Ancient chicken remains reveal the origins of virulence in Marek's disease virus

The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.

The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain

Genetic investigations of Upper Palaeolithic Europe have revealed a complex and transformative history of human population movements and ancestries, with evidence of several instances of genetic change across the European continent in the period following the Last Glacial Maximum (LGM). Concurrent with these genetic shifts, the post-LGM period is characterized by a series of significant climatic changes, population expansions and cultural diversification. Britain lies at the extreme northwest corner of post-LGM expansion and its earliest Late Glacial human occupation remains unclear. Here we present genetic data from Palaeolithic human individuals in the United Kingdom and the oldest human DNA thus far obtained from Britain or Ireland. We determine that a Late Upper Palaeolithic individual from Gough's Cave probably traced all its ancestry to Magdalenian-associated individuals closely related to those from sites such as El Mirón Cave, Spain, and Troisième Caverne in Goyet, Belgium. However, an individual from Kendrick's Cave shows no evidence of having ancestry related to the Gough’s Cave individual. Instead, the Kendrick’s Cave individual traces its ancestry to groups who expanded across Europe during the Late Glacial and are represented at sites such as Villabruna, Italy. Furthermore, the individuals differ not only in their genetic ancestry profiles but also in their mortuary practices and their diets and ecologies, as evidenced through stable isotope analyses. This finding mirrors patterns of dual genetic ancestry and admixture previously detected in Iberia but may suggest a more drastic genetic turnover in northwestern Europe than in the southwest.

The authors report genetic, archaeological and stable isotopic data from two late Palaeolithic individuals in Britain, from Gough's Cave and Kendrick's Cave. The individuals differ not only in their ancestry but also their diets, ecologies and mortuary practices, revealing diverse origins and lifeways among inhabitants of late Pleistocene Britain.

The problem with petrous? A consideration of the potential biases in the utilization of pars petrosa for ancient DNA analysis

Advances in NGS sequencing technologies, improved laboratory protocols and new bioinformatic workflows have seen huge increases in ancient DNA (aDNA) research on archaeological materials. A large proportion of aDNA work now utilizes the petrous portion of the temporal bone (pars petrosa), which is recognized as an excellent skeletal element for long-term ancient endogenous (host) DNA survival. This has been significant due to the often low endogenous content of other skeletal elements, meaning that large amounts of sequencing are frequently required to obtain sufficient genetic coverage. However, exclusive sampling of the petrous for aDNA analysis introduces a new set of potential biases into our scientific studies - and these issues are yet to be considered by ancient DNA researchers. This paper aims to outline the possible biases of utilizing petrous bones to undertake aDNA analyses and highlight how these complications may potentially be overcome in future research.

Author Correction: Ancient genomes indicate population replacement in Early Neolithic Britain

In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.

Ancient genomes indicate population replacement in Early Neolithic Britain

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.

Direct evidence of milk consumption from ancient human dental calculus

Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein β-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15^th century CE.

Pathogens and host immunity in the ancient human oral cavity

Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.

Pilot evaluation of anterior dynamic ultrasound screening for developmental dysplasia of the hip in an Australian regional hospital

INTRODUCTION

Developmental Dysplasia of the Hip (DDH) is the most common notifiable musculoskeletal birth defect in South Australia (SA). Despite routine screening by physical examination of the hips in the neonatal period and at 6 weeks of age, the risk of late diagnosis is increased in rural areas. It is assumed this is due to the examining doctors' reduced clinical expertise. Introducing Anterior Dynamic Ultrasound (ADUS) has reduced the late detection rates in Sweden to almost zero, and may benefit Australian infants in rural areas if routine screening was introduced. This study reports on a small implementation pilot in a SA regional hospital where volunteer postnatal mothers consented to their babies having ADUS examinations.

METHODS

The pilot was evaluated by collecting results of physical examination, ADUS, and surveying parental impressions of the screening test.

RESULTS

Hips of 86 infants underwent ADUS during the implementation pilot. Parents' perceptions were mainly very positive and indicated ADUS was an accessible and acceptable screening test. Of the hips scanned, three were found to have maximum movement of the femoral head of >3 mm and were deemed to demonstrate increased laxity. Four hips described as loose or mobile on clinical examination were found to be within normal limits of maximum mobility on ADUS.

CONCLUSIONS

This study has demonstrated that a larger scale implementation project would be feasible in regional Australia, and would enable researchers to better understand how to reduce the late diagnosis rate of DDH in rural areas.

