Brenneria bubanii sp. nov., isolated from decaying plant tissues.

Gram-negative, motile, rod-shaped bacterial strains (designated 4F2T and Kf) were isolated from decaying tissues of various deciduous tree species. Phylogenetic analyses based on their 16S rRNA gene sequences showed that the novel isolates belong to the genus Brenneria and showed highest (98.3 %) sequence similarity to Brenneria goodwinii. Isolate 4F2T formed a separate branch on the phylogenetic tree based on concatenated sequences of four housekeeping genes or whole genome sequences, clearly separate from Brenneria goodwinii, suggesting that novel isolates should belong to a novel species. Orthologous average nucleotide identity scores and in silico DNA-DNA hybridization values between isolate 4F2T and type strains of other species in the genus Brenneria were less than 85 and 30 %, respectively, significantly lower than the species boundary cut-off values (95 and 70 %). A negative reaction for ß-galactosidase, the ability to use dextrin and maltose as carbon sources, and an inability to use lactose are the main phenotypic characteristics that can be used to differentiate the novel isolates from B. goodwinii. Based on phenotypic and genotypic characteristics, isolates 4F2T and Kf belong to a novel species of the genus Brenneria, for which the name Brenneria bubanii sp. nov. is proposed. The type strain is 4F2T (=NCAIM B 02661T=LMG 32183T).

Fisheye transformation enhances deep-learning-based single-cell phenotyping by including cellular microenvironment.

Incorporating information about the surroundings can have a significant impact on successfully determining the class of an object. This is of particular interest when determining the phenotypes of cells, for example, in the context of high-throughput screens. We hypothesized that an ideal approach would consider the fully featured view of the cell of interest, include its neighboring microenvironment, and give lesser weight to cells that are far from the cell of interest. To satisfy these criteria, we present an approach with a transformation similar to those characteristic of fisheye cameras. Using this transformation with proper settings, we could significantly increase the accuracy of single-cell phenotyping, both in the case of cell culture and tissue-based microscopy images, and we present improved results on a dataset containing images of wild animals.

Cell lines and clearing approaches: a single-cell level 3D light-sheet fluorescence microscopy dataset of multicellular spheroids.

Nowadays, three dimensional (3D) cell cultures are widely used in the biological laboratories and several optical clearing approaches have been proposed to visualize individual cells in the deepest layers of cancer multicellular spheroids. However, defining the most appropriate clearing approach for the different cell lines is an open issue due to the lack of a gold standard quantitative metric. In this article, we describe and share a single-cell resolution 3D image dataset of human carcinoma spheroids imaged using a light-sheet fluorescence microscope. The dataset contains 90 multicellular cancer spheroids derived from 3 cell lines (i.e. T-47D, 5-8F, and Huh-7D12) and cleared with 5 different protocols, precisely ClearT, ClearT2, CUBIC, ScaleA2, and Sucrose. To evaluate image quality and light penetration depth of the cleared 3D samples, all the spheroids have been imaged under the same experimental conditions, labelling the nuclei with the DRAQ5 stain and using a Leica SP8 Digital LightSheet microscope. The clearing quality of this dataset was annotated by 10 independent experts and thus allows microscopy users to qualitatively compare the effects of different optical clearing protocols on different cell lines. It is also an optimal testbed to quantitatively assess different computational metrics evaluating the image quality in the deepest layers of the spheroids.

A quantitative metric for the comparative evaluation of optical clearing protocols for 3D multicellular spheroids.

3D multicellular spheroids quickly emerged as in vitro models because they represent the in vivo tumor environment better than standard 2D cell cultures. However, with current microscopy technologies, it is difficult to visualize individual cells in the deeper layers of 3D samples mainly because of limited light penetration and scattering. To overcome this problem several optical clearing methods have been proposed but defining the most appropriate clearing approach is an open issue due to the lack of a gold standard metric. Here, we propose a guideline for 3D light microscopy imaging to achieve single-cell resolution. The guideline includes a validation experiment focusing on five optical clearing protocols. We review and compare seven quality metrics which quantitatively characterize the imaging quality of spheroids. As a test environment, we have created and shared a large 3D dataset including approximately hundred fluorescently stained and optically cleared spheroids. Based on the results we introduce the use of a novel quality metric as a promising method to serve as a gold standard, applicable to compare optical clearing protocols, and decide on the most suitable one for a particular experiment.

