Pursuit of proteomic excellence and the excitement in Košice,Slovakia, at the 11th Central and Eastern European Proteomic Conference (CEEPC)

The Central and Eastern European Proteomic Conference (CEEPC) successfully launched its second decade of proteomics in Ko?ice, Slovakia with a program of systems biology, cellular, clinical, veterinary and sports proteomics. Whilst many conferences are struggling to attract participants, CEEPC with its outstanding track record and unique ‘family – feel’ packaged with excellent ambiance is thriving and bringing together proteomics experts from academia, industry, scientific specialties, clinics and precision medicine communities interested in resolving mysteries about protein functionalities in health and disease. CEEPC is also renowned for addressing humanitarian global healthcare issues, may it be ageing, chronic diseases or global epidemics. This year CEEPC intertwined with Ko?ice Peace Marathon’s pursuit of excellence in sports and initiatives including sports medicine and global peace.     

A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest,Hungary

The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented ‘state-of the-art’ proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.     

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference,Poznań, Poland

Every year since 2007, the Central and Eastern European Proteomic Conference (CEEPC) has excelled in representing state-of-the-art proteomics in and around Central and Eastern Europe, and linking it to international institutions worldwide. Its mission remains to contribute to all approaches of proteomics including traditional and often-revisited methodologies as well as the latest technological achievements in clinical, quantitative and structural proteomics with a view to systems biology of a variety of processes. The 9th CEEPC was held from June 15th to 18th, 2015, at the Institute of Bioorganic Chemistry, Polish Academy of Sciences in Poznań, Poland. The scientific program stimulated exchange of proteomic knowledge whilst the spectacular venue of the conference allowed participants to enjoy the cobblestoned historical city of Poznań.     

Abraham's Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry

For more than a century, Jews and non-Jews alike have tried to define the relatedness of contemporary Jewish people. Previous genetic studies of blood group and serum markers suggested that Jewish groups had Middle Eastern origin with greater genetic similarity between paired Jewish populations. However, these and successor studies of monoallelic Y chromosomal and mitochondrial genetic markers did not resolve the issues of within and between-group Jewish genetic identity. Here, genome-wide analysis of seven Jewish groups (Iranian, Iraqi, Syrian, Italian, Turkish, Greek, and Ashkenazi) and comparison with non-Jewish groups demonstrated distinctive Jewish population clusters, each with shared Middle Eastern ancestry, proximity to contemporary Middle Eastern populations, and variable degrees of European and North African admixture. Two major groups were identified by principal component, phylogenetic, and identity by descent (IBD) analysis: Middle Eastern Jews and European/Syrian Jews. The IBD segment sharing and the proximity of European Jews to each other and to southern European populations suggested similar origins for European Jewry and refuted large-scale genetic contributions of Central and Eastern European and Slavic populations to the formation of Ashkenazi Jewry. Rapid decay of IBD in Ashkenazi Jewish genomes was consistent with a severe bottleneck followed by large expansion, such as occurred with the so-called demographic miracle of population expansion from 50,000 people at the beginning of the 15^th century to 5,000,000 people at the beginning of the 19^th century. Thus, this study demonstrates that European/Syrian and Middle Eastern Jews represent a series of geographical isolates or clusters woven together by shared IBD genetic threads.     

Cross-linking/mass spectrometry as a new field and the proteomics information mountain of tomorrow

The European Proteomics Association (EuPA) 2012 Scientific Congress ‘New Horizons and Applications for Proteomics’, hosted by the British Society for Proteome Research (BSPR)

Glasgow, Scotland, UK, 12 July 2012

Cross-linking/mass spectrometry ended decades of method developments and entered the era of applications at this year’s European Proteomics Association meeting. The train has started moving, with successful applications of this tool by multiple pioneering laboratories addressing biological and structural problems. Proteomics, on the other side, sees ever increasing data volumes, leading to questions as to how to store the data mountain publically, use it and convert it into testable hypotheses. The European Proteomics Association meeting has been complementary to the American Society for Mass Spectrometry meeting in many ways, also thanks to its more manageable size and the vision of the organizers in inviting some of Europe’s best emerging minds.     

<Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated transformation and shoot regeneration in elite breeding lines of western shipper cantaloupe and honeydew melons (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.)

A reliable Agrobacterium-mediated transformation and shoot regeneration protocol was developed for breeding lines of commercially important western-shipper cantaloupe and honeydew melons, ‘F39’ and ‘150’, respectively. Different media were tested to select a shoot regeneration system for each of three elite breeding lines ‘F39’, ‘141’ and ‘TMS’. Murashige &; Skoog (MS) basal medium supplemented with 1 mg l^?1 benzyladenine (BA), 0.26 mg l^?1 abscisic acid (ABA) and 0.8 mg l^?1 indole-3-acetic acid (IAA) was used for shoot regeneration from cotyledonary explants in ‘F39’ and ‘150’. Kanamycin sensitivity as well as Timentin^? and Clavamox^® were evaluated using wild-type ‘F39’ and ‘150’ cotyledons. Kanamycin concentrations of 200 and 150 mg l^?1 were chosen as the threshold levels for ‘F39’ and ‘150’, respectively. No significant differences were found between Timentin^? and Clavamox^® in ‘F39’; however, Clavamox^® reduced the incidence of vitrification and increased the frequency of shoot elongation in ‘150’. A. tumefaciens strain EHA105, harboring pCNL56 carrying neomycin phosphotransferase II (nptII) and gusA reporter genes, was selected to establish a transformation protocol for ‘F39’ and ‘150’. Putative transformants were evaluated using β-glucuronidase (GUS) histochemical assay, polymerase chain reaction (PCR) and Southern blot analyses. Based on these parameters, the transformation efficiency for cantaloupe ‘F39’ was 0.3% and that for honeydew ‘150’ was 0.5%.     

5th BSPR‐EBI Meeting,Proteomics: From Technology to New Biology 8–10 July 2008, Wellcome Trust Conference Centre,Hinxton, Cambridge,UK

This paper reports on the 5^th joint British Society for Proteome Research (BSPR) and European Bioinformatics Institute (EBI) meeting which took place at the Wellcome Trust Conference Centre, Cambridge, UK, from the 8^th to 10^th July, 2008. As in previous years, the meeting attracted leading experts in the field who presented the latest cutting edge in proteomics. The meeting was entitled “Proteomics: From Technology to New Biology” taking into account the major transition proteomics has undergone in the past few years. In particular, the use of multiple reaction monitoring (MRM)‐based targeted experiments for absolute quantification and validation of proteins was the hot topic of the meeting. Attended by some 250 delegates, the conference was extremely well organised and provided a great opportunity for discussion and initiation of new collaborations.     

A pluralist challenge to “integrative medicine”: Feyerabend and Popper on the cognitive value of alternative medicine

This paper is a critique of ‘integrative medicine’ as an ideal of medical progress on the grounds that it fails to realise the cognitive value of alternative medicine. After a brief account of the cognitive value of alternative medicine, I outline the form of ‘integrative medicine’ defended by the late Stephen Straus, former director of the US National Centre for Complementary and Alternative Medicine. Straus’ account is then considered in the light of Zuzana Parusnikova’s recent criticism of ‘integrative medicine’ and her distinction between ‘cognitive’ and ‘opportunistic’ engagement with alternative medicine. Parusnikova warns that the medical establishment is guilty of ‘dogmatism’ and proposes that one can usefully invoke Karl Popper’s ‘critical rationalism’ as an antidote. Using the example of Straus, I argue that an appeal to Popper is insufficient, on the grounds that ‘integrative medicine’ can class as a form of cognitively-productive, critical engagement. I suggest that Parusnikova’s appeal to Popper should be augmented with Paul Feyerabend’s emphasis upon the role of ‘radical alternatives’ in maximising criticism. ‘Integrative medicine’ fails to maximise criticism because it ‘translates’ alternative medicine into the theories and terminology of allopathic medicine and so erodes its capacity to provide cognitively-valuable ‘radical alternatives’. These claims are then illustrated with a discussion of ‘traditional’ and ‘medical’ acupuncture. I conclude that ‘integrative medicine’ fails to exploit the cognitive value of alternative medicine and so should be rejected as an ideal of medical progress.     

