Paving the way to better understand the effects of prolonged spaceflight on operational performance and its neural bases

Space exploration objectives will soon move from low Earth orbit to distant destinations like Moon and Mars. The present work provides an up-to-date roadmap that identifies critical research gaps related to human behavior and performance in altered gravity and space. The roadmap summarizes (1) key neurobehavioral challenges associated with spaceflight, (2) the need to consider sex as a biological variable, (3) the use of integrative omics technologies to elucidate mechanisms underlying changes in the brain and behavior, and (4) the importance of understanding the neural representation of gravity throughout the brain and its multisensory processing. We then highlight the need for a variety of target-specific countermeasures, and a personalized administration schedule as two critical strategies for mitigating potentially adverse effects of spaceflight on the central nervous system and performance. We conclude with a summary of key priorities for the roadmaps of current and future space programs and stress the importance of new collaborative strategies across agencies and researchers for fostering an integrative cross- and transdisciplinary approach from cells, molecules to neural circuits and cognitive performance. Finally, we highlight that space research in neurocognitive science goes beyond monitoring and mitigating risks in astronauts but could also have significant benefits for the population on Earth.

Evolutionary genomics of oceanic island radiations

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.

Characteristics of young people accessing recently implemented Community Forensic Child and Adolescent Mental Health Services (F:CAMHS) in England: insights from national service activity data

Children and young people in contact with forensic child and adolescent mental health services present with more complex needs than young people in the general population. Recent policy in child and adolescent mental health has led to the implementation of new workstreams and programmes to improve service provision. This research examines the characteristics of children and young people referred to recently commissioned Community Forensic Child and Adolescent Services (F:CAMHS) and service activity during the first 24 months of service. The study is a national cohort study to describe the population and investigate service provision and access across England. Secondary data on 1311 advice cases and 1406 referrals are included in analysis. Findings show that 71.9% of the sample had accessed mainstream CAMHS before their referral, 50.9% had experienced/witnessed multiple traumatic events and 58.4% of young people presented with multiple difficulties. The results of the study highlight the complexity of the cohort and a need for interagency trauma-informed working. This is the first study to describe the characteristics of children and young people referred to Community F:CAMHS and provides valuable information on pathways and needs to inform service policy and provision.

Reproductive biology of wild and domesticated Ensete ventricosum: Further evidence for maintenance of sexual reproductive capacity in a vegetatively propagated perennial crop

Loss of sexual reproductive capacity has been proposed as a syndrome of domestication in vegetatively propagated crops, but there are relatively few examples from agricultural systems. In this study, we compare sexual reproductive capacity in wild (sexual) and domesticated (vegetative) populations of enset (Ensete ventricosum (Welw.) Cheesman), a tropical banana relative and Ethiopian food security crop. We examined floral and seed morphology and germination ecology across 35 wild and domesticated enset. We surveyed variation in floral and seed traits, including seed weight, viability and internal morphology, and germinated seeds across a range of constant and alternating temperature regimes to characterize optimum germination requirements. We report highly consistent floral allometry, seed viability, internal morphology and days to germination in wild and domesticated enset. However, seeds from domesticated plants responded to cooler temperatures with greater diurnal range. Shifts in germination behaviour appear concordant with a climatic envelope shift in the domesticated distribution. Our findings provide evidence that sexual reproductive capacity has been maintained despite long-term near-exclusive vegetative propagation in domesticated enset. Furthermore, certain traits such as germination behaviour and floral morphology may be under continued selection, presumably through rare sexually reproductive events. Compared to sexually propagated crops banked as seeds, vegetative crop diversity is typically conserved in living collections that are more costly and insecure. Improved understanding of sexual propagation in vegetative crops may have applications in germplasm conservation and plant breeding.

