Single-cell analysis of the nervous system at small and large scales with instant partitions.

Single-cell RNA sequencing is a new frontier across all biology, particularly in neuroscience. While powerful for answering numerous neuroscience questions, limitations in sample input size, and initial capital outlay can exclude some researchers from its application. Here, we tested a recently introduced method for scRNAseq across diverse scales and neuroscience experiments. We benchmarked against a major current scRNAseq technology and found that PIPseq performed similarly, in line with earlier benchmarking data. Across dozens of samples, PIPseq recovered many brain cell types at small and large scales (1,000-100,000 cells/sample) and was able to detect differentially expressed genes in an inflammation paradigm. Similarly, PIPseq could detect expected and new differentially expressed genes in a brain single cell suspension from a knockout mouse model; it could also detect rare, virally-la-belled cells following lentiviral targeting and gene knockdown. Finally, we used PIPseq to investigate gene expression in a nontraditional model species, the little skate (Leucoraja erinacea). In total, PIPSeq was able to detect single-cell gene expression changes across models and species, with an added benefit of large scale capture and sequencing of each sample.

Altered inflammasome activation in neonatal encephalopathy persists in childhood.

Neonatal encephalopathy (NE) is characterized by altered neurological function in term infants and inflammation plays an important pathophysiological role. Inflammatory cytokines interleukin (IL)-1ß, IL-1ra and IL-18 are activated by the nucleotide-binding and oligomerization domain (NOD)-, leucine-rich repeat domain (LRR)- and NOD-like receptor protein 3 (NLRP3) inflammasome; furthermore, we aimed to examine the role of the inflammasome multiprotein complex involved in proinflammatory responses from the newborn period to childhood in NE. Cytokine concentrations were measured by multiplex enzyme-linked immunosorbent assay (ELISA) in neonates and children with NE in the absence or presence of lipopolysaccharide (LPS) endotoxin. We then investigated expression of the NLRP3 inflammasome genes, NLRP3, IL-1ß and ASC by polymerase chain reaction (PCR). Serum samples from 40 NE patients at days 1 and 3 of the first week of life and in 37 patients at age 4-7 years were analysed. An increase in serum IL-1ra and IL-18 in neonates with NE on days 1 and 3 was observed compared to neonatal controls. IL-1ra in NE was decreased to normal levels at school age, whereas serum IL-18 in NE was even higher at school age compared to school age controls and NE in the first week of life. Percentage of LPS response was higher in newborns compared to school-age NE. NLRP3 and IL-1ß gene expression were up-regulated in the presence of LPS in NE neonates and NLRP3 gene expression remained up-regulated at school age in NE patients compared to controls. Increased inflammasome activation in the first day of life in NE persists in childhood, and may increase the window for therapeutic intervention.

Are viruses associated with disc herniation? A clinical case series.

BACKGROUND: There is some limited evidence for the presence of viruses in herniated disc material including a previous case series that claimed to provide "unequivocal evidence of the presence of herpes virus DNA in intervertebral disc specimens of patients with lumbar disc herniation suggesting the potential role of herpes viruses as a contributing factor to the pathogenesis of degenerative disc disease". This study has not been replicated. The objective of our study was to determine if viruses were present in herniated disc fragments in participants with a prior history of back pain. METHODS: We recruited fifteen participants with a history of prior low-back pain prior to undergoing disc herniation surgery in the lumbar spine. Harvested disc samples were subject to next generation sequencing for detection of both RNA and DNA viral pathogens. Additionally, samples were analysed by a broadly reactive PCR targeting herpesviral DNA. Ethics approval was granted by the Human Research Ethics Committees of both Murdoch University, and St John of God Hospital, Western Australia. RESULTS: Of the fifteen research participants, 8 were female. Mean age was 49.4 years (SD 14.5 yrs) with a range of 24-70 years. All participants had prior back pain with mean time since first ever attack being 8.8 years (SD 8.8 yrs). No samples contained significant DNA sequences relating to known human viral agents. Inconsequential retroviral sequences were commonly found and were a mixture of putative animal and human retroviral protein coding segments. All samples were negative for herpesvirus DNA when analysed by pan-herpesvirus PCR. CONCLUSIONS: This study found no viral pathogens in any intervertebral disc fragments of patients who had previous back pain and underwent discectomy for disc herniation and thus it is unlikely that viruses are associated with disc herniation, however given the contradiction between key studies enhanced replication of this experiment is recommended.