First Report of Colletotrichum godetiae Causing Anthracnose and Twig Blight on Persian Walnut in Hungary.

Persian walnut (Juglans regia L.) fruit with preharvest anthracnose symptoms, necrotic fruit stalks, and twigs with necrotic buds, and peaks were collected in a Hungarian orchard next to Nágocs, in September 2018. Disease incidence was approximately 15% on a Hungarian bred walnut cultivar 'Milotai 10'. Similar symptoms were found on Persian walnut in other locations (eg. Milota, Érd, Sarród, and Kocs). Acervuli were observed on necrotic lesions on fruit, and twigs with pale orange conidial masses. Conidia were hyaline, unicellular, and fusiform. Morphometric measurements of conidia showed mean length ± SD × width ± SD = 15.9 ± 1.7 × 4.5 ± 0.4 µm, length/width ratio 1:0.3 (n=100). The fungus was isolated from conidial masses on potato dextrose agar (PDA) medium amended with Chlorampenicol (25 mg/L). A total of 12 isolates were obtained as pure cultures by single-spore isolations and incubated at 23°C in dark for 10 days. The colonies were white to gray or grayish-orange on the upper side and with black spots on the reverse side. The isolates showed morphological characteristics of Colletotrichum acutatum in sensu lato (Jayawardena et al. 2016). Molecular analyses were conducted to identify the exact species. Internal transcribed spacer (ITS) region, actin (ACT), and calmodulin (CAL) partial genes were amplified by ITS1F/ITS4R, ACT512F/ACT783R and CAL1/CAL2 primers (White at al. 1990, Carbone and Kohn 1999, O'Donnell et al. 2000). The sequences of ITS region (GenBank Accession Nos: MK367398-99, MK367401-02) showed 100% identity with C. godetiae sequence. Based on ACT gene (GenBank Accession Nos: MK415991-92, MK415994-95) were 100% identity with the deposited C. godetiae type strains from walnut. The obtained sequences of CAL gene (GenBank Accession Nos: MK415998-99, MK416001-02) were same and showed 100% with other C. godetiae sequences from other host plants. The fungus was identified as Colletotrichum godetiae Neerg. Pathogenicity tests were accomplished in the field and under laboratory conditions (25°C on thermostat) on 10 green 'Milotai 10' walnut fruit, and 10 walnut twigs each. Tests were conducted on living trees, collected fruit, and two-year-old twigs by inserting mycelial agar plugs (5 mm in diameter) onto wounded pericarp tissues, which were then wrapped with wet cotton and parafilm. Wounded tissues on 5 fruit and 5 two-year-old twigs were treated with non-colonized PDA plugs as noninoculated controls. After 14 d necrotic lesions 9 to 17 mm in diameter developed on fruit on living trees. Lengths of 12 to 17 mm and width of 7 to 12 mm necrosis was measured on phloem of walnut twigs, and almost two times larger in cambium. No necrosis developed around control wounds. Koch's postulates were fulfilled with the reisolation of the pathogen from symptomatic tissues, isolates were identical morphologically and by sequence analysis of ITS region, ACT, and CAL partial genes to the original isolates. Damm et al. (2012) described two C. godetiae strains associated with walnut, one isolated in Austria and another one of unknown origin. An epidemic event of walnut anthracnose caused by Colletotrichum species mainly C. godetiae was reported in France (Da Lio et al. 2018). The pathogen was isolated from nuts, buds, insects, and stems. To our knowledge, this is the first report of anthracnose of walnut fruit caused by C. godetiae in Hungary. Anthracnose caused by C. godetiae, and previously reported C. fioriniae (Varjas et al. 2019) is becoming an increasing preharvest problem on Persian walnut in Hungary.

Software tools for 3D nuclei segmentation and quantitative analysis in multicellular aggregates.

Today, we are fully immersed into the era of 3D biology. It has been extensively demonstrated that 3D models: (a) better mimic the physiology of human tissues; (b) can effectively replace animal models; (c) often provide more reliable results than 2D ones. Accordingly, anti-cancer drug screenings and toxicology studies based on multicellular 3D biological models, the so-called "-oids" (e.g. spheroids, tumoroids, organoids), are blooming in the literature. However, the complex nature of these systems limit the manual quantitative analyses of single cells' behaviour in the culture. Accordingly, the demand for advanced software tools that are able to perform phenotypic analysis is fundamental. In this work, we describe the freely accessible tools that are currently available for biologists and researchers interested in analysing the effects of drugs/treatments on 3D multicellular -oids at a single-cell resolution level. In addition, using publicly available nuclear stained datasets we quantitatively compare the segmentation performance of 9 specific tools.

