Disease outbreak response: why epidemiology plays a central role.

The need to control transboundary animal disease outbreaks is widely recognised, as is the need for evidence-based decisions regarding which control measures to implement. Key data and information are required to inform this evidence base. To ensure effective communication of the evidence, a rapid process of collation, interpretation and translation is required. This paper describes how epidemiology can provide the framework through which relevant specialists can be engaged to this end, and highlights the central role of epidemiologists, with their unique combination of skills, in this process. It provides an example of an evidence team led by epidemiologists, namely the United Kingdom National Emergency Epidemiology Group, which was established to address this need. It then goes on to consider the different strands of epidemiology, the need for a wide multidisciplinary approach, and the importance of training and preparedness activities to facilitate rapid response.

La nécessité de contrôler les foyers de maladies animales transfrontalières est largement reconnue, tout comme celle de fonder la prise de décisions sur des données probantes pour la mise en oeuvre des mesures de contrôle. Afin de documenter cette base d'éléments probants, il est nécessaire d'obtenir un certain nombre de données et d'informations clés. Un processus rapide de collecte, d'interprétation et de traduction des données doit être mis en place afin de communiquer ces éléments probants de manière efficace. Les auteurs décrivent le cadre que l'épidémiologie peut apporter aux chercheurs pour s'engager sur cette voie ; ils soulignent le rôle central des épidémiologistes dans ce processus, grâce au faisceau unique de compétences dont ils disposent. Ils donnent l'exemple d'une équipe animée par des épidémiologistes travaillant sur les données probantes qui a été mise en place spécifiquement pour répondre à ce besoin : le Groupe national d'épidémiologie d'urgence du Royaume-Uni (National Emergency Epidemiology Group). Les auteurs concluent en menant une réflexion sur les différentes branches de l'épidémiologie, le besoin d'une approche pluridisciplinaire large et l'importance des activités de formation et de préparation pour une réponse rapide.

Hay coincidencia general en que hoy resulta imperativo combatir los brotes transfronterizos de enfermedades animales, al igual que es necesario contar con un sólido fundamento de datos factuales para tomar decisiones sobre las medidas de lucha que conviene implantar. Para generar esta base empírica hay que disponer de un conjunto esencial de datos e información y para comunicarla eficazmente se requiere un rápido proceso de recogida, interpretación y traducción. Los autores explican cómo puede la epidemiología constituir el marco de referencia desde el que trabajen para tal fin los distintos especialistas y destacan la función central que cumplen en este proceso los epidemiólogos, gracias a la singular combinación de competencias que presentan. A modo de ejemplo, describen un equipo dedicado al estudio de datos factuales que fue establecido, bajo la dirección de epidemiólogos, justamente para responder a esta necesidad: el Grupo nacional de respuesta epidemiológica a situaciones de emergencia del Reino Unido (National Emergency Epidemiology Group). Por último, tras detenerse en las distintas vertientes de la epidemiología, inciden en la necesidad de abordar la cuestión desde un planteamiento ampliamente pluridisciplinar y en la importancia que revisten las actividades de formación y preparación para facilitar una respuesta rápida.

Molecular phenotype and bleeding risks of an inherited platelet disorder in a family with a RUNX1 frameshift mutation.

INTRODUCTION: Inherited defects in RUNX1 are important causes of platelet function disorders. AIM: Our goals were to evaluate RUNX1-related platelet disorders among individuals evaluated for uncharacterized, inherited platelet function disorders and test a proof of concept that bleeding risks could be quantitatively estimated for typical families with an inherited platelet function disorder. METHODS: Index cases with an uncharacterized inherited platelet function disorder were subjected to exome sequencing with confirmation of RUNX1 mutations by Sanger sequencing. Laboratory findings were obtained from medical records and persistence of platelet non-muscle myosin heavy chain IIB (MYH10), a biomarker of RUNX1 defects, was assessed by Western blotting. Bleeding histories were assessed using standardized assessment tools. Bleeding risks were estimated as odds ratios (OR) using questionnaire data for affected individuals compared to controls. RESULTS: Among 12 index cases who had their exomes sequenced, one individual from a family with eight study participants had a c.583dup in RUNX1 that segregated with the disease and was predicted to cause a frameshift and RUNX1 haploinsufficiency. Unlike unaffected family members (n = 2), affected family members (n = 6) had increased bleeding scores and abnormal platelet aggregation and dense granule release responses to agonists but only some had thrombocytopenia and/or dense granule deficiency. This family's mutation was associated with persistence of MYH10 in platelets and increased risks (OR 11-440) for wound healing problems and mild bleeding symptoms, including bleeding interfering with lifestyle in women. CONCLUSION: Inherited platelet dysfunction due to a RUNX1 haploinsufficiency mutation significantly increases bleeding risks.

