Network deconvolution as a general method to distinguish direct dependencies in networks

Recognizing direct relationships between variables connected in a network is a pervasive problem in biological, social and information sciences as correlation-based networks contain numerous indirect relationships. Here we present a general method for inferring direct effects from an observed correlation matrix containing both direct and indirect effects. We formulate the problem as the inverse of network convolution, and introduce an algorithm that removes the combined effect of all indirect paths of arbitrary length in a closed-form solution by exploiting eigen-decomposition and infinite-series sums. We demonstrate the effectiveness of our approach in several network applications: distinguishing direct targets in gene expression regulatory networks; recognizing directly interacting amino-acid residues for protein structure prediction from sequence alignments; and distinguishing strong collaborations in co-authorship social networks using connectivity information alone. In addition to its theoretical impact as a foundational graph theoretic tool, our results suggest network deconvolution is widely applicable for computing direct dependencies in network science across diverse disciplines.National Institutes of Health (U.S.) (grant R01 HG004037)National Institutes of Health (U.S.) (grant HG005639)Swiss National Science Foundation (Fellowship)National Science Foundation (U.S.) (NSF CAREER Award 0644282

Side Chain Hydrophobicity Modulates Therapeutic Activity and Membrane Selectivity of Antimicrobial Peptide Mastoparan-X

The discovery of new anti-infective compounds is stagnating and multi-resistant bacteria continue to emerge, threatening to end the "antibiotic era". Antimicrobial peptides (AMPs) and lipo-peptides such as daptomycin offer themselves as a new potential class of antibiotics; however, further optimization is needed if AMPs are to find broad use as antibiotics. In the present work, eight analogues of mastoparan-X (MPX) were investigated, having side chain modifications in position 1, 8 and 14 to modulate peptide hydrophobicity. The self-association properties of the peptides were characterized, and the peptide-membrane interactions in model membranes were compared with the bactericidal and haemolytic properties. Alanine substitution at position 1 and 14 resulted in higher target selectivity (red blood cells versus bacteria), but also decreased bactericidal potency. For these analogues, the gain in target selectivity correlated to biophysical parameters showing an increased effective charge and reduction in the partitioning coefficient for membrane insertion. Introduction of an unnatural amino acid, with an octyl side chain by amino acid substitution, at positions 1, 8 and 14 resulted in increased bactericidal potency at the expense of radically reduced membrane target selectivity. Overall, optimized membrane selectivity or bactericidal potency was achieved by changes in side chain hydrophobicity of MPX. However, enhanced potency was achieved at the expense of selectivity and vice versa in all cases

The evolutionary significance of polyploidy

Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity

RNase 7 Contributes to the Cutaneous Defense against Enterococcus faecium

Background: Human skin is able to mount a fast response against invading microorganisms by the release of antimicrobial proteins such as the ribonuclease RNase 7. Because RNase 7 exhibits high activity against Enterococcus faecium the aim of this study was to further explore the role of RNase 7 in the cutaneous innate defense system against E. faecium. Methodology/Principal Findings: Absolute quantification using real-time PCR and ELISA revealed that primary keratinocytes expressed high levels of RNase 7. Immunohistochemistry showed RNase 7 expression in all epidermal layers of the skin with an intensification in the upper more differentiated layers. Furthermore, RNase 7 was secreted by keratinocytes in vitro and in vivo in a site-dependent way. RNase 7 was still active against E. faecium at low pH (5.5) or high NaCl (150 mM) concentration and the bactericidal activity of RNase 7 against E. faecium required no ribonuclease activity as shown by recombinant RNase 7 lacking enzymatic activity. To further explore the role of RNase 7 in cutaneous defense against E. faecium, we investigated whether RNase 7 contributes to the E. faecium killing activity of skin extracts derived from stratum corneum. Treatment of the skin extract with an RNase 7 specific antibody, which neutralizes the antimicrobial activity of RNase 7, diminished its E. faecium killing activity. Conclusions/Significance: Our data indicate that RNase 7 contributes to the E. faecium-killing activity of skin extracts an

COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia

Background: Microarrays are the main technology for large-scale transcriptional gene expression profiling, but the large bodies of data available in public databases are not useful due to the large heterogeneity. There are several initiatives that attempt to bundle these data into expression compendia, but such resources for bacterial organisms are scarce and limited to integration of experiments from the same platform or to indirect integration of per experiment analysis results. Methodology/Principal Findings: We have constructed comprehensive organism-specific cross-platform expression compendia for three bacterial model organisms (Escherichia coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium) together with an access portal, dubbed COLOMBOS, that not only provides easy access to the compendia, but also includes a suite of tools for exploring, analyzing, and visualizing the data within these compendia. It is freely available at http://bioi.biw.kuleuven.be/colombos. The compendia are unique in directly combining expression information from different microarray platforms and experiments, and we illustrate the potential benefits of this direct integration with a case study: extending the known regulon of the Fur transcription factor of E. coli. The compendia also incorporate extensive annotations for both genes and experimental conditions; these heterogeneous data are functionally integrated in the COLOMBOS analysis tools to interactively browse and query the compendia not only for specific genes or experiments, but also metabolic pathways, transcriptional regulation mechanisms, experimental conditions, biological processes, etc. Conclusions/Significance: We have created cross-platform expression compendia for several bacterial organisms and developed a complementary access port COLOMBOS, that also serves as a convenient expression analysis tool to extract useful biological information. This work is relevant to a large community of microbiologists by facilitating the use of publicly available microarray experiments to support their research

