Noncytotoxic orange and red/green derivatives of DsRed-Express2 for whole-cell labeling

<p>Abstract</p> <p>Background</p> <p>Whole-cell labeling is a common application of fluorescent proteins (FPs), but many red and orange FPs exhibit cytotoxicity that limits their use as whole-cell labels. Recently, a tetrameric red FP called DsRed-Express2 was engineered for enhanced solubility and was shown to be noncytotoxic in bacterial and mammalian cells. Our goal was to create derivatives of this protein with different spectral properties.</p> <p>Results</p> <p>Building on previous studies of DsRed mutants, we created two DsRed-Express2 derivatives: E2-Orange, an orange FP, and E2-Red/Green, a dual-color FP with both red and green emission. We show that these new FPs retain the low cytotoxicity of DsRed-Express2. In addition, we show that these new FPs are useful as second or third colors for flow cytometry and fluorescence microscopy.</p> <p>Conclusion</p> <p>E2-Orange and E2-Red/Green will facilitate the production of healthy, stably fluorescent cell lines and transgenic organisms for multi-color labeling studies.</p

Inhibition of nucleoporin member Nup214 expression by miR-133b perturbs mitotic timing and leads to cell death

Background: Nucleoporins mediate nucleocytoplasmic exchange of macromolecules and several have been assigned active mitotic functions. Nucleoporins can participate in various mitotic functions like spindle assembly, kinetochore organisation and chromosome segregation- important for genome integrity. Pathways to genome integrity are frequently deregulated in cancer and many are regulated in part by microRNAs. Indeed, altered levels of numerous microRNAs have frequently been associated with tumorigenesis. Here, we unveil a microRNA-mediated regulation of the nucleoporin Nup214 and its downstream effect on genome integrity. Methods: Databases/bioinformatic tools such as miRBase, Oncomine and RNAhybrid predicted Nup214 as a miR-133b target. To validate this, we used luciferase reporter assays, Real-Time PCR and immuno-blotting. Flow cytometry and immuno-blots of mitotic markers were used to analyse cell cycle pattern upon thymidine synchronization and miR-133b treatment. Mitotic indices and chromosomal abnormalities were assessed by immuno-fluorescence for FITC-tagged phospho-H3 as well as video-microscopy for GFP-tagged histone H4. Annexin V/propidium iodide staining, caspase3/ PARP cleavage and colony formation assays were done to investigate cell death upon either miR-133b transfection or NUP214 knockdown by siRNA. UPCI:SCC084, HCT116, HeLa-H4-pEGFP and HEK293 (human oral squamous cell carcinoma, colorectal, cervical carcinomas and embryonic kidney cell lines, respectively) were used. miR-133b and NUP214 expressions were validated in cancer cell lines and tissues by Real-Time PCR. Results: Examination of head and neck tumour tissues and cancer cell lines revealed that Nup214 and miR-133b expressions are negatively correlated. In vitro, Nup214 was significantly downregulated by ectopic miR-133b. This downregulation elevated mitotic indices and delayed degradation of mitotic marker proteins cyclinB1 and cyclinA and dephosphorylation of H3. Moreover, this mitotic delay enhanced chromosomal abnormalities and apoptosis. Conclusions: We have identified NUP214, a member of the massive nuclear pore complex, as a novel miR-133b target. Thus, we have shown a hitherto unknown microRNA regulation of mitosis mediated by a member of the nucleoporin family. Based on observations, we also raise some hypotheses regarding transport-dependent/independent functions of Nup214 in this study. Our results hence attempt to explain why miR-133b is generally downregulated in tumours and lay out the potential for Nup214 as a therapeutic target in the treatment of cancer

Ultrafast fluorescence resonance energy transfer in a bile salt aggregate: excitation wavelength dependence