Targeting and transforming major depression.

OBJECTIVE: To detail limitations to the construct of 'major depression', argue for repositioning it as a proxy for 'clinical depression' and then operationalize it and its principal constituent depressive subtypes, while preserving the DSM criteria-based format. METHOD: We summarize limitations to major depression being viewed as a diagnostic entity. Data from 391 clinically depressed patients were analysed to identify high-prevalence non-specific depressive symptoms to define 'clinical depression' as well as the features showing specificity to a melancholic depressive subtype. RESULTS: We identified a set of high-prevalence and generalized symptoms for defining clinical depression and with many being current criteria for major depression. We also developed a refined set of melancholic features and with their underlying distributions generating two classes that correlated strongly with clinical diagnoses of a melancholic or non-melancholic depression, thus validating its capacity to so differentiate. We append criteria sets for diagnosing clinical depression and its principal diagnostic subtypes (psychotic, melancholic and non-melancholic). CONCLUSION: This heuristic study reframes and modifies major depression's criteria set to define a domain of clinical depression with additional criteria and then allowing the delineation of three diagnostic subtypes. If this paradigm shift is accepted and further refined, greater precision in diagnosis, treatment and research would be anticipated.

The phenotypic manifestations of rare genic CNVs in autism spectrum disorder.

Significant evidence exists for the association between copy number variants (CNVs) and Autism Spectrum Disorder (ASD); however, most of this work has focused solely on the diagnosis of ASD. There is limited understanding of the impact of CNVs on the 'sub-phenotypes' of ASD. The objective of this paper is to evaluate associations between CNVs in differentially brain expressed (DBE) genes or genes previously implicated in ASD/intellectual disability (ASD/ID) and specific sub-phenotypes of ASD. The sample consisted of 1590 cases of European ancestry from the Autism Genome Project (AGP) with a diagnosis of an ASD and at least one rare CNV impacting any gene and a core set of phenotypic measures, including symptom severity, language impairments, seizures, gait disturbances, intelligence quotient (IQ) and adaptive function, as well as paternal and maternal age. Classification analyses using a non-parametric recursive partitioning method (random forests) were employed to define sets of phenotypic characteristics that best classify the CNV-defined groups. There was substantial variation in the classification accuracy of the two sets of genes. The best variables for classification were verbal IQ for the ASD/ID genes, paternal age at birth for the DBE genes and adaptive function for de novo CNVs. CNVs in the ASD/ID list were primarily associated with communication and language domains, whereas CNVs in DBE genes were related to broader manifestations of adaptive function. To our knowledge, this is the first study to examine the associations between sub-phenotypes and CNVs genome-wide in ASD. This work highlights the importance of examining the diverse sub-phenotypic manifestations of CNVs in ASD, including the specific features, comorbid conditions and clinical correlates of ASD that comprise underlying characteristics of the disorder.

Spectroscopic and Computational Insights on Catalytic Synergy in Bimetallic Aluminophosphate Catalysts.

A combined electronic structure computational and X-ray absorption spectroscopy study was used to investigate the nature of the active sites responsible for catalytic synergy in Co-Ti bimetallic nanoporous frameworks. Probing the nature of the molecular species at the atomic level has led to the identification of a unique Co-O-Ti bond, which serves as the loci for the superior performance of the bimetallic catalyst, when compared with its analogous monometallic counterpart. The structural and spectroscopic features associated with this active site have been characterized and contrasted, with a view to affording structure-property relationships, in the wider context of designing sustainable catalytic oxidations with porous solids.

Differentiating 'clinical' and 'non-clinical' depression.

