A panel consisting of three novel circulating lncRNAs,is it a predictive tool for gastric cancer?

Early detection is vital for prolonging 5‐year survival for patients with gastric cancer (GC). Numerous studies indicate that circulating long non‐coding RNAs (lncRNAs) can be used to diagnose malignant tumours. This study aimed to investigate the capacity of novel lncRNAs for diagnosing GC. A lncRNA microarray assay was used to screen differentially expressed lncRNAs between plasma of patients with GC and healthy controls. Plasma samples from 100 patients with healthy controls were used to construct a multiple‐gene panel. An additional 50 pairs of GC patients with healthy controls were used to evaluate the diagnostic accuracy of the panel. Expression levels of lncRNAs were quantified through real‐time polymerase chain reaction. The receiver operating characteristic curve and area under curve (AUC) were used to estimate the diagnostic capacity. We identified three lncRNAs, CTC‐501O10.1, AC100830.4 and RP11‐210K20.5 that were up‐regulated in the plasma of GC patients with AUCs 0.724, 0.730 and 0.737, respectively (P < .01). Based on the logistic regression model, the combined AUC of the three lncRNAs was 0.764. The AUC of the panel was 0.700 in the validation cohort. These findings indicate that plasma lncRNAs can serve as potential biomarkers for detection of GC.     

How is human cooperation different?

Although cooperation is a widespread phenomenon in nature, human cooperation exceeds that of all other species with regard to the scale and range of cooperative activities. Here we review and discuss differences between humans and non-humans in the strategies employed to maintain cooperation and control free-riders. We distinguish forms of cooperative behaviour based on their influence on the immediate payoffs of actor and recipient. If the actor has immediate costs and only the recipient obtains immediate benefits, we term this investment. If the behaviour has immediate positive effects for both actor and recipient, we call this a self-serving mutually beneficial behaviour or mutual cooperation. We argue that humans, in contrast to all other species, employ a wider range of enforcement mechanisms, which allow higher levels of cooperation to evolve and stabilize among unrelated individuals and in large groups. We also discuss proximate mechanisms underlying cooperative behaviour and focus on our experimental work with humans and our closest primate relatives. Differences in the proximate mechanisms also seem to contribute to explaining humans'' greater ability to cooperate and enforce cooperation.     

How replicable are mRNA expression QTL?

Applying quantitative trait analysis methods to genome-wide microarray-derived mRNA expression phenotypes in segregating populations is a valuable tool in the attempt to link high-level traits to their molecular causes. The massive multiple-testing issues involved in analyzing these data make the correct level of confidence to place in mRNA abundance quantitative trait loci (QTL) a difficult problem. We use a unique resource to directly test mRNA abundance QTL replicability in mice: paired recombinant inbred (RI) and F₂ data sets derived from C57BL/6J (B6) and DBA/2J (D2) inbred strains and phenotyped using the same Affymetrix arrays. We have one forebrain and one striatum data set pair. We describe QTL replication at varying stringencies in these data. For instance, 78% of mRNA expression QTL (eQTL) with genome-wide adjusted p ≤ 0.0001 in RI data replicate at a genome-wide adjusted p < 0.05 or better. Replicated QTL are disproportionately putatively cis-acting, and approximately 75% have higher apparent expression levels associated with B6 genotypes, which may be partly due to probe set generation using B6 sequence. Finally, we note that while trans-acting QTL do not replicate well between data sets in general, at least one cluster of trans-acting QTL on distal Chr 1 is notably preserved between data sets.     

How informative is the mouse for human gut microbiota research?

