Clustering gene-expression data with repeated measurements

Clustering is a common methodology for the analysis of array data, and many research laboratories are generating array data with repeated measurements. We evaluated several clustering algorithms that incorporate repeated measurements, and show that algorithms that take advantage of repeated measurements yield more accurate and more stable clusters. In particular, we show that the infinite mixture model-based approach with a built-in error model produces superior results.     

B7 costimulation molecules expressed from the herpes simplex virus 2 genome rescue immune induction in B7-deficient mice

The interaction between B7 costimulation molecules on antigen-presenting cells and CD28 on antigen-responsive T cells is essential for T-cell activation and maturation of immune responses to herpes simplex virus (HSV) infection. Vaccine-induced immune responses also depend upon adequate upregulation of B7 costimulation molecules, but this signal may be limiting for replication-defective virus vaccines. We investigated whether expression of B7 costimulation molecules by a prototypical replication-defective antiviral vaccine could enhance immune responses to the vaccine and whether B7-1 and B7-2 would be similarly effective. We altered an ICP8(-) replication-defective strain of HSV type 2 (HSV-2), 5BlacZ, to encode either murine B7-1 or B7-2. B7 molecule expression was detected on the surface of cells infected in vitro and at the RNA level in tissue of immunized mice. Immunization of B7-1/B7-2 knockout mice with B7-encoding virus modestly expanded the number of gamma interferon-producing T cells and significantly augmented class-switched HSV-specific antibody responses compared with the parental virus. Mice immunized with either B7-expressing virus showed less replication of challenge virus in the genital mucosa than mice immunized with 5BlacZ, markedly fewer signs of genital and neurological disease, and little weight loss. Virtually all mice immunized with B7-encoding virus survived challenge with a large dose of HSV-2, whereas most 5BlacZ-immunized mice succumbed to infection. These results indicate that protective immune responses can be enhanced by the inclusion of host B7 costimulation molecules in a prototypical replication-defective HSV vaccine against HSV-2 genital infection and that B7-1 and B7-2 induce immune responses with similar capacities to fight HSV-2 infection.     

Clitocine Reversal of P-Glycoprotein Associated Multi-Drug Resistance through Down-Regulation of Transcription Factor NF-κB in R-HepG2 Cell Line

Multidrug resistance(MDR)is one of the major reasons for failure in cancer chemotherapy and its suppression may increase the efficacy of therapy. The human multidrug resistance 1 (MDR1) gene encodes the plasma membrane P-glycoprotein (P-gp) that pumps various anti-cancer agents out of the cancer cell. R-HepG2 and MES-SA/Dx5 cells are doxorubicin induced P-gp over-expressed MDR sublines of human hepatocellular carcinoma HepG2 cells and human uterine carcinoma MES-SA cells respectively. Herein, we observed that clitocine, a natural compound extracted from Leucopaxillus giganteus, presented similar cytotoxicity in multidrug resistant cell lines compared with their parental cell lines and significantly suppressed the expression of P-gp in R-HepG2 and MES-SA/Dx5 cells. Further study showed that the clitocine increased the sensitivity and intracellular accumulation of doxorubicin in R-HepG2 cells accompanying down-regulated MDR1 mRNA level and promoter activity, indicating the reversal effect of MDR by clitocine. A 5'-serial truncation analysis of the MDR1 promoter defined a region from position -450 to -193 to be critical for clitocine suppression of MDR1. Mutation of a consensus NF-κB binding site in the defined region and overexpression of NF-κB p65 could offset the suppression effect of clitocine on MDR1 promoter. By immunohistochemistry, clitocine was confirmed to suppress the protein levels of both P-gp and NF-κB p65 in R-HepG2 cells and tumors. Clitocine also inhibited the expression of NF-κB p65 in MES-SA/Dx5. More importantly, clitocine could suppress the NF-κB activation even in presence of doxorubicin. Taken together; our results suggested that clitocine could reverse P-gp associated MDR via down-regulation of NF-κB.     

Adverse effects following anti–COVID-19 vaccination with mRNA-based BNT162b2 are alleviated by altering the route of administration and correlate with baseline enrichment of T and NK cell genes

Ensuring high vaccination and even booster vaccination coverage is critical in preventing severe Coronavirus Disease 2019 (COVID-19). Among the various COVID-19 vaccines currently in use, the mRNA vaccines have shown remarkable effectiveness. However, systemic adverse events (AEs), such as postvaccination fatigue, are prevalent following mRNA vaccination, and the underpinnings of which are not understood. Herein, we found that higher baseline expression of genes related to T and NK cell exhaustion and suppression were positively correlated with the development of moderately severe fatigue after Pfizer-BioNTech BNT162b2 vaccination; increased expression of genes associated with T and NK cell exhaustion and suppression reacted to vaccination were associated with greater levels of innate immune activation at 1 day postvaccination. We further found, in a mouse model, that altering the route of vaccination from intramuscular (i.m.) to subcutaneous (s.c.) could lessen the pro-inflammatory response and correspondingly the extent of systemic AEs; the humoral immune response to BNT162b2 vaccination was not compromised. Instead, it is possible that the s.c. route could improve cytotoxic CD8 T-cell responses to BNT162b2 vaccination. Our findings thus provide a glimpse of the molecular basis of postvaccination fatigue from mRNA vaccination and suggest a readily translatable solution to minimize systemic AEs.

Systemic adverse events, such as post-vaccination fatigue, are prevalent consequences of mRNA vaccination; why is this? This study shows that higher baseline expression of T and NK cell genes increases susceptibility to fatigue after mRNA vaccination, and that altering the route of vaccination may reduce the incidence of mRNA vaccine-associated systemic adverse events.     

