Targeted amplification and MinION nanopore sequencing of key azole and echinocandin resistance determinants of clinically relevant Candida spp. from blood culture bottles

The objective of the study was to evaluate the use of targeted multiplex Nanopore MinION amplicon re-sequencing of key Candida spp. from blood culture bottles to identify azole and echinocandin resistance associated SNPs. Targeted PCR amplification of azole (ERG11 and ERG3) and echinocandin (FKS) resistance-associated loci was performed on positive blood culture media. Sequencing was performed using MinION nanopore device with R9.4.1 Flow Cells. Twenty-eight spiked blood cultures (ATCC strains and clinical isolates) and 12 prospectively collected positive blood cultures with candidaemia were included. Isolate species included Candida albicans, Candida glabrata, Candida krusei, Candida parapsilosis, Candida tropicalis and Candida auris. SNPs that were identified on ERG and FKS genes using Snippy tool and CLC Genomic Workbench were correlated with phenotypic testing by broth microdilution (YeastOne™ Sensititre). Illumina whole-genome-sequencing and Sanger-sequencing were also performed as confirmatory testing of the mutations identified from nanopore sequencing data. There was a perfect agreement of the resistance-associated mutations detected by MinION-nanopore-sequencing compared to phenotypic testing for acquired resistance (16 with azole resistance; 3 with echinocandin resistance), and perfect concordance of the nanopore sequence mutations to Illumina and Sanger data. Mutations with no known association with phenotypic drug resistance and novel mutations were also detected.     

Restoration of morphological and functional integrity in the regenerating eye of the giant African land snail Achatina fulica

To determine whether vision returns to its original state following eye removal in Achatina fulica, light and electron microscope examinations, electrophysiological recordings and behavioural tests were carried out on the regenerating snails. Reparative morphogenesis can result in the restoration of the peripheral sense organ even in the absence of complete regrowth of the tentacle, but it can also lead to the formation of aberrant regenerates. We found that anatomically and ultrastructurally the eyes of the ‘most normal’ regenerates were basically the same as the original eyes. Under normal conditions each eye is composed of a principal and an accessory eye, both sharing a common cornea. The only difference between regenerated and native eyes is the smaller size of the former, as a result of a reduced number of retinal cells. Electroretinographic responses revealed that the molecular mechanism of phototransduction is restored, in principle, but that flicker fusion frequency in the regenerated eye is significantly lower than in the normal eye. The directional movement to a visual stimulus (a black stripe of 45° width) had not completely recovered even 6 months after amputation. This suggests that the central projections of the optic nerve had not become fully re‐established at the time of testing.     

Human Cone Light Sensitivity and Melatonin Rhythms Following 24-hour Continuous Illumination

This study investigates the possibility of an endogenous circadian rhythm in retinal cone function in humans. A full-field cone electroretinogram (ERG) was performed every 2?h for 24?h under continuous rod-saturating ambient white light (53 ±?30 lux; pupils dilated) in nine healthy subjects. Distinct circadian variations were superimposed upon a gradual decrease in cone responsiveness to light, demonstrated most reliably in the implicit times of b-wave and oscillatory potentials, and to a lesser extent in amplitude and a-wave implicit times. After mathematical correction of the linear trend, the cone response was found to be greatest around 20:00?h and least around 06:00?h. The phase of the ERG circadian rhythm was not synchronized with the phase of the salivary melatonin rhythm measured the previous evening. Melatonin levels measured under constant light on the day of ERG assessments were suppressed by 53% on average compared to melatonin profiles obtained previously under near-total darkness in seven participants. The progressive decline in cone responsiveness to light over the 24?h may reflect an adaptation of the cone-driven retinal system to constant light, although the mechanism is unclear. The endogenous rhythm of cone responsiveness to light may be used as an additional index of central or retinal circadian clock time. (Author correspondence: kvdani@mail.ru)     

The Drosophila melanogaster homolog of UBE3A is not imprinted in neurons

In mammals, expression of UBE3A is epigenetically regulated in neurons and expression is restricted to the maternal copy of UBE3A. A recent report claimed that Drosophila melanogaster UBE3A homolog (Dube3a) is preferentially expressed from the maternal allele in fly brain, inferring an imprinting mechanism. However, complex epigenetic regulatory features of the mammalian imprinting center are not present in Drosophila, and allele specific expression of Dube3a has not been documented. We used behavioral and electrophysiological analysis of the Dube3a loss-of-function allele (Dube3a^15b) to investigate Dube3a imprinting in fly neurons. We found that motor impairment (climbing ability) and a newly-characterized defect in synaptic transmission are independent of parental inheritance of the Dube3a^15b allele. Furthermore, expression analysis of coding single nucleotide polymorphisms (SNPs) in Dube3a did not reveal allele specific expression differences among reciprocal crosses. These data indicate that Dube3a is neither imprinted nor preferentially expressed from the maternal allele in fly neurons.     