Use of microwells to investigate the effect of quorum sensing on growth and antigen production in Bacillus anthracis Sterne 34F2

AIM

The aim of this study was to investigate the role of quorum sensing in Bacillus anthracis growth and toxin production.

METHODS AND RESULTS

A microwell plate culture method was developed to simulate the normal UK-licensed anthrax vaccine production run. Once established, sterile supernatant additions from a previous B. anthracis culture were made, and reductions in lag phase and early stimulation of the anthrax toxin component protective antigen (PA) were monitored using ELISA. The addition of the quorum-sensing inhibitor, fur-1, prolonged the lag phase and impeded PA production. Spin filters of various sizes were used to identify the molecular weight fraction of the sterile supernatant responsible for the autoinducer effect. A weight fraction between 5 and 10 kDa was responsible for the autoinducer effect; however, further identification using mass spectroscopy proved inconclusive.

CONCLUSIONS

Quorum sensing mediated by the autoinducer two molecule plays a significant role in both B. anthracis growth and toxin production.

SIGNIFICANCE AND IMPACT OF THE STUDY

While genomic analysis has eluded to the importance of LuxS and quorum sensing in anthrax, this is the first analysis using a production strain of B. anthracis and a quorum-sensing inhibitor to monitor the effect on growth and toxin production. This gives insights into anthrax pathogenicity and vaccine manufacture.

Distribution and clearance of bioadhesive formulations from the olfactory region in man: Effect of polymer type and nasal delivery device

There is an increasing need to identify novel approaches by which to improve the efficiency of drug transport from the nasal cavity (olfactory region) to the CNS, especially for treatment of central nervous system disorders. It is suggested, that one approach is the combination of active targeting of a bioadhesive formulation, that will retain the drug at the absorption site, potentially in combination with, an absorption enhancer. Two low methylated pectins, LM-5 and LM-12 were selected for evaluation as drug delivery systems, due to their ability to gel in the nasal cavity and their bioadhesive characteristics, together with chitosan G210, which acts both as a bioadhesive material and as an efficient absorption enhancer. It was found that all of the bioadhesive formulations were able to reach the olfactory region in the nasal cavity of human volunteers when delivered using a simple nasal drop device. Furthermore, the formulations displayed a significantly increased residence time on the epithelial surface. This was in contrast to a non-bioadhesive control delivered with the same device. In contrast, a pectin formulation administered with a nasal spray system did not show an increase in residence time in the olfactory region. It was further shown that the reproducibility of olfactory delivery of a polymer formulation was significantly better intra-subject than inter-subject.

Application of low dose rate pulsed fluoroscopy in cardiac pacing and electrophysiology: patient dose and image quality implications

The performance of a low dose rate pulsed fluoroscopy option and its successful application to cardiac pacing and electrophysiology is reported. Low dose rate 6.25 frames per second pulsed fluoroscopy was made available in two catheter laboratories at a specialist cardiac centre in February 2003, and was adopted as the standard imaging technique for cardiac pacing procedures. The image quality was found to be considerably poorer than conventional modern units, being very similar to that which would have been accepted as adequate performance 20 years ago, but at less than one-tenth of the dose rate. No problems with the clinical acceptance of this imaging mode for cardiac pacing and electrophysiology have been reported. The already low median patient dose-area product for pacing at this cardiac centre was further reduced by 50% with the introduction of this fluoroscopy option.

An association between the CTLA4 exon 1 polymorphism and early rheumatoid arthritis with autoimmune endocrinopathies

OBJECTIVE

To examine the allelic association of the single nucleotide polymorphism (CTLA4A/G) in exon 1 of the cytotoxic T lymphocyte antigen-4 (CTLA4) gene with early rheumatoid arthritis (RA).

METHODS

One hundred and twenty-three unrelated white probands with early RA from the north-east of England and 349 local ethnically matched controls were studied. The CTLA4A/G polymorphism was genotyped with a polymerase chain reaction (PCR) method and digestion with the restriction enzyme Bst71I. Probands were also screened by allele-specific PCR for alleles HLA DRB1*01 and DRB1*04.