OBJECTIVE: There has been increasing concern about extensions to the definition of 'clinical' depression, but little evident investigation as to how clinical and non-clinical depressive states might best be differentiated. This review considers the potential of many candidate symptom and non-symptom parameters. METHOD: We overview representative concerns and theories about the nature of psychiatric disorders before reviewing the potential utility of candidate parameters for differentiating clinical and non-clinical depressive states. RESULTS: While we detail limitations to all candidate parameters designed to distinguish between clinical and non-clinical depression, their actual utility may only be able to be judged by empirical testing across appropriate comparison groups. CONCLUSION: We argue for initial comparisons being made between prototypically defined categorical (i.e. psychotic, melancholic and bipolar) depressive disease states and residual non-melancholic clinical depressive states, before considering how each of those two clinical subsets might differ from non-clinical depressive mood states.

Cleaving depressive diseases from depressive disorders and non-clinical states.

OBJECTIVE: We sought to determine whether putative depressive diseases could be differentiated categorically from clinical depressive disorders and non-clinical mood states. METHOD: We interviewed volunteers who reported or denied any lifetime depressive mood state and analyzed data from the former group reporting on their 'most severe' depressive episode. We employed latent class analysis (LCA) to determine whether a two-class solution was supported and the contribution of individual variables to class allocations. RESULTS: All variables were significant predictors of class allocation. LCA-assigned Class I participants reported more depressive symptoms, had more distressing episodes and more lasting consequences, were more likely to view their depression as 'like a disease', and as being both disproportionately more severe and persistent in relation to any antecedent stressor. Validation involved comparison of LCA assignment with DSM-IV diagnosis for their most severe depressive episode. Of those assigned to Class I, 89% had a DSM diagnosis of melancholic, psychotic or bipolar depression. Class II had all those failing to meet criteria for a depressive episode and the majority of those with a non-melancholic depressive condition. CONCLUSION: Despite not including individual depressive symptoms, study variables strongly differentiated putative depressive diseases from a composite of clinical depressive conditions and subclinical depressive states.

Is essential fatty acid status in late pregnancy predictive of post-natal depression?

OBJECTIVE: We tested the hypothesis that abnormal levels of omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) during late pregnancy are associated with antenatal and post-natal depression. METHOD: We interviewed a sample of more than 900 women in late pregnancy. We assessed whether they met criteria for depression on a standardized measure of post-natal depression [the Edinburgh Post-natal Depression Scale (EPDS)] and met DSM-IV criteria for major depression and/or were in receipt of antidepressant medication. Blood was collected at that time to generate data on nine PUFA variables. Sample members were re-interviewed post-natally to determine depressive experience in the 3 months following the birth of their baby. RESULTS: Univariate associations were demonstrated between pre-natal depression categorized using DSM criteria and measures of blood fatty acids including total omega-3, the ratio of omega-6 to omega-3, docosahexaenoic acid (DHA) omega-3 and DHA plus eicosapentaenoic acid (EPA) omega-3. Such associations were not found post-natally, but different associations were quantified between EPDS-diagnosed depression and total omega-6, total omega-3 and EPA omega-3. In multivariate analyses, slight associations were maintained between EPDS and lower omega-3, lower EPA and higher omega-6 when neuroticism, stress during pregnancy, a lifetime episode of depression and older age were included in the analysis. CONCLUSION: Findings in such a large sample indicate that PUFA status in late pregnancy is only slightly linked with the risk of post-natal depression when depression was quantified by the EPDS. There were no associations between post-natal depression diagnosed by DSM criteria and any fatty acid variables.

Genetic dissection of Iddm26 in the spontaneously diabetic BBDP rat.

The 40 Mb T1D susceptibility locus Iddm26 was mapped to chromosome 2 through linkage analysis of a conditioned cross-intercross between the diabetes-prone BBDP and the diabetes-resistant ACI.BBDP-Iddm1,Iddm2 (ACI.1u.Lyp). It is flanked by Iddm32 and Iddm33, which control the kinetics of disease progression. To fine-map Iddm26 and characterize immune phenotypes controlled by this locus, several congenic sublines were generated carrying smaller, overlapping intervals spanning Iddm26 and fragments of Iddm32 and 33. Analysis of disease susceptibility, age of disease onset, and immune phenotypes in these sublines identified subloci regulating these different parameters. Two ACI.1u.Lyp-derived subloci, Iddm26.1 and Iddm26.2, imparted significant protection from diabetes, decreasing the cumulative incidence by as much as 57% and 28%, respectively. Iddm26.2, which overlaps with the human PTPN22 locus, only affected disease susceptibility, whereas Iddm26.1 also significantly affected disease kinetics, delaying T1D onset by more than 10 days compared with the parental BBDP strain. These Iddm26 subloci also regulated various immune phenotypes, including the proportion of splenic macrophages by Iddm26.1, and the proportion of activated T-cells in secondary lymphoid organs by Iddm26.2. The analysis of Iddm26 congenic animals in two different SPF facilities demonstrated that the influence of this locus on T1D is environment-dependent.

