Effects of arginine vasopressin on human anxiety and associations with sex, dose, and V1a-receptor genotype

RATIONALE

Arginine vasopressin (AVP) has dose- and sex-specific effects on social behavior, and variation in social responses is related to variation in the V1a receptor gene in animals. Whether such complexity also characterizes AVP effects on anxiety in humans, or whether V1a genotype is related to anxiety and/or AVP's ability to affect it, remains to be determined.

OBJECTIVE

To test if AVP has dose-dependent effects on anxiety in men and/or women and if a particular allele within the RS3 promoter region of the V1a receptor gene is associated with anxiety and/or AVP effects on anxiety.

METHOD

Men and women self-administered 20 IU or 40 IU intranasal arginine vasopressin (AVP) and placebo in a double-blind, within-subjects design, and State (SA) and Trait (TA) anxiety were measured 60 min later. PCR was used to identify allelic variation within the RS3 region of the V1a receptor gene.

RESULTS

AVP decreased SA in men across both doses, whereas only the lower dose had the same effect, across sexes, in individuals who carry at least one copy of a previously identified "risk" allele in the RS3 promoter of the V1a receptor gene. Additionally, after placebo, women who carried a copy of the allele displayed lower TA than women who did not, and AVP acutely increased TA scores in those women.

CONCLUSIONS

Exogenous AVP has modest sex- and dose-dependent effects on anxiety/affect in humans. Further, allelic variation in the V1a promoter appears associated with responsiveness to AVP's effects and, at least in women, to stable levels of anxiety/affect.

A nuclear genome assembly of an extinct flightless bird, the little bush moa

We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.

Convergent evolution of parrot plumage coloration

Parrots have remarkable plumage coloration that result in part from a unique ability to produce pigments called psittacofulvins that yield yellow to red feather colors. Little is known about the evolution of psittacofulvin-based pigmentation. Widespread color mutations of captive-bred parrots provide perfect opportunities to study the genetic basis of this trait. An earlier study on blue budgerigars, which do not possess psittacofulvins, reveals the involvement of an uncharacterized polyketide synthase (MuPKS) in yellow psittacofulvin synthesis. The blue phenotype had repeatedly appeared in different parrot species, similar to independent experimental replications allowing the study of convergent evolution and molecular mechanism of psittacofulvin-based pigmentation. Here, we investigated the genetic basis of the blue phenotypes in two species of Agapornis parrots, Fischer's lovebird (A. fischeri) and Yellow-collared lovebird (A. personatus). Using whole-genome data, we identified a single genomic region with size <2 Mb to be strongly associated with the color difference between blue and wild-type (WT) birds in both species. Surprisingly, we discovered that the mutation associated with the blue Agapornis phenotype was identical to the previously described substitution causing the functional change of MuPKS in budgerigars. Together with the evidence of shared blue-associated haplotypes and signatures of a selective sweep in this genomic region in both species, we demonstrated both de novo mutation and interspecific introgression play a role in the evolution of this trait in different Agapornis species. The convergent substitution in the same gene in both lovebirds and budgerigars also indicates a strong evolutionary constraint on psittacofulvin-based coloration.

Whole-genome analyses reveal past population fluctuations and low genetic diversities of the North Pacific albatrosses

Throughout the Plio-Pleistocene, climate change has impacted tropical marine ecosystems substantially, with even more severe impacts predicted in the Anthropocene. Although many studies have clarified demographic histories of seabirds in polar regions, the history of keystone seabirds of the tropics is unclear, despite the prominence of albatrosses (Diomedeidae, Procellariiformes) as the largest and most threatened group of oceanic seabirds. To understand the impact of climate change on tropical albatrosses, we investigated the evolutionary and demographic histories of all four North Pacific albatrosses and their prey using whole-genome analyses. We report a striking concordance in demographic histories among the four species, with a notable dip in effective population size at the beginning of the Pleistocene and a population expansion in the Last Glacial Period when sea levels were low, which resulted in increased potential coastal breeding sites. Abundance of the black-footed albatross dropped again during the Last Glacial Maximum, potentially linked to climate-driven loss of breeding sites and concordant genome-derived decreases in its major prey. We find very low genome-wide (π < 0.001) and adaptative genetic diversities across the albatrosses, with genes of the major histocompatibility complex close to monomorphic. We also identify recent selective sweeps at genes associated with hyperosmotic adaptation, longevity, and cognition and memory. Our study has shed light on the evolutionary and demographic histories of the largest tropical oceanic seabirds and provides evidence for their large population fluctuations and alarmingly low genetic diversities.

