Depressive symptoms and cognitive decline in older adults

OBJECTIVES

Few studies have examined the impact of late-life depression trajectories on specific domains of cognitive function. This study aims to delineate how different depressive symptom trajectories specifically affect cognitive function in older adults.

DESIGN

Prospective longitudinal cohort study.

SETTING

Australia and the United States of America.

PARTICIPANTS

In total, 11,035 community-dwelling older adults with a mean age of 75 years.

MEASUREMENTS

Depressive trajectories were modelled from depressive symptoms according to annual Centre for Epidemiological Studies Depression Scale 10 (CES-D-10) surveys. Four trajectories of depressive symptoms were identified: low ("nondepressed"), consistently mild ("subthreshold depression"), consistently moderate ("persistent depression"), and initially low but increasing ("emerging depression"). Global cognition (Modified Mini-Mental State Examination [3MS]), verbal fluency (Controlled Oral Word Association Test [COWAT]), processing speed (Symbol Digit Modalities Test [SDMT]), episodic memory (Hopkins Verbal Learning Test - Revised [HVLT-R]), and a composite z-score were assessed over a subsequent median 2 years.

RESULTS

Subthreshold depression predicted impaired performance on the SDMT (Cohen's d -0.04) and composite score (-0.03); emerging depression predicted impaired performance on the SDMT (-0.13), HVLT-R (-0.09), 3 MS (-0.08) and composite score (-0.09); and persistent depression predicted impaired performance on the SDMT (-0.08), 3 MS (-0.11), and composite score (-0.09).

CONCLUSIONS

Depressive symptoms are associated with later impaired processing speed. These effects are small. Diverse depression trajectories have different impacts on cognitive function.

Expanded statistical analysis plan for legacy and long-term effects of aspirin in the ASPREE-XT observational follow-up study of participants in the ASPREE randomized trial

The ASPREE randomized controlled trial (2010-2017) of 19,114 community-dwelling older adults without cardiovascular disease and significant disability compared daily 100mg aspirin to placebo. A total of 16,317 (93%) of 17,546 surviving and non-withdrawn participants agreed to continue regular study follow-up visits in the post-trial phase, named ASPREE-XT (2017-2024). We present a statistical analysis plan to underpin three main papers to report aspirin effects through to the fourth post-trial ASPREE-XT study visit with focus areas of: (1) death, dementia, and disability, (2) CVD events and bleeding, and (3) cancer. The focus of the plan is to estimate long-term (entire timespan of RCT plus post-trial) and legacy (post-trial period only) effects of aspirin in the setting of primary prevention for older individuals. Preliminary insights to these effects are presented that are based on data that has been reported to the study's observational study monitoring board however formal data lock is not expected until October 2023.

UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship

The human proteome comprises of all of the proteins produced by the sequences translated from the human genome with additional modifications in both sequence and function caused by nonsynonymous variants and posttranslational modifications including cleavage of the initial transcript into smaller peptides and polypeptides. The UniProtKB database (www.uniprot.org) is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information and presents a summary of experimentally verified, or computationally predicted, functional information added by our expert biocuration team for each protein in the proteome. Researchers in the field of mass spectrometry-based proteomics both consume and add to the body of data available in UniProtKB, and this review highlights the information we provide to this community and the knowledge we in turn obtain from groups via deposition of large-scale datasets in public domain databases.

POTENTIALLY INAPPROPRIATE MEDICATION USE INCREASES RISK OF INCIDENT DISABILITY IN HEALTHY OLDER ADULTS

Background

Efforts to minimize medication risks among older adults include avoidance of potentially inappropriate medications (PIMs). However, most PIMs research has focussed on aged or inpatient care, creating an evidence gap for community-dwelling older adults. To address this, we investigated the impact of PIMs use in the ASPREE clinical trial.

Methods

ASPREE enrolled 19,114 community-dwelling participants aged 70+ years (65+ if US minorities) without a history of major cardiovascular disease, cognitive impairment, and significant physical disability. PIMs was defined according to a modified 2019 AGS Beers Criteria. Cox proportional-hazards regression models were used to estimate the association between baseline PIMs exposure, and disability-free survival, death, disability, and hospitalization, with adjustment for comorbidities including frailty.