Lesion Volume in Relapsing Multiple Sclerosis is Associated with Perivascular Space Enlargement at the Level of the Basal Ganglia

BACKGROUND AND PURPOSE

Perivascular spaces surround the blood vessels of the brain and are involved in neuroimmune functions and clearance of metabolites via the glymphatic system of the brain. Enlarged perivascular spaces could be a marker of dysfunction in these processes and, therefore, are highly relevant to monitoring disease activity in MS. This study aimed to compare the number of enlarged perivascular spaces in people with relapsing MS with MR imaging markers of inflammation and brain atrophy.

MATERIALS AND METHODS

Fifty-nine patients (18 with clinically isolated syndrome, 22 with early and 19 with late relapsing-remitting MS) were scanned longitudinally (mean follow-up duration = 19.6 [SD, 0.5] months) using T2-weighted, T1-weighted, and FLAIR MR imaging. Two expert raters identified and counted enlarged perivascular spaces on T2-weighted MR images from 3 ROIs (the centrum semiovale, basal ganglia, and midbrain). Baseline and change with time in the number of enlarged perivascular spaces were correlated with demographics and lesion and brain volumes.

RESULTS

Late relapsing-remitting MS had a greater average number of enlarged perivascular spaces at baseline at the level of the basal ganglia (72.3) compared with early relapsing-remitting MS (60.5) and clinically isolated syndrome (54.7) (F = 3.4, P = .042), and this finding correlated with lesion volume (R = 0.44, P = .0004) but not brain atrophy (R = -0.16). Enlarged perivascular spaces increased in number with time in all regions, and the rate of increase did not differ among clinical groups.

CONCLUSIONS

Enlarged perivascular spaces at the level of the basal ganglia are associated with greater neuroinflammatory burden, and the rate of enlargement appears constant in patients with relapsing-remitting disease phenotypes.

Motor strategies and adiabatic invariants: The case of rhythmic motion in parabolic flights

The role of gravity in human motor control is at the same time obvious and difficult to isolate. It can be assessed by performing experiments in variable gravity. We propose that adiabatic invariant theory may be used to reveal nearly conserved quantities in human voluntary rhythmic motion, an individual being seen as a complex time-dependent dynamical system with bounded motion in phase space. We study an explicit realization of our proposal: An experiment in which we asked participants to perform ∞- shaped motion of their right arm during a parabolic flight, either at self-selected pace or at a metronome's given pace. Gravity varied between 0 and 1.8 g during a parabola. We compute the adiabatic invariants in the participant's frontal plane assuming a separable dynamics. It appears that the adiabatic invariant in vertical direction increases linearly with g, in agreement with our model. Differences between the free and metronome-driven conditions show that participants' adaptation to variable gravity is maximal without constraint. Furthermore, motion in the participant's transverse plane induces trajectories that may be linked to higher-derivative dynamics. Our results show that adiabatic invariants are relevant quantities to show the changes in motor strategy in time-dependent environments.

Adiabatic invariants drive rhythmic human motion in variable gravity

Voluntary human movements are stereotyped. When modeled in the framework of classical mechanics they are expected to minimize cost functions that may include energy, a natural candidate from a physiological point of view also. In time-changing environments, however, energy is no longer conserved-regardless of frictional energy dissipation-and it is therefore not the preferred candidate for any cost function able to describe the subsequent changes in motor strategies. Adiabatic invariants are known to be relevant observables in such systems, although they still need to be investigated in human motor control. We fill this gap and show that the theory of adiabatic invariants provides an accurate description of how human participants modify a voluntary, rhythmic, one-dimensional motion of the forearm in response to variable gravity (from 1 to 3g). Our findings suggest that adiabatic invariants may reveal generic hidden constraints ruling human motion in time-changing gravity.