Clinical and economic impact of a switch from high- to low-volume renal replacement therapy in patients with acute kidney injury.

High-intensity renal replacement therapy protocols in intensive care patients with acute kidney injury have failed to translate to improved patient outcomes when compared with lower-intensity protocols. This retrospective study explored the clinical and economic impacts of switching from a 30-35 ml.kg(-1) .h(-1) (high-volume) to a 20 ml.kg(-1) .h(-1) (low-volume) protocol. Patients (n = 366) admitted 12 months before (n = 187) and after (n = 179) the switch were included in the study. There was no difference in in-hospital mortality (77/187 (41%) vs 75/179 (42%), respectively, p = 0.92), intensive care unit mortality (55/187 (29%) vs 61/179 (34%), respectively, p = 0.40), duration of organ support or extent of renal recovery between the high- and low-volume cohorts. A 25% reduction in daily replacement fluid usage was observed, equating to a cost saving of over £27 000 per annum. In conclusion, a switch from high- to low-volume continuous haemodiafiltration had minimal effects on clinical outcomes and resulted in marked cost savings.

A new variant of gallbladder duplication mimicking a choledochal cyst: stepwise management of an unexpected surgical finding.

We present a case of previously unclassified duplicated gallbladder which posed a surgical challenge intraoperatively by mimicking a choledochal cyst. An intraoperative cholangiogram was performed followed by a simple cholecystectomy. No further dissection was performed to avoid bile duct injury and complication from the unconventional anatomy. Postoperative imaging and histology, followed by the second operation confirmed findings consistent with the duplicated gallbladder. Through this case, we have demonstrated the principles of safe cholecystectomy and the importance of a staged approach in an unanticipated encounter of anatomical uncertainty, as well as the description of a new variant of duplicated gallbladder.

Metabolomic associations of impaired awareness of hypoglycaemia in type 1 diabetes.

This study investigates impaired awareness of hypoglycaemia (IAH), a complication of insulin therapy affecting 20-40% of individuals with type 1 diabetes. The exact pathophysiology is unclear, therefore we sought to identify metabolic signatures in IAH to elucidate potential pathophysiological pathways. Plasma samples from 578 individuals of the Dutch type 1 diabetes biomarker cohort, 67 with IAH and 108 without IAH (NAH) were analysed using the targeted metabolomics Biocrates AbsoluteIDQ p180 assay. Eleven metabolites were significantly associated with IAH. Genome-wide association studies of these 11 metabolites identified significant single nucleotide polymorphisms (SNPs) in C22:1-OH and phosphatidylcholine diacyl C36:6. After adjusting for the SNPs, 11 sphingomyelins and phosphatidylcholines were significantly higher in the IAH group in comparison to NAH. These metabolites are important components of the cell membrane and have been implicated to play a role in cell signalling in diabetes. These findings demonstrate the potential role of phosphatidylcholine and sphingomyelins in IAH.

Epidemiology of healthcare-associated Pseudomonas aeruginosa in intensive care units: are sink drains to blame?