Results

At baseline, 7396 (39% of total) participants were prescribed at least one PIM. Compared with those unexposed, participants on a PIM at baseline were at an increased risk of persistent physical disability (Adjusted HR 1.47, 95%CI 1.21, 1.80) and hospitalization (Adjusted HR 1.26, 95%CI 1.20, 1.32), but had similar rates of disability free survival and death. These effects did not vary by polypharmacy status. PIMs exposure was associated with higher risk of disability followed by hospitalization (Adjusted HR 1.92, 95%CI 1.25, 2.96) as well as vice versa (Adjusted HR 1.54, 95%CI 1.15, 2.05). Conclusions: PIMs exposure is associated with increased risk of incident disability and hospitalization. Increased risk of disability prior to hospitalization suggests that PIMs use may start the disability cascade, emphasizing the importance of caution when prescribing PIMs for community-dwelling older adults.

The association between polypharmacy, frailty and disability-free survival in community-dwelling healthy older individuals

OBJECTIVES

Polypharmacy and frailty are two common geriatric conditions. In community-dwelling healthy older adults, we examined whether polypharmacy is associated with frailty and affects disability-free survival (DFS), assessed as a composite of death, dementia, or persistent physical disability.

METHODS

We included 19,114 participants (median age 74.0 years, IQR: 6.1 years) from ASPirin in Reducing Events in the Elderly (ASPREE) clinical trial. Frailty was assessed by a modified Fried phenotype and a deficit accumulation Frailty Index (FI). Polypharmacy was defined as concomitant use of five or more prescription medications. Multinomial logistic regression was used to examine the cross-sectional association between polypharmacy and frailty at base line, and Cox regression to determine the effect of polypharmacy and frailty on DFS over five years.

RESULTS

Individuals with polypharmacy (vs. <5 medications) were 55% more likely to be pre-frail (Relative Risk Ratio or RRR: 1.55; 95%Confidence Interval or CI:1.44, 1.68) and three times more likely to be frail (RRR: 3.34; 95%CI:2.64, 4.22) according to Fried phenotype. Frailty alone was associated with double risk of the composite outcome (Hazard ratio or HR: 2.16; 95%CI: 1.56, 2.99), but frail individuals using polypharmacy had a four-fold risk (HR: 4.24; 95%CI: 3.28, 5.47). Effect sizes were larger when frailty was assessed using the FI.

CONCLUSION

Polypharmacy was significantly associated with pre-frailty and frailty at baseline. Polypharmacy-exposed frailty increased the risk of reducing disability-free survival among older adults. Addressing polypharmacy in older people could ameliorate the impact of frailty on individuals' functional status, cognition and survival.

Associations between Metformin and Aspirin Use on Cancer Incidence and Mortality in Older Adults

Diabetes increases risk of malignancies, and this association increases with age. Metformin may protect against cancer development and progression, but results are mixed and limited to younger cohorts. We examined whether metformin, in the presence or absence of aspirin, reduces incident cancer and cancer-related mortality in older adults. ASPirin in Reducing Events in the Elderly (ASPREE) was a primary prevention trial of daily aspirin vs placebo which enrolled community-dwelling adults from Australia (70+ years) and the US (65+ years for minorities) followed for a median of 4.7 years. Invasive cancer was adjudicated by an expert panel. Cox proportional-hazards models, controlling for age at randomization and known cancer risk factors, were used to analyse the relationship between baseline metformin use, randomized treatment arm, cancer incidence (first in-trial cancer) and mortality. For participants with controlled diabetes, there was a significant reduction in cancer mortality in metformin users compared to nonusers (Adjusted [Adj] HR=0.24, 95%CI=0.07, 0.80), but not for cancer incidence (Adj HR=0.61, 95%CI=0.29, 1.27). For participants with uncontrolled diabetes, there was no significant difference in cancer incidence (Adj HR=0.95, 95%CI=0.66, 1.38) or mortality (Adj HR=1.18, 95%CI=0.62, 2.26) between metformin and non-metformin users. Uncontrolled diabetes, irrespective of metformin use, increased risk of cancer incidence and mortality compared to non-diabetics. Aspirin did not modify the effect of metformin on cancer incidence or mortality. Our findings show that metformin may have protective effects against cancer-related mortality for those older persons whose diabetes is well-controlled, and underscores the importance of diabetes control to minimise cancer risk.

