root traits in breeding and domestication of wild and exotic resources of L. angustifolius for stressful or poor soil environments.     

Novel promoter/transactivator configurations for macrolide- and streptogramin-responsive transgene expression in mammalian cells

Background

The recently developed heterologous macrolide‐ (E.REX system) and streptogramin‐ (PIP system) responsive gene regulation systems show significant differences in their regulation performance in diverse cell lines.

Methods

In order to provide optimal regulation modalities for a wide variety of mammalian cell lines, we have performed a detailed analysis of E.REX and PIP systems modified in (i) the transactivation domains of the antibiotic‐dependent transactivators, (ii) the type of minimal promoter used, and (iii) the spacing between the operator module and the minimal promoter.

Results

These novel E.REX and PIP regulation components showed not only dramatically improved regulation performance in some cell types, but also enabled their use in cell lines which had previously been inaccessible to regulated transgene expression.

Conclusions

Due to their modular set‐up the novel E.REX and PIP regulation systems presented here are most versatile and ready for future upgrades using different cell‐specific key regulation components. Copyright © 2002 John Wiley & Sons, Ltd.

     

Evaluation of water services system through LCA. A case study for Iasi City,Romania

Purpose

The main objective of this paper is to analyse through life cycle assessment (LCA), the entire water services system in Iasi City (Romania): a representative city for the problems faced by the water services sector in Romania. Furthermore, the study is aimed at demonstrating the usefulness of the LCA approach as a support instrument for water resources management.

Methods

The life cycle inventory (LCI) of the Iasi water system was organized considering the water system components, as well as their function related to the water use life cycle: before the tap system as production phase (water abstraction, transport, treatment and distribution) and after the tap section as post-use phase (wastewater collection, treatment and discharge). The foreground data describing the LCI processes were provided directly by the company operating the Iasi water system, while the data for the background processes were sourced or selected from Ecoinvent 2.0 database. The assessment considers the quantification of environmental impacts (according to the CML 2000 baseline and Ecological Scarcity 2006 methodologies) of water supply (abstraction, treatment and distribution) and wastewater disposal (collection and treatment) relative to 1 m³ of tap water.

Results and discussion

For this given system, the results have pointed out that the before the tap system generates higher impacts than the after tap system, mainly due to the energetic effort needed for water supply and the fairly high water losses in the distribution system. However, the after the tap system, specifically the discharge of treated wastewater is still responsible for many of the water-related impact such as Eutrophication (when using CML) or Emissions to surface waters (when using the Ecological Scarcity method). Apart from the LCA approach, this study presents several scenarios for the improvement of the environmental performance of the water services, such as: changing between water sources, improving the distribution system and upgrading the wastewater treatment plant.

Conclusions

This study has demonstrated the usefulness of LCA to describe, compare and predict the environmental performance of complex water services systems (and all its components). The results have provided a reference case for the environmental profile of Iasi city water system, and have enabled the identification of its improvement alternatives. Also, this study, which represents a premiere for Romania, has opened future research directions which may include the development perspectives of the Iasi water services system, as well as improvements of LCIA methodologies to better represent the local specific water-related impacts.     

QTLRel: an R Package for Genome-wide Association Studies in which Relatedness is a Concern

Background

Existing software for quantitative trait mapping is either not able to model polygenic variation or does not allow incorporation of more than one genetic variance component. Improperly modeling the genetic relatedness among subjects can result in excessive false positives. We have developed an R package, QTLRel, to enable more flexible modeling of genetic relatedness as well as covariates and non-genetic variance components.

Results

We have successfully used the package to analyze many datasets, including F₃₄ body weight data that contains 688 individuals genotyped at 3105 SNP markers and identified 11 QTL. It took 295 seconds to estimate variance components and 70 seconds to perform the genome scan on an Linux machine equipped with a 2.40GHz Intel(R) Core(TM)2 Quad CPU.

Conclusions

QTLRel provides a toolkit for genome-wide association studies that is capable of calculating genetic incidence matrices from pedigrees, estimating variance components, performing genome scans, incorporating interactive covariates and genetic and non-genetic variance components, as well as other functionalities such as multiple-QTL mapping and genome-wide epistasis.     

Metabolic Syndrome Components Are Associated with Intervertebral Disc Degeneration: The Wakayama Spine Study

Objective

The objective of the present study was to examine the associations between metabolic syndrome (MS) components, such as overweight (OW), hypertension (HT), dyslipidemia (DL), and impaired glucose tolerance (IGT), and intervertebral disc degeneration (DD).