Museomics and phylogenomics of lovebirds (Psittaciformes, Psittaculidae, Agapornis) using low-coverage whole-genome sequencing

Natural history collections contain specimens that provide important insights into studies of ecology and evolution. With the advancement of high-throughput sequencing, historical DNA (hDNA) from museum specimens has become a valuable source of genomic data to study the evolutionary history of organisms. Low-coverage whole genome sequencing (WGS) has been increasingly applied to museum specimens for analyzing organelle genomes, but is still uncommon for genotyping the nuclear DNA fraction. In this study, we applied low-coverage WGS to phylogenomic analyses of parrots in the genus Agapornis by including both modern samples and historical specimens of ∼100-year-old. Agapornis are small-sized African and Malagasy parrots with diverse characters. Earlier phylogenetic studies failed to resolve the positions of some key lineages, prohibiting a robust interpretation of the biogeography and evolution of these African parrots. Here, we demonstrated the use of low-coverage WGS for generating both mitochondrial and nuclear genomic data, and evaluated data quality differences between modern and historical samples. Our resolved Agapornis phylogeny indicates the ancestor of Agapornis likely colonized Madagascar from Australasia by trans-oceanic dispersal events before dispersing to the African continent. Genome-wide SNPs also allowed us to identify the parental origins of hybrid Agapornis individuals. This study demonstrates the potential of applying low-coverage WGS to phylogenomics and population genomics analyses and illustrates how including historical museum specimens can address outstanding questions regarding the evolutionary history of contemporary lineages.

Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird

Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here we assembled a high-quality genome and nasal epithelium transcriptome of the Leach's storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that ORs genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.

Arm Motor Recovery After Ischemic Stroke: A Focus on Clinically Distinct Trajectory Groups

BACKGROUND AND PURPOSE

Recovery of arm function poststroke is highly variable with some people experiencing rapid recovery but many experiencing slower or limited functional improvement. Current stroke prediction models provide some guidance for clinicians regarding expected motor outcomes poststroke but do not address recovery rates, complicating discharge planning. This study developed a novel approach to defining recovery groups based on arm motor recovery trajectories poststroke. In addition, between-group differences in baseline characteristics and therapy hours were explored.

METHODS

A retrospective cohort analysis was conducted where 40 participants with arm weakness were assessed 1 week, 6 weeks, 3 months, and 6 months after an ischemic stroke. Arm recovery trajectory groups were defined on the basis of timing of changes in the Fugl-Meyer Assessment Upper Extremity (FMA-UE), at least the minimal clinically important difference (MCID), 1 week to 6 weeks or 6 weeks to 6 months. Three recovery trajectory groups were defined: Fast (n = 19), Extended (n = 12), and Limited (n = 9). Between-group differences in baseline characteristics and therapy hours were assessed. Associations between baseline characteristics and group membership were also determined.

RESULTS

Three baseline characteristics were associated with trajectory group membership: FMA-UE, NIH Stroke Scale, and Barthel Index. The Fast Recovery group received the least therapy hours 6 weeks to 6 months. No differences in therapy hours were observed between Extended and Limited Recovery groups at any time points.

DISCUSSION AND CONCLUSIONS

Three clinically relevant recovery trajectory groups were defined using the FMA-UE MCID. Baseline impairment, overall stroke severity, and dependence in activities of daily living were associated with group membership and therapy hours differed between groups. Stratifying individuals by recovery trajectory early poststroke could offer additional guidance to clinicians in discharge planning.

(See Supplemental Digital Content 1 for Video Abstract, available at: http://links.lww.com/JNPT/A337.).

Abstract TMP38: Web Based Testing of Upper Extremity Movement for Patients Recovering After Stroke

Background: Studies of movement of the upper extremity for stroke patients currently require assessments with special equipment and trained assessors, limiting the accessibility. Hevelius is an experimental online platform designed to study human interaction with technology at a large scale. Our aim was to demonstrate the feasibility of using Hevelius for testing arm kinematics in stroke patients.