Gait Speed and Grip Strength Are Predictors of Cognitive Decline and Dementia in Older Individuals

Lower gait speed and grip strength are common in older adults. However, the results of lower motor function on cognitive outcomes have been mixed. We examined the longitudinal association between baseline slow gait speed and weak grip strength, alone and in combination, with risk of incident dementia or cognitive decline in a cohort of older adults. Participants (n=19,114) aged 70 and over (65 if U.S. minority) without documented evidence of dementia, significant cognitive impairment, physical disability or previous cardiovascular disease at baseline, were recruited from community settings. Incident dementia was adjudicated by an expert panel using DSM-IV criteria. Incident cognitive decline was defined as a persistent intra-individual decline in score of >1.5 SD from baseline on any of the cognitive tests. Using cox proportional hazard models, slow gait speed at baseline was associated with an increased risk of dementia (63%) and cognitive decline (43%), over a median 4.7 years. Weak grip strength was not as strong a predictor, but was also associated with risk (43% and 11%, respectively). Both outcomes showed higher risk for dementia than cognitive decline. There was no gender-specific interaction. When considered together (adjusted for one another), gait speed and grip strength were both independently associated with cognitive decline and dementia. The synergistic association of these physical measures, each of which is readily administered in the clinic or home, serve as effective early markers of increasing risk of cognitive decline and incident dementia and thus, should be considered for routine health assessments for older adults.

Trajectories of cognitive function and associated factors in community-dwelling older adults: a prospective study

There is variability in cognitive aging between individuals. This study aimed to investigate cognitive aging trajectories, the associated modifiable factors, and the association of these trajectories with dementia. Community-dwelling older adults (n=19,114) without dementia or major cognitive impairment at inclusion were followed for up to 7 years, with regular standardized cognitive assessments. Group-based (multi-) trajectory modeling identified distinct cognitive trajectories. Structural equation modeling (n=16,018) was used to analyze the associated predictors. Four to seven trajectories were identified per cognitive domain, with generally stable trajectories. Improvement in verbal fluency and minor psychomotor slowing were common. Substantial decline in global cognition and episodic memory were observed in a small proportion of individuals. The highest proportions of dementia cases were in trajectories with major decline in global cognition (56.9%) and memory (33.2%). A number of sociodemographic characteristics, health behaviors and chronic conditions were either directly or indirectly associated with cognitive change in older adults. This study found that some individuals appear resilient to cognitive decline even with advancing age, and that factors that promote healthy cognitive aging are not simply the absence of factors which confer risk for decline.

602Prevalence of cancer history and association with risk factors in a healthy older population

Background

The ASPirin in Reducing Events in the Elderly (ASPREE) study randomised healthy older individuals to 100mg aspirin or placebo, with clinical outcomes and disability-free survival endpoints. Detailed baseline data provides a rare opportunity to explore cancer burden and association with known cancer risk factors in this population.

Methods

At enrolment (2010-2014), self-reported personal cancer history, cancer type and cancer risk factor data were sought from 19,114 participants (Australia, n = 16,703; U.S., n = 2,411). Participants were healthy and expected to survive 5 years.

Results

Of those reporting a prior cancer diagnosis (18% women, 22% men), women were diagnosed younger (16% vs 6% of diagnoses &lt;50 years). Cancer prevalence increased with age. Prostate and breast cancer history were higher in U.S. participants; melanoma and colorectal cancer were higher in Australian participants. Cancer history prevalence was not associated with any common risk factors, but was associated with poor health ratings in men. Blood and breast cancer history was more common with past aspirin use.

Conclusions

Personal cancer history in healthy older ASPREE participants was as expected for the most common cancer types in the respective populations. The lack of alignment with known risk factors is attributable to survivor bias, driven by entry criteria, and to possible molecular differences in cancer between elderly and younger people.

Key messages

As the prevalence of cancer increases with age, the lack of alignment with known risk factors implies other factors play a significant role.