Fluorescence resonance energy transfer (FRET) from Coumarin 153 (C153) to Rhodamine 6G (R6G) in a secondary aggregate of a bile salt (sodium deoxycholate, NaDC) is studied by femtosecond up-conversion. The emission spectrum of C153 in NaDC is analysed in terms of two spectra-one with emission maximum at 480 nm which corresponds to a non-polar and hydrophobic site and another with maximum at ~530 nm which arises from a polar hydrophilic site. The time constants of FRET were obtained from the rise time of the emission of the acceptor (R6G). In the NaDC aggregate, FRET occurs in multiple time scales - 4 ps and 3700 ps. The 4 ps component is assigned to FRET from a donor (D) to an acceptor (A) held at a close distance (RDA ~ 17 Å) inside the bile salt aggregate. The 3700 ps component corresponds to a donor-acceptor distance ~48 Å. The long (~3700 ps) component may involve diffusion of the donor. With increase in the excitation wavelength (λex) from 375 to 435 nm, the relative contribution of the ultrafast component of FRET (~4 ps) increases from 3 to 40% with a concomitant decrease in the contribution of the ultraslow component (~3700 ps) from 97 to 60%. The λex dependence is attributed to the presence of donors at different locations. At a long λex (435 nm) donors in the highly polar peripheral region are excited. A short λ ex (375 nm) 'selects' donor at a hydrophobic location

Disseminated Histoplasmosis in an immuno- competent Individual

Disseminated histoplasmosis in an immunocompetent individual is a rare phenomenon. The microconidia of this dimorphic fungus are transmitted through inhalational route and undergo dissemination. Cytopenias in the background of immunocompetence is an extremely rare finding in disseminated histoplasmosis. Here, we report a case of disseminated histoplasmosis in an immunocompetent patient presenting with fever, hepatosplenomegaly and bicytopenia

A comprehensive model to predict mitotic division in budding yeasts

High-fidelity chromosome segregation during cell division depends on a series of concerted interdependent interactions. Using a systems biology approach, we built a robust minimal computational model to comprehend mitotic events in dividing budding yeasts of two major phyla: Ascomycota and Basidiomycota. This model accurately reproduces experimental observations related to spindle alignment, nuclear migration, and microtubule (MT) dynamics during cell division in these yeasts. The model converges to the conclusion that biased nucleation of cytoplasmic microtubules (cMTs) is essential for directional nuclear migration. Two distinct pathways, based on the population of cMTs and cortical dyneins, differentiate nuclear migration and spindle orientation in these two phyla. In addition, the model accurately predicts the contribution of specific classes of MTs in chromosome segregation. Thus we present a model that offers a wider applicability to simulate the effects of perturbation of an event on the concerted process of the mitotic cell division

High spin-polarization in a disordered novel quaternary Heusler alloy FeMnVGa

In this work, we report the successful synthesis of a Fe-based novel half-metallic quaternary Heusler alloy FeMnVGa and its structural, magnetic and transport properties probed through different experimental methods and theoretical technique. Density functional theory (DFT) calculations performed on different types of structure reveal that Type-2 ordered structure (space group: F-43m, Ga at 4a, V at 4b, Mn at 4c and Fe at 4d) possess minimum energy among all the ordered variants. Ab-initio simulations in Type 2 ordered structure further reveal that the compound is half-metallic ferromagnet (HMF) having a large spin-polarization (89.9 %). Neutron diffraction reveal that the compound crystalizes in disordered Type-2 structure (space group: Fm-3m) in which Ga occupy at 4a, V at 4b and Fe/Mn occupy 4c/4d sites with 50:50 proportions. The structural disorder is further confirmed by X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS),57Fe Mossbauer spectrometry results and DFT calculations. Magnetisation studies suggest that the compound orders ferromagnetically below TC ~ 293 K and the saturation magnetization follows Slater-Pauling rule. Mossbauer spectrometry, along with neutron diffraction suggest that Mn is the major contributor to the total magnetism in the compound consistent with the theoretical calculations. First principle calculations indicate that spin-polarization remain high (81.3 %) even in the presence of such large atomic disorder. The robustness of the HMF property in presence of disorder is a quite unique characteristic over other reported HMF in literature and make this compound quiet promising for spintronics applications