Sequential Processing for Organic Photovoltaics: Design Rules for Morphology Control by Tailored Semi‐Orthogonal Solvent Blends

Design rules are presented for significantly expanding sequential processing (SqP) into previously inaccessible polymer:fullerene systems by tailoring binary solvent blends for fullerene deposition. Starting with a base solvent that has high fullerene solubility, 2‐chlorophenol (2‐CP), ellipsometry‐based swelling experiments are used to investigate different co‐solvents for the fullerene‐casting solution. By tuning the Flory‐Huggins χ parameter of the 2‐CP/co‐solvent blend, it is possible to optimally swell the polymer of interest for fullerene interdiffusion without dissolution of the polymer underlayer. In this way solar cell power conversion efficiencies are obtained for the PTB7 (poly[(4,8‐bis[(2‐ethylhexyl)oxy]benzo[1,2‐b:4,5‐b′]dithiophene‐2,6‐diyl)(3‐fluoro‐2‐[(2‐ethylhexyl)carbonyl]thieno[3,4‐b]thiophenediyl)]) and PC₆₁BM (phenyl‐C₆₁‐butyric acid methyl ester) materials combination that match those of blend‐cast films. Both semicrystalline (e.g., P3HT (poly(3‐hexylthiophene‐2,5‐diyl)) and entirely amorphous (e.g., PSDTTT (poly[(4,8‐di(2‐butyloxy)benzo[1,2‐b:4,5‐b′]dithiophene‐2,6‐diyl)‐alt‐(2,5‐bis(4,4′‐bis(2‐octyl)dithieno[3,2‐b:2′3′‐d]silole‐2,6‐diyl)thiazolo[5,4‐d]thiazole)]) conjugated polymers can be processed into highly efficient photovoltaic devices using the solvent‐blend SqP design rules. Grazing‐incidence wide‐angle x‐ray diffraction experiments confirm that proper choice of the fullerene casting co‐solvent yields well‐ordered interdispersed bulk heterojunction (BHJ) morphologies without the need for subsequent thermal annealing or the use of trace solvent additives (e.g., diiodooctane). The results open SqP to polymer/fullerene systems that are currently incompatible with traditional methods of device fabrication, and make BHJ morphology control a more tractable problem.     

Utilization of oil palm decanter cake for cellulase and polyoses production

The abundance of oil palm decanter cake (OPDC) is a problem in oil palm mills. However, this lignocellulosic biomass can be utilized for cellulase and polyoses production. The effectiveness of chemical and physical pretreatment in reducing the lignin content was studied by saccharification using a Celluclast 1.5 L and scanning electron microscope. Physicochemical pretreatment of OPDC with 1% (w/v) NaOH and autoclaving at 121°C for 20 min increased potential polyoses produced to 52.5% and removed 28.7% of the lignin content. The optimized conditions for cellulase production by a locally isolated fungus were a time of 120 h, a substrate of untreated OPDC, a spore concentration of 1 × 10⁷ spore/mL, a temperature of 30°C, and a pH between 7.0 and 7.5. Trichoderma asperellum UPM1 produced carboxymethylcellulase (CMCase), ??-glucosidase and filter paper activity (FPase) in the following concentrations: 17.35, 0.53, and 0.28 U/mL, respectively. Aspergillus fumigatus UPM2 produced the CMCase, ??-glucosidase and FPase in the following amounts: 10.93, 0.76, and 0.24 U/mL. The cellulases from T. asperellum UPM1 produced 2.33 g/L of polyoses and the cellulases from A. fumigatus UPM2 produced 4.37 g/L of polyoses.     

Enhanced autophagy from chronic toxicity of iron and mutant A53T α-synuclein: implications for neuronal cell death in Parkinson disease

Parkinson disease (PD), a prevalent neurodegenerative motor disorder, is characterized by the rather selective loss of dopaminergic neurons and the presence of α-synuclein-enriched Lewy body inclusions in the substantia nigra of the midbrain. Although the etiology of PD remains incompletely understood, emerging evidence suggests that dysregulated iron homeostasis may be involved. Notably, nigral dopaminergic neurons are enriched in iron, the uptake of which is facilitated by the divalent metal ion transporter DMT1. To clarify the role of iron in PD, we generated SH-SY5Y cells stably expressing DMT1 either singly or in combination with wild type or mutant α-synuclein. We found that DMT1 overexpression dramatically enhances Fe(2+) uptake, which concomitantly promotes cell death. This Fe(2+)-mediated toxicity is aggravated by the presence of mutant α-synuclein expression, resulting in increased oxidative stress and DNA damage. Curiously, Fe(2+)-mediated cell death does not appear to involve apoptosis. Instead, the phenomenon seems to occur as a result of excessive autophagic activity. Accordingly, pharmacological inhibition of autophagy reverses cell death mediated by Fe(2+) overloading. Taken together, our results suggest a role for iron in PD pathogenesis and provide a mechanism underlying Fe(2+)-mediated cell death.     

Mitochondrial autophagy is an HIF-1-dependent adaptive metabolic response to hypoxia

Autophagy is a process by which cytoplasmic organelles can be catabolized either to remove defective structures or as a means of providing macromolecules for energy generation under conditions of nutrient starvation. In this study we demonstrate that mitochondrial autophagy is induced by hypoxia, that this process requires the hypoxia-dependent factor-1-dependent expression of BNIP3 and the constitutive expression of Beclin-1 and Atg5, and that in cells subjected to prolonged hypoxia, mitochondrial autophagy is an adaptive metabolic response which is necessary to prevent increased levels of reactive oxygen species and cell death.