BACKGROUND: Pseudomonas aeruginosa (PA) is a common cause of healthcare-associated infection (PA-HAI) in the intensive care unit (ICU). AIM: To describe the epidemiology of PA-HAI in ICUs in Ontario, Canada, and to identify episodes of sink-to-patient PA transmission. METHODS: This was a prospective cohort study of patients in six ICUs from 2018 to 2019, with retrieval of PA clinical isolates, and PA-screening of antimicrobial-resistant organism surveillance rectal swabs, and of sink drain, air, and faucet samples. All PA isolates underwent whole-genome sequencing. PA-HAI was defined using US National Healthcare Safety Network criteria. ICU-acquired PA was defined as PA isolated from specimens obtained ≥48 h after ICU admission in those with prior negative rectal swabs. Sink-to-patient PA transmission was defined as ICU-acquired PA with close genomic relationship to isolate(s) previously recovered from sinks in a room/bedspace occupied 3-14 days prior to collection date of the relevant patient specimen. FINDINGS: Over ten months, 72 PA-HAIs occurred among 60/4263 admissions. The rate of PA-HAI was 2.40 per 1000 patient-ICU-days; higher in patients who were PA-colonized on admission. PA-HAI was associated with longer stay (median: 26 vs 3 days uninfected; P < 0.001) and contributed to death in 22/60 cases (36.7%). Fifty-eight admissions with ICU-acquired PA were identified, contributing 35/72 (48.6%) PA-HAIs. Four patients with five PA-HAIs (6.9%) had closely related isolates previously recovered from their room/bedspace sinks. CONCLUSION: Nearly half of PA causing HAI appeared to be acquired in ICUs, and 7% of PA-HAIs were associated with sink-to-patient transmission. Sinks may be an under-recognized reservoir for HAIs.

Global warming triggers the loss of a key Arctic refugium.

We document the rapid transformation of one of the Earth's last remaining Arctic refugia, a change that is being driven by global warming. In stark contrast to the amplified warming observed throughout much of the Arctic, the Hudson Bay Lowlands (HBL) of subarctic Canada has maintained cool temperatures, largely due to the counteracting effects of persistent sea ice. However, since the mid-1990s, climate of the HBL has passed a tipping point, the pace and magnitude of which is exceptional even by Arctic standards, exceeding the range of regional long-term variability. Using high-resolution, palaeolimnological records of algal remains in dated lake sediment cores, we report that, within this short period of intense warming, striking biological changes have occurred in the region's freshwater ecosystems. The delayed and intense warming in this remote region provides a natural observatory for testing ecosystem resilience under a rapidly changing climate, in the absence of direct anthropogenic influences. The environmental repercussions of this climate change are of global significance, influencing the huge store of carbon in the region's extensive peatlands, the world's southern-most polar bear population that depends upon Hudson Bay sea ice and permafrost for survival, and native communities who rely on this landscape for sustenance.

Three genetic systems controlling growth, development and productivity of rice (Oryza sativa L.): a reevaluation of the 'Green Revolution'.

The Green Revolution (GR-I) included worldwide adoption of semi-dwarf rice cultivars (SRCs) with mutant alleles at GA20ox2 or SD1 encoding gibberellin 20-oxidase. Two series of experiments were conducted to characterize the pleiotropic effects of SD1 and its relationships with large numbers of QTLs affecting rice growth, development and productivity. The pleiotropic effects of SD1 in the IR64 genetic background for increased height, root length/mass and grain weight, and for reduced spikelet fertility and delayed heading were first demonstrated using large populations derived from near isogenic IR64 lines of SD1. In the second set of experiments, QTLs controlling nine growth and yield traits were characterized using a new molecular quantitative genetics model and the phenotypic data of the well-known IR64/Azucena DH population evaluated across 11 environments, which revealed three genetic systems: the SD1-mediated, SD1-repressed and SD1-independent pathways that control rice growth, development and productivity. The SD1-mediated system comprised 43 functional genetic units (FGUs) controlled by GA. The SD1-repressed system was the alternative one comprising 38 FGUs that were only expressed in the mutant sd1 backgrounds. The SD1-independent one comprised 64 FGUs that were independent of SD1. GR-I resulted from the overall differences between the former two systems in the three aspects: (1) trait/environment-specific contributions; (2) distribution of favorable alleles for increased productivity in the parents; and (3) different responses to (fertilizer) inputs. Our results suggest that at 71.4 % of the detected loci, a QTL resulted from the difference between a functional allele and a loss-of-function mutant, whereas at the remaining 28.6 % of loci, from two functional alleles with differentiated effects. Our results suggest two general strategies to achieve GR-II (1) by further exploiting the genetic potential of the SD1-repressed and SD1-independent pathways and (2) by restoring the SD1-mediated pathways, or 'back to the nature' to fully exploit the genetic diversity of those loci in the SD1-mediated pathways which are virtually inaccessible to most rice-breeding programs worldwide that are exclusively based on sd1.

The superiority of antidepressant medication to cognitive behavior therapy in melancholic depressed patients: a 12-week single-blind randomized study.