The microbiota of the human gut is gaining broad attention owing to its association with a wide range of diseases, ranging from metabolic disorders (e.g. obesity and type 2 diabetes) to autoimmune diseases (such as inflammatory bowel disease and type 1 diabetes), cancer and even neurodevelopmental disorders (e.g. autism). Having been increasingly used in biomedical research, mice have become the model of choice for most studies in this emerging field. Mouse models allow perturbations in gut microbiota to be studied in a controlled experimental setup, and thus help in assessing causality of the complex host-microbiota interactions and in developing mechanistic hypotheses. However, pitfalls should be considered when translating gut microbiome research results from mouse models to humans. In this Special Article, we discuss the intrinsic similarities and differences that exist between the two systems, and compare the human and murine core gut microbiota based on a meta-analysis of currently available datasets. Finally, we discuss the external factors that influence the capability of mouse models to recapitulate the gut microbiota shifts associated with human diseases, and investigate which alternative model systems exist for gut microbiota research.KEY WORDS: Gut microbiota, Humanized mouse models, Mouse core gut microbiota, Mouse models, Mouse pan-gut microbiota     

How random is a highly denatured protein?

There has been renewed interest in determining the physicochemical properties of denatured states of proteins. In many denatured states there is evidence for the existence of nonrandom configurational distributions. Here we examine the small-angle neutron scattering profile of yeast phosphoglycerate kinase in the native state and in highly denaturing conditions. We show that the denatured protein scattering profile can be interpreted using a model developed for synthetic polymers in which the chain behaves as a random coil in a good solvent, i.e. with excluded volume interactions. The implications of this result for our appreciation of the protein folding process are discussed.     

How predictive is a cervical smear suggesting glandular neoplasia?

The prevalence of endocervical adenocarcinoma and its precursors has increased, in part due to increased diagnostic awareness of these lesions. To date, limited information has been published regarding the predictive value of glandular abnormalities in cervical smears. This study details the histological follow up of 418 cervical smears showing glandular abnormality, reported in our department over a six year period from 1993 to 1998. Histological follow up was available for 395 of the 418 smears (94.50%). The overall positive predictive value (PPV) for this group of smears was 72.66% for either significant glandular or squamous pathology (at least low grade cervical glandular intraepithelial neoplasia or CIN2 on follow up biopsy), and 55.70% for significant glandular pathology alone. Examination of subcategories of abnormal glandular smear showed that the PPV increased with the degree of abnormality reported within the smears.     

How distributed is visual category information in human occipito-temporal cortex? An fMRI study

We used fMRI to study the distribution of object category information in the ventral visual pathway. Extending the findings of, we find that categories of stimuli can be distinguished by the pattern of activation they elicit across this entire pathway, even when the stimuli within a category differ in viewpoint, exemplar, or image format. However, regions within the ventral visual pathway are neither interchangeable nor equipotential. Although the FFA and PPA permit excellent discrimination between preferred versus nonpreferred stimuli (e.g., faces-bottles and houses-bottles, respectively), we find that neither region alone permits accurate discrimination between pairs of nonpreferred stimuli (e.g., bottles-shoes). These findings indicate that the ventral visual pathway is not homogeneous, but contains some regions (including FFA and PPA) that are primarily involved in the analysis of a single class of stimulus.     

How blind is double-blind? A study of fish oil versus placebo

The distinctive aftertaste associated with fish oil preparations used in clinical trials of omega-3 fatty acids may weaken the double-blind. This double-blind pilot study was designed to examine whether normal subjects could correctly 'guess' if they were receiving capsules containing concentrated fish oil or capsules of pure olive oil. The informed consent was designed to give subjects ambiguous expectations about what oil they might be receiving to examine whether this would influence their guess. Despite a marked difference in taste experience, there was no significant difference in correct guesses between the two groups. The results suggest that altering subjects' expectations could further improve the validity of the double-blind.     

YKL-40 protein expression in normal adult human tissues – an immunohistochemical study

YKL-40, a 40 kDa plasma protein, is secreted by macrophages, neutrophils, chondrocytes, vascular smooth muscle cells and cancer cells. High plasma YKL-40 is found in patients with inflammatory diseases and cancer, but it is not known how the protein is expressed in tissues. This immunohistochemical study was carried out with the purpose of mapping and grading cytoplasmic expression of YKL-40 in normal human tissue. Bovine serum albumin had to be used for pre-incubation in order to eliminate background staining of YKL-40. The majority of cells were stained, but the intensity varied, not just among different cell types but also within the same cell type. Cells known for exerting a high metabolic activity, i.e., high producing cells or cells with high turn-over, tended to show the most intense cytoplasmic staining, which was weak or lacking in cells with no or little activity. Many of these positive cells probably contribute to the YKL-40 found in plasma in healthy subjects in accordance with previous findings on their in vitro production of the protein. In conclusion, all cells with a functioning nucleus appeared to be capable of expressing YKL-40 in their cytoplasm, the intensity of which was dependent on cellular activity. An erratum to this article can be found at     

How much can physics do for protein design?