RESULTS

The frequency of the G allele at CTLA4A/G was significantly increased in probands with early RA compared with controls [43 vs 36%; P=0.028, odds ratio (OR) 1.35, 95% confidence interval (CI) 1.01-1.82]. Most of this increased frequency was attributable to RA individuals with coexisting autoimmune thyroid disease or type 1 diabetes (58 vs 36% in controls; P=0.005, OR 2.50, CI 1.29-4.84). The frequency of the G allele in RA patients without autoimmune endocrinopathy was 40%, which was not significantly different from that in controls (P=0.140).

CONCLUSION

The association between the CTLA4 G allele and early RA is largely explained by individuals with RA who have coexisting autoimmune endocrinopathies.

Characterization of the exosporium of Bacillus cereus

Exosporium components from endospores of Bacillus cereus ATCC 10876 were purified and separated by gel electrophoresis. Several of the proteins for which N-terminal sequences were recovered were found to have homologues in protein databases which have been demonstrated to have enzymic activity in other organisms. Amongst these is a zinc metalloprotease, immune inhibitor A, already described in B. thuringiensis. This has been shown to be present in an active 73 kDa form on the exosporium of B. cereus. Other proteins associated with the exosporium include the molecular chaperone GroEL and a homologue of RocA (1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)) of B. subtilis. Although these are unlikely to represent integral structural proteins of the exosporium, the observation that they are selectively present in the spore surface layer suggests that this layer may have functional significance.

Fungal galectins, sequence and specificity of two isolectins from Coprinus cinereus

Galectins are members of a genetically related family of beta-galactoside-binding lectins. At least eight distinct mammalian galectins have been identified. More distantly related, but still conserving amino acid residues critical for carbohydrate-binding, are galectins in chicken, eel, frog, nematode, and sponge. Here we report that galectins are also expressed in a species of fungus, the inky cap mushroom, Coprinus cinereus. Two dimeric galectins are expressed during fruiting body formation which are 83% identical to each other in amino acid sequence and conserve all key residues shared by members of the galectin family. Unlike most galectins, these have no N-terminal post-translational modification and no cysteine residues. We expressed one of these as a recombinant protein and studied its carbohydrate-binding specificity using a novel nonradioactive assay. Binding specificity has been well studied for a number of other galectins, and like many of these, the recombinant C. cinereus galectin shows particular affinity for blood group A structures. These results demonstrate not only that the galectin gene family is evolutionarily much older than previously realized but also that fine specificity for complex saccharide structures has been conserved. Such conservation implies that galectins evolved to perform very basic cellular functions, presumably by interaction with glycoconjugates bearing complex lactoside carbohydrates resembling blood group A.

The effects of hemispheric asymmetries and depression on the perception of emotion

The present study investigated hemispheric asymmetries in the perception of positive and negative emotion. The moderating effect of depression on hemispheric asymmetries was also examined. Forty undergraduates were presented with happy and sad faces using a bilateral visual half-field design. Subjects were classified as depressed or nondepressed based on scores on the Beck Depression Inventory. For nondepressed subjects, a right hemisphere advantage emerged for the speed of processing open and close-mouth sad expressions. For depressed subjects a right hemisphere advantage emerged for the speed of processing open-mouth sad expressions. In addition, a right hemisphere advantage for accuracy in identifying sad expressions was found for all subjects. No visual field differences were found for processing happy expressions.

The impact of change on violent patients

This article describes how a continuing care ward attempted to deal with an increase in levels of violence towards staff and looks at how changes that were taking place on the ward may have contributed to a reduction in this problem. Possible lessons for the future management of this group of patients and reduction of violence are drawn from the discussion.

Cloning and differential expression during the sexual cycle of a meiotic endonuclease-encoding gene from the basidiomycete Coprinus cinereus

The naturally synchronous meiosis of the fungus, Coprinus cinereus, provides an ideal system for the investigation of differential gene expression in relation to meiosis and fruiting body development. We have cloned a cDNA from the fruiting body of C. cinereus encoding the 12-kDa subunit of a meiotic endonuclease (mENase). The identification of the 12-kDa subunit cDNA clone was achieved by the mENase antiserum against a lambda gt11 cDNA expression library. It was confirmed by a direct match of the amino acid (aa) sequence obtained from purified 12-kDa polypeptide with the nucleotide sequence. Northern blot analysis using the cDNA clone as a probe showed that the mENase-encoding gene (MenA) for the 12-kDa subunit was expressed mainly in fruiting bodies and at a very low level in the asexual vegetative mycelium. In addition, it was differentially expressed in the early meiotic stages. The MenA transcript was most abundant in fruiting body primordia prior to the premeiotic S-phase; it remained high from karyogamy to early pachytene, declined drastically by late pachytene and diplotene, and was undetectable by sterigma stage. Western blot analysis showed that the mENase protein was produced at a very low level in mycelium; it was produced in great quantity during the early meiotic stages and decreased to a low level at the end of meiosis.