Defining immigrant newcomers in new destinations: symbolic boundaries in Williamsburg,Virginia

Abstract

This article examines media representations of immigration in Williamsburg, Virginia, a ‘new immigrant destination’ in the USA. Through a content analysis of coverage in Williamsburg's local newspaper, we explore how reporters, columnists and readers draw on nationally and internationally circulating discourses to produce public interpretations of immigration issues and construct symbolic boundaries between and among in-groups and ‘others’ in the community. ‘National boundaries drawn locally’ captures how media actors use nationally recognizable frames to interpret local issues and define the parameters of community and national belonging. ‘Localized symbolic boundaries’ take their meanings from place-based, cultural understandings, specific economic conditions and demographics in the local setting. Newspaper discussions in Williamsburg distinguish between ‘deserving’ foreign student workers (primarily from Eastern Europe and Asia) and ‘undeserving’, racialized, Latino ‘others’. Our analysis advances theories of boundary construction and holds implications for the politics of belonging more generally in other immigrant-receiving contexts.     

The Burden Attributable to Mental and Substance Use Disorders as Risk Factors for Suicide: Findings from the Global Burden of Disease Study 2010

Background

The Global Burden of Disease Study 2010 (GBD 2010) identified mental and substance use disorders as the 5^th leading contributor of burden in 2010, measured by disability adjusted life years (DALYs). This estimate was incomplete as it excluded burden resulting from the increased risk of suicide captured elsewhere in GBD 2010''s mutually exclusive list of diseases and injuries. Here, we estimate suicide DALYs attributable to mental and substance use disorders.

Methods

Relative-risk estimates of suicide due to mental and substance use disorders and the global prevalence of each disorder were used to estimate population attributable fractions. These were adjusted for global differences in the proportion of suicide due to mental and substance use disorders compared to other causes then multiplied by suicide DALYs reported in GBD 2010 to estimate attributable DALYs (with 95% uncertainty).

Results

Mental and substance use disorders were responsible for 22.5 million (14.8–29.8 million) of the 36.2 million (26.5–44.3 million) DALYs allocated to suicide in 2010. Depression was responsible for the largest proportion of suicide DALYs (46.1% (28.0%–60.8%)) and anorexia nervosa the lowest (0.2% (0.02%–0.5%)). DALYs occurred throughout the lifespan, with the largest proportion found in Eastern Europe and Asia, and males aged 20–30 years. The inclusion of attributable suicide DALYs would have increased the overall burden of mental and substance use disorders (assigned to them in GBD 2010 as a direct cause) from 7.4% (6.2%–8.6%) to 8.3% (7.1%–9.6%) of global DALYs, and would have changed the global ranking from 5^th to 3^rd leading cause of burden.

Conclusions

Capturing the suicide burden attributable to mental and substance use disorders allows for more accurate estimates of burden. More consideration needs to be given to interventions targeted to populations with, or at risk for, mental and substance use disorders as an effective strategy for suicide prevention.     

Correlation of urinary inflammatory and oxidative stress markers in very low birth weight infants with subsequent development of bronchopulmonary dysplasia