A Mixed-Methods Realist Evaluation of the Implementation and Impact of Community Forensic CAMHS to Manage Risk for Young People With Forensic and Mental Health Needs: Study Protocol

Introduction: Young people in contact with forensic child and adolescent mental health services present with more complex needs than young people in the general population. Recent policy has led to the implementation of new workstreams and programmes to improve service provision for this cohort. This paper aims to present the protocol for a national study examining the impact and implementation of Community Forensic Child and Adolescent Mental Health Services (F:CAMHS). Methods and analysis: The study will use a mixed-methods Realist Evaluation design. Quantitative service activity and feedback data will be collected from all 13 sites, as well as questionnaires from staff. Non-participant observations and qualitative interviews will be conducted with staff, young people and parents/guardians from four focus study sites. An economic evaluation will examine whether Community F:CAMHS provides good value for money. The results will be triangulated to gain an in-depth understanding of young people's, parents/guardians' and staff experiences of the service. Ethics and dissemination: Ethical approval was granted by the Health Research Association and UCL Ethics. The results will be disseminated via project reports, feedback to sites, peer-reviewed journal publications and conference presentations.

The gravitational imprint on sensorimotor planning and control

Humans excel at learning complex tasks, and elite performers such as musicians or athletes develop motor skills that defy biomechanical constraints. All actions require the movement of massive bodies. Of particular interest in the process of sensorimotor learning and control is the impact of gravitational forces on the body. Indeed, efficient control and accurate internal representations of the body configuration in space depend on our ability to feel and anticipate the action of gravity. Here we review studies on perception and sensorimotor control in both normal and altered gravity. Behavioral and modeling studies together suggested that the nervous system develops efficient strategies to take advantage of gravitational forces across a wide variety of tasks. However, when the body was exposed to altered gravity, the rate and amount of adaptation exhibited substantial variation from one experiment to another and sometimes led to partial adjustment only. Overall, these results support the hypothesis that the brain uses a multimodal and flexible representation of the effect of gravity on our body and movements. Future work is necessary to better characterize the nature of this internal representation and the extent to which it can adapt to novel contexts.

Forensic mental health services for children and adolescents: Rationale and development

This article outlines the rationale for dedicated specialist services for high-risk young people about whom there may be family or professional concerns in relation to mental disorder. It provides an overview of the development and remit of such services and emphasises the need for them to form part of overall service provision for children and young people.

Learning Objectives

• Greater understanding of the scope and emphasis of forensic child and adolescent mental health services (FCAMHS)

• Greater understanding of the different statutory jurisdictions that frequently apply in the cases of high-risk young people

• Greater understanding of the importance of initial service accessibility for concerned professionals and for authoritative understanding by FCAMHS of the wide variety of circumstances in which high-risk young people may find themselves

Direction-dependent activation of the insular cortex during vertical and horizontal hand movements

The planning of any motor action requires a complex multisensory processing by the brain. Gravity - immutable on Earth - has been shown to be a key input to these mechanisms. Seminal fMRI studies performed during visual perception of falling objects and self-motion demonstrated that humans represent the action of gravity in parts of the cortical vestibular system; in particular, the insular cortex and the cerebellum. However, little is known as to whether a specific neural network is engaged when processing non-visual signals relevant to gravity. We asked participants to perform vertical and horizontal hand movements without visual control, while lying in a 3T-MRI scanner. We highlighted brain regions activated in the processing of vertical movements, for which the effects of gravity changed during execution. Precisely, the left insula was activated in vertical movements and not in horizontal movements. Moreover, the network identified by contrasting vertical and horizontal movements overlapped with neural correlates previously associated to the processing of simulated self-motion and visual perception of the vertical direction. Interestingly, we found that the insular cortex activity is direction-dependent which suggests that this brain region processes the effects of gravity on the moving limbs through non-visual signals.

