Lessons from genetics: interpreting complex phenotypes in RNAi screens

Mammalian cell biology is witnessing a new era in which cellular processes are explained through dynamic networks of interacting cellular components. In this fast-pacing field, where image-based RNAi screening is taking a central role, there is a strong need to improve ways to capture such interactions in space and time. Cell biologists traditionally depict these events by confining themselves to the level of a single cell, or to many population-averaged cells. Similarly, classical geneticists observe and interpret phenotypes in a single organism to delineate signaling processes, but have also described genetic phenomena in populations of organisms. The analogy in the two approaches inspired us to draw parallels with, and take lessons from concepts in classical genetics.     

The Notch ligands DLL1 and JAG2 act synergistically to regulate hair cell development in the mammalian inner ear

The mammalian auditory sensory epithelium, the organ of Corti, contains sensory hair cells and nonsensory supporting cells arranged in a highly patterned mosaic. Notch-mediated lateral inhibition is the proposed mechanism for creating this sensory mosaic. Previous work has shown that mice lacking the Notch ligand JAG2 differentiate supernumerary hair cells in the cochlea, consistent with the lateral inhibitory model. However, it was not clear why only relatively modest increases in hair cell production were observed in Jag2 mutant mice. Here, we show that another Notch ligand, DLL1, functions synergistically with JAG2 in regulating hair cell differentiation in the cochlea. We also show by conditional inactivation that these ligands probably signal through the NOTCH1 receptor. Supernumerary hair cells in Dll1/Jag2 double mutants arise primarily through a switch in cell fate, rather than through excess proliferation. Although these results demonstrate an important role for Notch-mediated lateral inhibition during cochlear hair cell patterning, we also detected abnormally prolonged cellular proliferation that preferentially affected supporting cells in the organ of Corti. Our results demonstrate that the Notch pathway plays a dual role in regulating cellular differentiation and patterning in the cochlea, acting both through lateral inhibition and the control of cellular proliferation.     

Multidimensional analysis of Drosophila wing variation in Evolution Canyon

Environmental stress has been suggested to be a major evolutionary force, both through inducing strong selection and because of its direct impact on developmental buffering processes that alter the evolvability of organisms. In particular, temperature has attracted much attention because of its importance as an ecological feature and the relative ease with which it can be experimentally manipulated in the lab. Evolution Canyon, Lower Nahal Oren, Israel, is a well studied natural site where ecological parameters are suspected to drive evolutionary differentiation. In this study, using Drosophila melanogaster isofemale lines derived from wild flies collected on both slopes of the canyon, we investigated the effect of developmental temperature upon the different components of phenotypic variation of a complex trait: the wing. Combining geometric and traditional morphometrics, we find only limited evidence for a differentiation among slopes. Investigating simultaneously phenotypic plasticity, genetic variation among isofemale lines, variation among individuals and fluctuating asymmetry, we could not identify a consistent effect of the stressful conditions encountered on the south facing slope. The prevailing structuring effect is that of the experimentally manipulated temperature which clearly influences wing mean size and shape. Variability, in contrast, is not consistently affected by temperature. Finally, we investigated the specific relationship between individual variation and fluctuating asymmetry. Using metric multi-dimensional scaling we show that the related patterns of wing shape variation are not identical, supporting the view that the underlying developmental processes are to a certain extent different.     

Electron‐Beam‐Evaporated Nickel Oxide Hole Transport Layers for Perovskite‐Based Photovoltaics

High‐quality charge carrier transport materials are of key importance for stable and efficient perovskite‐based photovoltaics. This work reports on electron‐beam‐evaporated nickel oxide (NiO_x) layers, resulting in stable power conversion efficiencies (PCEs) of up to 18.5% when integrated into solar cells employing inkjet‐printed perovskite absorbers. By adding oxygen as a process gas and optimizing the layer thickness, transparent and efficient NiO_x hole transport layers (HTLs) are fabricated, exhibiting an average absorptance of only 1%. The versatility of the material is demonstrated for different absorber compositions and deposition techniques. As another highlight of this work, all‐evaporated perovskite solar cells employing an inorganic NiO_x HTL are presented, achieving stable PCEs of up to 15.4%. Along with good PCEs, devices with electron‐beam‐evaporated NiO_x show improved stability under realistic operating conditions with negligible degradation after 40 h of maximum power point tracking at 75 °C. Additionally, a strong improvement in device stability under ultraviolet radiation is found if compared to conventional perovskite solar cell architectures employing other metal oxide charge transport layers (e.g., titanium dioxide). Finally, an all‐evaporated perovskite solar mini‐module with a NiO_x HTL is presented, reaching a PCE of 12.4% on an active device area of 2.3 cm².     

Deficiency in ethanolamine plasmalogen leads to altered cholesterol transport

Plasmalogens are a major sub-class of ethanolamine and choline phospholipids in which the sn-1 position has a long chain fatty alcohol attached through a vinyl ether bond. These phospholipids are proposed to play a role in membrane fusion-mediated events. In this study, we investigated the role of the ethanolamine plasmalogen plasmenylethanolamine (PlsEtn) in intracellular cholesterol transport in Chinese hamster ovary cell mutants NRel-4 and NZel-1, which have single gene defects in PlsEtn biosynthesis. We found that PlsEtn was essential for specific cholesterol transport pathways, those from the cell surface or endocytic compartments to acyl-CoA/cholesterol acyltransferase in the endoplasmic reticulum. The movement of cholesterol from the endoplasmic reticulum or endocytic compartments to the cell surface was normal in PlsEtn-deficient cells. Also, vesicle trafficking was normal in PlsEtn-deficient cells, as measured by fluid phase endocytosis and exocytosis, as was the movement of newly-synthesized proteins to the cell surface. The mutant cholesterol transport phenotype was due to the lack of PlsEtn, since it was corrected when NRel-4 cells were transfected with a cDNA encoding the missing enzyme or supplied with a metabolic intermediate that enters the PlsEtn biosynthetic pathway downstream of the defect. Future work must determine the precise role that plasmalogens have on cholesterol transport to the endoplasmic reticulum.     