Exploring structural features of the interaction between the scorpion toxinCnErg1 and ERG K+ channels

The gamma-KTx-type scorpion toxins specific for K+ channels were found to interact with ERG channels on the turret region, while alpha-KTx3.2 Agitoxin-2 binds to the pore region of the Shaker K+ channel, and alpha-KTx5.3 BmP05 binds to the intermediate region of the small-conductance calcium-activated K-channel (SK(Ca)). In order to explore the critical residues for gamma-KTx binding, we determined the NMR structure of native gamma-KTx1.1 (CnErg1), a 42 amino acid residues scorpion toxin isolated from the venom of the Mexican scorpion Centruro?des noxius Hoffmann, and we used computational evolutionary trace (ET) analysis to predict possible structural and functional features of interacting surfaces. The 1H-NMR three-dimensional solution structure of native ergtoxin (CnErg1) was solved using a total of 452 distance constraints, 13 3J(NH-Halpha) and 10 hydrogen bonds. The structure is characterized by 2 segments of alpha-helices and a triple-stranded antiparallel beta-sheet stabilized by 4 disulfide bridges. The ET and structural analysis provided indication of the presence of two important amino acid residue clusters, one hydrophobic and the other hydrophilic, that should be involved in the surface contact between the toxin and the channel. Some features of the proposed interacting surface are discussed.     

Lipid function in plant cell polarity

The establishment and maintenance of cell polarity play pivotal roles during plant development. During the past five years, proteins that are required for different aspects of plant cell polarity have been identified. However, the functions of lipids and their interactions with proteins that mediate polarity remained largely unaddressed. Recent genetic studies have discovered cell and tissue polarity mutants that have defects in sterol composition, glycosylphosphatidylinositol-anchored proteins, glycosylphosphatidylinositol biosynthesis and phospholipid signalling. Analyses of the affected gene products have provided a first glance at the roles of lipids in cell polarity signalling, as well as in the trafficking and anchoring of polar proteins.     

Appearance of ocular electrical responses during development of cavernicolous and epigaeic opilionids (Arachnida)

The appearance of the electroretinogram was established during the development of two species of opilionids, an epigaeic species, Pachylus chilensis, and a cavernicolous one, Ischyropsalis luteipes. In nymphs and adults of the two species, electroretinograms of about the same amplitude can be recorded. During embryonic and larval development they are quite different. In Ischyropsalis luteipes, it is impossible to record an electrical response before hatching. In Pachylus chilensis on the other hand an initial inconstant and very small response occurs from the 50th hour of development of the retina and can always be recorded from the 72nd hour. In older embryos, the response has a progressively greater amplitude, but remains a simple negative wave. On the tenth day, when the first synaptic relays appear, the electroretinogram takes the shape of that of the adult. Given that transmission electronic microscopy cannot detect differences between the microvilli of these two species, it is tempting to compare Ischyropsalis luteipes lack of response with that of the mutant norp A of Drosophila melanogaster in which transmission electron microscopy shows no marked difference, whereas freeze-etching shows a very low number of intramembranous particles.     

角鲨烯合成酶特异性mU6-siRNA真核表达载体的构建及鉴定

利用RNA干扰技术靶向构建角鲨烯合成酶基因ERG9特异性真核表达载体。将针对粟酒裂殖酵母(Schizosaccharomyces pombe Linder)ERG9不同部位所设计的3对siRNA序列通过重组技术克隆到质粒mU6 pro中构建真核表达重组体mU6 ERG9 siRNA1、2、3,转化DH5α菌株扩增,提取质粒通过限制性酶切和测序分析对重组表达载体进行鉴定,分析结果表明3个表达载体的设计基因插入正确,成功构建了ERG9特异性真核表达载体mU6 ERG9 siRNA,重组体的成功构建为在裂殖酵母细胞中靶向RNA干扰角鲨烯的合成从而提高辅酶Q10合成途径的代谢通量打下基础。     

Multifocal Electroretinograms

A limitation of traditional full-field electroretinograms (ERG) for the diagnosis of retinopathy is lack of sensitivity. Generally, ERG results are normal unless more than approximately 20% of the retina is affected. In practical terms, a patient might be legally blind as a result of macular degeneration or other scotomas and still appear normal, according to traditional full field ERG. An important development in ERGs is the multifocal ERG (mfERG). Erich Sutter adapted the mathematical sequences called binary m-sequences enabling the isolation from a single electrical signal an electroretinogram representing less than each square millimeter of retina in response to a visual stimulus¹.Results that are generated by mfERG appear similar to those generated by flash ERG. In contrast to flash ERG, which best generates data appropriate for whole-eye disorders. The basic mfERG result is based on the calculated mathematical average of an approximation of the positive deflection component of traditional ERG response, known as the b-wave¹. Multifocal ERG programs measure electrical activity from more than a hundred retinal areas per eye, in a few minutes. The enhanced spatial resolution enables scotomas and retinal dysfunction to be mapped and quantified.In the protocol below, we describe the recording of mfERGs using a bipolar speculum contact lens.Components of mfERG systems vary between manufacturers. For the presentation of visible stimulus, some suitable CRT monitors are available but most systems have adopted the use of flat-panel liquid crystal displays (LCD). The visual stimuli depicted here, were produced by a LCD microdisplay subtending 35 - 40 degrees horizontally and 30 - 35 degrees vertically of visual field, and calibrated to produce multifocal flash intensities of 2.7 cd s m^-2. Amplification was 50K. Lower and upper bandpass limits were 10 and 300 Hz. The software packages used were VERIS versions 5 and 6.