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Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex 398 (CC398) is the dominant livestock-associated (LA) MRSA lineage in European livestock and an increasing cause of difficult-to-treat human disease. LA-CC398 MRSA evolved from a diverse human-associated methicillin-sensitive population, and this transition from humans to livestock was associated with three mobile genetic elements (MGEs). In this study, we apply transposon-directed insertion site sequencing (TraDIS), a high-throughput transposon mutagenesis approach, to investigate genetic signatures that contribute to LA-CC398 causing disease in humans. We identified 26 genes associated with LA-CC398 survival in human blood and 47 genes in porcine blood. We carried out phylogenetic reconstruction on 1,180 CC398 isolates to investigate the genetic context of all identified genes. We found that all genes associated with survival in human blood were part of the CC398 core genome, while 2/47 genes essential for survival in porcine blood were located on MGEs. Gene SAPIG0966 was located on the previously identified Tn916 transposon carrying a tetracycline resistance gene, which has been shown to be stably inherited within LA-CC398. Gene SAPIG1525 was carried on a phage element, which in part, matched phiSa2wa_st1, a previously identified bacteriophage carrying the Panton-Valentine leucocidin (PVL) virulence factor. Gene deletion mutants constructed in two LA-CC398 strains confirmed that the SAPIG0966 carrying Tn916 and SAPIG1525 were important for CC398 survival in porcine blood. Our study shows that MGEs that carry antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for host adaptation. IMPORTANCE CC398 is the dominant type of methicillin-resistant Staphylococcus aureus (MRSA) in European livestock and a growing cause of human infections. Previous studies have suggested MRSA CC398 evolved from human-associated methicillin-sensitive Staphylococcus aureus and is capable of rapidly readapting to human hosts while maintaining antibiotic resistance. Using high-throughput transposon mutagenesis, our study identified 26 and 47 genes important for MRSA CC398 survival in human and porcine blood, respectively. Two of the genes important for MRSA CC398 survival in porcine blood were located on mobile genetic elements (MGEs) carrying resistance or virulence genes. Our study shows that these MGEs carrying antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for blood infection and host adaptation.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli.Author SummaryAntimicrobial resistance (AMR) is one of the biggest global health threats humanity is facing. Understanding the emergence and spread of AMR between different bacterial species is crucial for the development of effective countermeasures. In this paper we describe a user-friendly, affordable and comprehensive (laboratory and bioinformatics) workflow that is able to identify, associate and track AMR genes in bacteria. We demonstrate the efficiency and reliability of the method by comparing 50 faecal microbiomes from pig farms with high-antibiotic use (conventional farms), and 50 faecal microbiomes from pig farms with low-antibiotic use (organic farms). Our method provides a novel approach to resistance gene tracking, that also leads to the generation of high quality metagenomic assembled genomes that includes genes on mobile genetic elements, such as plasmids, that would not otherwise be included in these assembled genomes.

The United Kingdom has prohibited the prophylactic use of antibiotics in agriculture but they are still critical for disease control. It is thus vital to understand the effects of antibiotic treatment on antimicrobial resistance (AMR) spread. Hi-C metagenomic sequencing can help identify AMR genes in animal microbiomes and assign plasmid-based genes to their bacterial hosts. Leveraging Hi-C, we sequence antibiotically-treated pig microbiomes through time to identify dynamic trends in AMR gene prevalence. Fecal samples were collected at time points prior to and following antibiotic treatment in 6 farms across England when pigs presented with illness. Control samples were collected from 2 of these farms at multiple time points without treatment. Samples were processed using a bioinformatic pipeline that outputs assemblies with information on taxonomic classification and presence/absence of an AMR allele. 115 AMR alleles across 11 antibiotic classes were included. The bacterial species in highest abundance/farm belonged to order Bacteroidales (45.9-53.1%). Tetracycline resistance alleles showed the highest prevalence/farm (28.4-52.8%). No significant association between bacterial species abundance and time point, and AMR allele prevalence and time point was found in all farms (χ2 p>.05). The distribution of the number of AMR alleles/assembly was significantly higher between the first and last time point in 4/6 treated farms and 1/2 control farms (Wilcoxan rank sum p Key messages Ensuring that the responsible use of antibiotics does not drastically affect AMR mobilization is key to preserving the efficacy of therapeutics in agriculture. While acquisition of resistance genes over time is seen it cannot conclusively be tied to treatment; Minimal microbiome perturbation post treatment implies that therapeutic antibiotic use is warranted.

Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases. We aimed to identify the optimal method for isolating small (&lt, 200 nm) EVs from human urine prior to small RNA analysis. EVs from filtered healthy volunteer urine were concentrated using three methods: ultracentrifugation (UC), a precipitation-based kit (PR), and ultrafiltration (UF). EVs were further purified by size-exclusion chromatography (SEC). EV preparations were analysed with transmission electron microscopy (TEM), Western blotting, nanoparticle tracking analysis (NTA) and an Agilent Bioanalyzer Small RNA kit. UF yielded the highest number of particles both before and after SEC. Small RNA analysis from UF-concentrated urine identified two major peaks at 10–40 nucleotides (nt) and 40–80 nt. In contrast, EV preparations obtained after UC, PR or SEC combined with any concentrating method, contained predominantly 40–80 nt sized small RNA. Protein fractions from UF+SEC contained small RNA of 10–40 nt in size (consistent with miRNAs). These data indicate that most of the microRNA-sized RNAs in filtered urine are not associated with small-sized EVs, and highlights the importance of removing non-vesicular proteins and RNA from urine EV preparations prior to small RNA analysis.

Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana’s Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14.

Funder: CHDI Foundation; doi: http://dx.doi.org/10.13039/100005725, Huntington’s disease (HD) is characterised by progressive symptoms including cognitive deficits and sleep/wake disturbances reflected in an abnormal electroencephalography (EEG). Modafinil, a wake-promoting and cognitive-enhancing drug, has been considered as a treatment for HD. We used HD (R6/2) mice to investigate the potential for using modafinil to treat sleep-wake disturbance in HD. R6/2 mice show sleep-wake and EEG changes similar to those seen in HD patients, with increased rapid eye movement sleep (REMS), decreased wakefulness/increased non-REMS (NREMS), and pathological changes in EEG spectra, particularly an increase in gamma power. We recorded EEG from R6/2 and wild-type mice treated with modafinil acutely (with single doses between 25 and 100 mg/kg; at 12 and 16 weeks of age), or chronically (64 mg/kg modafinil/day from 6 to 15 weeks). Acutely, modafinil increased wakefulness in R6/2 mice and restored NREMS to wild-type levels at 12 weeks. It also suppressed the pathologically increased REMS. This was accompanied by decreased delta power, increased peak frequency of theta, and increased gamma power. At 16 weeks, acute modafinil also restored wakefulness and NREMS to wild-type levels. However, whilst REMS decreased, it did not return to normal levels. By contrast, in the chronic treatment group, modafinil-induced wakefulness was maintained at 15 weeks (after 9 weeks of treatment). Interestingly, chronic modafinil also caused widespread suppression of power across the EEG spectra, including a reduction in gamma that increases pathologically in R6/2 mice. The complex EEG effects of modafinil in R6/2 mice should provide a baseline for further studies to investigate the translatability of these result to clinical practice.

Details of the functional mechanisms of intrinsically disordered proteins (IDPs) in living cells is an area not frequently investigated. Here, we dissect the molecular mechanism of action of an IDP in cells by detailed structural analyses based on an in-cell nuclear magnetic resonance experiment. We show that the ID stress protein (IDSP) A. thaliana Early Response to Dehydration (ERD14) is capable of protecting E. coli cells under heat stress. The overexpression of ERD14 increases the viability of E. coli cells from 38.9% to 73.9% following heat stress (50 &deg, C &times, 15 min). We also provide evidence that the protection is mainly achieved by protecting the proteome of the cells. In-cell NMR experiments performed in E. coli cells show that the protective activity is associated with a largely disordered structural state with conserved, short sequence motifs (K- and H-segments), which transiently sample helical conformations in vitro and engage in partner binding in vivo. Other regions of the protein, such as its S segment and its regions linking and flanking the binding motifs, remain unbound and disordered in the cell. Our data suggest that the cellular function of ERD14 is compatible with its residual structural disorder in vivo.

A form of hereditary cerebellar ataxia has recently been described in the Norwegian Buhund dog breed. This study aimed to identify the genetic cause of the disease. Whole-genome sequencing of two Norwegian Buhund siblings diagnosed with progressive cerebellar ataxia was carried out, and sequences compared with 405 whole genome sequences of dogs of other breeds to filter benign common variants. Nine variants predicted to be deleterious segregated among the genomes in concordance with an autosomal recessive mode of inheritance, only one of which segregated within the breed when genotyped in additional Norwegian Buhunds. In total this variant was assessed in 802 whole genome sequences, and genotyped in an additional 505 unaffected dogs (including 146 Buhunds), and only four affected Norwegian Buhunds were homozygous for the variant. The variant identified, a T to C single nucleotide polymorphism (SNP) (NC_006585.3:g.88890674T>C), is predicted to cause a tryptophan to arginine substitution in a highly conserved region of the potassium voltage-gated channel interacting protein KCNIP4. This gene has not been implicated previously in hereditary ataxia in any species. Evaluation of KCNIP4 protein expression through western blot and immunohistochemical analysis using cerebellum tissue of affected and control dogs demonstrated that the mutation causes a dramatic reduction of KCNIP4 protein expression. The expression of alternative KCNIP4 transcripts within the canine cerebellum, and regional differences in KCNIP4 protein expression, were characterised through RT-PCR and immunohistochemistry respectively. The voltage-gated potassium channel protein KCND3 has previously been implicated in spinocerebellar ataxia, and our findings suggest that the Kv4 channel complex KCNIP accessory subunits also have an essential role in voltage-gated potassium channel function in the cerebellum and should be investigated as potential candidate genes for cerebellar ataxia in future studies in other species., Author summary Hereditary ataxias, which are a group of disorders characterised by incoordination of movement, are typically incurable and there are often no disease-modifying treatments available. Canine hereditary ataxias are a notable group of movement disorders in dogs, and represent well characterised naturally occurring disease models of ataxia that can help improve our understanding of the underlying biology of the disorder in both dogs and humans. We used the whole genome sequences of two affected siblings to investigate the genetic cause of a slowly progressive form of hereditary ataxia in the Norwegian Buhund dog breed, and identified a single base change within the KCNIP4 gene. We have characterised the expression of KCNIP4 in the dog, and investigated the effect of the identified mutation. This gene has not previously been implicated in inherited ataxia in any species, and our findings suggest that this and related genes represent potential candidates for ataxia in future studies in other species. Our findings will allow dog breeders to avoid producing affected dogs, reduce the disease allele frequency, and eventually eliminate the disease from the breed, through the use of a DNA test.

