Infant sitting postural control appears robust across changes in surface context

Aim of the study: Independent sitting requires the control of the involved body segments over the base of support using information obtained from the three sensory systems (visual, vestibular, and somatosensory). The contribution of somatosensory information in infant sitting has not been explored. To address this gap, we altered the context of the sitting support surface and examined the infants’ immediate postural responses.

Materials and methods: Ten 7-month-old typically developing infants sat on compliant and firm surfaces in one session. Spatial, frequency, and temporal measures of postural control were obtained using center of pressure data.

Results Our results suggest that infants’ postural sway is not immediately affected by the different types of foam surface while sitting.

Conclusions: It seems that mature sitter infants are able to adapt to different environmental constraints by disregarding the distorted somatosensory information from the support surface and relying more on their remaining senses (visual and vestibular) to control their sitting posture.     

Protein biomarkers for subtyping breast cancer and implications for future research

Introduction: Breast cancer subtypes are currently defined by a combination of morphologic, genomic, and proteomic characteristics. These subtypes provide a molecular portrait of the tumor that aids diagnosis, prognosis, and treatment escalation/de-escalation options. Gene expression signatures describing intrinsic breast cancer subtypes for predicting risk of recurrence have been rapidly adopted in the clinic. Despite the use of subtype classifications, many patients develop drug resistance, breast cancer recurrence, or therapy failure.

Areas covered: This review provides a summary of immunohistochemistry, reverse phase protein array, mass spectrometry, and integrative studies that are revealing differences in biological functions within and between breast cancer subtypes. We conclude with a discussion of rigor and reproducibility for proteomic-based biomarker discovery.

Expert commentary: Innovations in proteomics, including implementation of assay guidelines and standards, are facilitating refinement of breast cancer subtypes. Proteomic and phosphoproteomic information distinguish biologically functional subtypes, are predictive of recurrence, and indicate likelihood of drug resistance. Actionable, activated signal transduction pathways can now be quantified and characterized. Proteomic biomarker validation in large, well-designed studies should become a public health priority to capitalize on the wealth of information gleaned from the proteome.     

GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

We live in an age of access to more information than ever before. This can be a double-edged sword. Increased access to information allows for more informed and empowered researchers, while information overload becomes an increasingly serious risk. Thus, there is a need for intelligent information retrieval systems that can summarize relevant and reliable textual sources to satisfy a user's query. Question answering is a specialized type of information retrieval with the aim of returning precise short answers to queries posed as natural language questions. We present a review and comparison of three biomedical question answering systems: askHERMES (http://www.askhermes.org/), EAGLi (http://eagl.unige.ch/EAGLi/), and HONQA (http://services.hon.ch/cgi-bin/QA10/qa.pl).     

Opinion Practical and ethical considerations for students conducting ecological research involving wildlife

This commentary outlines relevant changes to the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes for ecologists and students active in field‐based wildlife research. All field‐based activities that require the approval of an Animal Ethics Committee (AEC) have now been detailed within the revised Code of Practice. Researchers and their students are required to give explicit consideration to the humane principles of replacement, reduction and refinement within their experimental protocols as a part of the AEC permission procedure. University‐based researchers also have obligations to train graduate students in the ethical as well as the practical components of wildlife research. In promoting this educational aim, a summary of ethical considerations in wildlife research is offered as a basis for discussion: the regulatory framework of research animal welfare (including an introduction to the Code of Practice, the AEC process and some thoughts on experimental design); and the humane principles on which the Code of Practice is based. Some practical considerations for field work relevant to students’ research training are also described.     

Cancer biomarker discovery and translation: proteomics and beyond

Introduction: Cancer is often diagnosed at late stages when the chance of cure is relatively low and although research initiatives in oncology discover many potential cancer biomarkers, few transition to clinical applications. This review addresses the current landscape of cancer biomarker discovery and translation with a focus on proteomics and beyond.

Areas covered: The review examines proteomic and genomic techniques for cancer biomarker detection and outlines advantages and challenges of integrating multiple omics approaches to achieve optimal sensitivity and address tumor heterogeneity. This discussion is based on a systematic literature review and direct participation in translational studies.

