The Signal Sequence Coding Region Promotes Nuclear Export of mRNA

In eukaryotic cells, most mRNAs are exported from the nucleus by the transcription export (TREX) complex, which is loaded onto mRNAs after their splicing and capping. We have studied in mammalian cells the nuclear export of mRNAs that code for secretory proteins, which are targeted to the endoplasmic reticulum membrane by hydrophobic signal sequences. The mRNAs were injected into the nucleus or synthesized from injected or transfected DNA, and their export was followed by fluorescent in situ hybridization. We made the surprising observation that the signal sequence coding region (SSCR) can serve as a nuclear export signal of an mRNA that lacks an intron or functional cap. Even the export of an intron-containing natural mRNA was enhanced by its SSCR. Like conventional export, the SSCR-dependent pathway required the factor TAP, but depletion of the TREX components had only moderate effects. The SSCR export signal appears to be characterized in vertebrates by a low content of adenines, as demonstrated by genome-wide sequence analysis and by the inhibitory effect of silent adenine mutations in SSCRs. The discovery of an SSCR-mediated pathway explains the previously noted amino acid bias in signal sequences and suggests a link between nuclear export and membrane targeting of mRNAs

A zeolitic imidazolate framework with conformational variety

We show via structural considerations and DFT calculations that for a zeolitic imidazolate framework (ZIF) with sodalite (SOD) topology, [Zn(dcim)2]-SOD (dcim = 4,5-dichloroimidazolate), structural models of an infinite number of hypothetical conformational polymorphs with distinct linker orientations can be generated, which can be interconverted most likely only via reconstructive structural transitions. The relative total energies suggest that some of those polymorphs might be synthetically accessible. Efforts in that direction led to the synthesis of new trigonal 1 and previously known cubic 2 with improved crystallinity. According to structural analyses based on powder X-ray diffraction (PXRD) methods supported by NMR spectroscopy, 1 is the most stable of the theoretically predicted SOD-type framework conformers (isostructural to ZIF-7), whereas 2, at variance with a recent proposal, is a SOD-type material with a high degree of orientational disorder of the dcim linker units. The statistics of the linker orientations in 2 is close to that in 1, indicating that the disorder in 2 is not random. Rather, crystals of 2 are likely twins consisting of nanoscopic domains of trigonal 1 that are deformed to a cubic metric, with linker disorder located in the domain interfaces. As structural differences appear to be more related to characteristics of real as opposed to ideal crystal structures, we propose to not consider 1 and 2 as true conformational polymorphs. Systematic investigations of solvent mixtures led to the discovery of intermediate materials of 1 and 2. The PXRD patterns and SEM images indicate that they belong to a complete series of structural intermediates. Differences in the Ar adsorption/desorption behaviours reveal that 1, in contrast to 2, is a flexible ZIF framework.DFG/Priority Program/141

Exclusion of Mucorales Co-Infection in a Patient with Aspergillus flavus Sinusitis by Fluorescence In Situ Hybridization (FISH)

Invasive fungal infections are associated with increased mortality in hematological patients. Despite considerable advances in antifungal therapy, the evaluation of suspected treatment failure is a common clinical challenge requiring extensive diagnostic testing to rule out potential causes, such as mixed infections. We present a 64-year-old patient with secondary AML, diabetes mellitus, febrile neutropenia, and sinusitis. While cultures from nasal tissue grew Aspergillus flavus, a microscopic examination of the tissue was suggestive of concomitant mucormycosis. However, fluorescence in situ hybridization (FISH) using specific probes targeting Aspergillus and Mucorales species ruled out mixed infection. This was confirmed by specific qPCR assays amplifying the DNA of Aspergillus, but not of Mucorales. These results provided a rational basis for step-down targeted therapy, i.e., the patient received posaconazole after seven days of calculated dual therapy with liposomal amphotericin B and posaconazole. Despite clinical response to the antifungal therapy, he died due to the progression of the underlying disease within two weeks after diagnosis of fungal infection. Molecular diagnostics applied to tissue blocks may reveal useful information on the etiology of invasive fungal infections, including challenging situations, such as with mixed infections. A thorough understanding of fungal etiology facilitates targeted therapy that may improve therapeutic success while limiting side effects.Peer Reviewe

Expression divergence measured by transcriptome sequencing of four yeast species

<p>Abstract</p> <p>Background</p> <p>The evolution of gene expression is a challenging problem in evolutionary biology, for which accurate, well-calibrated measurements and methods are crucial.</p> <p>Results</p> <p>We quantified gene expression with whole-transcriptome sequencing in four diploid, prototrophic strains of <it>Saccharomyces </it>species grown under the same condition to investigate the evolution of gene expression. We found that variation in expression is gene-dependent with large variations in each gene's expression between replicates of the same species. This confounds the identification of genes differentially expressed across species. To address this, we developed a statistical approach to establish significance bounds for inter-species differential expression in RNA-Seq data based on the variance measured across biological replicates. This metric estimates the combined effects of technical and environmental variance, as well as Poisson sampling noise by isolating each component. Despite a paucity of large expression changes, we found a strong correlation between the variance of gene expression change and species divergence (R²= 0.90).</p> <p>Conclusion</p> <p>We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects.</p> <p>GEO Accession Number: GSE32679</p

High Failure Rates of Concomitant Periprosthetic Joint Infection and Extensor Mechanism Disruption