Methods: Stroke patients (time from stroke 6 weeks to 1 year) with upper extremity weakness with an NIH Stroke Scale contralesional arm motor (5A or 5B) score of 2 or less were tested on Hevelius. Participants engaged in a Point-And-Click task. Thirty-two kinematic features of movement from continuous, target-driven mouse movement were collected in the arms contralesional and ipsilesional to stroke and compared to data from with health controls. Upper extremity Fugl-Meyer (UE-FM), NIH Stroke Scale (NIHSS), 9-Hole-Peg as well as patient reported outcomes (via Stroke Impact Scale) were collected during the same research visits.

Results: In a total sample of N = 19 patients with upper extremity weakness after stroke who performed Hevelius testing, the median age was 66 (range 47 - 81) with 70% male participants. Nine participants had strokes affecting their dominant arm. LASSO method was used for regression to simultaneously performs feature selection and fitting of a linear model. Score estimates on Hevelius platform correlated strongly on linear regression modeling with clinical scores (from r=0.675 for arm portion of NIHSS ). There was also correlation with 9-Hole-Peg (r=0.581) and no clear correlation with UE-FM, modified Rankin score and Stroke Impact Scale. Five of the 9 patients with dominant arm affected by stroke had NIHSS of 0 and UE-FM of 66. Abnormal movement kinematics were detected in both the contralesional and ipsilesional arms when compared to healthy controls.

Conclusions: Characteristics of arm movement are essential to the understanding of motor recovery after stroke. Our study demonstrates subtle deficits of arm movement in task-directed testing that were not captured with traditional measures of stroke recovery.

Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

Interdisciplinary Stroke Recovery Research: The Perspective of Occupational Therapists in Acute Care

As acute stroke treatments advance, more people survive the initial stroke event and live with long-term neurological impairments that impact functional outcomes and quality of life. In accordance with International Classification of Functioning (ICF), living with long-term neurological impairments can limit survivors' activity performance and restrict participation in valued life roles and routines. Research focused on longitudinal analysis of functional measures and outcomes after stroke are critical for determining early indicators of long-term participation and quality of life and guiding rehabilitation resource allocation. As core members of the interdisciplinary stroke recovery treatment team throughout the post-acute care continuum, occupational therapists (OTs) directly address stroke survivors' ability to participate in meaningful daily activities to promote function and quality of life. Just as in clinical care in which multidisciplinary, team-based perspectives are vital, OTs provide invaluable perspectives for stroke recovery research. Here we describe OTs' role in a collaborative, interdisciplinary research study aimed at comprehensively understanding upper extremity motor recovery after stroke and its impact on individuals across the post-acute care continuum. This article discusses the importance of the OTs' perspectives in conducting interdisciplinary, longitudinal stroke recovery research. The challenges, strategies and recommendations for future directions of advancing the role of OTs in multidisciplinary stroke recovery research are highlighted. We use this perspective as a call to action to the stroke recovery field to incorporate OTs as members of the research team and for OTs to provide their perspectives on ongoing stroke recovery research.

Convergent regulatory evolution and loss of flight in paleognathous birds

A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.

Abstract TP363: Early Changes in Stroke Severity: Characterization and Impact on Patient-Centered Stroke Outcomes

Introduction: Early changes in NIH stroke scale (NIHSS) within the first days after ischemic stroke have been associated with clinical outcomes, however association with patient-centered outcomes is unknown. Predicting outcomes is important for decisions after the acute period. We sought to characterize the magnitude of early NIHSS change and identify its impact on 90-day Stroke Impact Scale-16 (SIS).

Methods: Data were collected as part of an ongoing single-center study of recovery for patients with upper extremity weakness. NIHSS at time of presentation (presentation NIHSS) was obtained by chart review and NIHSS at time of enrollment (enrollment NIHSS) was assessed prior to acute hospital discharge. We collected demographic, treatment, imaging, and 90-day outcomes. We used a linear regression to determine the relationship of early NIHSS improvement (presentation-enrollment NIHSS) with 90-day SIS and dichotomized the dataset (early NIHSS improvement ≥3 vs not) to compare predefined clinical variables hypothesized to be early improvement predictors.

Results: Study participants (n=72) had median presentation NIHSS of 6 (IQR4-13) and median enrollment NIHSS of 6 (IQR4-10) with a mean of 2.7+/-2.5 days between timepoints. Seventeen subjects improved by ≥3 and 16 worsened by ≥3. Acute treatments were endovascular therapy (ET, n=10) and thrombolysis (tPA, n=16). Early NIHSS improvement was associated with better 90-day SIS (p=0.012). This association remained when subjects who underwent ET or tPA were excluded (p=0.046). Subjects with early NIHSS improvement ≥3 were less likely to have hypertension (15 vs 85%, p=0.039) and more likely to have undergone ET (60 vs 40%, p=0.010), but there were no differences in tPA treatment, infarct volume, days between timepoints, age, or other medical history.

