The Oleaginous Yeast Meyerozyma guilliermondii BI281A as a New Potential Biodiesel Feedstock: Selection and Lipid Production Optimization

A high throughput screening (HTS) methodology for evaluation of cellular lipid content based on Nile red fluorescence reads using black background 96-wells test plates and a plate reader equipment allowed the rapid intracellular lipid estimation of strains from a Brazilian phylloplane yeast collection. A new oleaginous yeast, Meyerozyma guilliermondii BI281A, was selected, for which the gravimetric determination of total lipids relative to dry weight was 52.38% for glucose or 34.97% for pure glycerol. The lipid production was optimized obtaining 108 mg/L of neutral lipids using pure glycerol as carbon source, and the strain proved capable of accumulating oil using raw glycerol from a biodiesel refinery. The lipid profile showed monounsaturated fatty acids (MUFA) varying between 56 or 74% in pure or raw glycerol, respectively. M. guilliermondii BI281A bears potential as a new biodiesel feedstock.

DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation

DNA barcoding is a global initiative for species identification through sequencing of short DNA sequence markers. Sequences of two loci, ITS and LSU, were generated as barcode data for all (ca. 9k) yeast strains included in the CBS collection, originally assigned to ca. 2 000 species. Taxonomic sequence validation turned out to be the most severe bottleneck due to the large volume of generated trace files and lack of reference sequences. We have analysed and validated CBS strains and barcode sequences automatically. Our analysis shows that there were 6 and 9.5 % of CBS yeast species that could not be distinguished by ITS and LSU, respectively. Among them, ∼3 % were indistinguishable by both loci. Except for those species, both loci were successfully resolving yeast species as the grouping of yeast DNA barcodes with the predicted taxonomic thresholds was more than 90 % similar to the grouping with respect to the expected taxon names. The taxonomic thresholds predicted to discriminate yeast species were 98.41 % for ITS and 99.51 % for LSU. To discriminate current yeast genera, thresholds were 96.31 % for ITS and 97.11 % for LSU. Using ITS and LSU barcodes, we were also able to show that the recent reclassifications of basidiomycetous yeasts in 2015 have made a significant improvement for the generic taxonomy of those organisms. The barcodes of 4 730 (51 %) CBS yeast strains of 1 351 (80 %) accepted yeast species that were manually validated have been released to GenBank and the CBS-KNAW website as reference sequences for yeast identification.

Assessing the network connectivity of modifier ions in metaphosphate glass melts: A dynamic light scattering study of Na-Zn mixtures

Photon correlation spectroscopy conducted on polymeric metaphosphate melts [NaPO₃]_1-y[Zn(PO₃)₂]_y shows a systematic decrease in glass fragility as the more strongly bonding Zn cation replaces the more weakly bonding Na cation as a crosslinking agent between PO₃ chains. This decrease is similar to that observed previously in Na-Al melts and the decrease in fragility for both systems is shown to be fully consistent with a recently reported universal pattern of fragility in network forming glasses as a function of network connectivity. Unique to the Na-Zn system is the appearance of an ultraslow relaxation in the dynamic structure factor (slower than the viscoelastic decay) that is not present in either Na-Al or Na-Li metaphosphate mixtures. This relaxation appears to originate from the diffusion of the Zn cation within the melt which is partially coupled to the oxide network. Taken together, these results underscore the need to distinguish between network-forming cations of high ionic bond strength that contribute to the connectivity of the oxide network and those of lower bond strength that do not contribute.

Efficacy of intravenous immunoglobulin in the treatment of persistent BK viremia and BK virus nephropathy in renal transplant recipients

BK virus-associated nephropathy (BKVN) can cause clinically significant viral infection in renal transplant recipients, leading to allograft dysfunction and loss. The usual management of BKVN involves the reduction of immunosuppression and the addition of leflunomide, quinolones, and cidofovir, but the rate of graft loss remains high. The aim of this study was to assess the impact of treatment with intravenous human immunoglobulin (IVIG) on the outcome of BKVN in renal transplant recipients. Upon diagnosis of BKVN, patients remained on anti-polyomavirus treatment, consisting of the reduction of immunosuppression and the use of leflunomide therapy. Treatment with IVIG was given only to patients who did not respond to 8 weeks of the adjustment of immunosuppression and leflunomide. All 30 patients had persistent BKV viremia and BKVN with their mean BK viral loads higher than the baseline (range, 15,000-2 million copies/mL). Mean peak BK load was 205,314 copies/mL compared with 697 copies/mL after 1 year of follow-up. Twenty-seven patients (90%) had a positive response in clearing viremia. The actuarial patient and graft survival rates after 12 months were 100% and 96.7%, respectively. IVIG administration appeared to be safe and effective in treating BKV viremia and BKVN and preventing graft loss in patients who had inadequate response to immunosuppression reduction and leflunomide therapy.