Design

The present study included 928 participants (308 men, 620 women) of the 1,011 participants in the Wakayama Spine Study. DD on magnetic resonance imaging was classified according to the Pfirrmann system. OW, HT, DL, and IGT were assessed using the criteria of the Examination Committee of Criteria for MS in Japan.

Results

Multivariable logistic regression analysis revealed that OW was significantly associated with cervical, thoracic, and lumbar DD (cervical: odds ratio [OR], 1.28; 95% confidence interval [CI], 0.92–1.78; thoracic: OR, 1.75; 95% CI, 1.24–2.51; lumbar: OR, 1.87; 95% CI, 1.06–3.48). HT and IGT were significantly associated with thoracic DD (HT: OR, 1.54; 95% CI, 1.09–2.18; IGT: OR, 1.65; 95% CI, 1.12–2.48). Furthermore, subjects with 1 or more MS components had a higher OR for thoracic DD compared with those without MS components (vs. no component; 1 component: OR, 1.58; 95% CI, 1.03–2.42; 2 components: OR, 2.60; 95% CI, 1.62–4.20; ≥3 components: OR, 2.62; 95% CI, 1.42–5.00).

Conclusion

MS components were significantly associated with thoracic DD. Furthermore, accumulation of MS components significantly increased the OR for thoracic DD. These findings support the need for further studies of the effects of metabolic abnormality on DD.     

Automating curation using a natural language processing pipeline

Background:

The tasks in BioCreative II were designed to approximate some of the laborious work involved in curating biomedical research papers. The approach to these tasks taken by the University of Edinburgh team was to adapt and extend the existing natural language processing (NLP) system that we have developed as part of a commercial curation assistant. Although this paper concentrates on using NLP to assist with curation, the system can be equally employed to extract types of information from the literature that is immediately relevant to biologists in general.

Results:

Our system was among the highest performing on the interaction subtasks, and competitive performance on the gene mention task was achieved with minimal development effort. For the gene normalization task, a string matching technique that can be quickly applied to new domains was shown to perform close to average.

Conclusion:

The technologies being developed were shown to be readily adapted to the BioCreative II tasks. Although high performance may be obtained on individual tasks such as gene mention recognition and normalization, and document classification, tasks in which a number of components must be combined, such as detection and normalization of interacting protein pairs, are still challenging for NLP systems.

     

Boundary cells regulate a switch in the expression of FGF3 in hindbrain rhombomeres

Background  

During formation of the vertebrate central nervous system, the hindbrain is organized into segmental units, called rhombomeres (r). These cell-lineage restricted segments are separated by a subpopulation of cells known as boundary cells. Boundary cells display distinct molecular and cellular properties such as an elongated shape, enriched extracellular matrix components and a reduced proliferation rate compared to intra-rhombomeric cells. However, little is known regarding their functions and the mechanisms that regulate their formation.     

Time-frequency component analysis of somatosensory evoked potentials in rats

Background  

Somatosensory evoked potential (SEP) signal usually contains a set of detailed temporal components measured and identified in a time domain, giving meaningful information on physiological mechanisms of the nervous system. The purpose of this study is to measure and identify detailed time-frequency components in normal SEP using time-frequency analysis (TFA) methods and to obtain their distribution pattern in the time-frequency domain.     

A potential tocopherol acetate loaded palm oil esters-in-water nanoemulsions for nanocosmeceuticals

Background  

Cosmeceuticals are cosmetic-pharmaceutical hybrids intended to enhance health and beauty of the skin. Nanocosmeceuticals use nano-sized system for the delivery of active ingredients to the targeted cells for better penetration. In this work, nanoemulsion from palm oil esters was developed as a delivery system to produce nanocosmeceuticals. The stability of the resulting formulation was tested using various methods. In addition, the effect of components i.e. Vitamin E and Pluronic F-68 on the formulation was also studied.     

A meta‐analysis of nestedness and turnover components of beta diversity across organisms and ecosystems

Aim

The number of studies investigating the nestedness and turnover components of beta diversity has increased substantially, but our general understanding of the drivers of turnover and nestedness remains elusive. Here, we examined the effects of species traits, spatial extent, latitude and ecosystem type on the nestedness and turnover components of beta diversity.

Location

Global.

Time period

1968–2017.

Major taxa studied

From bacteria to mammals.

Methods

From the 99 studies that partition total beta diversity into its turnover and nestedness components, we assembled 269 and 259 data points for the pairwise and multiple site beta‐diversity metrics, respectively. Our data covered a broad variation in species dispersal type, body size and trophic position. The data were from freshwater, marine and terrestrial realms, and encompassed geographical areas from the tropics to near polar regions. We used linear modelling as a meta‐regression tool to analyse the data.