Conclusion: This analysis confirms that there are substantial changes in NIHSS in the first days after stroke. Early NIHSS improvement was associated with better 90-day SIS, even when excluding subjects who underwent treatment with ET or tPA suggesting this association also exists for subjects with spontaneous improvement. Early NIHSS improvement may be a useful prognostic tool for patient-centered outcomes after stroke.

Pervasive Correlated Evolution in Gene Expression Shapes Cell and Tissue Type Transcriptomes

The evolution and diversification of cell types is a key means by which animal complexity evolves. Recently, hierarchical clustering and phylogenetic methods have been applied to RNA-seq data to infer cell type evolutionary history and homology. A major challenge for interpreting this data is that cell type transcriptomes may not evolve independently due to correlated changes in gene expression. This nonindependence can arise for several reasons, such as common regulatory sequences for genes expressed in multiple tissues, that is, pleiotropic effects of mutations. We develop a model to estimate the level of correlated transcriptome evolution (LCE) and apply it to different data sets. The results reveal pervasive correlated transcriptome evolution among different cell and tissue types. In general, tissues related by morphology or developmental lineage exhibit higher LCE than more distantly related tissues. Analyzing new data collected from bird skin appendages suggests that LCE decreases with the phylogenetic age of tissues compared, with recently evolved tissues exhibiting the highest LCE. Furthermore, we show correlated evolution can alter patterns of hierarchical clustering, causing different tissue types from the same species to cluster together. To identify genes that most strongly contribute to the correlated evolution signal, we performed a gene-wise estimation of LCE on a data set with ten species. Removing genes with high LCE allows for accurate reconstruction of evolutionary relationships among tissue types. Our study provides a statistical method to measure and account for correlated gene expression evolution when interpreting comparative transcriptome data.

Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics

Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.

Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites

One of the most startling discoveries in avian molecular phylogenetics is that the volant tinamous are embedded in the flightless ratites, but this topology remains controversial because recent morphological phylogenies place tinamous as the closest relative of a monophyletic ratite clade. Here, we integrate new phylogenomic sequences from 1,448 nuclear DNA loci totaling almost 1 million bp from the extinct little bush moa, Chilean tinamou, and emu with available sequences from ostrich, elegant crested tinamou, four neognaths, and the green anole. Phylogenetic analysis using standard homogeneous models and heterogeneous models robust to common topological artifacts recovered compelling support for ratite paraphyly with the little bush moa closest to tinamous within ratites. Ratite paraphyly was further corroborated by eight independent CR1 retroposon insertions. Analysis of morphological characters reinterpreted on a 27-gene paleognath topology indicates that many characters are convergent in the ratites, probably as the result of adaptation to a cursorial life style.

Partial reductions in mechanical loading yield proportional changes in bone density, bone architecture, and muscle mass

Although the musculoskeletal system is known to be sensitive to changes in its mechanical environment, the relationship between functional adaptation and below-normal mechanical stimuli is not well defined. We investigated bone and muscle adaptation to a range of reduced loading using the partial weight suspension (PWS) system, in which a two-point harness is used to offload a tunable amount of body weight while maintaining quadrupedal locomotion. Skeletally mature female C57Bl/6 mice were exposed to partial weight bearing at 20%, 40%, 70%, or 100% of body weight for 21 days. A hindlimb unloaded (HLU) group was included for comparison in addition to age-matched controls in normal housing. Gait kinematics was measured across the full range of weight bearing, and some minor alterations in gait from PWS were identified. With PWS, bone and muscle changes were generally proportional to the degree of unloading. Specifically, total body and hindlimb bone mineral density, calf muscle mass, trabecular bone volume of the distal femur, and cortical area of the femur midshaft were all linearly related to the degree of unloading. Even a load reduction to 70% of normal weight bearing was associated with significant bone deterioration and muscle atrophy. Weight bearing at 20% did not lead to better bone outcomes than HLU despite less muscle atrophy and presumably greater mechanical stimulus, requiring further investigation. These data confirm that the PWS model is highly effective in applying controllable, reduced, long-term loading that produces predictable, discrete adaptive changes in muscle and bone of the hindlimb.