Brachycephalic breeds are often in the news due to the challenges and ethical issues surrounding conformation-related disease in these breeds. An exponential rise in ownership of brachycephalic breeds has occurred in recent years, particularly of French bulldogs, where kennel club registrations have increased by 3000 per cent over the past 10 years in the UK. The increase in popularity of these breeds has led to increased awareness of conformation-related health issues seen in some brachycephalic dogs. Brachycephalic obstructive airway syndrome (BOAS) is perhaps the most obvious conformation-related health issue, but other welfare issues include: skin fold pyoderma; shallow orbits with protruding globes, leading to increased risk of corneal ulceration and globe prolapse; hemivertebrae, which may be accompanied by spinal cord compression; Chiari-like malformation; dystocia; and dental malocclusion. Upper airway obstruction, or BOAS, has been predominantly documented in extreme brachycephalic breeds, specifically the bulldog, French bulldog and pug. BOAS may manifest as respiratory noise, dyspnoea, exercise intolerance, heat sensitivity, sleep disorders, cyanosis or collapse.1 The prevalence of these diseases among the brachycephalic breeds is difficult to assess as many are not recognised by owners2 and some are accepted by veterinary surgeons as normal for the breed. Although many breeds, including the French bulldog, pug and bulldog, have health schemes which the breed clubs are promoting, only a small proportion of the pet population is Kennel Club registered. The increased demand for these dogs has resulted in a lucrative puppy trade where the focus may be on money rather than health. The general practice surveillance data generated from schemes such as VetCompass have shown that extreme brachycephalic breeds die younger than equivalent sized dogs, with a higher proportion of deaths due to upper respiratory disease.3 However, the value of such information depends on accurate, consistent reporting of lesions which, …

Sleep disruption is a common invisible symptom of neurological dysfunction in Huntington's disease (HD) that takes an insidious toll on well-being of patients. Here we used electroencephalography (EEG) to examine sleep in 6 year old OVT73 transgenic sheep (Ovis aries) that we used as a presymptomatic model of HD. We hypothesized that despite the lack of overt symptoms of HD at this age, early alterations of the sleep-wake pattern and EEG powers may already be present. We recorded EEG from female transgenic and normal sheep (5/group) during two undisturbed ‘baseline’ nights with different lighting conditions. We then recorded continuously through a night of sleep disruption and the following 24 h (recovery day and night). On baseline nights, regardless of whether the lights were on or off, transgenic sheep spent more time awake than normal sheep particularly at the beginning of the night. Furthermore, there were significant differences between transgenic and normal sheep in both EEG power and its pattern of distribution during non-rapid eye movement (NREM) sleep. In particular, there was a significant decrease in delta (0.5–4 Hz) power across the night in transgenic compared to normal sheep, and the distributions of delta, theta and alpha oscillations that typically dominate the EEG in the first half of the night of normal sheep were skewed so they were predominant in the second, rather than the first half of the night in transgenic sheep. Interestingly, the effect of sleep disruption on normal sheep was also to skew the pattern of distribution of EEG powers so they looked more like that of transgenic sheep under baseline conditions. Thus it is possible that transgenic sheep exist in a state that resemble a chronic state of physiological sleep deprivation. During the sleep recovery period, normal sheep showed a significant ‘rebound’ increase in delta power with frontal dominance. A similar rebound was not seen in transgenic sheep, suggesting that their homeostatic response to sleep deprivation is abnormal. Although sleep abnormalities in early stage HD patients are subtle, with patients often unaware of their existence, they may contribute to impairment of neurological function that herald the onset of disease. A better understanding of the mechanisms underlying EEG abnormalities in early stage HD would give insight into how, and when, they progress into the sleep disorder. The transgenic sheep model is ideally positioned for studies of the earliest phase of disease when sleep abnormalities first emerge.

Objective To determine prognostic indicators for the surgical treatment of brachycephalic obstructive airway syndrome (BOAS) and to compare the prognosis of 2 multilevel surgical procedures. Study Design Prospective clinical study. Sample Population Client-owned pugs, French bulldogs, and bulldogs (n = 50). Methods Noninvasive whole-body barometric plethysmography (WBBP) was used to assess respiratory function before, 1 month and 6 months after upper airway corrective surgery. Postoperatively, BOAS indices (ie, ascending severity score generated from WBBP data, 0%-100%) that equaled to or exceeded the cut-off values of BOAS in the diagnostic models were considered to have a “poor prognosis.” A multivariate logistic regression was used to assess predictors for prognosis. Results The median BOAS indices decreased after surgery (from 76% to 63%, P