Abstract

Currently, bronchopulmonary dysplasia (BPD) occurs almost exclusively in pre-term infants. In addition to prematurity, other factors like oxygen toxicity and inflammation can contribute to the pathogenesis. This study aimed to compare urinary inflammatory and oxidative stress markers between the no/mild BPD group and moderate/severe BPD group and between BPD cases with significant early lung disease like respiratory distress syndrome (RDS) (‘classic’ BPD) and with minimal early lung disease (‘atypical’ BPD). A total of 60 patients who were a gestational age < 30 weeks or a birth weight < 1250 g were included. Urine samples were obtained on the 1^st, 3^rd and 7^th day of life and measured the levels of leukotriene E₄ (LTE₄) and 8-hydroxydeoxyguanosine (8-OHdG). The 8-OHdG values on the 3^rd day showed significant correlation to duration of mechanical ventilation. The 8-OHdG levels on the 7^th day were the independent risk factor for developing moderate/severe BPD. In ‘classic’ BPD, the 8-OHdG values on the 3^rd day were higher than those of ‘atypical’ BPD. In ‘atypical’ BPD, the LTE₄ values on the 7^th day were higher than the values in ‘classic’ BPD. These results suggest that oxidative DNA damage could be the crucial mechanism in the pathogenesis of current BPD and the ongoing inflammatory process could be an important mechanism in ‘atypical’ BPD.     

The IDIP framework for assessing protein function and its application to the prion protein

The quest to determine the function of a protein can represent a profound challenge. Although this task is the mandate of countless research groups, a general framework for how it can be approached is conspicuously lacking. Moreover, even expectations for when the function of a protein can be considered to be ‘known’ are not well defined. In this review, we begin by introducing concepts pertinent to the challenge of protein function assignments. We then propose a framework for inferring a protein's function from four data categories: ‘inheritance’, ‘distribution’, ‘interactions’ and ‘phenotypes’ (IDIP). We document that the functions of proteins emerge at the intersection of inferences drawn from these data categories and emphasise the benefit of considering them in an evolutionary context. We then apply this approach to the cellular prion protein (PrP^C), well known for its central role in prion diseases, whose function continues to be considered elusive by many investigators. We document that available data converge on the conclusion that the function of the prion protein is to control a critical post-translational modification of the neural cell adhesion molecule in the context of epithelial-to-mesenchymal transition and related plasticity programmes. Finally, we argue that this proposed function of PrP^C has already passed the test of time and is concordant with the IDIP framework in a way that other functions considered for this protein fail to achieve. We anticipate that the IDIP framework and the concepts analysed herein will aid the investigation of other proteins whose primary functional assignments have thus far been intractable.     

Complex migration and breeding strategies in an elusive bird species illuminated by genetic and isotopic markers

Unlike the annual bi‐directional movements of over 200 bird species within the Palaearctic–Afrotropical region, irregular movements such as irruptive migration with a low degree of philopatry are reported for a variety of species depending on highly seasonal and unpredictable resources. These flexible movements allow for itinerant breeding – consecutive breeding attempts in two or more geographically different regions during the same annual reproductive cycle. In order to illuminate migratory and breeding strategies of the erratic wetland species Baillon's crake Zapornia pusilla across the W‐Palaearctic–Afrotropical region, we used a set of six DNA microsatellites as well as δ²H_f values of individuals sampled at one African and four European breeding sites. We investigated the degree of genetic population structure within and among different sites and assigned individuals’ feathers of unknown origin to their probable moulting (hence breeding) site using a likelihood approach. We found three genetic clusters, differentiating into one ‘European’ and two ‘African’ populations. Connectivity between the sampling sites was probable as genetic ‘African’ individuals were found in breeding conditions in Europe and vice versa. Likewise, assigned moulting locations based on δ²H isoscapes suggested trans‐continental movements as well as moulting and possibly breeding by the same individual both in African and European breeding grounds. Both isotopic and genetic data reveal the Baillon's crake pursue a complex migration and breeding strategy, allowing as well for irruptive movements and itinerant breeding across the W‐Palaearctic–Afrotropical region. However, a better knowledge about the species’ distribution as well as a more comprehensive data set, including samples from the southern and eastern boundaries of the distribution area would be necessary to improve the spatial resolution to the precision required to unambiguously infer migration directions and extent of exchange between African and European breeding grounds.     

Mining the fecal proteome: from biomarkers to personalised medicine

Introduction: Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance.

Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current ‘Proteomics Toolbox’, explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform.

Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.     

Spatial scale affects bioclimate model projections of climate change impacts on mountain plants

Plant species have responded to recent increases in global temperatures by shifting their geographical ranges poleward and to higher altitudes. Bioclimate models project future range contractions of montane species as suitable climate space shifts uphill. The species–climate relationships underlying such models are calibrated using data at either ‘macro’ scales (coarse resolution, e.g. 50 km × 50 km, and large spatial extent) or ‘local’ scales (fine resolution, e.g. 50 m × 50 m, and small spatial extent), but the two approaches have not been compared. This study projected macro (European) and local models for vascular plants at a mountain range in Scotland, UK, under low (+1.7 °C) and high (+3.3 °C) climate change scenarios for the 2080s. Depending on scenario, the local models projected that seven or eight out of 10 focal montane species would lose all suitable climate space at the site. However, the European models projected such a loss for only one species. The cause of this divergence was investigated by cross‐scale comparisons of estimated temperatures at montane species' warm range edges. The results indicate that European models overestimated species' thermal tolerances because the input coarse resolution climate data were biased against the cold, high‐altitude habitats of montane plants. Although tests at other mountain ranges are required, these results indicate that recent large‐scale modelling studies may have overestimated montane species' ability to cope with increasing temperatures, thereby underestimating the potential impacts of climate change. Furthermore, the results suggest that montane species persistence in microclimatic refugia might not be as widespread as previously speculated.     

Meeting Report of the 2nd International Workshop on 2‐D DIGE Applications in Proteomics

The second international workshop on “2‐D DIGE Applications in Proteomics” took place at the Medizinisches Proteom‐Center, Ruhr‐Universität Bochum, from February 27^th to March 2^nd, 2007. The four day “hands‐on” course was addressed to all interested scientists from the field of Proteomics, inter alia to members of HUPO and DGPF, with a greater focus on image analysis and statistical analysis of 2‐D DIGE experiments.     

Ebola,COVID‐19 and Africa: What we expected and what we got

Democratic Republic of the Congo’s fight with Ebola was just settling when WHO declared COVID‐19 to be a global pandemic on March 12, 2020. This has caused concomitant setbacks in the treatment and control of major health issues like HIV, tuberculosis, measles, and malaria in the country. This, coupled with civil unrest and risk to the safety of the health workers, is a 'perfect storm' waiting to unfold. Military contingents as peacekeepers are having the most difficult time, handling the situation, in the wake of risks involved.     

Tu Youyou winning the Nobel Prize: Ethical research on the value and safety of traditional Chinese medicine

In 2015, the Chinese pharmacologist, Tu Youyou, was awarded the Nobel Prize for Physiology or Medicine for the discovery of artemisinin. Traditional Chinese medicine (TCM) was the source of inspiration for Tu's discovery and provides an opportunity for the world to know more about TCM as a source of medical knowledge and practice. In this article, the value of TCM is evaluated from an ethical perspective. The characteristics of ‘jian, bian, yan, lian’ are explored in the way they promote accessibility and economic efficiency for TCM. The article also examines how the increased use and prevalence of TCM reflects the scientific, cultural, and ethical values of TCM and their increasing attraction in meeting major challenges to medicine and health systems currently and in the future. The article discusses safety issues within TCM, which is a controversial area, and also comments on some shortcomings and challenges which pose difficulties for more widespread and greater uptake of TCM-derived clinical or therapeutic interventions. The article concludes that TCM is generally safe if it is used according to TCM theory and where such applications are cognizant of the strengths and weaknesses of TCM. TCM has important bioethical values which may inform potential measures for meeting challenges facing global health care systems and the article argues that it can have an increasing role in improving human health.     

What does race do?

In writing on ‘John Rex's Main Mistake’, Michael Banton reveals more about Banton than he does about Rex. I use Banton's discussion of the differences between his own and John Rex's ‘mistakes’ to explore why, in my view, race continues to have analytical purchase in a purportedly ‘post-racial’ age