Haploinsufficiency predictions without study bias

Any given human individual carries multiple genetic variants that disrupt protein-coding genes, through structural variation, as well as nucleotide variants and indels. Predicting the phenotypic consequences of a gene disruption remains a significant challenge. Current approaches employ information from a range of biological networks to predict which human genes are haploinsufficient (meaning two copies are required for normal function) or essential (meaning at least one copy is required for viability). Using recently available study gene sets, we show that these approaches are strongly biased towards providing accurate predictions for well-studied genes. By contrast, we derive a haploinsufficiency score from a combination of unbiased large-scale high-throughput datasets, including gene co-expression and genetic variation in over 6000 human exomes. Our approach provides a haploinsufficiency prediction for over twice as many genes currently unassociated with papers listed in Pubmed as three commonly-used approaches, and outperforms these approaches for predicting haploinsufficiency for less-studied genes. We also show that fine-tuning the predictor on a set of well-studied ‘gold standard’ haploinsufficient genes does not improve the prediction for less-studied genes. This new score can readily be used to prioritize gene disruptions resulting from any genetic variant, including copy number variants, indels and single-nucleotide variants.     

Functional enrichment analysis with structural variants: pitfalls and strategies

Interpreting the phenotypic consequences of human structural variation remains challenging. Functional enrichment analysis, which can identify functional enrichments among genes affected by structural variants, is providing significant biological insights into the genotype-phenotype relationship. In this review, we discuss the different approaches and choices in the application of this technique to human structural variation. We consider the importance of choosing the right background distribution for detection, the significance of the gene selection criteria, the effects of tissue-specific gene length biases and discuss sources of functional annotations with a focus on Gene Ontology and mouse phenotypic resources. Throughout this review, we highlight potential sources of significant bias that are of particular concern to the analysis of structural variants, and illustrate the importance of examining the expectations upon which enrichment analysis techniques depend.     

Tumor-Endothelial Cell Three-dimensional Spheroids: New Aspects to Enhance Radiation and Drug Therapeutics

Classic cancer research for several decades has focused on understanding the biology of tumor cells in vitro. However, extending these findings to in vivo settings has been impeded owing to limited insights on the impact of microenvironment on tumor cells. We hypothesized that tumor cell biology and treatment response would be more informative when done in the presence of stromal components, like endothelial cells, which exist in the tumor microenvironment. To that end, we have developed a system to grow three-dimensional cultures of GFP-4T1 mouse mammary tumor and 2H11 murine endothelial cells in hanging drops of medium in vitro. The presence of 2H11 endothelial cells in these three-dimensional cocultures was found to sensitize 4T1-GFP tumor cells to chemotherapy (Taxol) and, at the same time, protect cells from ionizing radiation. These spheroidal cultures can also be implanted into the dorsal skinfold window chamber of mice for fluorescence imaging of vascularization and disease progression/treatment response. We observed rapid neovascularization of the tumor-endothelial spheroids in comparison to tumor spheroids grown in nude mice. Molecular analysis revealed pronounced up-regulation of several proangiogenic factors in the tumor tissue derived from the tumor-endothelial spheroids compared with tumor-only spheroids. Furthermore, the rate of tumor growth from tumor-endothelial spheroids in mice was faster than the tumor cell-only spheroids, resulting in greater metastasis to the lung. This three-dimensional coculture model presents an improved way to investigate more pertinent aspects of the therapeutic potential for radiation and/or chemotherapy alone and in combination with antiangiogenic agents.     

MVPA is associated with lower weight gain in 8-10 year old children: a prospective study with 1 year follow-up

Background

Studies relating physical activity (PA) to weight gain in children have produced mixed results, although there is some evidence for stronger associations with more intense physical activities. The present study tested the hypothesis that weight gain over one year in 8–10 year olds would be more strongly predicted by moderate and vigorous physical activity (MVPA) than total physical activity (total PA) or sedentary behaviour.

Methodology

Participants were 280 children taking part in the Physical Exercise and Appetite in Children Study (PEACHES). Weight status was assessed using body mass index (BMI), fat mass index (FMI), and waist circumference (WC) in school Year 4 (baseline; age 8.7 yrs) and Year 5 (follow-up; age 9.7 yrs). Physical activity was measured at baseline using the Actigraph GT1M accelerometer to assess total PA (mean accelerometers counts per minute), MVPA; ≥4000 counts per minute) and sedentary time (<100 counts per minute).