Objectives: High-level β-lactam resistance in methicillin-resistant Staphylococcus aureus is mediated in the majority of strains by a mecA or mecC gene. In this study, we identified ten mec gene negative MRSA human isolates from Austria and eleven bovine isolates from the UK showing high levels of β-lactam resistance and sought to understand the molecular basis of the resistance observed. Methods: Different antimicrobial resistance testing methods (disk diffusion, Etest and Vitek®2) were used to establish the β-lactam resistance profiles for the isolates and the isolates were further investigated by whole-genome sequencing. Results: A number of mutations (including novel ones) in penicillin-binding proteins, AcrB, YjbH and pbp4-promoter were identified in the resistant isolates but not in closely related susceptible isolates. Importantly, a truncation in the c-di-AMP phosphodiesterase enzyme, GdpP, was identified in seven of the ten Austrian isolates and ten of the eleven UK isolates. Complementation of four representative isolates with an intact copy of gdpP gene restored susceptibility to penicillins and abolished the growth defects caused by the truncation. Conclusion: This study reports naturally occurring inactivation of GdpP protein in S. aureus of both human and animal origins, and demonstrated clinical relevance to a previously reported association between this truncation and increased β-lactam resistance and impaired bacterial growth in laboratory generated mutants. It also highlights possible limitations of genomic determination of antibiotic susceptibility based on single gene presence or absence when choosing the appropriate antimicrobial treatment for patients.

Background A novel test using whole-body barometric plethysmography (WBBP) was developed recently to diagnose brachycephalic obstructive airway syndrome (BOAS) in unsedated French bulldogs. Hypothesis/Objectives The hypotheses of this study were: (1) respiratory characteristics are different between healthy nonbrachycephalic dogs and brachycephalic dogs; and among pugs, French bulldogs, and bulldogs; and (2) obesity and stenotic nares are risk factors for BOAS. The main objective was to establish a diagnostic test for BOAS in these 3 breeds. Animals A total of 266 brachycephalic dogs (100 pugs, 100 French bulldogs, and 66 bulldogs) and 28 nonbrachycephalic dogs. Methods Prospective study. Exercise tolerance tests with respiratory functional grading, and WBBP were performed on all dogs. Data from WBBP were associated with functional grades to train quadratic discriminant analysis tools to assign dogs to BOAS+ and BOAS- groups. A BOAS index (0–100%) was calculated for each dog. Receiver operating characteristic (ROC) curves were used to evaluate classification ability. Results Minute volume was decreased significantly in asymptomatic pugs (P = .009), French bulldogs (P = .026), and bulldogs (P < .0001) when compared to nonbrachycephalic controls. Respiratory characteristics were different among breeds and affected dogs had a significant increase in trace variation. The BOAS index predicted BOAS status for each breed with 94–97% (95% confidence interval [CI], 88.9–100%) accuracy (area under the ROC curve). Both obesity (P = .04) and stenotic nares (P = .004) were significantly associated with BOAS. Conclusions and Clinical Importance The WBBP can be used as a clinical tool to diagnose BOAS noninvasively and objectively.

The Ca(2+) -binding protein S100A4 interacts with the C terminus of nonmuscle myosin IIA (NMIIA) causing filament disassembly, which is correlated with an increased metastatic potential of tumor cells. Despite high sequence similarity of the three NMII isoforms, S100A4 discriminates against binding to NMIIB. We searched for structural determinants of this selectivity. Based on paralog scanning using phage display, we identified a single position as major determinant of isoform selectivity. Reciprocal single amino acid replacements showed that at position 1907 (NMIIA numbering), the NMIIA/NMIIC-specific alanine provides about 60-fold higher affinity than the NMIIB-specific asparagine. The structural background of this can be explained in part by a communication between the two consecutive α-helical binding segments. This communication is completely abolished by the Ala-to-Asn substitution. Mutual swapping of the disordered tailpieces only slightly affects the affinity of the NMII chimeras. Interestingly, we found that the tailpiece and position 1907 act in a nonadditive fashion. Finally, we also found that the higher stability of the C-terminal coiled-coil region of NMIIB also discriminates against interaction with S100A4. Our results clearly show that the isoform-selective binding of S100A4 is determined at multiple levels in the structure of the three NMII isoforms and the corresponding functional elements of NMII act synergistically with one another resulting in a complex interaction network. The experimental and in silico results suggest two divergent evolutionary pathways: NMIIA and NMIIB evolved to possess S100A4-dependent and -independent regulations, respectively.

Computed tomography (CT) is used to document upper airway lesions in dogs with brachycephalic obstructive airway syndrome. The presence of an endotracheal tube during CT scanning is often required for general anesthesia. We hypothesized that the endotracheal tube placement would change the soft tissue dimensions of the upper airway. The aims of this prospective, method comparison study were to evaluate the reliability of the previously reported upper airway CT measurements with endotracheal tube placement, and to propose measurements that are minimally affected by the endotracheal tube. Twenty brachycephalic dogs were included in this study. Each dog underwent head/neck CT with an endotracheal tube, followed by a second scan without the endotracheal tube. Ten measurements of the soft palate, nasopharynx, and trachea were performed. Tracheal dimension was significantly larger with the endotracheal tube compared to without, whereas the soft palate cross-sectional area was significantly smaller with the endotracheal tube than without the endotracheal tube. The influence of the endotracheal tube on the caudal nasopharynx cross-sectional (transverse-sectional) area varied with a mean proportional absolute difference of 35%. Rostral soft palate thickness, tracheal perimeter, and cross-sectional area of the rostral nasopharynx were the measurements least affected by the endotracheal tube (intraclass correlation coefficient = 0.964, 0.967, and 0.951, respectively). Therefore, we proposed that these three measurements may be most useful for future brachycephalic obstructive airway syndrome studies that require CT scanning of intubated animals. However, with endotracheal tube placement, measurements of soft palate length, caudal nasopharyngeal cross-sectional area, and trachea height and width may not be reliable.