Results

Pairwise turnover, multiple site turnover and total beta diversity all decreased significantly with latitude. In contrast, multiple site nestedness showed a positive relationship with latitude. Beta‐diversity components did not generally differ among the realms. The turnover component and total beta diversity increased with spatial extent, whereas nestedness was scale invariant for pairwise metrics. Multiple site beta‐diversity components did not vary with spatial extent. Surprisingly, passively dispersed organisms had lower turnover and total beta diversity than flying organisms. Body size showed a relatively weak relationship with beta diversity but had important interactions with trophic position, thus also affecting beta diversity via interactive effects. Producers had significantly higher average pairwise turnover and total beta diversity than carnivores.

Main conclusions

The present results provide evidence that species turnover, being consistently the larger component of total beta diversity, and nestedness are related to the latitude of the study area and intrinsic organismal features. We showed that two beta‐diversity components had generally opposing patterns with regard to latitude. We highlight that beta‐diversity partition may give additional insights into the underlying causes of spatial variability in biotic communities compared with total beta diversity alone.     

Deficits in Executive and Memory Processes in Delusional Disorder: A Case-Control Study

Objective

Delusional disorder has been traditionally considered a psychotic syndrome that does not evolve to cognitive deterioration. However, to date, very little empirical research has been done to explore cognitive executive components and memory processes in Delusional Disorder patients. This study will investigate whether patients with delusional disorder are intact in both executive function components (such as flexibility, impulsivity and updating components) and memory processes (such as immediate, short term and long term recall, learning and recognition).

Methods

A large sample of patients with delusional disorder (n = 86) and a group of healthy controls (n = 343) were compared with regard to their performance in a broad battery of neuropsychological tests including Trail Making Test, Wisconsin Card Sorting Test, Colour-Word Stroop Test, and Complutense Verbal Learning Test (TAVEC).

Results

When compared to controls, cases of delusional disorder showed a significantly poorer performance in most cognitive tests. Thus, we demonstrate deficits in flexibility, impulsivity and updating components of executive functions as well as in memory processes. These findings held significant after taking into account sex, age, educational level and premorbid IQ.

Conclusions

Our results do not support the traditional notion of patients with delusional disorder being cognitively intact.     

Antimicrobial peptides effectively kill a broad spectrum of <Emphasis Type="Italic">Listeria monocytogenes</Emphasis> and <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> strains independently of origin,sub-type,or virulence factor expression

Background  

Host defense peptides (HDPs), or antimicrobial peptides (AMPs), are important components of the innate immune system that bacterial pathogens must overcome to establish an infection and HDPs have been suggested as novel antimicrobial therapeutics in treatment of infectious diseases. Hence it is important to determine the natural variation in susceptibility to HDPs to ensure a successful use in clinical treatment regimes.     

Is impaired energy regulation the core of the metabolic syndrome in various ethnic groups of the USA and Taiwan?

Background

The metabolic syndrome (MetS) concept is widely used in public health and clinical settings without an agreed pathophysiology. We have re-examined the MetS in terms of body fuels, so as to provide a coherent cross-cultural pathogenesis.

Methods

National Health and Nutrition Examination Survey (NHANES 2001-2) with n = 2254 and Taiwanese National Health Interview Survey (NHIS) sub-set for hypertension, hyperglycemia and hyperlipidemia assessment (TwSHHH 2002), n = 5786, were used to compare different ethnicities according to NCEP-ATPIII (NCEP-tw) criteria for METS. Exploratory factor analysis (EFA) using principal components (PC) was employed to differentiate and unify MetS components across four ethnicities, gender, age-strata, and urban-rural settings.

Results

The first two factors from the PC analysis (PCA) accounted for from 55.2% (non-Hispanic white) to 63.7% (Taiwanese) of the variance. Rotated factor loadings showed that the six MetS components provided three clusters: the impaired energy regulation (IER) components (waist circumference, WC, fasting triglycerides, TG, and fasting plasma glucose, FPG), systolic and diastolic blood pressures (BPs), and HDL-cholesterol, where the IER components accounted for 25-26% of total variance of MetS components. For the three US ethnic subgroups, factor 1 was mainly determined by IER and HDL-cholesterol, and factor 2 was related to the BP components. For Taiwanese, IER was determinant for both factors, and BPs and HDL-cholesterol were related to factors 1 and 2 respectively.

Conclusions

There is a MetS core which unifies populations. It comprises WC, TG and FPG as a core, IER, which may be expressed and modulated in various second order ways.