Principal Findings

After adjustment for baseline BMI, SES, sex and ethnicity, MVPA was significantly associated with follow–up BMI (adjusted β = −0.07; p = 0.002). This association was independent of total PA or sedentary time. Similar results were observed for FMI; again MVPA was significantly associated with follow up FMI (β = −0.16; p = 0.001) independent of total PA or sedentary time. The pattern was similar for WC (β = −0.07), but the association between MVPA and WC did not reach significance at p = 0.06.

Conclusion

The results of this study strongly support promotion of MVPA in children.     

Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function

The Major Histocompatibility Complex (MHC) plays an important role in the human immune system. The MHC is involved in the antigen presentation system assisting T cells to identify foreign or pathogenic proteins. However, an MHC molecule binding a self-peptide may incorrectly trigger an immune response and cause an autoimmune disease, such as multiple sclerosis. Understanding the molecular mechanism of this process will greatly assist in determining the aetiology of various diseases and in the design of effective drugs. In the present study, we have used the Fresno semi-empirical scoring function and modify the approach to the prediction of peptide-MHC binding by using open-source and public domain software. We apply the method to HLA class II alleles DR15, DR1, and DR4, and the HLA class I allele HLA A2. Our analysis shows that using a large set of binding data and multiple crystal structures improves the predictive capability of the method. The performance of the method is also shown to be correlated to the structural similarity of the crystal structures used. We have exposed some of the obstacles faced by structure-based prediction methods and proposed possible solutions to those obstacles. It is envisaged that these obstacles need to be addressed before the performance of structure-based methods can be on par with the sequence-based methods.     

Exposure of Salmonella enterica serovar Typhimurium to high level biocide challenge can select multidrug resistant mutants in a single step

Background

Biocides are crucial to the prevention of infection by bacteria, particularly with the global emergence of multiply antibiotic resistant strains of many species. Concern has been raised regarding the potential for biocide exposure to select for antibiotic resistance due to common mechanisms of resistance, notably efflux.

Methodology/Principal Findings

Salmonella enterica serovar Typhimurium was challenged with 4 biocides of differing modes of action at both low and recommended-use concentration. Flow cytometry was used to investigate the physiological state of the cells after biocide challenge. After 5 hours exposure to biocide, live cells were sorted by FACS and recovered. Cells recovered after an exposure to low concentrations of biocide had antibiotic resistance profiles similar to wild-type cells. Live cells were recovered after exposure to two of the biocides at in-use concentration for 5 hours. These cells were multi-drug resistant and accumulation assays demonstrated an efflux phenotype of these mutants. Gene expression analysis showed that the AcrEF multidrug efflux pump was de-repressed in mutants isolated from high-levels of biocide.

Conclusions/Significance

These data show that a single exposure to the working concentration of certain biocides can select for mutant Salmonella with efflux mediated multidrug resistance and that flow cytometry is a sensitive tool for identifying biocide tolerant mutants. The propensity for biocides to select for MDR mutants varies and this should be a consideration when designing new biocidal formulations.     

Stem/progenitor and intermediate cell types and the origin of human prostate cancer

Theories of cell lineage in human prostatic epithelium, based on protein expression, propose that basal and luminal cells: 1) are either independently capable of self-renewal or 2) arise from stem cells expressing a full spectrum of proteins (p63, cytokeratins CK5/14, CK8/18, and glutathione-S-transferase-pi [GST-pi]) similar to cells of the embryonic urogenital sinus (UGS). Such embryonic-like stem cells are thought to give rise to mature basal cells and secretory luminal cells. By single cell cloning of an immortalized, normal human prostate-derived, non-tumorigenic RWPE-1 cell line, we isolated and characterized two epithelial cell types, WPE-stem and WPE-int. WPE-stem cells show: i) strong, sixfold greater nuclear expression of p63; ii) nearly twofold greater expression of CK14; iii) threefold less CK18, and iv) low androgen receptor (AR) expression as compared with WPE-int cells. WPE-stem cells are androgen-independent for growth and survival. WPE-int cells express very low p63 and CK5/14, and high CK18. WPE-int cells are androgen-independent for growth and survival but are highly responsive as shown by androgen induction of AR and prostate specific antigen (PSA). Compared with WPE-int cells, WPE-stem cells are smaller and show more rapid growth. WPE-stem cells can grow in an anchorage-independent manner in agar with 4.5-fold greater cloning efficiency and as free floating "prostaspheres" in liquid medium; and express over 40-fold higher matrix metalloproteinase-2 activity. These results indicate that WPE-stem cells express several features characteristic of stem/progenitor cells present in the UGS and in adult prostatic epithelium. In contrast, WPE-int cells have an intermediate, committed phenotype on the pathway to luminal cell differentiation. We propose that in normal prostatic epithelium, cells exist at many stages in a continuum of differentiation progressing from stem cells to definitive basal and luminal cells. Establishment and characterization of clones of human prostatic epithelial cells provide novel models for determining cell lineages, the origin of prostate cancer, and for developing new strategies for tumor prevention and treatment.     