Why do biting horseflies prefer warmer hosts? tabanids can escape easier from warmer targets.

Blood-sucking horseflies (tabanids) prefer warmer (sunlit, darker) host animals and generally attack them in sunshine, the reason for which was unknown until now. Recently, it was hypothesized that blood-seeking female tabanids prefer elevated temperatures, because their wing muscles are quicker and their nervous system functions better at a warmer body temperature brought about by warmer microclimate, and thus they can more successfully avoid the host's parasite-repelling reactions by prompt takeoffs. To test this hypothesis, we studied in field experiments the success rate of escape reactions of tabanids that landed on black targets as a function of the target temperature, and measured the surface temperature of differently coloured horses with thermography. We found that the escape success of tabanids decreased with decreasing target temperature, that is escape success is driven by temperature. Our results explain the behaviour of biting horseflies that they prefer warmer hosts against colder ones. Since in sunshine the darker the host the warmer its body surface, our results also explain why horseflies prefer sunlit dark (brown, black) hosts against bright (beige, white) ones, and why these parasites attack their hosts usually in sunshine, rather than under shaded conditions.

3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images.

SUMMARY: Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids and embryos) show that the precision of the segmentation reaches the level of a human expert. AVAILABILITY AND IMPLEMENTATION: 3D-Cell-Annotator is implemented in CUDA/C++ as a patch for the segmentation module of MITK. The 3D-Cell-Annotator enabled MITK distribution can be downloaded at: www.3D-cell-annotator.org. It works under Windows 64-bit systems and recent Linux distributions even on a consumer level laptop with a CUDA-enabled video card using recent NVIDIA drivers. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer.

Single-cell segmentation is typically a crucial task of image-based cellular analysis. We present nucleAIzer, a deep-learning approach aiming toward a truly general method for localizing 2D cell nuclei across a diverse range of assays and light microscopy modalities. We outperform the 739 methods submitted to the 2018 Data Science Bowl on images representing a variety of realistic conditions, some of which were not represented in the training data. The key to our approach is that during training nucleAIzer automatically adapts its nucleus-style model to unseen and unlabeled data using image style transfer to automatically generate augmented training samples. This allows the model to recognize nuclei in new and different experiments efficiently without requiring expert annotations, making deep learning for nucleus segmentation fairly simple and labor free for most biological light microscopy experiments. It can also be used online, integrated into CellProfiler and freely downloaded at www.nucleaizer.org. A record of this paper's transparent peer review process is included in the Supplemental Information.

Attractiveness of thermally different, uniformly black targets to horseflies: Tabanus tergestinus prefers sunlit warm shiny dark targets.

From a large distance tabanid flies may find their host animal by means of its shape, size, motion, odour, radiance and degree of polarization of host-reflected light. After alighting on the host, tabanids may use their mechano-, thermo-, hygro- and chemoreceptors to sense the substrate characteristics. Female tabanids prefer to attack sunlit against shady dark host animals, or dark against bright hosts for a blood meal, the exact reasons for which are unknown. Since sunlit darker surfaces are warmer than shady ones or sunlit/shady brighter surfaces, the differences in surface temperatures of dark and bright as well as sunlit and shady hosts may partly explain their different attractiveness to tabanids. We tested this observed warmth preference in field experiments, where we compared the attractiveness to tabanids (Tabanus tergestinus) of a warm and a cold shiny black barrel imitating dark hosts with the same optical characteristics. Using imaging polarimetry, thermography and Schlieren imaging, we measured the optical and thermal characteristics of both barrels and their small-scale models. We recorded the number of landings on these targets and measured the time periods spent on them. Our study revealed that T. tergestinus tabanid flies prefer sunlit warm shiny black targets against sunlit or shady cold ones with the same optical characteristics. These results support our new hypothesis that a blood-seeking female tabanid prefers elevated temperatures, partly because her wing muscles are more rapid and her nervous system functions better (due to faster conduction velocities and synaptic transmission of signals) in a warmer microclimate, and thus, she can avoid the parasite-repelling reactions of host animals by a prompt take-off.

Nectar- and stigma exudate-specific expression of an acidic chitinase could partially protect certain apple cultivars against fire blight disease.