OBJECTIVE: To pursue the previously long-standing but formally untested clinical view that melancholia is preferentially responsive to antidepressant medication in comparison with psychotherapy [specifically Cognitive Behavior Therapy (CBT)]. Second, to determine whether a broader action antidepressant medication sequencing regimen is superior to a Selective Serotonin Reuptake Inhibitor (SSRI) alone. METHOD: We sought to recruit a large sample of participants with melancholic depression for a 12-week trial but inclusion criteria compromised recruitment and testing the second hypothesis. The first hypothesis was evaluated by comparing 18 participants receiving antidepressant medication to 11 receiving CBT. Primary study measures were the Hamilton Rating Scale for Depression (HAM-D) and the Hamilton Endogenous Subscale (HES), rated blindly, while several secondary measures also evaluated outcome. RESULTS: Participants receiving medication had a superior 12-week outcome to those receiving CBT, with significant differences present on primary measures as early as 4 weeks. At trial conclusion, the percentage improvement in HAM-D scores was 61.1% vs. 34.4%, respectively [Number Needed to Treat (NNT) = 3.7] and with those in receipt of medication returning non-significantly higher HAM-D responder (66.6% vs. 36.4%, NNT = 2.8) and remission (66.7% vs. 45.4%, NNT = 4.7) rates. CONCLUSION: As the sample size was small and participants evidenced only moderate levels of depression severity, the study risked being underpowered and idiosyncratic. Despite the small sample, the superiority of antidepressant medication to CBT in those with a melancholic depression was distinctive in this pilot study.

HostSeq: a Canadian whole genome sequencing and clinical data resource.

HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experience. The mandate of HostSeq is to support the Canadian and international research communities in their efforts to understand the risk factors for disease and associated health outcomes and support the development of interventions such as vaccines and therapeutics. HostSeq is a collaboration among 13 independent epidemiological studies of SARS-CoV-2 across five provinces in Canada. Aggregated data collected by HostSeq are made available to the public through two data portals: a phenotype portal showing summaries of major variables and their distributions, and a variant search portal enabling queries in a genomic region. Individual-level data is available to the global research community for health research through a Data Access Agreement and Data Access Compliance Office approval. Here we provide an overview of the collective project design along with summary level information for HostSeq. We highlight several statistical considerations for researchers using the HostSeq platform regarding data aggregation, sampling mechanism, covariate adjustment, and X chromosome analysis. In addition to serving as a rich data source, the diversity of study designs, sample sizes, and research objectives among the participating studies provides unique opportunities for the research community.

Role of the PD-1 pathway in the immune response.

Understanding immunoregulatory mechanisms is essential for the development of novel interventions to improve long-term allograft survival. Programmed death 1 (PD-1) and its ligands, PD-L1 and PD-L2, have emerged as critical inhibitory signaling pathways that regulate T cell response and maintain peripheral tolerance. PD-1 signaling inhibits alloreactive T cell activation, and can promote induced regulatory T cell development. Furthermore, the upregulation of PD-L1 on nonhematopoietic cells of the allograft may actively participate in the inhibition of immune responses and provide tissue-specific protection. In murine transplant models, this pathway has been shown to be critical for the induction and maintenance of graft tolerance. In this review, we discuss the current knowledge of the immunoregulatory functions of PD-1 and its ligands and their therapeutic potential in transplantation.

Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types.

To explore types, levels and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA and simple sequence repeat (SSR) loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, whereas expressed sequence tags are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.

Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus.

Full-length genome sequencing of pathogenic and attenuated (for chickens) avian coronavirus infectious bronchitis virus (IBV) strains of the same serotype was conducted to identify genetic differences between the pathotypes. Analysis of the consensus full-length genome for three different IBV serotypes (Ark, GA98, and Mass41) showed that passage in embryonated eggs, to attenuate the viruses for chickens, resulted in 34.75-43.66% of all the amino acid changes occurring in nsp 3 within a virus type, whereas changes in the spike glycoprotein, thought to be the most variable protein in IBV, ranged from 5.8 to 13.4% of all changes. The attenuated viruses did not cause any clinical signs of disease and had lower replication rates than the pathogenic viruses of the same serotype in chickens. However, both attenuated and pathogenic viruses of the same serotype replicated similarly in embryonated eggs, suggesting that mutations in nsp 3, which is involved in replication of the virus, might play an important role in the reduced replication observed in chickens leading to the attenuated phenotype.