Physics and physical chemistry are an important thread in computational protein design, complementary to knowledge-based tools. They provide molecular mechanics scoring functions that need little or no ad hoc parameter readjustment, methods to thoroughly sample equilibrium ensembles, and different levels of approximation for conformational flexibility. They led recently to the successful redesign of a small protein using a physics-based folded state energy. Adaptive Monte Carlo or molecular dynamics schemes were discovered where protein variants are populated as per their ligand-binding free energy or catalytic efficiency. Molecular dynamics have been used for backbone flexibility. Implicit solvent models have been refined, polarizable force fields applied, and many physical insights obtained.     

Increased expression of FcγRI/CD64 on circulating monocytes parallels ongoing inflammation and nephritis in lupus

Introduction  

The high-affinity receptor for IgG Fcγ/CD64 is critical for the development of lupus nephritis (LN). Cross-linking Fc receptor on recruited monocytes by IgG-containing immune complexes is a key step in immune-complex-mediated nephritis in systemic lupus erythematosus (SLE). The goal of this study was to determine whether expression of Fc receptor (FcγR) I on circulating monocytes is associated with systemic inflammation and renal disease in SLE patients.     

Mitochondrial gene history and mRNA localization: is there a correlation?

Phylogenetic studies of the yeast mitochondrial proteome have shown a complex evolutionary scenario, in which proteins of bacterial origin form complexes with proteins of eukaryotic origin. Exciting new results from whole-genome microarray studies of subcellular mRNA localizations have shown that mRNAs that are of putative bacterial origin are mainly translated on polysomes that are associated with the mitochondrion, whereas those of eukaryotic origin are generally translated on free cytosolic polysomes. Understanding these newly discovered relationships promises insights into old questions about organelle origins and mRNA localization in the eukaryotic cell.     

Is mass spectrometry ready for proteome-wide protein expression analysis?

Recent advances in mass spectrometry will soon allow routine analysis of protein expression levels. How close are we to true quantitative proteomics?     

How important is DNA replication for mutagenesis?

Rates of mutation and substitution in mammals are generally greater in the germ lines of males. This is usually explained as resulting from the larger number of germ cell divisions during spermatogenesis compared with oogenesis, with the assumption made that mutations occur primarily during DNA replication. However, the rate of cell division is not the only difference between male and female germ lines, and mechanisms are known that can give rise to mutations independently of DNA replication. We investigate the possibility that there are other causes of male-biased mutation. First, we show that patterns of variation at approximately 5,200 short tandem repeat (STR) loci indicate a higher mutation rate in males. We estimate a ratio of male-to-female mutation rates of approximately 1.9. This is significantly greater than 1 and supports a greater rate of mutation in males, affecting the evolution of these loci. Second, we show that there are chromosome-specific patterns of nucleotide and dinucleotide composition in mammals that have been shaped by mutation at CpG dinucleotides. Comparable patterns occur in birds. In mammals, male germ lines are more methylated than female germ lines, and these patterns indicate that differential methylation has played a role in male-biased vertebrate evolution. However, estimates of male mutation bias obtained from both classes of mutation are substantially lower than estimates of cell division bias from anatomical data. This discrepancy, along with published data indicating slipped-strand mispairing arising at STR loci in nonreplicating DNA, suggests that a substantial percentage of mutation may occur in nonreplicating DNA.     

How early is firing required for wiring?

Activity is known to be important for the refinement of neural connections in the developing brain. In this issue of Neuron, Hanson and Landmesser provide evidence that GABA-dependent spontaneous bursting of motor neurons in the embryonic spinal cord is required for the correct execution of an early axon pathfinding decision.