Presence of several plasmids in the fungus Ascobolus immersus, and homologies with the linear plasmid pA1

DNA analysis of several genetically unstable strains of the fungus Ascobolus immersus revealed the presence of at least seven different plasmids. These plasmids ranged from 2 to 20 kb in size, and showed homology to one of them, pA1. In 18 stocks directly isolated from nature, two-thirds harboured plasmids ranging from 3 to 17 kb. Plasmids with homology to pA1 had similar molecular masses (about 8.5 kb). A possible mechanism of plasmid formation from chromosomal DNA is discussed.     

Ultrastructural analysis of the in vitro differentiation of female rat preadipocytes

In an attempt to characterize the preadipocytes of the adipose tissue of female rat, we studied by electron microscopy the differentiation of the cells into mature adipocytes in in vitro cultures. The preadipocytes arose from the stroma-vascular fraction of perirenal and perigenital adipose tissue. Culture of the preadipocytes in an enriched medium consisting of Dulbecco's medium supplemented with 10% fetal calf serum, antibiotics, rat triglycerides (0.5%), insulin (290 nM) and Tween 80 (0.1 mg/ml) induced their adipose conversion. The morphology of preadipocytes changed progressively. They accumulated fat granules, droplets and finally globules, which fused together. The cell organelles featured qualitative and quantitative modifications. The nucleus migrated with most mitochondria and a part of the Golgi system towards the cell periphery; the rough endoplasmic reticulum, dilated at the initial stage of differentiation became less and less conspicuous; the perinuclear Golgi system was dispersed between lipid droplets during fat accumulation; thick bundles of microfilaments, localized beneath the plasma membrane disappeared; large lipid droplets were surrounded by a network of microfilaments; many microvesicles and some "rosettes" typical of mature adipocytes could be observed. Nevertheless, the ultrastructural criteria did not allow to clearly discriminate the undifferentiated cells: early preadipocytes (without lipid droplets), adipoblasts and fibroblasts, all of these being probably present in the culture system.     

A geographically variable model of hemlock woolly adelgid spread

The hemlock woolly adelgid (HWA) (Adelges tsugae) has spread through the range of eastern hemlock (Tsuga canadensis) leaving dead hemlock trees in its wake. We combined county and previously unavailable township level infestation records with geographic variables including plant hardiness zone, elevation, forest cover type, urbanization, precipitation, temperature, and hemlock range in a geographic information system to build models linking HWA spread to the structure and characteristics of the environment. We explored the connections between site variables and spread rate using quantile regression, Tobit regression, a parametric model for heterogeneous error variance, and classification and regression tree modeling. The results show that since 1990 HWA has spread at a rate closer to 12.5 km/yr rather than the 20–30 km/yr previously estimated, however spread rates vary significantly with environmental variables. County-based data show a faster rate of range expansion in the south, 15.6 km/yr, and very slow spread in the northern part of the current range of HWA. The rate of spread based on township records for Pennsylvania and north is 8.13 km/yr. Our study suggests that HWA spreads more slowly in colder areas, with a mean minimum temperature of  − 26.1°C (plant hardiness zone 5B) delineating areas of slower range expansion. HWA also spreads more slowly during cold years, those with lower than average mean January temperatures. Our analysis demonstrates the value of quantile regression, Tobit regression, and classification and regression tree models for understanding the spread of invasive, exotic insects.     