Phytoplankton and zooplankton as indicators of water quality in Discovery Bay,Jamaica

Several investigations exist which use planktonic communities as indicators of water quality in Jamaican and Caribbean Bays, however, few are conducted before there are obvious effects of eutrophication. Therefore, most of our ‘baseline’ data are for bays already severely affected by pollution. This study was conducted to assess water quality in Discovery Bay, Jamaica, before there were severe signs of eutrophication. The bay was monitored over a 12-month period (October 1995–September 1996) using 10 stations. Physicochemical data indicated a well mixed upper 5 m of water column, below which discontinuities in temperature/salinity profiles indicated the influence of colder, more saline waters associated with deep offshore currents. Physicochemical variables were within the range for oligotrophic systems with a tendency towards mesotrophic in localized areas close to the shoreline. Signs of anthropogenic stress were associated with the eastern, southwestern and western sections of the bay. Of the over 120 species of phytoplankton found in the waters of Discovery Bay, most were neritic/oceanic and diatoms dominated while 11 were found to be potentially harmful species. While these harmful species occurred at all stations they occurred most frequently at stations on the eastern side of the bay. About 107 zooplankton species were identified, 52 of which were copepods. The species also represented a mix of neritic and oceanic taxa and mean abundances for the area ranged from 1077 m⁻³ at the mouth of the bay to 3794 m⁻³ close to the south shore (station 6). Generally stations closest to shore had greater zooplankton abundances than centrally located bay stations and stations close to oceanic influence. Acartia tonsa and Lucifer faxoni showed greatest densities at shoreline areas of the bay while Oithona plumifera, Undinula vulgaris and Temora stylifera were important at stations closest to oceanic influences. These species were thus considered as indicators of these different areas within the bay. From physicochemical data and the planktonic assemblage, Discovery Bay cannot be considered polluted, it is still more accurately classified as generally pristine with mesotrophic zones in the eastern and southeastern sections of the bay. These data therefore provide a real baseline of conditions for similar tropical coastal embayments.     

Bidirectional electron transfer in photosystem I: accumulation of A0- in A-side or B-side mutants of the axial ligand to chlorophyll A0

Photosystem I contains two potential electron transfer pathways between P(700) and F(X). These branches are made up of the electron transfer chain components A, A(0), and A(1). The primary electron acceptor A(0) is a chlorophyll a monomer that could be one or both of the two chlorophyll molecules, eC-A(3)/eC-B(3), identified in the 2.5 A resolution structure. The eC-A(3)/eC-B(3) chlorophylls are both coordinated by the sulfur atom of a methionine. This coordination is highly unusual, as interactions between the acid Mg(2+) and the soft base sulfur are weak. The eC-A(3)/eC-B(3) chlorophylls also are located close to one of the connecting chlorophylls that may link the antenna and the electron transfer chain chlorophylls. Due to their location in the structure, the eC-A(3)/eC-B(3) chlorophylls may play a role in both excitation energy transfer and electron transfer. To test the role of the eC-A(3)/eC-B(3) chlorophylls in electron transfer, Met-684 of PsaA and Met-664 of PsaB have been changed to His, Ser, and Leu. Replacement of either M(A684) or M(B664) results in a significant alteration in growth phenotype. The His and Leu mutants are very light sensitive in the presence of oxygen. Growth is impaired to a greater extent in the B-side mutants. However, all of the mutants are able to grow anaerobically at comparable rates. The His and Ser mutants all accumulate PSI at a level similar to that of wild type, whereas the Leu mutants have reduced amounts of PSI. Ultrafast transient absorbance measurements show that the (A(0)(-) - A(0)) difference signal accumulates in the MH(A684) and MH(B664) mutants under neutral conditions, demonstrating that electron transfer between A(0)(-) and A(1) is blocked or significantly slowed. The results show that both the A-branch and the B-branch of the ETC are active in PSI from Chlamydomonas reinhardtii.