443Factors associated with frailty in a relatively healthy community-dwelling older adults

Background

Frailty is gaining importance as a predictor of disability and mortality in aged adults, and becoming frail poses a challenge for healthy aging. We investigated the prevalence and factors associated with pre-frail and frail status in a large study cohort of community-dwelling healthy older adults from Australia and the United States.

Methods

A total of 19,114 individuals (87% Australian and 56% women) aged 65 years or older enrolled in a primary prevention clinical trial were evaluated. Frailty status was classified using the modified Fried phenotype criteria comprising exhaustion, body mass index, grip strength, gait speed and physical activity. Prevalence and factors associated with frailty status (e.g., demographic characteristics and lifestyle factors) were reported using descriptive statistics along with a logistic regression model.

Results

At baseline, 39.0% (95% CI: 38.3, 39.7) of older trial participants were pre-frail and 2.2% (95% CI: 2.0, 2.4) were frail, respectively. Women were more likely to be frail (65.1% vs. 36.9%) and prefrail (58.0% vs. 42.0%) than men. Lower levels of education (&lt;12 years), living alone, ethnic minorities, current smoking and past alcohol use were some of the factors which were common among frail or prefrail.

Conclusions

Despite being a relatively healthy cohort, more than one-third of the older trial participants were pre-frail, which was more prevalent among specific subgroups of individuals. This study emphasizes the high burden of the prefrailty status even among a healthy cohort of community-dwelling older people.

Key messages

The burden of prefrailty is high, even among a healthy cohort of older people in the communities.

OP0015 GENOMIC RISK SCORE FOR ADVANCED OSTEOARTHRITIS IN OLDER ADULTS

Background:

Osteoarthritis (OA) is a major cause of disability, with treatment options mostly limited to advanced disease when joint replacement is indicated. Recent genome-wide association analysis more than doubled the number of OA-associated variants identified (1, 2), extending the feasibility of identification of high-risk individuals.

Objectives:

Including these variants, we calculated polygenic risk scores (PRSs) and performed validation in a well-characterised population of older individuals.

Methods:

We calculated PRSs for knee and hip OA respectively, using joint replacement surgeries as markers of advanced disease in 12,724 older individuals of European descent in the ASPREE trial. We considered in-trial joint replacement (hospitalizations during median 4.7 years follow-up) and pre-trial joint replacement from self-reported medical history. Multivariable models examined the effect of PRS as a continuous variable (per standard deviation [SD]) and categorical variable (low-risk [0-20%], medium-risk [21-80%], high-risk [81-100%] groups), adjusting for age, sex and BMI.

Results:

Mean population age at baseline was 75 years and 54.9% of participants were female. In total, 1478 (11.6%) participants had knee replacements and 1324 (10.4%) had hip replacements. Female sex, higher BMI and age were associated with higher risk of knee and hip replacements. PRSs as continuous variables per SD were associated with knee (odds ratio [OR] 1.11, 95% confidence interval [CI] 1.04-1.17) and hip (OR 1.18, 95% CI 1.11-1.25) replacements. We found meaningfully different rates of knee or hip joint replacement occurring between low-, medium- and high-risk PRS groups. Participants in the high-risk PRS group, compared with the low, had a higher risk of knee replacements (OR=1.35, CI 1.12-1.62), and hip replacements (OR 1.66, 95% CI 1.37-2.02). We found no interaction between PRS and sex, and no collinearity between PRS and BMI, suggesting PRS is an independent risk factor for OA.

Conclusion:

Joint-specific genomic risk scores predict advanced OA in older adults, independent of age, sex and BMI. Stronger associations are observed for hip versus knee OA. Our study provides some of the first evidence of potential clinical utility of genomic risk prediction for OA, which may help identify individuals who would benefit most from targeted clinical management and preventive intervention.