OBJECTIVE To evaluate the effectiveness of laser-assisted turbinectomy (LATE) in treating brachycephalic obstructive airway syndrome (BOAS) and to investigate the potential indications. STUDY DESIGN Prospective clinical study. SAMPLE POPULATION Client-owned pugs, French bulldogs, and English bulldogs (n = 57). METHODS A BOAS index was obtained from whole-body barometric plethysmography before BOAS conventional multilevel surgery (CMS) and 2-6 months post-CMS. Dogs with BOAS index >50% and BOAS functional grades II-III after CMS were considered candidates for LATE. A BOAS index was repeated 2-6 months after LATE. Intranasal lesions and a measurement of soft tissue proportion at the rostral entrance of choanae (STC) were recorded on the basis of computed tomography images. Logistic regressions were used to assess the intranasal predictors for being LATE candidates. RESULTS Twenty-nine of 57 dogs were candidates for LATE, all of which were pugs or French bulldogs. The median BOAS index of dogs that were operated on (20/29 candidates) decreased from 67% post-CMS to 42% after LATE (P

Extremely brachycephalic, or short-muzzled, dog breeds such as pugs, French bulldogs, and bulldogs are prone to the conformation-related respiratory disorder-brachycephalic obstructive airway syndrome (BOAS). Affected dogs present with a wide range of clinical signs from snoring and exercise intolerance, to life-threatening events such as syncope. In this study, conformational risk factors for BOAS that could potentially aid in breeding away from BOAS were sought. Six hundred and four pugs, French bulldogs, and bulldogs were included in the study. Soft tape measurements of the head and body were used and the inter-observer reproducibility was evaluated. Breed-specific models were developed to assess the associations between the conformational factors and BOAS status based on functional grading. The models were further validated by means of a BOAS index, which is an objective measurement of respiratory function using whole-body barometric plethysmography. The final models have good predictive power for discriminating BOAS (-) and BOAS (+) phenotypes indicated by the area under the curve values of >80% on the receiver operating curves. When other factors were controlled, stenotic nostrils were associated with BOAS in all three breeds; pugs and bulldogs with higher body condition scores (BCS) had a higher risk of developing BOAS. Among the standardized conformational measurements (i.e. craniofacial ratio (CFR), eye width ratio (EWR), skull index (SI), neck girth ratio (NGR), and neck length ratio (NLR)), for pugs EWR and SI, for French bulldogs NGR and NLR, and for bulldogs SI and NGR showed significant associations with BOAS status. However, the NGR in bulldogs was the only significant predictor that also had satisfactory inter-observer reproducibility. A NGR higher than 0.71 in male bulldogs was predictive of BOAS with approximately 70% sensitivity and specificity. In conclusion, stenotic nostrils, BCS, and NGR were found to be valid, easily applicable predictors for BOAS (+).

Several cellular processes rely on the fine tuning of actin cytoskeleton. A central component in the regulation of this cellular machinery is the ADF-H domain proteins. Despite sharing the same domain, ADF-H domain proteins produce a diverse functional landscape in the regulation of the actin cytoskeleton. Recent findings emphasize that the functional and structural features of these proteins can differ not only between ADF-H families but even within the same family. The structural and evolutional background of this functional diversity is poorly understood. This review focuses on the specific functional characteristics of ADF-H domain proteins and how these features can be linked to structural differences in the ADF-H domain and also to different conformational transitions in actin. In the light of recent discoveries we pay special attention to the ADF/cofilin proteins to find tendencies along which the functional and structural diversification is governed through the evolution.

Several multi-target drugs used in treating psychiatric disorders, such as antidepressants (e.g. agomelatine, trazodone, nefazodone, amitriptyline, mirtazapine, mianserin, fluoxetine) or most atypical antipsychotics, have 5-hydroxytryptamine 2C (5-HT2C) receptor-blocking property. Adaptive changes in 5-HT2C receptor-mediated functions are suggested to contribute to therapeutic effects of selective serotonin reuptake inhibitor (SSRI) antidepressants after weeks of treatment, at least in part. Beyond the mediation of anxiety and other functions, 5-HT2C receptors are involved in sleep regulation. Anxiety-related adaptive changes caused by antidepressants have been studied extensively, although sleep- and electroencephalography (EEG)-related functional studies are still lacking. The aim of this study was to investigate the effects of chronic SSRI treatment on 5-HT2C receptor antagonist-induced functions in different vigilance stages and on quantitative EEG (Q-EEG) spectra. Rats were treated with a single dose of the selective 5-HT2C receptor antagonist SB-242084 (1 mg/kg, i.p.) or vehicle at the beginning of passive phase following a 20-day-long SSRI (escitalopram; 10 mg/kg/day, osmotic minipump) or VEHICLE pretreatment. Fronto-parietal electroencephalogram, electromyogram and motility were recorded during the first 3 h of passive phase. We found that the chronic escitalopram pretreatment attenuated the SB-242084-caused suppression in rapid eye movement sleep (REMS). On the contrary, the 5-HT2C receptor antagonist-induced elevations in passive wake and theta (5-9 Hz) power density during active wake and REMS were not affected by the SSRI. In conclusion, attenuation in certain, but not all vigilance- and Q-EEG-related functions induced by the 5-HT2C receptor antagonist, suggests dissociation in 5-HT2C receptor adaptation.