Expert commentary: Identifying aggressive cancers early on requires improved sensitivity and implementation of biomarkers representative of tumor heterogeneity. During the last decade of genomic and proteomic research, significant advancements have been made in next generation sequencing and mass spectrometry techniques. This in turn has led to a dramatic increase in identification of potential genomic and proteomic cancer biomarkers. However, limited successes have been shown with translation of these discoveries into clinical practice. We believe that the integration of these omics approaches is the most promising molecular tool for comprehensive cancer evaluation, early detection and transition to Precision Medicine in oncology.     

Spaceflight induced changes in the human proteome

Introduction: Spaceflight is one of the most extreme conditions encountered by humans: Individuals are exposed to radiation, microgravity, hypodynamia, and will experience isolation. A better understanding of the molecular processes induced by these factors may allow us to develop personalized countermeasures to minimize risks to astronauts.

Areas covered: This review is a summary of literature searches from PubMed, NASA, Roskosmos and the authors’ research experiences and opinions. The review covers the available proteomic data on the effects of spaceflight factors on the human body, including both real space missions and ground-based model experiments.

Expert commentary: Overall, the authors believe that the present background, methodology and equipment improvements will enhance spaceflight safety and support accumulation of new knowledge on how organisms adapt to extreme conditions.     

Integrative analysis of the colorectal cancer proteome: potential clinical impact

Introduction: Colorectal cancer (CRC) is one of the common types of cancer that affects a significant proportion of the population and is a major contributor to cancer related mortality. The relatively poor survival rate of CRC could be improved through the identification of clinically useful biomarkers.

Areas covered: This review highlights the need for biomarkers and discusses recent proteomics discoveries in the aspects of CRC clinical practice including diagnosis, prognosis, therapy, screening and molecular pathological epidemiology (MPE). Studies have been evaluated in relation to biomarker target, methodology, sample selection, limitations, and potential impact. Finally, the progress in proteomic approaches is briefly discussed and the main difficulties facing the translation of proteomics biomarkers into the clinical practice are highlighted.

Expert commentary: The establishment of specific guidelines, best practice recommendations and the improvement in proteomic strategies will significantly improve the prospects for developing clinically useful biomarkers.     

Head-to-head comparison of cardiac troponin T and troponin I in patients without acute coronary syndrome: a systematic review

Background: Cardiac-specific troponin T (cTnT) and troponin I (cTnI) are considered diagnostically equal in patients with acute coronary syndrome (ACS). The aim of this systematic review was to compare the prevalence and prognostic strength of elevations of cTnT and cTnI in patients with other conditions than ACS.

Methods: A systemic review was conducted in concordance with the PRISMA guidelines. The studies were identified by searching PubMed, EMBASE and Cochrane Central Register, from May to August 2016. Studies measuring both cTnT and cTnI in populations without ACS were eligible.

Results: Twenty-nine studies were included (n?=?25,859). Seventeen studies reported on prognostic information with follow-up time ranging for 30?d–5?years. Elevation above the 99th percentile (reference value for a healthy population) in non-ACS population was reported to be 0–39% for cTnI and 40–100% for cTnT. Elevation of cTnT tends to be a superior predictor for all-cause mortality and elevation of cTnI tends to be a superior predictor for cardiovascular related mortality.

Discussion: In the absence of ACS, elevation of cTnT is more frequent than elevation of cTnI.

Conclusion: Both cTnT and cTnI elevations have important prognostic information regarding morbidity, cardiac mortality and all-cause mortality.     

The macroecology of animal versus wind pollination: ecological factors are more important than historical climate stability

Background: The relative frequency of wind- and animal-pollinated plants a non-randomly distributed across the globe and numerous hypotheses have been raised for the greater occurrence of wind pollination in some habitats and towards higher latitudes. To date, however, there has been no comprehensive global investigation of these hypotheses.

Aims: Investigating a range of hypotheses for the role of biotic and abiotic factors as determinants of the global variation in animal vs. wind pollination.

Methods: We analysed 67 plant communities ranging from 70º north to 34º south. For these we determined habitat type, species richness, insularity, topographic heterogeneity, current climate and late-quaternary climate change. The predictive effects of these factors on the proportion of wind- and animal-pollinated plants were tested using correlations, ordinary least squares (OLS) and logistic regression analyses with information-theoretic model selection.