References:

[1]Tachmazidou I, Hatzikotoulas K, Southam L, et al. 2019. Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data. Nat Genet, 51, 230-236

[2]Zengini E, Hatzikotoulas K, Tachmazidou I, et al. 2018. Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis. Nat Genet, 50, 549-558

Disclosure of Interests:

None declared

Evidence for Niche Differentiation in the Environmental Responses of Co-occurring Mucoromycotinian Fine Root Endophytes and Glomeromycotinian Arbuscular Mycorrhizal Fungi

Fine root endophytes (FRE) were traditionally considered a morphotype of arbuscular mycorrhizal fungi (AMF), but recent genetic studies demonstrate that FRE belong within the subphylum Mucoromycotina, rather than in the subphylum Glomeromycotina with the AMF. These findings prompt enquiry into the fundamental ecology of FRE and AMF. We sampled FRE and AMF in roots of Trifolium subterraneum from 58 sites across temperate southern Australia. We investigated the environmental drivers of composition, richness, and root colonization of FRE and AMF by using structural equation modelling and canonical correspondence analyses. Root colonization by FRE increased with increasing temperature and rainfall but decreased with increasing phosphorus (P). Root colonization by AMF increased with increasing soil organic carbon but decreased with increasing P. Richness of FRE decreased with increasing temperature and soil pH. Richness of AMF increased with increasing temperature and rainfall but decreased with increasing soil aluminium (Al) and pH. Aluminium, soil pH, and rainfall were, in decreasing order, the strongest drivers of community composition of FRE; they were also important drivers of community composition of AMF, along with temperature, in decreasing order: rainfall, Al, temperature, and soil pH. Thus, FRE and AMF showed the same responses to some (e.g. soil P, soil pH) and different responses to other (e.g. temperature) key environmental factors. Overall, our data are evidence for niche differentiation among these co-occurring mycorrhizal associates.

First Cryo-Scanning Electron Microscopy Images and X-Ray Microanalyses of Mucoromycotinian Fine Root Endophytes in Vascular Plants

AIMS

Arbuscule-producing fine root endophytes (FRE) (previously incorrectly Glomus tenue) were recently placed within subphylum Mucoromycotina; the first report of arbuscules outside subphylum Glomeromycotina. Here, we aimed to estimate nutrient concentrations in plant and fungal structures of FRE and to test the utility of cryo-scanning electron microscopy (cryoSEM) for studying these fungi.

METHODS

We used replicated cryoSEM and X-ray microanalysis of heavily colonized roots of Trifolium subterraneum.

RESULTS

Intercellular hyphae and hyphae in developed arbuscules were consistently very thin; 1.35 ± 0.03 μm and 0.99 ± 0.03 μm in diameter, respectively (mean ± SE). Several intercellular hyphae were often adjacent to each other forming "hyphal ropes." Developed arbuscules showed higher phosphorus concentrations than senesced arbuscules and non-colonized structures. Senesced arbuscules showed greatly elevated concentrations of calcium and magnesium.

CONCLUSION

While uniformly thin hyphae and hyphal ropes are distinct features of FRE, the morphology of fully developed arbuscules, elevated phosphorus in fungal structures, and accumulation of calcium with loss of structural integrity in senesced arbuscules are similar to glomeromycotinian fungi. Thus, we provide evidence that FRE may respond to similar host-plant signals or that the host plant may employ a similar mechanism of association with FRE and AMF.

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions

The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website ( www.ebi.ac.uk/intact ), and will be continuously updated as research on COVID-19 progresses.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

MOTIVATION

Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalization of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signalling information, focus on capturing, organizing and displaying signalling interactions by representing them as binary, causal relationships between biological entities. The curation efforts that build these individual databases demand a concerted effort to ensure interoperability among resources.

RESULTS

Aware of the enormous benefits of standardization efforts in the molecular interaction research field, representatives of the signalling network community agreed to extend the PSI-MI controlled vocabulary to include additional terms representing aspects of causal interactions. Here, we present a common standard for the representation and dissemination of signalling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI tab-delimited format, now designated PSI-MITAB 2.8. We define the new term 'causal interaction', and related child terms, which are children of the PSI-MI 'molecular interaction' term. The new vocabulary terms in this extended PSI-MI format will enable systems biologists to model large-scale signalling networks more precisely and with higher coverage than before.

AVAILABILITY AND IMPLEMENTATION

PSI-MITAB 2.8 format and the new reference implementation of PSICQUIC are available online (https://psicquic.github.io/ and https://psicquic.github.io/MITAB28Format.html).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions

The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses.