Narcolepsy is a chronic sleep disorder, likely with an autoimmune component. During 2009 and 2010, a link between A(H1N1)pdm09 Pandemrix vaccination and onset of narcolepsy was suggested in Scandinavia. In this study, we searched for autoantibodies related to narcolepsy using a neuroanatomical array: rat brain sections were processed for immunohistochemistry/double labeling using patient sera/cerebrospinal fluid as primary antibodies. Sera from 89 narcoleptic patients, 52 patients with other sleep-related disorders (OSRDs), and 137 healthy controls were examined. Three distinct patterns of immunoreactivity were of particular interest: pattern A, hypothalamic melanin-concentrating hormone and proopiomelanocortin but not hypocretin/orexin neurons; pattern B, GABAergic cortical interneurons; and pattern C, mainly globus pallidus neurons. Altogether, 24 of 89 (27%) narcoleptics exhibited pattern A or B or C. None of the patterns were exclusive for narcolepsy but were also detected in the OSRD group at significantly lower numbers. Also, some healthy controls exhibited these patterns. The antigen of pattern A autoantibodies was identified as the common C-terminal epitope of neuropeptide glutamic acid-isoleucine/α-melanocyte-stimulating hormone (NEI/αMSH) peptides. Passive transfer experiments on rat showed significant effects of pattern A human IgGs on rapid eye movement and slow-wave sleep time parameters in the inactive phase and EEG θ-power in the active phase. We suggest that NEI/αMSH autoantibodies may interfere with the fine regulation of sleep, contributing to the complex pathogenesis of narcolepsy and OSRDs. Also, patterns B and C are potentially interesting, because recent data suggest a relevance of those brain regions/neuron populations in the regulation of sleep/arousal.

The prion protein (PrP)—known for its central role in transmissible spongiform encephalopathies—has been reported to possess two nuclear localization signals and localize in the nuclei of certain cells in various forms. Although these data are superficially contradictory, it is apparent that nuclear forms of the prion protein can be found in cells in either the healthy or the diseased state. Here we report that Shadoo (Sho)—a member of the prion protein superfamily—is also found in the nucleus of several neural and non-neural cell lines as visualized by using an YFP-Sho construct. This nuclear localization is mediated by the (25-61) fragment of mouse Sho encompassing an (RXXX)8 motif. Bioinformatic analysis shows that the (RXXX)n motif (n=7-8) is a highly conserved and characteristic part of mammalian Shadoo proteins. Experiments to assess if Sho enters the nucleus by facilitated transport gave no decisive results: the inhibition of active processes that require energy in the cell, abolishes nuclear but not nucleolar accumulation. However, the (RXXX)8 motif is not able to mediate the nuclear transport of large fusion constructs exceeding the size limit of the nuclear pore for passive entry. Tracing the journey of various forms of Sho from translation to the nucleus and discerning the potential nuclear function of PrP and Sho requires further studies.

The development of genetic methods broadens the scope of non-invasive sample types. Large shed feathers are good material for genetic analyses, since they are easy to collect and a single feather can provide a sufficient amount of DNA for PCR-based methods. Previous studies have demonstrated that feather quality and type affect the DNA quality extracted from the feather tips. Besides the tip, the superior umbilicus part of the shaft is also proposed as an appropriate source of DNA. In our study, we examined whether some feather parameters (physical condition, type and size) and storage time affect amplification success of DNA extracted from the superior umbilicus of shed Eastern Imperial Eagle (Aquila heliaca) feathers. We also tested the effects of sunlight, temperature and humidity on DNA extracted from Domestic Goose (Anser anser domesticus) feathers with amplification of fragments of various sizes, modelling the environmental conditions of the moulting season. While good quality feathers usually provided sufficient DNA, the usability of the DNA extracted from moderate quality feathers were affected by feather type. DNA quality was influenced in order of importance by humidity, direct sunlight and heat. Our findings support the usability of DNA samples derived from the superior umbilicus of shed feathers, and help to schedule field work by careful consideration of our results about feather quality and environmental factors.

The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance (primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins., SCOPUS: ar.j, info:eu-repo/semantics/published

The propensity of α-synuclein to form amyloid plays an important role in Parkinson's disease. Three familial mutations, A30P, E46K, and A53T, correlate with Parkinson's disease. Therefore, unraveling the structural effects of these mutations has basic implications in understanding the molecular basis of the disease. Here, we address this issue through comparing details of the hydration of wild-type α-synuclein and its A53T mutant by a combination of wide-line NMR, differential scanning calorimetry, and molecular dynamics simulations. All three approaches suggest a hydrate shell compatible with a largely disordered state of both proteins. Its fine details, however, are different, with the mutant displaying a somewhat higher level of hydration, suggesting a bias to more open structures, favorable for protein-protein interactions leading to amyloid formation. These differences disappear in the amyloid state, suggesting basically the same surface topology, irrespective of the initial monomeric state.