High Throughput Discovery of Solar Fuels Photoanodes in the CuO–V2O5 System

Solar photoelectrochemical generation of fuel is a promising energy technology yet the lack of an efficient, robust photoanode remains a primary materials challenge in the development and deployment of solar fuels generators. Metal oxides comprise the most promising class of photoanode materials, but no known material meets the demanding requirements of low band gap energy, photoelectrocatalysis of the oxygen evolution reaction (OER), and stability under highly oxidizing conditions. Here, the identification of new photoelectroactive materials is reported through a strategic combination of combinatorial materials synthesis, high‐throughput photoelectrochemistry, optical spectroscopy, and detailed electronic structure calculations. Four photoelectrocatalyst phases, α ‐Cu₂V₂O₇, β ‐Cu₂V₂O_7, γ ‐Cu₃V₂O₈, and Cu₁₁V₆O₂₆, are reported with band gap energy at or below 2 eV. The photoelectrochemical properties and 30 min stability of these copper vanadate phases are demonstrated in three different aqueous electrolytes (pH 7, pH 9, and pH 13), with select combinations of phase and electrolyte exhibiting unprecedented photoelectrocatalytic stability for metal oxides with sub‐2 eV band gap. Through integration of experimental and theoretical techniques, new structure‐property relationships are determined and establish CuO–V₂O₅ as the most prominent composition system for OER photoelectrocatalysts, providing crucial information for materials genomes initiatives and paving the way for continued development of solar fuels photoanodes.     

The Isomerase Active Site of Cyclophilin A Is Critical for Hepatitis C Virus Replication

Cyclosporine A and nonimmunosuppressive cyclophilin (Cyp) inhibitors such as Debio 025, NIM811, and SCY-635 block hepatitis C virus (HCV) replication in vitro. This effect was recently confirmed in HCV-infected patients where Debio 025 treatment dramatically decreased HCV viral load, suggesting that Cyps inhibitors represent a novel class of anti-HCV agents. However, it remains unclear how these compounds control HCV replication. Recent studies suggest that Cyps are important for HCV replication. However, a profound disagreement currently exists as to the respective roles of Cyp members in HCV replication. In this study, we analyzed the respective contribution of Cyp members to HCV replication by specifically knocking down their expression by both transient and stable small RNA interference. Only the CypA knockdown drastically decreased HCV replication. The re-expression of an exogenous CypA escape protein, which contains escape mutations at the small RNA interference recognition site, restored HCV replication, demonstrating the specificity for the CypA requirement. We then mutated residues that reside in the hydrophobic pocket of CypA where proline-containing peptide substrates and cyclosporine A bind and that are vital for the enzymatic or the hydrophobic pocket binding activity of CypA. Remarkably, these CypA mutants fail to restore HCV replication, suggesting for the first time that HCV exploits either the isomerase or the chaperone activity of CypA to replicate in hepatocytes and that CypA is the principal mediator of the Cyp inhibitor anti-HCV activity. Moreover, we demonstrated that the HCV NS5B polymerase associates with CypA via its enzymatic pocket. The study of the roles of Cyps in HCV replication should lead to the identification of new targets for the development of alternate anti-HCV therapies.Hepatitis C virus (HCV)² is the main contributing agent of acute and chronic liver diseases worldwide (1). Primary infection is often asymptomatic or associated with mild symptoms. However, persistently infected individuals develop high risks for chronic liver diseases such as hepatocellular carcinoma and liver cirrhosis (1). The combination of IFNα and ribavirin that serves as current therapy for chronically HCV-infected patients