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.

In vitro rescue of FGA deletion by lentiviral transduction of an afibrinogenemic patient's hepatocytes

BACKGROUND

Congenital afibrinogenemia is a rare inherited autosomal recessive disorder in which a mutation in one of three genes coding for the fibrinogen polypeptide chains Aα, Bβ and γ results in the absence of a functional coagulation protein. A patient with congenital afibrinogenemia, resulting from an FGA homozygous gene deletion, underwent an orthotopic liver transplant that resulted in complete restoration of normal hemostasis. The patient's explanted liver provided a unique opportunity to further investigate a potential novel treatment modality.

OBJECTIVE

To explore a targeted gene therapy approach for patients with congenital afibrinogenemia.

METHODS AND RESULTS

At the time of transplant, the patient's FGA-deficient hepatocytes were isolated and transduced with lentiviral vectors encoding the human fibrinogen Aα-chain. FGA-transduced hepatocytes produced fully functional fibrinogen in vitro.

CONCLUSIONS

Orthotopic liver transplantation is a possible rescue treatment for failure of on-demand fibrinogen replacement therapy. In addition, we provide evidence that hepatocytes homozygous for a large FGA deletion can be genetically modified to restore Aα-chain protein expression and secrete a functional fibrinogen hexamer.

Short communication. The role of animal-sourced insulin in the treatment of type 1 diabetes and its availability

As a result of a number of factors, the treatment of insulin-dependent diabetes has moved away from using insulin of beef or pork origin to using recombinant (biosynthetic) insulin preparations. However, some people with type 1 diabetes can manage their diabetes better using animal-sourced insulin. Despite dwindling options and decreased production, animal-sourced insulin (and pork insulin in particular) is still available on the Canadian market. This communication describes the actions taken by Health Canada with respect to the availability of animal insulin.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.

Database URL:http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353

MycoBank gearing up for new horizons

MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software.

Circularly polarized luminescence microscopy for the imaging of charge and spin diffusion in semiconductors

Room temperature electronic diffusion is studied in 3 μm thick epitaxial p(+) GaAs lift-off films using a novel circularly polarized photoluminescence microscope. The method is equivalent to using a standard optical microscope and provides a contactless means to measure both the charge (L) and spin (L(s)) diffusion lengths simultaneously. The measured values of L and L(s) are in excellent agreement with the spatially averaged polarization and a sharp reduction in these two quantities (L from 21.3 to 1.2 μm and L(s) from 1.3 to 0.8 μm) is found with increasing surface recombination velocity. Outward diffusion results in a factor of 10 increase in the polarization at the excitation spot. The range of materials to which the technique can be applied, as well as a comparison with other existing methods for the measurement of spin diffusion, is discussed.

Anatomy of the subtalar joint and imaging of talo-calcaneal coalition

Talo-calcaneal coalitions may be intra-articular or extra-articular in position and may be classified as fibrous, cartilaginous or osseous in morphology. Fibrous coalitions, particularly extra-articular talo-calcaneal coalitions, may have cross-sectional imaging findings that resemble normal anatomic variants, particularly the medial talo-calcaneal ligament and to a lesser extent the presence of an accessory articular facet between the posterior margin of the sustentaculum and postero-medial process of the talus. Typically, in the adult fibrous coalition, there will be some osseous deformity at the entheses, allowing differentiation from a medial talo-calcaneal ligament. The anatomy of the subtalar joint and its ligamentous supports, normal anatomic variations and their corresponding imaging appearance are reviewed in the first part of this article. In the second part, the various forms of talo-calcaneal coalition and their imaging appearance are reviewed.