Anatomy transformed.

This paper arose from exhibitions in Oxford and Dublin and comprises three experiments which look at the relationship between anatomy and art. In the first experiment, a passport photograph, photographic portrait and portrait in oils, all of the same sitter, show how artistic input transforms anatomy from a mere likeness into works of art. In the second, the reverse is true, as computer techniques render idealized old master images anatomically accurate. The third experiment addresses the biomechanical consequences of anatomical variation and shows that vehicular design is based on mean body shapes, and so it is the average, rather than the idealized, form that is safer in a collision.

Prevalence, risk factors and antimicrobial resistance of Salmonella diarrhoeal infection among children in Thi-Qar Governorate, Iraq.

We conducted a hospital-based cross-sectional study among children aged <5 years in Thi-Qar Governorate, south-eastern Iraq, in order to examine the prevalence, risk factors and antimicrobial resistance associated with gastroenteritis caused by Salmonella infection. From 320 diarrhoea cases enrolled between March and August 2016, 33 (10·3%, 95% confidence interval (CI) 8·4-12·4) cases were stool culture-positive for non-typhoidal Salmonella enterica. The most commonly identified serovar was Typhimurium (54%). Multivariable logistic regression analysis indicated that the odds of Salmonella infection in children from households supplied by pipe water was 4·7 (95% CI 1·6-13·9) times higher compared with those supplied with reverse osmosis treated water. Similarly, children from households with domestic animals were found to have a higher odds (OR 10·5; 95% CI 3·8-28·4) of being Salmonella stool culture-positive. The likelihood of Salmonella infection was higher (OR 3·9; 95% CI 1·0-6·4) among children belonging to caregiver with primary vs. tertiary education levels. Lower odds (OR 0·4; 95% CI 0·1-0·9) of Salmonella infection were associated with children exclusively breast fed as compared with those exclusively bottle fed. Salmonella infection was three times lower (95% CI 0·1-0·7) in children belonging to caregiver who reported always washing hands after cleaning children following defecation, vs. those belonging to caregivers who did not wash hands. The antimicrobial resistance profile by disc diffusion revealed that non-susceptibility to tetracycline (78·8%), azithromycin (66·7%) and ciprofloxacin (57·6%) were the most commonly seen, and 84·9% of Salmonella isolates were classified as multi-drug resistant. This is the first study on prevalence and antimicrobial resistance of Salmonella infection among children in this setting. This work provides specific epidemiological data which are crucial to understand and combat paediatric diarrhoea in Iraq.

Prevalence and characteristics of paediatric Type 2 diabetes in the Republic of Ireland.

OBJECTIVE: To establish the prevalence of paediatric Type 2 diabetes in the Republic of Ireland and describe patient demographics, initial presentation, management, outcomes, comorbidities and complications. METHODS: Using a standardized proforma we conducted a cross-sectional survey of children and adolescents aged < 16 years with a diagnosis of Type 2 diabetes between October and December 2015 in each of the 19 centres in the Republic of Ireland responsible for the care of children with diabetes. RESULTS: Twelve cases of Type 2 diabetes were identified, giving a prevalence in children aged <16 years of 1.2/100 000 (95% CI 0.6 to 2). Six of these children (50%) were white, two (33%) of whom were members of the travelling community. Four (33%) were of black ethnicity. The prevalence of Type 2 diabetes in traveller children was 16.1/100 000 (95% CI 1.9 to 58.1) and was similar to that in black children, a known high-risk group, which was 13.3/100 000 (95% CI 3.6 to 34.1). The median current HbA1c value was 51 mmol/mol (6.8%) and four (33%) of the children achieved the International Society for Pediatric and Adolescent Diabetes target HbA1c of ≤48 mmol/mol (6.5%). Seven (59%) children were managed on metformin monotherapy, three (25%) were managed on insulin and metformin in combination, and two (16%) were receiving dietary management. CONCLUSION: This was the first national study to estimate the prevalence of childhood Type 2 diabetes in Ireland. Despite their white ethnicity, traveller children appear to be a high-risk group, but this finding requires further study.

Alphaherpesvirus-associated disease in greater bilbies (Macrotis lagotis).