not only has a low success rate (about 50%) (2) but is often associated with serious side effects (2). There is thus an urgent need for the development of novel anti-HCV treatments (2).The immunosuppressive drug cyclosporine A (CsA) was reported to be clinically effective against HCV (3). Controlled trials showed that a combination of CsA with IFNα is more effective than IFNα alone, especially in patients with a high viral load (4, 5). Moreover, recent in vitro studies provided evidence that CsA prevents both HCV RNA replication and HCV protein production in an IFNα-independent manner (6–10). CsA exerts this anti-HCV activity independently of its immunosuppressive activity because the nonimmunosuppressive Cyp inhibitors such as Debio 025, NIM811, and SCY-635 also block HCV RNA and protein production (9, 11–14). Unlike CsA, these molecules do not display calcineurin affinity and specifically inhibit the peptidyl-prolyl cis-trans-isomerase (PPIase) Cyps. Most importantly, recent clinical data demonstrated that Debio 025 dramatically decreased HCV viral load (3.6 log decrease) in patients coinfected with HCV and HIV (15). This 14-day Debio 025 treatment (1200 mg orally administered twice daily) was effective against the three genotypes (genotypes 1, 3, and 4) represented in the study. More recently, the anti HCV effect of Debio 025 in combination with peginterferon α 2a (peg-IFNα2a) was investigated in treatment-inexperienced patients with chronic hepatitis C. Debio 025 (600 mg administered once daily) in combination with peg-IFNα2a (180 μg/week) for 4 weeks induced a continuous decay in viral load that reached −4.61 ± 1.88 IU/ml in patients with genotypes 1 and 4 and −5.91 ± 1.11 IU/ml in patients with genotypes 2 and 3 at week 4 (16). The Debio 025 findings are critical because they suggest that Cyp inhibitors represent a novel class of anti-HCV agents. However, it remains unclear how these compounds control HCV replication. The fact that several recent studies using small RNA interference knockdown approaches suggest that Cyps are critical for the HCV life cycle (9, 17, 18) strongly implies that there is a direct or indirect link between the CsA- and CsA derivative-mediated inhibitory effect on HCV replication and host Cyps.The discovery 20 years ago of the first cellular protein showing PPIase activity (19) was entirely unrelated to the discovery of CypA as an intracellular protein possessing a high affinity for CsA (20). It is only a few years later that Fischer et al. (21) demonstrated that the 18-kDa protein with PPIase activity and CypA represent a single unique protein. All Cyps contain a common domain of 109 amino acids, called the Cyp-like domain, which is surrounded by domains specific to each Cyp members and which dictates their cellular compartmentalization and function (22). Bacteria, fungi, insects, plants, and mammals contain Cyps, which all have PPIase activity and are structurally conserved (22). To date, 16 Cyp members have been identified, and 7 of them are found in humans: CypA, CypB, CypC, CypD, CypE, Cyp40, and CypNK (22).Although there is a growing body of evidence that Cyps control HCV replication in human hepatocytes, a major disagreement currently exists on the respective roles of Cyp members in HCV replication. One study suggests that CypB, but not CypA, is critical for HCV replication (17), another suggests that CypA, but not CypB and CypC, is critical for HCV replication (18), and a third study suggests that three Cyps, CypA, B, and C, are all required for HCV replication (9). Thus, although it becomes evident that Cyps serve as HCV co-factors, their respective contributions and roles in the HCV life cycle remain to be determined. An understanding of the mechanisms that control the Cyp inhibitor-mediated anti-HCV effect is imperative because it will provide new alternate anti-HCV therapies and shed light on the still poorly understood early and late steps of the HCV life cycle.     