Characterization and locus-specific typing of MHC class I genes in the red-billed gull (Larus scopulinus) provides evidence for major, minor, and nonclassical loci

A major challenge facing studies of major histocompatibility complex (MHC) evolution in birds is the difficulty in genotyping alleles at individual loci, and the consequent inability to investigate sequence variation and selection pressures for each gene. In this study, four MHC class I loci were isolated from the red-billed gull (Larus scopulinus), representing both the first characterized MHCI genes within Charadriiformes (shorebirds, gulls, and allies) and the first full-length MHCI sequences described outside Galloanserae (gamebirds + waterfowl). Complete multilocus genotypes were obtained for 470 individuals using a combination of reference-strand conformation analysis and direct sequencing of gene-specific amplification products, and variation of peptide-binding region (PBR) exons was surveyed for all loci. Each gene is transcribed and has conserved sequence features characteristic of antigen-presenting MHCI molecules. However, higher allelic variation, a more even allele frequency distribution, and evidence of positive selection acting on a larger number of PBR residues suggest that only one locus (Lasc-UAA) functions as a major classical MHCI gene. Lasc-UBA, with more limited variation and PBR motifs that encompass a subset of Lasc-UAA diversity, was assigned a putative minor classical function, whereas the divergent and largely invariant binding-groove motifs of Lasc-UCA and -UDA are suggestive of nonclassical loci with specialized ligand-binding roles.

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

Molecular sexing of prey remains permits a test of sex-biased predation in a wintering population of western sandpipers

Population sex ratios in monogamous birds are often male biased. One factor that can affect population sex ratios is sex-biased predation. However, most estimates of sex-biased predation in birds have focused on species with obvious sexual colour dimorphism or body size dimorphism. Data on sexually monomorphic birds are generally lacking. In the present study, we adopt a PCR-based sexing procedure to help test for sex-biased predation in a wintering population of western sandpipers (Calidris mauri), a shorebird that shows only subtle sexual size dimorphism. Specifically, by comparing the a priori determined sex ratio of live birds wintering at a site in western Mexico to the molecular estimate obtained from depredated birds at this same site, we were able to perform a population-specific test for sex bias in predator-induced mortality. The proportion of females estimated from living (ca. 25%) versus dead (ca. 24%) individuals was in fact not significantly different, indicating that the strong male bias in this population is not due to differential predation. However, molecular sexing of prey remains is a hitherto unexploited test of sex-biased predation in birds, and is potentially applicable to any species for which prey remains can be gathered. We discuss our results in the context of alternate ecological hypotheses for population sex biases.

A set of BAC clones spanning the human genome

Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC clones spanning the human genome. The clone set provides coverage for at least 98% of the human fingerprint map, 99% of the current assembled sequence and has an effective resolving power of 79 kb. We have made the clone set publicly available, anticipating that it will generally facilitate FISH or array-CGH-based identification and characterization of chromosomal alterations relevant to disease.

Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome

As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

The Genome sequence of the SARS-associated coronavirus

We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.

Meeting the challenge of unscheduled outpatient visits

Cancer patients receive multimodal therapy and treatments on an ongoing basis in free-standing cancer centers, infusion centers, and oncology offices and at home. To serve those who require unscheduled evaluation for treatment effects, one hospital developed a program to receive those visits on an inpatient cancer unit.

Evolution of fetal ventricular aneurysms and diverticula of the heart: an echocardiographic study

Due to the rarity of congenital ventricular diverticula and aneurysms, their natural history remains unclear. An excellent prognosis has been suggested for those cases diagnosed during fetal life: From October 1992 to January 1996 seven fetuses were diagnosed with ventricular diverticula or aneurysms. Gestational age ranged from 18 to 36 weeks. The indications for fetal echocardiogram were cardiomegaly, abnormal four-chamber view, a large pericardial effusion, and hydrothorax. Echocardiography revealed a moderate sized apical left ventricular aneurysm (2), a small subvalvular right ventricular diverticulum (1), small apical right ventricular diverticulum (2), a large submitral left ventricular aneurysm (1), and a large diverticulum arising from the lateral free wall of the left ventricle (1). Decreased left ventricular function was detected in three fetuses with left ventricular aneurysms. Two fetuses with large lesions, developed hydrops and died in utero. Postnatal echocardiograms confirmed prenatal findings in all survivors. All infants remained asymptomatic, with age on follow-up from 8 to 24 months. An accurate diagnosis of ventricular diverticula and aneurysms is feasible prenatally. Outcome depends on the size and progression of the lesion. The presence of a large pericardial effusion in three cases with a diverticula was noted.