MAIN CONCLUSION: Certain apple cultivars accumulate to high levels in their nectar and stigma exudate an acidic chitinase III protein that can protect against pathogens including fire blight disease causing Erwinia amylovora. To prevent microbial infections, flower nectars and stigma exudates contain various antimicrobial compounds. Erwinia amylovora, the causing bacterium of the devastating fire blight apple disease, is the model pathogen that multiplies in flower secretions and infects through the nectaries. Although Erwinia-resistant apples are not available, certain cultivars are tolerant. It was reported that in flower infection assay, the 'Freedom' cultivar was Erwinia tolerant, while the 'Jonagold' cultivar was susceptible. We hypothesized that differences in the nectar protein compositions lead to different susceptibility. Indeed, we found that an acidic chitinase III protein (Machi3-1) selectively accumulates to very high levels in the nectar and the stigma exudate of the 'Freedom' cultivar. We show that three different Machi3-1 alleles exist in apple cultivars and that only the 5B-Machi3-1 allele expresses the Machi3-1 protein in the nectar and the stigma exudate. We demonstrate that the 5B-Machi3-1 allele was introgressed from the Malus floribunda 821 clone into different apple cultivars including the 'Freedom'. Our data suggest that MYB-binding site containing repeats of the 5B-Machi3-1 promoter is responsible for the strong nectar- and stigma exudate-specific expression. As we found that in vitro, the Machi3-1 protein impairs growth and biofilm formation of Erwinia at physiological concentration, we propose that the Machi3-1 protein could partially protect 5B-Machi3-1 allele containing cultivars against Erwinia by inhibiting the multiplication and biofilm formation of the pathogen in the stigma exudate and in the nectar.

Environmental properties of cells improve machine learning-based phenotype recognition accuracy.

To answer major questions of cell biology, it is often essential to understand the complex phenotypic composition of cellular systems precisely. Modern automated microscopes produce vast amounts of images routinely, making manual analysis nearly impossible. Due to their efficiency, machine learning-based analysis software have become essential tools to perform single-cell-level phenotypic analysis of large imaging datasets. However, an important limitation of such methods is that they do not use the information gained from the cellular micro- and macroenvironment: the algorithmic decision is based solely on the local properties of the cell of interest. Here, we present how various features from the surrounding environment contribute to identifying a cell and how such additional information can improve single-cell-level phenotypic image analysis. The proposed methodology was tested for different sizes of Euclidean and nearest neighbour-based cellular environments both on tissue sections and cell cultures. Our experimental data verify that the surrounding area of a cell largely determines its entity. This effect was found to be especially strong for established tissues, while it was somewhat weaker in the case of cell cultures. Our analysis shows that combining local cellular features with the properties of the cell's neighbourhood significantly improves the accuracy of machine learning-based phenotyping.

Acute effects and after-effects of acoustic coordinated reset neuromodulation in patients with chronic subjective tinnitus.

Chronic subjective tinnitus is an auditory phantom phenomenon characterized by abnormal neuronal synchrony in the central auditory system. As shown computationally, acoustic coordinated reset (CR) neuromodulation causes a long-lasting desynchronization of pathological synchrony by downregulating abnormal synaptic connectivity. In a previous proof of concept study acoustic CR neuromodulation, employing stimulation tone patterns tailored to the dominant tinnitus frequency, was compared to noisy CR-like stimulation, a CR version significantly detuned by sparing the tinnitus-related pitch range and including substantial random variability of the tone spacing on the frequency axis. Both stimulation protocols caused an acute relief as measured with visual analogue scale scores for tinnitus loudness (VAS-L) and annoyance (VAS-A) in the stimulation-ON condition (i.e. 15 min after stimulation onset), but only acoustic CR neuromodulation had sustained long-lasting therapeutic effects after 12 weeks of treatment as assessed with VAS-L, VAS-A scores and a tinnitus questionnaire (TQ) in the stimulation-OFF condition (i.e. with patients being off stimulation for at least 2.5 h). To understand the source of the long-lasting therapeutic effects, we here study whether acoustic CR neuromodulation has different electrophysiological effects on oscillatory brain activity as compared to noisy CR-like stimulation under stimulation-ON conditions and immediately after cessation of stimulation. To this end, we used a single-blind, single application, cross over design in 18 patients with chronic tonal subjective tinnitus and administered three different 16-minute stimulation protocols: acoustic CR neuromodulation, noisy CR-like stimulation and low frequency range (LFR) stimulation, a CR type stimulation with deliberately detuned pitch and repetition rate of stimulation tones, as control stimulation. We measured VAS-L and VAS-A scores together with spontaneous EEG activity pre-, during- and post-stimulation. Under stimulation-ON conditions acoustic CR neuromodulation and noisy CR-like stimulation had similar effects: a reduction of VAS-L and VAS-A scores together with a decrease of auditory delta power and an increase of auditory alpha and gamma power, without significant differences. In contrast, LFR stimulation had significantly weaker EEG effects and no significant clinical effects under stimulation-ON conditions. The distinguishing feature between acoustic CR neuromodulation and noisy CR-like stimulation were the electrophysiological after-effects. Acoustic CR neuromodulation caused the longest significant reduction of delta and gamma and increase of alpha power in the auditory cortex region. Noisy CR-like stimulation had weaker and LFR stimulation hardly any electrophysiological after-effects. This qualitative difference further supports the assertion that long-term effects of acoustic CR neuromodulation on tinnitus are mediated by a specific disruption of synchronous neural activity. Furthermore, our results indicate that acute electrophysiological after-effects might serve as a marker to further improve desynchronizing sound stimulation.