Background Patients presenting with both chronic periprosthetic joint infection (PJI) and extensor mechanism disruption (EMD) pose a significant challenge. As there is little in the literature regarding outcomes of patients with concomitant PJI and EMD, we performed a multicenter study to evaluate the outcomes. Methods Sixty patients with concomitant diagnoses of PJI and EMD were evaluated from 5 institutions. Patient demographics, presentation type, surgical management, and outcomes including recurrent infections, final surgery, and ambulatory status were documented. Results Fifty-three of 60 patients had an attempted extensor mechanism reconstruction/repair (EMR) of which 12 (23%) were successful, averaging 3.5 (range, 2-7) intervening surgeries. Forty-one patients (77%) were considered failures with recurrence of infection as most common failure (80%); 26 ended in fusion, 10 in above knee amputation, 3 with chronic resection arthroplasty, and 2 with chronic spacers/EMD. Seven patients had no attempt at EMR but proceeded directly to fusion (n = 6) or amputation (n = 1). There was no statistical difference between groups that had success or failure of EMR in age, American Society of Anesthesiologists Physical Status Classification System, or body mass index. Conclusion Our study demonstrates that concomitant EMD and PJI is a dreaded combination with poor outcomes regardless of treatment. Eradication of infection and reconstruction of the extensor mechanism often require numerous surgeries and despite great effort often end in failure. Consideration of early fusion or amputation may be preferable in some patients to avoid the morbidity and mortality of repeated surgeries

A Critical Site in the Core of the CCR5 Chemokine Receptor Required for Binding and Infectivity of Human Immunodeficiency Virus Type 1

Like the CCR5 chemokine receptors of humans and rhesus macaques, the very homologous (∼98–99% identical) CCR5 of African green monkeys (AGMs) avidly binds β-chemokines and functions as a coreceptor for simian immunodeficiency viruses. However, AGM CCR5 is a weak coreceptor for tested macrophage-tropic (R5) isolates of human immunodeficiency virus type 1 (HIV-1). Correspondingly, gp120 envelope glycoproteins derived from R5 isolates of HIV-1 bind poorly to AGM CCR5. We focused on a unique extracellular amino acid substitution at the juncture of transmembrane helix 4 (TM4) and extracellular loop 2 (ECL2) (Arg for Gly at amino acid 163 (G163R)) as the likely source of the weak R5 gp120 binding and HIV-1 coreceptor properties of AGM CCR5. Accordingly, a G163R mutant of human CCR5 was severely attenuated in its ability to bind R5 gp120s and to mediate infection by R5 HIV-1 isolates. Conversely, the R163G mutant of AGM CCR5 was substantially strengthened as a coreceptor for HIV-1 and had improved R5 gp120 binding affinity relative to the wild-type AGM CCR5. These substitutions at amino acid position 163 had no effect on chemokine binding or signal transduction, suggesting the absence of structural alterations. The 2D7 monoclonal antibody has been reported to bind to ECL2 and to block HIV-1 binding and infection. Whereas 2D7 antibody binding to CCR5 was unaffected by the G163R mutation, it was prevented by a conservative ECL2 substitution (K171R), shared between rhesus and AGM CCR5s. Thus, it appears that the 2D7 antibody binds to an epitope that includes Lys-171 and may block HIV-1 infection mediated by CCR5 by occluding an HIV-1-binding site in the vicinity of Gly-163. In summary, our results identify a site for gp120 interaction that is critical for R5 isolates of HIV-1 in the central core of human CCR5, and we propose that this site collaborates with a previously identified region in the CCR5 amino terminus to enable gp120 binding and HIV-1 infections

Cancer targeting with biomolecules: a comparative study of photodynamic therapy efficacy using antibody or lectin conjugated phthalocyanine-PEG gold nanoparticles

The functionalisation of therapeutic nanoparticle constructs with cancer-specific biomolecules can enable selective tumour accumulation and targeted treatment. Water soluble gold nanoparticles (ca. 4 nm) stabilised by a mixed monolayer of a hydrophobic zinc phthalocyanine photosensitiser (C11Pc) and hydrophilic polyethylene glycol (PEG) have been prepared. The C11Pc-PEG gold nanoparticle constructs were further functionalised with jacalin, a lectin specific for the cancer-associated Thomsen–Friedenreich (T) carbohydrate antigen, or with monoclonal antibodies specific for the human epidermal growth factor receptor-2 (HER-2). The two biofunctionalised nanoparticle conjugates produced similar levels of singlet oxygen upon irradiation at 633 nm. Importantly, both nanoparticle conjugates demonstrated extensive, yet comparable, phototoxicity in HT-29 colorectal adenocarcinoma cells (80–90%) and in SK-BR-3 breast adenocarcinoma cells (>99%). Non-conjugated C11Pc-PEG gold nanoparticles were only minimally phototoxic. Lysosomal colocalisation studies performed with the HT-29 colon cancer cells and the SK-BR-3 breast cancer cells revealed that both nanoparticle conjugates were partially localised within acidic organelles, which is typical of receptor-mediated endocytosis. The similarity of the targeted PDT efficacy of the two biofunctionalised C11Pc-PEG gold nanoparticles is discussed with respect to targeting ligand binding affinity and cell surface antigen density as key determinants of targeting efficiency. This study highlights how targeting small cell-surface molecules, such as the T antigen, can mediate a selective photodynamic treatment response which is similar to that achieved when targeting overexpressed protein receptors, such as HER-2. The high prevalence of the T antigen present on the cellular surface of primary tumours emphasises the broad potential applications for lectin-targeted therapies