A mycorrhizal revolution

It has long been postulated that symbiotic fungi facilitated plant migrations onto land through enhancing the scavenging of mineral nutrients and exchanging these for photosynthetically fixed organic carbon. Today, land plant-fungal symbioses are both widespread and diverse. Recent discoveries show that a variety of potential fungal associates were likely available to the earliest land plants, and that these early partnerships were probably affected by changing atmospheric CO₂ concentrations. Here, we evaluate current hypotheses and knowledge gaps regarding early plant-fungal partnerships in the context of newly discovered fungal mutualists of early and more recently evolved land plants and the rapidly changing views on the roles of plant-fungal symbioses in the evolution and ecology of the terrestrial biosphere.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

BACKGROUND

Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes.

RESULTS

The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal.

CONCLUSIONS

PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

JAMI: a Java library for molecular interactions and data interoperability

Background

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types.

Results

A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats.

Conclusion

Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI’s model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

Fine root endophytes under scrutiny: a review of the literature on arbuscule-producing fungi recently suggested to belong to the Mucoromycotina

Fine root endophytes (FRE) are arbuscule-forming fungi presently considered as a single species-Glomus tenue in the Glomeromycota (Glomeromycotina)-but probably belong within the Mucoromycotina. Thus, FRE are the only known arbuscule-forming fungi not within the arbuscular mycorrhizal fungi (AMF; Glomeromycotina) as currently understood. Phylogenetic differences between FRE and AMF could reflect ecological differences. To synthesize current ecological knowledge, we reviewed the literature on FRE and identified 108 papers that noted the presence of FRE and, in some, the colonization levels for FRE or AMF (or both). We categorized these records by geographic region, host-plant family and environment (agriculture, moderate-natural, low-temperature, high-altitude and other) and determined their influence on the percentage of root length colonized by FRE in a meta-analysis. We found that FRE are globally distributed, with many observations from Poaceae, perhaps due to grasses being widely distributed. In agricultural environments, colonization by FRE often equalled or exceeded that of AMF, particularly in Australasia. In moderate-natural and high-altitude environments, average colonization by FRE (~10%) was lower than that of AMF (~35%), whereas in low-temperature environments, colonization was similar (~20%). Several studies suggested that FRE can enhance host-plant phosphorus uptake and growth, and may be more resilient than AMF to environmental stress in some host plants. Further research is required on the functioning of FRE in relation to the environment, host plant and co-occurring AMF and, in particular, to examine whether FRE are important for plant growth in stressful environments. Targeted molecular primers are urgently needed for further research on FRE.

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative–molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset.

Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach

The epidermal growth factor receptor (EGFR) kinase is generally considered to be activated by either ligand-induced dimerisation or a ligand-induced conformational change within pre-formed dimers. Ligand-induced higher-order EGFR oligomerisation or clustering has been reported but it is not clear how EGFR oligomers, as distinct from EGFR dimers, influence signaling outputs. To address this question, we combined measures of receptor clustering (microscopy; image correlation spectroscopy) and phosphorylation (Western blots) with modelling of mass-action chemical kinetics. A stable BaF/3 cell-line that contains a high proportion (>90%) of inactive dimers of EGFR-eGFP but no secreted ligand and no other detectable ErbB receptors was used as the model cell system. EGF at concentrations of greater than 1 nM was found to cluster EGFR-eGFP dimers into higher-order complexes and cause parallel increases in EGFR phosphorylation. The kinetics of EGFR clustering and phosphorylation were both rapid, plateauing within 2 minutes after stimulation with 30 nM EGF. A rule-based model was formulated to interpret the data. This model took into account ligand binding, ligand-induced conformational changes in the cytosolic tail, monomer-dimer-trimer-tetramer transitions via ectodomain- and kinase-mediated interactions, and phosphorylation. The model predicts that cyclic EGFR tetramers are the predominant phosphorylated species, in which activated receptor dimers adopt a cyclic side-by-side orientation, and that receptor kinase activation is stabilised by the intramolecular interactions responsible for cyclic tetramerization.

