Recent successes illustrate the role of mass spectrometry-based proteomics as an indispensable tool for molecular and cellular biology and for the emerging field of systems biology. These include the study of protein-protein interactions via affinity-based isolations on a small and proteome-wide scale, the mapping of numerous organelles, the concurrent description of the malaria parasite genome and proteome, and the generation of quantitative protein profiles from diverse species. The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.

Mass spectrometry-based proteomics

Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts have already produced a wealth of data. As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery. This paper describes a novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes. The method is based on vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions according to given parameters. The algorithm has the advantage over other graph clustering methods of having a directed mode that allows fine-tuning of clusters of interest without considering the rest of the network and allows examination of cluster interconnectivity, which is relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces cerevisiae was used for evaluation. Dense regions of protein interaction networks can be found, based solely on connectivity data, many of which correspond to known protein complexes. The algorithm is not affected by a known high rate of false positives in data from high-throughput interaction techniques. The program is available from ftp://ftp.mshri.on.ca/pub/BIND/Tools/MCODE
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An automated method for finding molecular complexes in large protein interaction networks.

We are in the midst of a technological revolution whereby, for the first time, researchers can link daily word use to a broad array of real-world behaviors. This article reviews several computerized text analysis methods and describes how Linguistic Inquiry and Word Count (LIWC) was created and validated. LIWC is a transparent text analysis program that counts words in psychologically meaningful categories. Empirical results using LIWC demonstrate its ability to detect meaning in a wide variety of experimental settings, including to show attentional focus, emotionality, social relationships, thinking styles, and individual differences.

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The psychological meaning of words: LIWC and computerized text analysis methods

A fundamental goal of cell biology is to define the functions of proteins in the context of compartments that organize them in the cellular environment. Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories, and provide localization information for 70% of previously unlocalized proteins. Analysis of this high-resolution, high-coverage localization data set in the context of transcriptional, genetic, and protein-protein interaction data helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.

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Global analysis of protein localization in budding yeast

Given the functional interdependencies between the molecular components in a human cell, a disease is rarely a consequence of an abnormality in a single gene, but reflects the perturbations of the complex intracellular and intercellular network that links tissue and organ systems. The emerging tools of network medicine offer a platform to explore systematically not only the molecular complexity of a particular disease, leading to the identification of disease modules and pathways, but also the molecular relationships among apparently distinct (patho)phenotypes. Advances in this direction are essential for identifying new disease genes, for uncovering the biological significance of disease-associated mutations identified by genome-wide association studies and full-genome sequencing, and for identifying drug targets and biomarkers for complex diseases.

Network Medicine: A Network-Based Approach to Human Disease

This work was part funded by the Centre for Research and Evidence on Security Threats (ESRC Award: ES/N009614/1). Direct correspondence to Paul J. Taylor, Department of Psychology, Lancaster University, Lancaster, U.K. LA1 4YF (e-mail p.j.taylor@lancaster.ac.uk). Comment [SVV1]: AU: Please note that your article has been edited to be consistent with the style and preferences of CPP and the other articles included in this issue.

/pdf/same-kind-of-different-affordances-terrorism-and-the-r3htfpl76a.pdf

Same kind of different: affordances, terrorism, and the Internet

Synaptic transmission is highly plastic and subject to regulation by a wide variety of neuromodulators and neuropeptides. In the present study, we have examined the role of isoforms of the cytochrome b561 homologue called no extended memory (nemy) in regulation of synaptic strength and plasticity at the neuromuscular junction (NMJ) of third instar larvae in Drosophila. Specifically, we generated two independent excisions of nemy that differentially affect the expression of nemy isoforms. We show that the nemy45 excision, which specifically reduces the expression of the longest splice form of nemy, leads to an increase in stimulus evoked transmitter release and altered synaptic plasticity at the NMJ. Conversely, the nemy26.2 excision, which appears to reduce the expression of all splice forms except the longest splice isoform, shows a reduction in stimulus evoked transmitter release, and enhanced synaptic plasticity. We further show that nemy45 mutants have reduced levels of amidated peptides similar to that observed in peptidyl-glycine hydryoxylating mono-oxygenase (PHM) mutants. In contrast, nemy26.2 mutants show no defects in peptide amidation but rather display a decrease in Tyramine β hydroxylase activity (TβH). Taken together, these results show non-redundant roles for the different nemy isoforms and shed light on the complex regulation of neuromodulators.

/pdf/distinct-regulation-of-transmitter-release-at-the-drosophila-5fk0j2zbbc.pdf

Distinct Regulation of Transmitter Release at the Drosophila NMJ by Different Isoforms of nemy.

Reports about repeated experiences tend to include more schematic information than information about specific instances. However, investigators in both forensic and intelligence settings typically seek specific over general information. We tested a multi-method interviewing format (MMIF) to facilitate recall and particularisation of repeated events through the use of the self-generated cues mnemonic, the timeline technique, and follow-up questions. Over separate sessions, 150 adult participants watched four scripted films depicting a series of meetings in which a terrorist group planned attacks and planted explosive devices. For half of our sample, the third witnessed event included two deviations (one new detail and one changed detail). A week later, participants provided their account using the MMIF, the timeline technique with self-generated cues, or a free recall format followed by open-ended questions. As expected, more information was reported overall in the MMIF condition compared to the other format conditions, for two types of details, correct details, and correct gist details. The reporting of internal intrusions was comparable across format conditions. Contrary to hypotheses, the presence of deviations did not benefit recall or source monitoring. Our findings have implications for information elicitation in applied settings and for future research on adults’ retrieval of repeated events.

Facilitating recall and particularisation of repeated events in adults using a multi-method interviewing format

Criminal profiling: granfalloons and gobbledygook

Two experiments explore the effect of law enforcement officers’ communication errors and their response strategies on a suspect’s trust in the officer; established rapport and hostility; and, the amount and quality of information shared. Students were questioned online by an exam board member about exam fraud (Nstudy1  = 188) or by a police negotiator after they had stolen money and barricaded themselves (Nstudy2  = 184). Unknown to participants, the online utterances of the law enforcement officer were pre-programmed to randomly assign them to a condition in a 2(Error: factual, judgment) × 3(Response: contradict, apologize, accept) factorial design, or to control where no error was made. Our findings show that making (judgment) errors seem more detrimental for affective trust and rapport in a suspect interview, while no such effects appeared in a crisis negotiation. Notably, we found a positive effect of errors, as more information was being shared. The ultimate effect of the error was dependent on the response: accept was effective in re-establishing rapport and decreasing hostility, while contradict threatens it. Accept seems more effective for the willingness to provide information in a suspect interview, while apologize seems more effective for affective trust and rapport in a crisis negotiation.

https://www.tandfonline.com/doi/pdf/10.1080/1068316X.2017.1390112

Paul J. Taylor

Papers

Same kind of different: affordances, terrorism, and the Internet

Distinct Regulation of Transmitter Release at the Drosophila NMJ by Different Isoforms of nemy.

Facilitating recall and particularisation of repeated events in adults using a multi-method interviewing format

Criminal profiling: granfalloons and gobbledygook

Communication error management in law enforcement interactions:a receiver’s perspective