In chronic myeloid leukemia (CML), the best characterized imatinib resistance mechanisms are BCR-ABL tyrosine kinase domain mutations and clonal evolution, but recently alternative splicing of BCR-ABL was also proposed as a mechanism for imatinib resistance. Among recently reported BCR-ABL splice variants, exon 7 deletion (Δexon7) was characterized in this study. The frequency of Δexon7 was investigated in 30 healthy controls and in 76 CML patients at different time points of the disease course by four different molecular genetic methods (direct sequencing, fragment analysis, allele-specific and quantitative PCR). The functionality and viability of the variant protein was tested by bioinformatic prediction. The Δexon7 was abundantly detected with similar frequency in healthy controls, in imatinib naive and resistant CML patients on BCR-ABL and also on the nontranslocated ABL. The detection rate of Δexon7 (varying between 17 and 100%) was highly dependent on the expression levels of BCR-ABL or ABL and the sensitivity of detection method. According to secondary structure prediction by bioinformatic methods, the exon 7 deleted mRNA is a target for nonsense-mediated decay, and the translated protein is likely to be nonfunctional and unstable. Taken together all the above observations, we concluded that Δexon7 is a common splice variant not associating with imatinib resistance.

According to current estimations ∼95% of multi-exonic human protein-coding genes undergo alternative splicing (AS). However, for 4000 human proteins in PDB, only 14 human proteins have structures of at least two alternative isoforms. Surveying these structural isoforms revealed that the maximum insertion accommodated by an isoform of a fully ordered protein domain was 5 amino acids, other instances of domain changes involved intrinsic structural disorder. After collecting 505 minor isoforms of human proteins with evidence for their existence we analyzed their length, protein disorder and exposed hydrophobic surface. We found that strict rules govern the selection of alternative splice variants aimed to preserve the integrity of globular domains: alternative splice sites (i) tend to avoid globular domains or (ii) affect them only marginally or (iii) tend to coincide with a location where the exposed hydrophobic surface is minimal or (iv) the protein is disordered. We also observed an inverse correlation between the domain fraction lost and the full length of the minor isoform containing the domain, possibly indicating a buffering effect for the isoform protein counteracting the domain truncation effect. These observations provide the basis for a prediction method (currently under development) to predict the viability of splice variants.

Numerous human genes display dual coding within alternatively spliced regions, which give rise to distinct protein products that include segments translated in more than one reading frame. To resolve the ensuing protein structural puzzle, we identified 67 human genes with alternative splice variants comprising a dual-coding region at least 75 nucleotides in length and analyzed the structural status of the protein segments they encode. The inspection of their amino acid composition and predictions by the IUPred and PONDR® VSL2 algorithms suggest a high propensity for structural disorder in dual-coding regions. In the case of +1 frameshifts, the average level of disorder in the two frames is similarly high (47.2% in the ancestral frame, 58.2% in the derived frame, with the average level of disorder in human proteins being approximately 30%), whereas in the case of -1 frameshifts, there is a significant tendency to become more disordered upon shifting the frame (16.7% in the ancestral frame, 56.3% in the derived frame). The regions encoded by the derived frame are mostly disordered (disorder percentage > 50%) in 39 out of 62 cases, which strongly suggests that structural disorder enables these protein products to exist and function without the need of a highly evolved 3D fold. The potential advantages are also demonstrated by the appearance of novel functions and the high incidence of transcripts escaping nonsense-mediated decay. By discussing several examples, we demonstrate that dual coding may be an effective mechanism for the evolutionary appearance of novel intrinsically disordered regions with new functions.

The Topology Data Bank of Transmembrane Proteins (TOPDB) is the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information currently available. It contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins. TOPDB collects details of various experiments that were carried out to learn about the topology of particular transmembrane proteins. In addition to experimental data from the literature, an extensive collection of structural data was also compiled from PDB and from PDBTM. Because topology information is often incomplete, for each protein in the database the most probable topology that is consistent with the collected experimental constraints was also calculated using the HMMTOP transmembrane topology prediction algorithm. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. The web interface of TOPDB includes tools for searching, relational querying and data browsing as well as for visualization. TOPDB is designed to bridge the gap between the number of transmembrane proteins available in sequence databases and the publicly accessible topology information of experimentally or computationally studied transmembrane proteins. TOPDB is available at http://topdb.enzim.hu.

Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein-protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural-functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as 'interaction specialists'.

Understanding the molecular mechanisms of the regulation of cell cycle is a central issue in molecular cell biology, due to its fundamental role in the existence of cells. The regulatory circuits that make decisions on when a cell should divide are very complex and particularly subtly balanced in eukaryotes, in which the harmony of many different cells in an organism is essential for life. Several hundred proteins are involved in these processes, and a great deal of studies attests that most of them have functionally relevant intrinsic structural disorder. Structural disorder imparts many functional advantages on these proteins, and we discuss it in detail that it is involved in all key steps from signaling through the cell membrane to regulating transcription of proteins that execute timely responses to an ever-changing environment.