Sec12 Binds to Sec16 at Transitional ER Sites

COPII vesicles bud from an ER domain known as the transitional ER (tER). Assembly of the COPII coat is initiated by the transmembrane guanine nucleotide exchange factor Sec12. In the budding yeast Pichia pastoris, Sec12 is concentrated at tER sites. Previously, we found that the tER localization of P. pastoris Sec12 requires a saturable binding partner. We now show that this binding partner is Sec16, a peripheral membrane protein that functions in ER export and tER organization. One line of evidence is that overexpression of Sec12 delocalizes Sec12 to the general ER, but simultaneous overexpression of Sec16 retains overexpressed Sec12 at tER sites. Additionally, when P. pastoris Sec12 is expressed in S. cerevisiae, the exogenous Sec12 localizes to the general ER, but when P. pastoris Sec16 is expressed in the same cells, the exogenous Sec12 is recruited to tER sites. In both of these experimental systems, the ability of Sec16 to recruit Sec12 to tER sites is abolished by deleting a C-terminal fragment of Sec16. Biochemical experiments confirm that this C-terminal fragment of Sec16 binds to the cytosolic domain of Sec12. Similarly, we demonstrate that human Sec12 is concentrated at tER sites, likely due to association with a C-terminal fragment of Sec16A. These results suggest that a Sec12–Sec16 interaction has a conserved role in ER export

Reduced SPAG17 Expression in Systemic Sclerosis Triggers Myofibroblast Transition and Drives Fibrosis

Systemic sclerosis (SSc) is a clinically heterogeneous fibrotic disease with no effective treatment. Myofibroblasts are responsible for unresolving synchronous skin and internal organ fibrosis in SSc, but the drivers of sustained myofibroblast activation remain poorly understood. Using unbiased transcriptome analysis of skin biopsies, we identified the downregulation of SPAG17 in multiple independent cohorts of patients with SSc, and by orthogonal approaches, we observed a significant negative correlation between SPAG17 and fibrotic gene expression. Fibroblasts and endothelial cells explanted from SSc skin biopsies showed reduced chromatin accessibility at the SPAG17 locus. Remarkably, mice lacking Spag17 showed spontaneous skin fibrosis with increased dermal thickness, collagen deposition and stiffness, and altered collagen fiber alignment. Knockdown of SPAG17 in human and mouse fibroblasts and microvascular endothelial cells was accompanied by spontaneous myofibroblast transformation and markedly heightened sensitivity to profibrotic stimuli. These responses were accompanied by constitutive TGF-β pathway activation. Thus, we discovered impaired expression of SPAG17 in SSc and identified, to our knowledge, a previously unreported cell-intrinsic role for SPAG17 in the negative regulation of fibrotic responses. These findings shed fresh light on the pathogenesis of SSc and may inform the search for innovative therapies for SSc and other fibrotic conditions through SPAG17 signaling

Soil conservation issues in India

Despite years of study and substantial investment in remediation and prevention, soil erosion continues to be a major environmental problem with regard to land use in India and elsewhere around the world. Furthermore, changing climate and/or weather patterns are exacerbating the problem. Our objective was to review past and current soil conservation programmes in India to better understand how production-, environmental-, social-, economic- and policy-related issues have affected soil and water conservation and the incentives needed to address the most critical problems. We found that to achieve success in soil and water conservation policies, institutions and operations must be co-ordinated using a holistic approach. Watershed programmes have been shown to be one of the most effective strategies for bringing socio-economic change to different parts of India. Within both dryland and rainfed areas, watershed management has quietly revolutionized agriculture by aligning various sectors through technological soil and water conservation interventions and land-use diversification. Significant results associated with various watershed-scale soil and water conservation programmes and interventions that were effective for reducing land degradation and improving productivity in different parts of the country are discussed