CASE REPORT: A captive breeding colony of 9 greater bilbies (Macrotis lagotis) exhibited mild upper respiratory signs and sudden deaths with 100% mortality over a 2-week period. Histologically, acute necrotising and erosive epithelial lesions throughout the upper respiratory system and bronchi were associated with eosinophilic intranuclear inclusion bodies. Inclusions were also present in hepatocytes and adrenocortical cells, but were not always associated with necrosis. Transmission electron microscopy of lung sections revealed nucleocapsids forming arrays within some nuclei. A pan-herpesvirus PCR yielded a 440-bp product, with sequencing confirming homology with the alphaherpesviruses. Viral culture in a marsupial cell line resulted in cytopathic effect consistent with an alphaherpesvirus. CONCLUSION: This is the first report of a herpesvirus-associated disease in greater bilbies.

Avian influenza in Australia: a summary of 5 years of wild bird surveillance.

BACKGROUND: Avian influenza viruses (AIVs) are found worldwide in numerous bird species, causing significant disease in gallinaceous poultry and occasionally other species. Surveillance of wild bird reservoirs provides an opportunity to add to the understanding of the epidemiology of AIVs. METHODS: This study examined key findings from the National Avian Influenza Wild Bird Surveillance Program over a 5-year period (July 2007-June 2012), the main source of information on AIVs circulating in Australia. RESULTS: The overall proportion of birds that tested positive for influenza A via PCR was 1.9 ± 0.1%, with evidence of widespread exposure of Australian wild birds to most low pathogenic avian influenza (LPAI) subtypes (H1-13, H16). LPAI H5 subtypes were found to be dominant and widespread during this 5-year period. CONCLUSION: Given Australia's isolation, both geographically and ecologically, it is important for Australia not to assume that the epidemiology of AIV from other geographic regions applies here. Despite all previous highly pathogenic avian influenza outbreaks in Australian poultry being attributed to H7 subtypes, widespread detection of H5 subtypes in wild birds may represent an ongoing risk to the Australian poultry industry.

Evidence for episodic acidification effects on migrating Atlantic salmon Salmo salar smolts.

Field studies were conducted to determine levels of gill aluminium as an index of acidification effects on migrating Atlantic salmon Salmo salar smolts in the north-eastern U.S.A. along mainstem river migration corridors in several major river basins. Smolts emigrating from the Connecticut River, where most (but not all) tributaries were well buffered, had low or undetectable levels of gill aluminium and high gill Na(+) /K(+) -ATPase (NKA) activity. In contrast, smolts emigrating from the upper Merrimack River basin where most tributaries are characterized by low pH and high inorganic aluminium had consistently elevated gill aluminium and lower gill NKA activity, which may explain the low adult return rates of S. salar stocked into the upper Merrimack catchment. In the Sheepscot, Narraguagus and Penobscot Rivers in Maine, river and year-specific effects on gill aluminium were detected that appeared to be driven by underlying geology and high spring discharge. The results indicate that episodic acidification is affecting S. salar smolts in poorly buffered streams in New England and may help explain variation in S. salar survival and abundance among rivers and among years, with implications for the conservation and recovery of S. salar in the north-eastern U.S.A. These results suggest that the physiological condition of outmigrating smolts may serve as a large-scale sentinel of landscape-level recovery of atmospheric pollution in this and other parts of the North Atlantic region.

Migratory patterns of hatchery and stream-reared Atlantic salmon Salmo salar smolts in the Connecticut River, U.S.A.

The timing of downstream migration and detection rates of hatchery-reared Atlantic salmon Salmo salar smolts and stream-reared smolts (stocked 2 years earlier as fry) were examined in the Connecticut River (U.S.A.) using passive integrated transponder (PIT) tags implanted into fish and then detected at a downstream fish bypass collection facility at Turners Falls, MA (river length 192 km). In two successive years, hatchery-reared smolts were released in mid-April and early May at two sites: the West River (river length 241 km) or the Passumpsic (river length 450 km). Hatchery-reared smolts released higher in the catchment arrived 7 to 14 days later and had significantly lower detection rates than smolts stocked lower in the catchment. Hatchery-reared smolts released 3 weeks apart at the same location were detected downstream at similar times, indicating that early-release smolts had a lower average speed after release and longer residence time. The size and gill Na(+) /K(+) -ATPase (NKA) activity of smolts at the time of release were significantly greater for detected fish (those that survived and migrated) than for those that were not detected. Stream-reared pre-smolts (>11·5 cm) from four tributaries (length 261-551 km) were tagged in autumn and detected during smolt migration the following spring. Stream-reared smolts higher in the catchment arrived later and had significantly lower detection rates. The results indicate that both hatchery and stream-reared smolts from the upper catchment will arrive at the mouth of the river later and experience higher overall mortality than fish from lower reaches, and that both size and gill NKA activity are related to survival during downstream migration.