Cross talk between hedgehog and epithelial–mesenchymal transition pathways in gastric pit cells and in diffuse-type gastric cancers

We previously reported hedgehog (Hh) signal activation in the mucus-secreting pit cell of the stomach and in diffuse-type gastric cancer (GC). Epithelial–mesenchymal transition (EMT) is known to be involved in tumour malignancy. However, little is known about whether and how both signallings cooperatively act in diffuse-type GC. By microarray and reverse transcription–PCR, we investigated the expression of those Hh and EMT signalling molecules in pit cells and in diffuse-type GCs. How both signallings act cooperatively in those cells was also investigated by the treatment of an Hh-signal inhibitor and siRNAs of Hh and EMT transcriptional key regulator genes on a mouse primary culture and on human GC cell lines. Pit cells and diffuse-type GCs co-expressed many Hh and EMT signalling genes. Mesenchymal-related genes (WNT5A, CDH2, PDGFRB, EDNRA, ROBO1, ROR2, and MEF2C) were found to be activated by an EMT regulator, SIP1/ZFHX1B/ZEB2, which was a target of a primary transcriptional regulator GLI1 in Hh signal. Furthermore, we identified two cancer-specific Hh targets, ELK1 and MSX2, which have an essential role in GC cell growth. These findings suggest that the gastric pit cell exhibits mesenchymal-like gene expression, and that diffuse-type GC maintains expression through the Hh–EMT pathway. Our proposed extensive Hh–EMT signal pathway has the potential to an understanding of diffuse-type GC and to the development of new drugs

Associated tears of the lateral meniscus in anterior cruciate ligament injuries: risk factors for different tear patterns

BACKGROUND: The pattern of lateral meniscus tears observed in anterior cruciate ligament (ACL)-injured subjects varies greatly and determines subsequent management. Certain tear patterns with major biomechanical consequences should be repaired in a timely manner. Knowledge about risk factors for such tears may help to identify patients in the early posttraumatic phase and subsequently may improve clinical results. METHODS: A database of 268 patients undergoing primary ACL reconstruction was used to identify all patients with isolated ACL tears and patients with an associated tear of the lateral meniscus. Patients who underwent surgery >6 months after the injury were excluded. Based on the arthroscopic appearance of the lateral meniscus, patients were assorted to one of three groups: ‘no tear,’ ‘minor tear,’ and ‘major tear.’ Tear patterns defined as major included root tears, complete radial tears, and unstable longitudinal tears including bucket-handle tears. Univariate analysis was performed by comparing the three groups with regard to gender, age, height, weight, BMI, type of injury (high-impact sport, low-impact sport, and not sports related), and mechanism of injury (non-contact vs. contact). Multivariate logistic regression was carried out to identify independent risk factors for minor and major meniscal tears and to calculate odds ratios (OR). RESULTS: Two hundred fifteen patients met the inclusion and exclusion criteria. Of those, 56% had isolated ACL tears, 27% had associated minor tears, and 17% had associated major tears of the lateral meniscus. Univariate analysis revealed significant differences between the three groups for gender (p = 0.002), age groups (p = 0.026), and mechanism of injury (p < 0.001). A contact injury mechanism was a risk factor for minor tears (OR: 4.28) and major tears (OR: 18.49). Additional risk factors for major tears were male gender (OR: 7.38) and age <30 years (OR: 5.85). CONCLUSION: Male patients, patients <30 years, and particularly patients who sustained a contact injury have a high risk for an associated major lateral meniscus tear. Special attention is therefore necessary in those patients and early referral to magnetic resonance imaging and/or arthroscopy is recommended to allow meniscus repair in a timely manner

Intimate Partner Violence Victimization Among Non-Heterosexuals: Prevalence and Associations With Mental and Sexual Well-Being

This study focused on intimate partner violence (IPV) among non-heterosexuals in Flanders. Prevalence rates were explored and compared with heterosexual IPV using a first representative sample consisting of 1690 heterosexuals and non-heterosexual individuals. A second convenience sample consisting of 2401 non-heterosexual individuals was used to determine differences between women and men and to explore associations between IPV and victims' well-being. Physical and psychological IPV inflicted by the current/former partner were reported by 14.5 and 57.9 % of the non-heterosexuals, respectively. Non-heterosexuals and heterosexuals were equally likely to report physical and psychological IPV. Furthermore, non-heterosexual women and men reported similar physical, sexual, and psychological IPV. However, female victims experienced more frequent acts of psychological IPV. IPV was negatively associated with victims' well-being

Disorders of intestinal rotation and fixation (“malrotation”)

Malrotation with volvulus is one of the true surgical emergencies of childhood. Prompt radiological diagnosis is often paramount to achieving a good outcome. An understanding of the normal and anomalous development of the midgut provides a basis for understanding the pathophysiology and the clinical presentation of malrotation and malrotation complicated by volvulus. In this essay, the radiologic findings of malrotation and volvulus are reviewed and illustrated with particular attention to the child with equivocal imaging findings.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46708/1/247_2004_Article_1279.pd