Aortic valve replacement with pulmonary autograft in children and adults

Aortic valve replacement with a conventional prosthesis is still flawed with complications, especially in children and young adults. Complex aortic root enlargement (Konno) is often needed because of small aortic diameter. The poor compliance with anticoagulation by teenagers and the risks associated with this made us look at alternative techniques. From November 1990 to June 1994, 70 patients were considered for pulmonary autografts in our institution; 64 underwent the procedure with one death and one failure to implant. Short-term results are excellent, with minimal gradient in 90% and minimal regurgitation in 96% of the patients. The long-term follow-up, hopefully, will confirm the superiority of this procedure over more conventional replacement.

Lobectomy in the treatment of the scimitar syndrome

The scimitar syndrome is a congenital anomaly that consists mainly of total or partial anomalous venous drainage of the right lung to the inferior vena cava. We report the case of an 8-year-old girl diagnosed at birth as having a scimitar syndrome and who presented with recurrent right lower lung infections. She underwent resection of the lower half of her right lung without diversion of the anomalous venous drainage of the upper portion of the lung. She improved rapidly postoperatively and the shunt fraction diminished.

Abnormal distribution of pulmonary blood flow after the Glenn shunt or Fontan procedure: risk of development of arteriovenous fistulae

Since the Fontan procedure results in low pulsatile pulmonary blood flow similar to that seen in patients with a Glenn shunt, it may also be associated with abnormal distribution of flow to the lower lung lobes and with the development of pulmonary arteriovenous fistulae (PAVF). In 12 patients 0.8 to 4.5 years after Fontan procedure and in 20 patients 0.2 to 18 years after receipt of Glenn shunts we assessed ventilation (with 133Xe) and perfusion (after a peripheral injection of 99mTc-macroaggregated albumin) to compare upper to lower lobe distribution of blood flow with that in a control group. The presence of PAVF was assessed by radionuclide activity in kidneys and the brain and by a two-dimensional echocardiographic contrast study. A decreased upper/lower lobe perfusion ratio was noted in 13 of 20 patients with Glenn shunts (65%) and correlated with the time after surgery (p less than .05). Despite the shorter follow-up period, two of 12 (16%) patients who had undergone the Fontan procedure also had a decreased upper/lower lobe perfusion ratio, and one of these developed right heart failure. Brain and kidney radionuclide counts above control values were observed in all patients with Glenn shunts and in 11 of 12 patients who had the Fontan operation. However, in only five of 20 (25%) patients with Glenn shunts were PAVF confirmed by the two-dimensional echocardiographic contrast study. Three of the five patients with PAVF had Glenn shunts of long duration.(ABSTRACT TRUNCATED AT 250 WORDS)

Absence of placental transfer of l-triiodothyronine (T3) in the rat

To detect placental transfer of L-triiodothyronine (T3) in pregnant rats, we injected 1 muCi [125I]T3 on the 16th, 18th, and 20th day of gestation. Three hours after the injection, which corresponds to the equilibrium time determined by a method of constant infusion, the pregnant rats and their fetuses were killed. The [125I]T3 was extracted from the serum or the homogenate by butanol extractions and alkaline washes. The transfer rate was calculated from the quantity of [125I]T3 in the serum of the fetuses after 3 hr and from the maternal metabolic clearance rate (8.19 +/- 0.45 ml/hr/100 g body weight; mean +/- SEM). At the 16th day of gestation, the placental transfer of T3 was 0.82 +/- 0.11% of the total maternal clearance rate/litter weight; it was 1.05 +/- 0.25% at the 18th day of gestation and 0.58 +/- 0.10% at the 20th day of gestation. There were no significant differences between these results. The maternal T3 concentration was 68.27 +/- 20.6 ng/100 ml and its production rate was 5.57 +/- 0.31 ng/hr/100 g; with these data we calculated a maternal-fetal T3 transfer of 46 +/- 6 pg/hr. Furthermore, there was no T3 transfer observed when the mother received 1.9 mug unlabeled T3, which led to a significant rise in maternal T3 concentration (68.27 +/- 20.6 ng to 102.23 +/- 7.41 ng/100 ml; P less than 0.01); there was no detectable T3 in the fetal serum. From these results we conclude that there is minimal or no placental transfer of T3 in the rat and that the hypothalamic-pituitary-thyroid axis of the fetus develops autonomously.