Silver nanoparticles defeat p53-positive and p53-negative osteosarcoma cells by triggering mitochondrial stress and apoptosis.

Loss of function of the tumour suppressor p53 observed frequently in human cancers challenges the drug-induced apoptotic elimination of cancer cells from the body. This phenomenon is a major concern and provides much of the impetus for current attempts to develop a new generation of anticancer drugs capable of provoking apoptosis in a p53-independent manner. Since silver nanoparticles (AgNPs) possess unique cytotoxic features, we examined, whether their activity could be exploited to kill tumour suppressor-deficient cancer cells. Therefore, we investigated the effects of AgNPs on osteosarcoma cells of different p53 genetic backgrounds. As particle diameters might influence the molecular mechanisms leading to AgNP-induced cell death we applied 5 nm and 35 nm sized citrate-coated AgNPs. We found that both sized AgNPs targeted mitochondria and induced apoptosis in wild-type p53-containing U2Os and p53-deficient Saos-2 cells. According to our findings AgNPs are able to kill osteosarcoma cells independently from their actual p53 status and induce p53-independent cancer cell apoptosis. This feature renders AgNPs attractive candidates for novel chemotherapeutic approaches.

Silver nanoparticles modulate ABC transporter activity and enhance chemotherapy in multidrug resistant cancer.

The emergence of multidrug resistant (MDR) cancer phenotypes dramatically attenuates the efficiency of antineoplastic drug treatments often leading to the failure of chemotherapy. Therefore there is an urgent need to engineer new therapeutically useful agents and propose innovative approaches able to defeat resistant cancer cells. Although the remarkable anti-cancer features of silver nanoparticles (AgNPs) have already been delineated their impact on MDR cancer has never been investigated. Herein, we report that AgNPs have notable anti-proliferative effect and induce apoptosis mediated cell death both in drug sensitive and in MDR cancer cells. Furthermore we show evidence that AgNPs exert an inhibitory action on the efflux activity of MDR cancer cells which feature could be exploited to enhance drug accumulation. We verified synergistic interactions of AgNPs with six different antineoplastic agents on drug resistant cells which emphasizes the excellent potential of AgNPs as combinational partners in the chemotherapy of MDR cancer. FROM THE CLINICAL EDITOR: The treatment of cancer often fails due to the development of multidrug resistant (MDR) cancer cells. Hence, novel approaches are being investigated to combat drug resistant cancer cells. One particular method studied here uses silver nanoparticles (AgNPs). The authors showed that AgNPs had anti-proliferative effect and ?exerted an inhibitory action on ABC transporter. The findings could suggest the possible use of AgNPs in combination with other chemotherapeutic agents in the clinical setting.

Reversing pathologically increased EEG power by acoustic coordinated reset neuromodulation.