Porcine circovirus-associated disease in weaner pigs in Western Australia.

OBJECTIVE: To report the occurrence and pathology of porcine circovirus type 2 (PCV2)-associated disease (PCVAD) of postweaning pigs in two Australian pig herds. METHODS: Mortality data from two commercial piggeries that experienced higher than normal postweaning illthrift and mortalities were examined. Gross and histopathological examinations were performed on the index cases, and at weekly intervals thereafter for a period of 10 weeks. Specimens were submitted to the laboratory for routine diagnostic testing and for exclusion of porcine reproductive and respiratory syndrome virus (PRRSV). The genomes of two strains of PCV2 isolated during testing were sequenced. RESULTS: Mortality rates in weaned, 5-12-week-old pigs spiked significantly during mid to late 2007. This increase in the mortalities was mainly attributed to salmonella-associated diarrhoea and illthrift. Salmonellosis was diagnosed in 73/110 cases inclusive of both piggeries. Many pigs also had chronic granulomatous lymphadenitis and diffuse histiocytic interstitial pneumonia consistent with PCVAD and associated with varying amounts of PCV2 antigen and inclusion bodies. All samples tested for PRRSV were negative. Sequence analysis of the PCV2 isolates showed strain differences between piggeries. CONCLUSION: This report describes the first outbreaks of PCVAD in growing pigs in Western Australia (WA) and describes lesions not previously seen in this laboratory. It also describes the first isolation of a PCV2 group 1 virus in WA associated with PCVAD. Although the outbreaks of PCVAD occurred with concurrent salmonellosis, the two diseases were unrelated. Neither of the outbreaks met the Australian case definition for the diagnosis of postweaning multisystemic wasting syndrome.

Genetic variants associated with neutrophil function in aggressive periodontitis and healthy controls.

BACKGROUND: Genetic polymorphisms that influence neutrophil function were proposed as possible risk factors for aggressive periodontitis (AgP). The aim of this study is to test whether a clinical diagnosis and specific genetic variants are associated with neutrophil activity in subjects with AgP and healthy subjects. METHODS: This study describes the results of neutrophil analyses performed in 40 subjects (20 subjects with AgP and 20 healthy control subjects). Neutrophils were extracted from peripheral blood and analyzed in a masked manner for phagocytosis and oxidative burst by flow cytometry in response to Escherichia coli, Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), and Porphyromonas gingivalis. Genomic DNA was extracted and genotyped for the nicotinamide adenine dinucleotide phosphate p22 phagocytic oxidase subunit (p22(phox)) cytochrome b alpha gene (CYBA) C242T, crystallizable gamma fragment (Fcgamma)IIa H/R, and FcgammaIIIb neutrophil antigen (NA)1/NA2 polymorphisms. RESULTS: Analyses in pairs of white subjects (n = 24) revealed that patients with AgP exhibited a higher oxidative burst in response to E. coli (P = 0.002) and P. gingivalis (P = 0.002) compared to healthy control subjects. The p22(phox) CYBA 242 T allele was associated with an oxidative burst in response to the challenge by two strains of A. actinomycetemcomitans (P = 0.018 and P = 0.046). The FcgammaIIa polymorphism was associated with the phagocytic index of E. coli (P = 0.024). CONCLUSION: This study confirms previous reports of a higher oxidative burst associated with AgP and presented preliminary evidence that genetic factors may influence neutrophil function in patients with AgP and healthy individuals.

Estimation of infectious dose and viral shedding rates for infectious pancreatic necrosis virus in Atlantic salmon, Salmo salar L., post-smolts.

Infectious dose and shedding rates are important parameters to estimate in order to understand the transmission of infectious pancreatic necrosis virus (IPNV). Bath challenge of Atlantic salmon post-smolts was selected as the route of experimental infection as this mimics a major natural route of exposure to IPNV infection. Doses ranging from 10(2) to 10(-4) 50% end-point tissue culture infectious dose (TCID(50)) mL(-1) sea water were used to estimate the minimum infectious dose for a Scottish isolate of IPNV. The minimum dose required to induce infection in Atlantic salmon post-smolts was <10(-1) TCID(50) mL(-1) by bath immersion (4 h at 10 degrees C). The peak shedding rate for IPNV following intraperitoneal challenge using post-smolts was estimated to be 6.8 x 10(3) TCID(50) h(-1) kg(-1) and occurred 11 days post-challenge. This information may be incorporated into mathematical models to increase the understanding of the dispersal of IPNV from marine salmon sites.