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

Background

Systems biology has embraced computational modeling in response to the quantitative nature and increasing scale of contemporary data sets. The onslaught of data is accelerating as molecular profiling technology evolves. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) is a community effort to catalyze discussion about the design, application, and assessment of systems biology models through annual reverse-engineering challenges.

Methodology and Principal Findings

We describe our assessments of the four challenges associated with the third DREAM conference which came to be known as the DREAM3 challenges: signaling cascade identification, signaling response prediction, gene expression prediction, and the DREAM3 in silico network challenge. The challenges, based on anonymized data sets, tested participants in network inference and prediction of measurements. Forty teams submitted 413 predicted networks and measurement test sets. Overall, a handful of best-performer teams were identified, while a majority of teams made predictions that were equivalent to random. Counterintuitively, combining the predictions of multiple teams (including the weaker teams) can in some cases improve predictive power beyond that of any single method.

Conclusions

DREAM provides valuable feedback to practitioners of systems biology modeling. Lessons learned from the predictions of the community provide much-needed context for interpreting claims of efficacy of algorithms described in the scientific literature.     

CLN6, which is associated with a lysosomal storage disease, is an endoplasmic reticulum protein

The neuronal ceroid lipofuscinoses (NCLs) are severe inherited neurodegenerative disorders affecting children. In this disease, lysosomes accumulate autofluorescent storage material and there is death of neurons. Five types of NCL are caused by mutations in lysosomal proteins (CTSD, CLN1/PPT1, CLN2/TTPI, CLN3 and CLN5), and one type is caused by mutations in a protein that recycles between the ER and ERGIC (CLN8). The CLN6 gene underlying a variant of late infantile NCL (vLINCL) was recently identified. It encodes a novel 311 amino acid transmembrane protein. Antisera raised against CLN6 peptides detected a protein of 30 kDa by Western blotting of human cells, which was missing in cells from some CLN6 deficient patients. Using immunofluorescence microscopy, CLN6 was shown to reside in the endoplasmic reticulum (ER). CLN6 protein tagged with GFP at the C-terminus and expressed in HEK293 cells was also found within the ER. Investigation of the effect of five CLN6 disease mutations that affect single amino acids showed that the mutant proteins were retained in the ER. These data suggest that CLN6 is an ER resident protein, the activity of which, despite this location, must contribute to lysosomal function.     

RFX1 and NF-1 associate with P sequences of the human growth hormone locus in pituitary chromatin

The human GH family consists of five genes, including the placental chorionic somatomammotropins (CS), within a single locus on chromosome 17. Based on nuclease sensitivity, the entire GH/CS locus is accessible in pituitary chromatin, yet only GH-N is expressed. Previously, we reported a P sequence element (263P) capable of repressing placental CS promoter activity in transfected pituitary (GC) cells. Regions of protein binding within 263P include P sequence elements A and B (PSE-A and PSE-B), and we reported nuclear factor-1 (NF-1) recognition of PSE-B. We now provide evidence for multiple interactions on PSE-A, including binding of the regulatory factor X (RFX) family. Disruption of the RFX site within 263P blunts repressor activity in transfected GC cells; however, repression is only abolished when both PSE-A/RFX and PSE-B/NF-1 sites are mutated. The capacity of RFX and NF-1 to participate in a novel common complex is further suggested by coimmunoprecipitation of RFX1 and epitope-tagged NF-1 family members. Finally, we confirm the association of NF-1 and RFX1 with P sequences in human pituitary tissue by chromatin immunoprecipitation. Taken together, our data suggest that an inverse relationship exists between 263P and CS promoter histone hyperacetylation and the association of these factors in vivo.     

Bioavailability of selenium from meat and broccoli as determined by retention and distribution of 75Se

The concentration of selenium (Se), an essential nutrient, is variable in foods, depending, in part, on how and where foods are produced; some foods accumulate substantial amounts of Se when produced on high-Se soils. The chemical form of Se also differs among foods. Broccoli is a Se-accumulating plant that contains many methylated forms of Se, and Se bioavailability from broccoli has been reported to be low. Red meats such as pork or beef could accumulate Se when the animal is fed high-Se diets, and Se from such meats has been reported to be highly bioavailable for selenoprotein synthesis. In a further attempt to characterize the utilization of Se from broccoli and meats such as pork or beef, we have fed rats diets adequate (0.1 μg Se/g diet) in Se or high in Se (1.5 μg S/g diet), with the Se source being either high-Se broccoli or beef. Rats were then given test meals of broccoli or pork intrinsically labeled with ⁷⁵Se. When dietary Se was nutritionally adequate (0.1 μg/g diet), more ⁷⁵Se from pork than broccoli was retained in tissues; however, there were no significant differences in whole-body retention when dietary Se was high (1.5 μg/g diet). A significantly greater percentage of ⁷⁵Se from broccoli than pork was excreted in the urine and dietary Se did not affect urinary excretion of broccoli ⁷⁵Se, but the amount excreted from pork varied directly with dietary Se intake. Radiolabeled ⁷⁵Se derived from pork effectively labeled selenoproteins in all tissues examined, but ⁷⁵Se from broccoli was undetectable in selenoproteins. These differences in retention and distribution of Se from broccoli or pork are consistent with reported differences in bioavailability of Se from beef and broccoli. They also suggest that there are fewer differences in bioavailability when Se is consumed in supranutritional amounts.