Acoustic Coordinated Reset (CR) neuromodulation is a patterned stimulation with tones adjusted to the patient's dominant tinnitus frequency, which aims at desynchronizing pathological neuronal synchronization. In a recent proof-of-concept study, CR therapy, delivered 4-6 h/day more than 12 weeks, induced a significant clinical improvement along with a significant long-lasting decrease of pathological oscillatory power in the low frequency as well as γ band and an increase of the α power in a network of tinnitus-related brain areas. As yet, it remains unclear whether CR shifts the brain activity toward physiological levels or whether it induces clinically beneficial, but nonetheless abnormal electroencephalographic (EEG) patterns, for example excessively decreased δ and/or γ. Here, we compared the patients' spontaneous EEG data at baseline as well as after 12 weeks of CR therapy with the spontaneous EEG of healthy controls by means of Brain Electrical Source Analysis source montage and standardized low-resolution brain electromagnetic tomography techniques. The relationship between changes in EEG power and clinical scores was investigated using a partial least squares approach. In this way, we show that acoustic CR neuromodulation leads to a normalization of the oscillatory power in the tinnitus-related network of brain areas, most prominently in temporal regions. A positive association was found between the changes in tinnitus severity and the normalization of δ and γ power in the temporal, parietal, and cingulate cortical regions. Our findings demonstrate a widespread CR-induced normalization of EEG power, significantly associated with a reduction of tinnitus severity.

Lonsdalea quercina subsp. populi subsp. nov., isolated from bark canker of poplar trees.

Seven Gram-negative bacterial strains were isolated from oozing bark canker of poplar (Populus × euramericana) trees in Hungary. They showed high (>98.3%) 16S rRNA gene sequence similarity to Lonsdalea quercina; however, they differed from this species in several phenotypic characteristics. Multilocus sequence analysis based on three housekeeping genes (gyrB, atpD and infB) revealed, and DNA-DNA hybridization analysis confirmed, that this group of bacterial strains forms a distinct lineage within the species Lonsdalea quercina. A detailed study of phenotypic and physiological characteristics confirmed the separation of isolates from poplars from other subspecies of L. quercina; therefore, a novel subspecies, Lonsdalea quercina subsp. populi, type strain NY060(T) (=DSM 25466(T)=NCAIM B 02483(T)), is proposed.

Phenotypic variability of patients homozygous for the GJB2 mutation 35delG cannot be explained by the influence of one major modifier gene.

Hereditary hearing loss (HL) is a very heterogeneous trait, with 46 gene identifications for non-syndromic HL. Mutations in GJB2 cause up to half of all cases of severe-to-profound congenital autosomal recessive non-syndromic HL, with 35delG being the most frequent mutation in Caucasians. Although a genotype-phenotype correlation has been established for most GJB2 genotypes, the HL of 35delG homozygous patients is mild to profound. We hypothesise that this phenotypic variability is at least partly caused by the influence of modifier genes. By performing a whole-genome association (WGA) study on 35delG homozygotes, we sought to identify modifier genes. The association study was performed by comparing the genotypes of mild/moderate cases and profound cases. The first analysis included a pooling-based WGA study of a first set of 255 samples by using both the Illumina 550K and Affymetrix 500K chips. This analysis resulted in a ranking of all analysed single-nucleotide polymorphisms (SNPs) according to their P-values. The top 250 most significantly associated SNPs were genotyped individually in the same sample set. All 192 SNPs that still had significant P-values were genotyped in a second independent set of 297 samples for replication. The significant P-values were replicated in nine SNPs, with combined P-values between 3 x 10(-3) and 1 x 10(-4). This study suggests that the phenotypic variability in 35delG homozygous patients cannot be explained by the effect of one major modifier gene. Significantly associated SNPs may reflect a small modifying effect on the phenotype. Increasing the power of the study will be of greatest importance to confirm these results.

Photorhabdus temperata subsp. cinerea subsp. nov., isolated from Heterorhabditis nematodes.

During the characterization of symbiotic bacteria of Hungarian entomopathogenic nematode isolates, a number of bacteria (including strain 3107(T)) isolated from Heterorhabditis downesi and Heterorhabditis megidis showed only moderate 16S rRNA gene sequence similarity to the type strains of all described Photorhabdus species and subspecies. On the basis of the 16S rRNA gene sequence, the phylogenetic relationships of these isolates were uncertain, because of the low bootstrap values. Using gyrB sequences for phylogenetic analysis, these isolates were shown to be part of the species Photorhabdus temperata, with clear separation from both Palaearctic and American strains (phylogenetic distances are 6.9 and 7.9 %, respectively). Physiological properties and carbon-source utilization profiles supported the phylogenetic position of these strains; therefore, a novel subspecies, Photorhabdus temperata subsp. cinerea subsp. nov. is proposed, with the type strain 3107(T) (=DSM 19724(T) =NCAIM B 02271(T)).