Interactions of CcdB with DNA gyrase. Inactivation of Gyra, poisoning of the gyrase-DNA complex, and the antidote action of CcdA.

The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. We have reconstituted the inactive GyrA-CcdB complex by denaturation and renaturation of the purified GyrA dimer in the presence of CcdB. This inactivating interaction involves the N-terminal domain of GyrA, because similar inactive complexes were formed by denaturing and renaturing N-terminal fragments of the GyrA protein in the presence of CcdB. Single amino acid mutations, both in GyrA and in CcdB, that prevent CcdB-induced DNA cleavage also prevent formation of the inactive complexes, indicating that some essential interaction sites of GyrA and of CcdB are common to both the poisoning and the inactivation processes. Whereas the lethal effect of CcdB is most probably due to poisoning of the gyrase-DNA complex, the inactivation pathway may prevent cell death through formation of a toxin-antitoxin-like complex between CcdB and newly translated GyrA subunits. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein. The products of treating the inactive GyrA-CcdB complex with CcdA are free GyrA and a CcdB-CcdA complex of approximately 44 kDa, which may correspond to a (CcdB)2(CcdA)2 heterotetramer.

Transference paradigms at play in psychoanalytically oriented group therapy with female adult survivors of childhood sexual abuse.

This article presents a psychoanalytically oriented model of group treatment for female adult survivors of childhood sexual abuse. Two key treatment issues--the survivor's struggle to trust her own mind and her tenacious allegiance to an omnipotent, all-bad self-representation--are used to illustrate ways in which the transference/countertransference matrix of the group permits members to enact, identify, and work through central internalized relational configurations. The group therapist's role is to maintain transitionality, a focus on process, and the capacity for play.

Reverse gyrase from Methanopyrus kandleri. Reconstitution of an active extremozyme from its two recombinant subunits.

Reverse gyrases are ATP-dependent type I 5'-topoisomerases that positively supercoil DNA. Reverse gyrase from Methanopyrus kandleri is unique as the first heterodimeric type I 5'-topoisomerase described, consisting of a 138-kDa subunit involved in the hydrolysis of ATP (RgyB) and a 43-kDa subunit that forms the covalent complex with DNA during the topoisomerase reaction (RgyA). Here we report the reconstitution of active reverse gyrase from the two recombinant proteins overexpressed in Escherichia coli. Both proteins have been purified by column chromatography to >90% homogeneity. RgyB has a DNA-dependent ATPase activity at high temperature (80 degrees C) and is independent of the presence of RgyA. RgyA alone has no detectable activity. The addition of RgyA to RgyB reconstitutes positive supercoiling activity, but the RgyB and RgyA subunits form a stable heterodimer only after being heated together. This is the first case in which it has been possible to reconstitute an active heterodimeric enzyme of a hyperthermophilic prokaryote from recombinant proteins.

The interaction of the F plasmid killer protein, CcdB, with DNA gyrase: induction of DNA cleavage and blocking of transcription.

We have studied the interaction of the F plasmid killer protein CcdB with its intracellular target DNA gyrase. We confirm that CcdB can induce DNA cleavage by gyrase and show that this cleavage reaction requires ATP hydrolysis when the substrate is linear DNA, but is independent of hydrolysis when negatively supercoiled DNA is used. The 64 kDa domain of the gyrase A protein, which can catalyse DNA cleavage in the presence of the B protein and quinolone drugs, is unable to cleave DNA in the presence of CcdB unless the C-terminal 33 kDa domain of the gyrase A protein is also present. CcdB-induced DNA cleavage by gyrase requires a minimum length of DNA (> approximately 160 bp), whereas in the presence of quinolone drugs gyrase can cleave much shorter DNA molecules. We show that CcdB, like quinolones, can form a complex with gyrase which can block transcription by RNA polymerase. A model for the interaction of CcdB with gyrase involving the trapping of a post-strand-passage intermediate is suggested. We conclude that CcdB can stabilise a cleavage complex between DNA gyrase and DNA in a manner distinct from quinolones but, like the quinolone-induced cleavage complex, the CcdB-stabilised complex can also form a barrier to the passage of polymerases.