Lateral orientation, eye movements and dichotic listening

Past studies have found that lateral orientation (eye or head turn) may influence hemispheric asymmetry on the dichotic listening task. The present work studied the effects of forced head and eye turn on a consonant-vowel dichotic test. Spontaneous conjugate lateral eye movements (CLEM) in response to questions were also measured. The subjects were 29 male and 25 female right-handed university students. The dichotic test was administered using a forced-attention method rather than free recall in order to control for attentional bias. As predicted, right lookers on the CLEM test, showed an enhanced right ear advantage while left lookers showed a diminished right ear advantage. This suggests that characteristic hemispheric arousal may enhance or inhibit asymmetry on perceptual laterality tests. No relationship was found between dichotic listening and forced head or eye turning. It was noted that past experiments may have failed to control for the attentional bias introduced by having the head or eyes turned to one direction.

Ginger root--a new antiemetic. The effect of ginger root on postoperative nausea and vomiting after major gynaecological surgery

The effectiveness of ginger (Zingiber officinale) as an antiemetic agent was compared with placebo and metoclopramide in 60 women who had major gynaecological surgery in a double-blind, randomised study. There were statistically significantly fewer recorded incidences of nausea in the group that received ginger root compared with placebo (p less than 0.05). The number of incidences of nausea in the groups that received either ginger root or metoclopramide were similar. The administration of antiemetic after operation was significantly greater in the placebo group compared to the other two groups (p less than 0.05).

Conjugate lateral eye movements: a second look

It has been suggested that conjugate lateral eye movements (CLEM) are related to cerebral lateralization. Two types of research have developed: studies examining individual differences (hemisphericity) and studies examining the type of questions used to elicit eye movements (hemispheric specialization). In a 1978 review, Ehrlichman and Weinberger questioned the notion that CLEM is related to cerebral lateralization, particularly with regard to individual differences. However, since their review, a substantial number of studies have been published which are pertinent to the validity of CLEM. The following paper reviewed the validity of CLEM through three avenues, neurophysiological evidence, relationships with other measures of laterality and relation to spatial and verbal stimuli. Overall, it was concluded that there is sufficient evidence to support the CLEM model. Converging evidence from studies on EEG, electrical stimulation, ablation, brain damage, sodium amytal testing, blood flow, positron emission tomography, dichotic listening, and visual half fields was found to be, for the most part, supportive. The results for verbal and spatial task performance were mixed. Studies examining verbal abilities or a verbal to spatial comparison were generally supportive. The findings for spatial abilities alone were more equivocal. Evidence on question-type was found to be weak but positive, with about half the studies showing the predicted asymmetry and the other half reporting nonsignificant results. The implications of an interaction between hemisphericity or characteristic arousal and hemispheric specialization were also discussed.

Torque and cerebral lateralization: a questionable link

Past research has suggested that torque (the tendency to draw circles in a clockwise direction) may be indicative of less cerebral lateralization. This notion is based on the finding that left-handers demonstrate a greater incidence of torque than right-handers. The present study attempted to investigate this relationship using both conjugate lateral eye movements (CLEM) and handedness as indices of cerebral lateralization. Subjects were 40 male and 40 female right-handed and 16 male and 16 female nonright-handed university students. Consistent with past studies, torque was significantly related to handedness, with nonright-handers demonstrating a greater incidence of torque. However, no relationship between torque and CLEM was found. On the basis of these findings, it is argued that the observed relationship between torque and handedness may be due more to muscle mechanics of the hands rather than any relationship with cerebral lateralization.

A psychogeriatric assessment program. III. Clinical and experimental psychologic aspects

Variables stemming from standard psychologic tests, psychophysiologic tests, and operant conditioning procedures were employed in assessing the status of 80 psychogeriatric patients with either organic brain syndromes or functional psychoses. Differences were observed in the responses between the two groups. In general, the performance of the patients with organic brain syndromes was more deviant than that of the patients with functional psychoses, and the performance of the hospitalized geriatric patients (regardless of diagnosis) was worse than that of the normal control groups.