Distinctive ligand-binding specificities of tandem PA14 biomass-sensory elements from Clostridium thermocellum and Clostridium clariflavum

Cellulolytic clostridia use a highly efficient cellulosome system to degrade polysaccharides. To regulate genes encoding enzymes of the multi-enzyme cellulosome complex, certain clostridia contain alternative sigma I (σ^I) factors that have cognate membrane-associated anti-σ^I factors (RsgIs) which act as polysaccharide sensors. In this work, we analyzed the structure-function relationship of the extracellular sensory elements of Clostridium (Ruminiclostridium) thermocellum and Clostridium clariflavum (RsgI3 and RsgI4, respectively). These elements were selected for comparison, as each comprised two tandem PA14-superfamily motifs. The X-ray structures of the PA14 modular dyads from the two bacterial species were determined, both of which showed a high degree of structural and sequence similarity, although their binding preferences differed. Bioinformatic approaches indicated that the DNA sequence of promoter of sigI/rsgI operons represents a strong signature, which helps to differentiate binding specificity of the structurally similar modules. The σ^I4-dependent C. clariflavum promoter sequence correlates with binding of RsgI4_PA14 to xylan and was identified in genes encoding xylanases, whereas the σ^I3-dependent C. thermocellum promoter sequence correlates with RsgI3_PA14 binding to pectin and regulates pectin degradation-related genes. Structural similarity between clostridial PA14 dyads to PA14-containing proteins in yeast helped identify another crucial signature element: the calcium-binding loop 2 (CBL2), which governs binding specificity. Variations in the five amino acids that constitute this loop distinguish the pectin vs xylan specificities. We propose that the first module (PA14^A) is dominant in directing the binding to the ligand in both bacteria. The two X-ray structures of the different PA14 dyads represent the first reported structures of tandem PA14 modules.     

Comparison of the performance of horizontal and vertical flow constructed wetland planted with Rhynchospora corymbosa

Treatment performance of horizontal flow (HF) and vertical flow (VF) constructed wetland planted with Rhynchospora corymbosa were compared. The average porosity of the CW beds were 0.55, hydraulic retention time (HRT) of 3?days, hydraulic loading rate (HLR) and Organic Loading rate were 0.058?m/day and 3.96 (g·BOD/m²·day), respectively with a volumetric flow rate of 0.14 m³/day. The pollutant concentration of graywater before and after its introduction to the CWs was measured using standard sampling and analyses methods. The mean removal efficiencies (RE) for HF and VF CWs were BOD, 35% and 35.4%; COD, 61.9% and 56.7%; TN, 87% and 92%; TP, 95% and 65%; TSS, 86% and 59.6%; pH, 8.8% and 12.8%, respectively. The graywater was highly contaminated in terms of nutrient and organic load. The mean values of the parameters tested for different CWs were significantly different (P?≤?0.05). This comparative study favored HF over VF Constructed wetland with HF found to be a viable alternative for graywater treatment for organics, nutrients and suspended solids removal. The result provided insight into the performance of CWs planted with R. corymbosa.     

Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1

Background

Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels.

Methodology/Principal Findings

The R. flavefaciens FD-1 genome was sequenced to 29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into 119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs), polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated, 135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three multi-modular xylanases ({"type":"entrez-protein","attrs":{"text":"ORF01222","term_id":"1178790230","term_text":"ORF01222"}}ORF01222, {"type":"entrez-protein","attrs":{"text":"ORF03896","term_id":"1178792974","term_text":"ORF03896"}}ORF03896, and {"type":"entrez-protein","attrs":{"text":"ORF01315","term_id":"1178790325","term_text":"ORF01315"}}ORF01315) exhibited the highest levels of up-regulation.

Conclusions/Significance

The genomic evidence indicates that R. flavefaciens FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a cellulosome architecture. Functional analysis of the genome has revealed that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components.     

Loss of RBPj in Postnatal Excitatory Neurons Does Not Cause Neurodegeneration or Memory Impairments in Aged Mice

Previous studies suggest that loss of γ-secretase activity in postnatal mouse brains causes age-dependent memory impairment and neurodegeneration. Due to the diverse array of γ-secretase substrates, it remains to be demonstrated whether loss of cleavage of any specific substrate(s) is responsible for these defects. The bulk of the phenotypes observed in mammals deficient for γ-secretase or exposed to γ-secretase inhibitors are caused by the loss of Notch receptor proteolysis. Accordingly, inhibition of Notch signaling is the main cause for untoward effects for γ-secretase inhibitors as therapeutics for Alzheimer’s disease. Therefore, we wished to determine if loss of canonical Notch signaling is responsible for the age-dependent neurodegeneration observed upon γ-secrectase deficiency in the mouse brain. We generated postnatal forebrain-specific RBPj conditional knockout (cKO) mice using the CamKII-Cre driver and examined behavior and brain pathology in 12–18 month old animals. Since all four mammalian Notch receptor homologues signal via this DNA binding protein, these mice lack canonical Notch signaling. We found that loss of RBPj in mature excitatory neurons was well tolerated, with no evidence for neurodegeneration or of learning and memory impairment in mice aged up to 18 months. The only phenotypic deficit we observed in the RBPj-deficient mice was a subtle abnormality in olfactory preferences, particularly in females. We conclude that the loss of canonical Notch signaling through the four receptors is not responsible for age-dependent neurodegeneration or learning and memory deficits seen in γ-secretase deficient mice.