Previous studies have shown that population analyses in Hungary can be of great importance from the viewpoint of the examination of population differentiation. This study provides additional population genetic data of the Hungarian population on the thirteen CODIS core STR loci and on two penta STRs (PentaE, PentaD). Allele frequency and profile databases were generated for four population samples. Comparing the allele frequency values by G-statistic, calculating the FST indices and with the pair-wise comparisons of inter-population molecular variance (AMOVA) the four Hungarian populations could be distinguished.

Non-invasive sampling is a useful tool for genetic analyses of endangered and1or elusive species, but it is often inapplicable due to the low quality and quantity of the DNA obtained. In this study we show that the blood clot located in the superior umbilicus of the feather shaft is a better source of DNA than the previously used tip samples from moulted feathers. We found that feather clots from museum specimens provided results nearly as good as footpad and better than those from the more commonly used museum skin snips. Feather clots proved to be a good source of DNA for genetic analysis that will significantly facilitate genetic monitoring of wild bird populations.

Hereditary angioneurotic edema (HAE) is an autosomal dominant disorder characterized by episodic local subcutaneous and submucosal edema and is caused by the deficiency of the activated C1 esterase inhibitor protein (C1-INH or C1INH; approved gene symbol SERPING1). Published C1-INH mutations are represented in large universal databases (e.g., OMIM, HGMD), but these databases update their data rather infrequently, they are not interactive, and they do not allow searches according to different criteria. The HAEdb, a C1-INH gene mutation database (http://hae.biomembrane.hu) was created to contribute to the following expectations: 1) help the comprehensive collection of information on genetic alterations of the C1-INH gene; 2) create a database in which data can be searched and compared according to several flexible criteria; and 3) provide additional help in new mutation identification. The website uses MySQL, an open-source, multithreaded, relational database management system. The user-friendly graphical interface was written in the PHP web programming language. The website consists of two main parts, the freely browsable search function, and the password-protected data deposition function. Mutations of the C1-INH gene are divided in two parts: gross mutations involving DNA fragments >1 kb, and micro mutations encompassing all non-gross mutations. Several attributes (e.g., affected exon, molecular consequence, family history) are collected for each mutation in a standardized form. This database may facilitate future comprehensive analyses of C1-INH mutations and also provide regular help for molecular diagnostic testing of HAE patients in different centers.

The 8-10 million European Roma/Gypsies are a founder population of common origins that has subsequently split into multiple socially divergent and geographically dispersed Gypsy groups. Unlike other founder populations, whose genealogy has been extensively documented, the demographic history of the Gypsies is not fully understood and, given the lack of written records, has to be inferred from current genetic data. In this study, we have used five disease loci harboring private Gypsy mutations to examine some missing historical parameters and current structure. We analyzed the frequency distribution of the five mutations in 832-1,363 unrelated controls, representing 14 Gypsy populations, and the diversification of chromosomal haplotypes in 501 members of affected families. Sharing of mutations and high carrier rates supported a strong founder effect, and the identity of the congenital myasthenia 1267delG mutation in Gypsy and Indian/Pakistani chromosomes provided the best evidence yet of the Indian origins of the Gypsies. However, dramatic differences in mutation frequencies and haplotype divergence and very limited haplotype sharing pointed to strong internal differentiation and characterized the Gypsies as a founder population comprising multiple subisolates. Using disease haplotype coalescence times at the different loci, we estimated that the entire Gypsy population was founded approximately 32-40 generations ago, with secondary and tertiary founder events occurring approximately 16-25 generations ago. The existence of multiple subisolates, with endogamy maintained to the present day, suggests a general approach to complex disorders in which initial gene mapping could be performed in large families from a single Gypsy group, whereas fine mapping would rely on the informed sampling of the divergent subisolates and searching for the shared genomic region that displays the strongest linkage disequilibrium with the disease.

Hereditary angioedema (HAE), a rare but life-threatening condition, manifests as acute attacks of facial, laryngeal, genital, or peripheral swelling or abdominal pain secondary to intra-abdominal edema. Resulting from mutations affecting C1 esterase inhibitor (C1-INH), inhibitor of the first complement system component, attacks are not histamine-mediated and do not respond to antihistamines or corticosteroids. Low awareness and resemblance to other disorders often delay diagnosis; despite availability of C1-INH replacement in some countries, no approved, safe acute attack therapy exists in the United States. The biennial C1 Esterase Inhibitor Deficiency Workshops resulted from a European initiative for better knowledge and treatment of HAE and related diseases. This supplement contains work presented at the third workshop and expanded content toward a definitive picture of angioedema in the absence of allergy. Most notably, it includes cumulative genetic investigations; multinational laboratory diagnosis recommendations; current pathogenesis hypotheses; suggested prophylaxis and acute attack treatment, including home treatment; future treatment options; and analysis of patient subpopulations, including pediatric patients and patients whose angioedema worsened during pregnancy or hormone administration. Causes and management of acquired angioedema and a new type of angioedema with normal C1-INH are also discussed. Collaborative patient and physician efforts, crucial in rare diseases, are emphasized. This supplement seeks to raise awareness and aid diagnosis of HAE, optimize treatment for all patients, and provide a platform for further research in this rare, partially understood disorder.