Molecular mechanisms accounting for fibrinogen deficiency: from large deletions to intracellular retention of misfolded proteins

Fibrinogen, the soluble precursor of fibrin, which is the main protein constituent of the blood clot, is synthesized in hepatocytes in the form of a hexamer composed of two sets of three polypeptides (Aalpha, Bbeta, and gamma). Each polypeptide is encoded by a distinct gene, FGA, FGB and FGG, all three clustered in a region of 50 kb on 4q32. Congenital afibrinogenemia is characterized by the complete absence of fibrinogen. The first causative mutation for this disease was identified in Geneva in a non-consanguineous Swiss family in 1999: the four patients were homozygous for a large deletion in the fibrinogen cluster, which eliminated almost the entire FGA genomic sequence. Mutations in the fibrinogen genes may lead to deficiency of fibrinogen by several mechanisms: acting at the DNA level, at the RNA level by affecting mRNA splicing or stability, or at the protein level by affecting protein synthesis, assembly or secretion. Recent reviews have provided helpful updates for the rapidly growing number of causative mutations identified in patients with fibrinogen deficiencies, either afibrinogenemia or hypofibrinogenemia. The aim of this review is to highlight specifically the subset of mutations that allow fibrinogen chain synthesis and hexamer assembly but impair secretion. Indeed, functional studies of these mutations have shed light on the specific sequences and structures in the fibrinogen molecule involved in the quality control of fibrinogen secretion.

Hypofibrinogenaemia caused by a novel FGG missense mutation (W253C) in the gamma chain globular domain impairing fibrinogen secretion

BACKGROUND

Inherited disorders of fibrinogen are rare and affect either the quantity (hypofibrinogenaemia and afibrinogenaemia) or the quality of the circulating fibrinogen (dysfibrinogenaemia). Extensive allelic heterogeneity has been found for all three disorders: in congenital afibrinogenaemia >30 mutations, the majority in FGA, have been identified in homozygosity or in compound heterozygosity. Several mutations have also been identified in patients with hypofibrinogenaemia; many of these are heterozygous carriers of afibrinogenaemia null mutations.

OBJECTIVE

To report the case of a patient from Slovakia diagnosed with hypofibrinogenaemia characterised by fibrinogen concentrations of around 0.7 g/l.

RESULTS

The patient was found to be heterozygous for a novel missense mutation W253C (W227C in the mature protein) in the C-terminal globular domain of the fibrinogen gamma chain. Co-expression of the W253C FGG mutant cDNA (fibrinogen Bratislava) in combination with wild-type FGA and FGB cDNAs showed that fibrinogen molecules containing the mutant gamma chain can assemble intracellularly but are not secreted into the media, confirming the causative nature of the identified mutation.

CONCLUSIONS

Current analysis of fibrinogen Bratislava indicates that the domains important for the processes of hexamer assembly and hexamer secretion should not be considered as strictly restricted to one or other fibrinogen chain.

Differential expression of LMO4 protein in Alzheimer's disease

The molecular bases of late-onset and sporadic Alzheimer's disease (AD) still have to be unraveled. Among putative candidates for molecular variations in AD, we propose LMO4 protein, a transcription regulator, involved in multiple protein complexes. We investigated changes in LMO4 immunoreactivity in vulnerable brain regions of AD cases and controls of comparable age. Immunocytochemical analysis revealed a high level of LMO4 expression in the entorhinal cortex (EC) and in the CA1 hippocampal region of the control brains and a consistent decrease in the AD brains, correlated with the amount of neurofibrillary tangles (NFT) degenerating neurones and the severity of senile plaques deposition. The decrease in LMO4 immunoreactivity resulted both from weaker immunoreactive signals and from a loss of immunoreactive neurones. LMO4 immunocytochemical staining appeared not to be colocalized with NFT in a majority of neurones. Its expression was weak in the dentate gyrus and stronger in CA3-4, two regions with no or low numbers of NFT, but there was no decrease in AD compared to control cases. In the frontal cortex, the ventro-infero-median region (area 12) showed a greater LMO4 expression than the polar one (area 9), but no decrease in AD was observed. As LMO4 has been proposed to inhibit cellular differentiation, it can be hypothesized that a reduced expression is associated in EC and CA1 with attempts of diseased neurones to differentiate (e.g. compensatory neuritogenesis). Taken together, these data indicate that LMO4 protein is involved in the complexity of the disease phenotype, at least as a secondary factor.