Results: The proportion of animal-pollinated plant species was positively associated with plant species richness and current temperature. Furthermore, in forest, animal pollination was positively related to precipitation. Historical climate was only weakly and idiosyncratically correlated with animal pollination.

Conclusion: Results were consistent with the hypothesised reduced chance for wind-transported pollen reaching conspecific flowers in species-rich communities, fewer constraints on nectar production in warm and wet habitats, and reduced relative effectiveness of wind dispersal in humid areas. There was little evidence of a legacy of historical climate change affecting these patterns.     

Breeding biology of Western Bonelli’s Warblers Phylloscopus bonelli in the Mediterranean region

Capsule: The Western Bonelli’s Warbler Phylloscopus bonelli has a nest success of only 25% in the core of its range in western Europe.

Aims: To investigate the breeding biology of Western Bonelli’s Warbler P. bonelli, focusing on possible altitude effects and potential reproductive problems.

Methods: Three Western Bonelli’s Warbler populations were monitored during the 2012 and 2013 breeding seasons in the massif range of Sierra Nevada, Spain. We determined all the breeding parameters and calculated daily survival and success rates for each reproductive period.

Results: The three studied populations did not differ in any breeding parameters. Altitude showed a positive relationship with clutch size and duration of incubation period, but a negative relationship with nestling tarsus growth and body mass gain. Daily survival rates during incubation and nestling periods were similar to those of common warblers, but the species presented a low breeding success of 25%.

Conclusion: The absence of differences among the three populations suggests that the information provided here could be representative of its distribution in the woodlands of Sierra Nevada. The novel and detailed information reported is crucial not only for expanding our understanding of this species but also to draw attention to the potential risks that it might face in the near future, considering the reduction that this species has suffered in Sierra Nevada during recent decades.     

Advances in the Chromosome-Centric Human Proteome Project: looking to the future

Introduction: The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on ‘missing proteins (MPs)’, which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs.

Areas covered: We will cover the scope, historic background, progress, challenges and future prospects of C-HPP. This review also addresses the question of how we can best improve the methodological approaches, select the optimal biological samples, and recommend stringent protocols for the identification and characterization of MPs. A new strategy for functional analysis of some of those annotated proteins having unknown function will also be discussed.

Expert commentary: If the project moves well by reshaping the original goals, the current working modules and team work in the proposed extended planning period, it is anticipated that a progressively more detailed draft of an accurate chromosome-based proteome map will become available with functional information.     

Recent advances in the metabolomic study of bladder cancer

Introduction: Metabolomics is a chemical process, involving the characterization of metabolites and cellular metabolism. Recent studies indicate that numerous metabolic pathways are altered in bladder cancer (BLCA), providing potential targets for improved detection and possible therapeutic intervention. We review recent advances in metabolomics related to BLCA and identify various metabolites that may serve as potential biomarkers for BLCA.

Areas covered: In this review, we describe the latest advances in defining the BLCA metabolome and discuss the possible clinical utility of metabolic alterations in BLCA tissues, serum, and urine. In addition, we focus on the metabolic alterations associated with tobacco smoke and racial disparity in BLCA.

Expert commentary: Metabolomics is a powerful tool which can shed new light on BLCA development and behavior. Key metabolites may serve as possible markers of BLCA. However, prospective validation will be needed to incorporate these markers into clinical care.     

Molybdenum-containing nitrite reductases: Spectroscopic characterization and redox mechanism

Objectives: This review summarizes the spectroscopic results, which will provide useful suggestions for future research. In addition, the fields that urgently need more information are also advised.

Background: Nitrite-NO-cGMP has been considered as an important signaling pathway of NO in human cells. To date, all the four known human molybdenum-containing enzymes, xanthine oxidase, aldehyde oxidase, sulfite oxidase, and mitochondrial amidoxime-reducing component, have been shown to function as nitrite reductases under hypoxia by biochemical, cellular, or animal studies. Various spectroscopic techniques have been applied to investigate the structure and catalytic mechanism of these enzymes for more than 20 years.

Methods: We summarize the published data on the applications of UV-vis and EPR spectroscopies, and X-ray crystallography in studying nitrite reductase activity of the four human molybdenum-containing enzymes.

Results: UV-vis has provided useful information on the redox active centers of these enzymes. The utilization of EPR spectroscopy has been critical in determining the coordination and redox status of the Mo center during catalysis. Despite the lack of substrate-bound crystal structures of these nitrite reductases, valuable structural information has been obtained by X-ray crystallography.