Differential and synergistic effects of epidermal growth factor receptor antibodies on unliganded ErbB dimers and oligomers

Antibodies directed against the epidermal growth factor receptor (EGFR) offer a potentially powerful therapeutic approach against cancers driven by the EGFR pathway. EGFR antibodies are believed to halt cell surface activation by blocking ligand-induced receptor tyrosine kinase activation, i.e., ligand binding, a change in conformation, or the monomer-dimer transition. In this work, we demonstrate that wild-type EGFR and the truncated de2-7-EGFR (tumor-associated mutant) formed unliganded homo-oligomers and examined the effects of two clinically relevant antibodies on the conformation and quaternary state of these ligand-free EGFR oligomers on the surface of cells. The EGFR antibodies were mAb528, a ligand-blocking antibody that binds domain III, and mAb806, a conformationally sensitive antibody that binds near the dimer interface in domain II. We used a model cellular system, BaF/3 cells, with GFP-tagged receptors in the absence of interference from secreted ligands or other erbB receptor members. Different antibody-mediated effects (conformational transition, receptor cross-linking, or receptor dissociation) were distinguished by combining two complementary biophysical techniques: image correlation spectroscopy (submicrometer scale clustering) and homo-Forster resonance energy transfer (association and/or conformation on a 1-10 nm scale). mAb528 cross-linked EGFR into an inactive EGFR dimer of dimers but had no effect when added to de2-7-EGFR oligomers. mAb806 had a minor effect on EGFR dimers as expected from its poor binding to a conformationally shielded epitope on wtEGFR but bound de2-7-EGFR oligomers, causing a conformational change in the intracellular C-terminal GFP-tagged tail. The combination of the two antibodies had synergistic effects, increasing the level of cross-linking of de2-7-EGFR, but did not lead to enhanced cross-linking of EGFR. The results reveal new modes of receptor-antibody interactions for EGFR and de2-7-EGFR.

The IntAct molecular interaction database in 2010

IntAct is an open-source, open data molecular interaction database and toolkit. Data is abstracted from the literature or from direct data depositions by expert curators following a deep annotation model providing a high level of detail. As of September 2009, IntAct contains over 200.000 curated binary interaction evidences. In response to the growing data volume and user requests, IntAct now provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.

IntAct--open source resource for molecular interaction data

IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126 000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from .

Epidermal growth factor receptor: association of extracellular domain negatively regulates intracellular kinase activation in the absence of ligand

The epidermal growth factor receptor (EGFR) plays an important role in many types of human cancers. Receptor amplification, autocrine activation and/or deletion of exons 2-7 of EGFR gene have all been associated with tumor development. The traditional model of EGFR activation via ligand induced dimerization and consequential kinase activation does not provide full understanding of its tumorigenicity. The main function of the receptor extracellular domain (ECD) has been thought to be ligand recognition and binding. We report that the EGFR ECD, through its association also negatively regulates the activity of the intracellular kinase in the absence of ligand. Even in the absence of its ligands, the EGF receptor forms homodimers, however, the ECD prevents constitutive receptor kinase activation through its intrinsic ligand-independent interaction. The removal of this domain, either partial or total, results in constitutive activation of the receptor kinase as observed by its phosphorylation in intact cells. Furthermore, EGF receptors truncated in the ECD induce phosphorylation of the wild-type full-length receptor, indicating an inter-molecular inhibitory mechanism by the receptor ECD. The tumor associated delta2-7EGFR mutant also dimerizes with and phosphorylates the wild type EGFR in the absence of ligand. Thus, in addition to its role in ligand recognition, EGFR ECD interacts with each other, imposing an inhibitory effect on the activation of the intracellular kinase.

Poison ivy/oak dermatitis. Use of polyamine salts of a linoleic acid dimer for topical prophylaxis

Closed patch tests were used to evaluate the ability of 156 different preparations (based on 22 different chemicals) to prevent poison ivy dermatitis. Several polyamine salts of a linoleic acid dimer were identified that were totally able to prevent the usual dermatitis in approximately 70% of subjects. The effectiveness of the preparations improved when the antigen and the protectant were washed off within eight to 12 hours, instead of remaining on the skin for 48 hours. When washed off, and depending on the protectant, concentration, and vehicle used, several of the preparations were totally able to prevent a dermatitis in a range of 56% to 100% of subjects tested. Further work with these compounds may greatly benefit the many people currently plagued by their allergy to poison ivy and poison oak.