Conclusions: To fully understand the catalytic mechanisms of these physiologically/pathologically important nitrite reductases, structural studies on substrate-redox center interaction are needed.     

Applications of MALDI-TOF mass spectrometry in clinical proteomics

Introduction: The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics.

Areas covered: This review aims to provide an updated overview of MALDI-TOF MS applications in clinical proteomics. The most relevant features of this analysis have been discussed, highlighting both pre-analytical and analytical factors that are crucial in proteomics studies. Particular emphasis is placed on biofluids proteomics for biomarkers discovery and on recent progresses in clinical microbiology, drug monitoring, and minimal residual disease (MRD).

Expert commentary: Despite some analytical limitations, the latest technological advances together with the easiness of use, the low time and low cost consuming and the high throughput are making MALDI-TOF MS instruments very attractive for the clinical practice. These features offer a significant potential for the routine of the clinical laboratory and ultimately for personalized medicine.     

Use of GPS tags to describe the home ranges,migration routes,stop-over locations and breeding area of Taiga Bean Geese Anser fabalis fabalis wintering in central Scotland

Capsule: Taiga Bean Geese Anser fabalis fabalis wintering near Falkirk, Scotland staged in Denmark, Norway and Sweden and summered in central Sweden.

Aims: To determine the migration routes, timing of movements, breeding area and home ranges of Taiga Bean Geese wintering near Falkirk, Scotland.

Methods: Ten Taiga Bean Geese, caught on the wintering grounds in Scotland, were marked with neck collars carrying global positioning system (GPS) tags. A further 21 geese were fitted with individually marked plastic neck collars. GPS location data were collected and field counts and searches for individually marked geese were undertaken to provide detailed information on their location throughout the year.

Results: Seven GPS tags provided information away from Scotland, indicating that two migration routes were used en route to the breeding grounds in Dalarna, Sweden. During the non-breeding season, the total home range of the geese was approximately 466?km², although the total area within agricultural fields used by the geese may have been as small as 13?km².

Conclusions: The timing of movements, migration routes, breeding area and identification of important stop-over sites for this wintering population are described for the first time.     

MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers

SUMMARY: Mitochondrial and Other Useful SEquences (MOUSE) is an integrated and comprehensive compilation of mtDNA from hypervariable regions I and II and of the low recombining nuclear loci Xq13.3 from about 11 200 humans and great apes, whose geographic and if applicable, linguistic classification is stored with their aligned sequences and publication details. The goal is to provide population geneticists and genetic epidemiologists with a comprehensive and user friendly repository of sequences and population information that is usually dispersed in a variety of other sources. AVAILABILITY: http://www.gen-epi.de/mouse. SUPPLEMENTARY INFORMATION: Documentation and detailed information on population subgroups is available on the homepage: http://www.gen-epi.de/mouse     

Mapping the human skeletal muscle proteome: progress and potential

Introduction: Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies.

Areas covered: This review critically analyses studies performed on muscle to date and identifies what still remains unknown or poorly investigated in physiological and pathological states, such as training, aging, metabolic disorders and muscular dystrophies.

Expert commentary: Efforts should be made on biological fluid analyses targeting low abundant/low molecular weight fragments generated from muscle cell disruption to improve diagnosis and clinical monitoring. From a methodological point of view, particular attention should be paid to improve the characterization of intact proteins and unknown post translational modifications to better understand the molecular mechanisms of muscle disorders.     

RETRACTED ARTICLE: A review of 45 candidate genes: Association of single nucleotide polymorphism to schizophrenia Risk

The following article has been retracted from publication in the Taylor & Francis journal New Genetics and Society. I. Priya, S. Sharma, I. Sharma, R. Mahajan and N. Kapoor, A review of 45 candidate genes: association of single nucleotide polymorphism to schizophrenia risk, New Genetics and Society https://doi.org/10.1080/14636778.2018.1481740. Version of Record published online 13 July 2018.

The editorial office of the journal inadvertently processed the paper through the online submission system without proper peer review or requisite checks. This has now been remedied and the journal and publishers apologise to the authors that this occurred. Journal processes and checks have now been reviewed and updated so that all best efforts are made to ensure this does not occur again.

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