The effects of flooding on dioxin and PCB levels in food produced on industrial river catchments

This research examined the effect of regular flooding upon PCDD/F and PCB levels in milk, beef and lamb, produced on the floodplains of industrial river catchments. Our unique dataset included more than 200 samples analysed for PCDD/Fs and PCBs over two data collection phases (1998-1999 & 2008-2010) from working farms. A robust paired study design was adopted with samples taken from flood-prone farms and nearby control farms not subject to flooding. On industrial river catchments regular flooding is associated with higher PCDD/F and PCB levels in soils and grass. This contamination may be transferred to food but the impact varied by food type. These contrasts may be due to physiological differences between animals, the ages at which they are sent to market and differences in animal husbandry. To minimise the risks of producing food on flood-prone land in industrial river catchments, as well as on any land with elevated PCDD/F and PCB levels, this research suggests a number of options. The choice of livestock may be important and as an example in our study beef cattle accumulated PCDD/Fs to a higher degree than sheep. Land management may also play a role and could include minimising the time that livestock spend on such land or feeding commercial feed, low in PCDD/Fs and PCBs, where appropriate.

The effects of river flooding on dioxin and PCBs in beef

In 2008-2010, samples of meat from 40 beef cattle, along with grass, soil and commercial feed, taken from ten matched pairs of flood-prone and control farms, were analysed for PCDD/Fs and PCBs. Concentrations were higher in soil and grass from flood-prone farms. The beef samples from flood-prone farms had total TEQ levels about 20% higher than on control farms. A majority of flood-prone farms (7/10) had higher median levels in beef than on the corresponding control farm. This first controlled investigation into PCDD/F and PCB contamination in beef produced on flood-prone land, presents robust evidence that flooding is a contaminant transfer mechanism to cattle raised on river catchments with a history of urbanisation and industrialisation. PCDD/F and PCB sources in these river systems are likely to be a result of the legacy of contamination from previous industrialisation, as well as more recent combustion activity or pollution events.

Seasonal variations in the levels of PCDD/Fs, PCBs and PBDEs in cows' milk

The first detailed investigation into seasonal variations in PCDD/F, PCB and PBDE concentrations in cows' milk from individual farms was conducted. From August 2009 milk samples were taken at 6 weeks intervals from the bulk tank of 2 farms over a period of one year. Samples of dietary inputs including commercial feed, grass, silage and soil were also collected at 6 weekly intervals from each farm. Detailed animal husbandry information was additionally obtained. For all these samples total TEQ, ∑ICES6 and the ∑7 PBDE congeners was calculated. The results demonstrated that the concentrations of these sets of compounds fluctuate notably over short periods in cows' milk. This variability was such that the highest observed concentrations were nearly double the lowest concentrations detected for both PCDD/Fs and PCBs and PBDEs. Fluctuations between extremes were observed over time periods as short as 6 weeks. Some, but not all, of these variations may be explained by changes in the contaminant concentrations of dietary inputs consumed by the cattle. Changes in contaminant inputs from grass and silage were identified as being the most important source of these fluctuations. Given this variability, the results from PCDD/F and PCB and PBDE monitoring studies may be highly dependent upon when the individual samples were taken. The results have important implications for total diet studies and sampling design.

Respiratory arrest and oversedation in an adolescent given intramuscular clonazepam for rapid tranquillization

Many young people in forensic adolescent units require intramuscular medication for rapid tranquillization. The efficacy and safety of the medications used is not well reported in this age group. Here we report a case of a 14-year-old girl experiencing severe oversedation and respiratory compromise on two occasions following intramuscular clonazepam.

Incidents in an adolescent forensic secure inpatient service

There has been increased research in recent years on incidents within adolescent inpatient psychiatric units, although findings to date have been somewhat inconsistent. We analysed all reported incidents by 37 consecutively discharged patients from a mixed sex adolescent forensic hospital. Findings include a very high overall rate of incidents. A small number of female patients with emerging emotionally unstable personality disorder accounted for the majority of violent incidents and other incidents. Almost all the patients assaulted someone during their admission. Patients on civil sections of the Mental Health Act had just as many incidents as patients on forensic sections. The vast majority of assaults were on staff. Peak times for incidents were the end of each day when education sessions were timetabled and the beginning of the night shift.

Effects of river flooding on polybrominated diphenyl ether (PBDE) levels in cows' milk, soil, and grass

The first investigation into PBDE levels in food produced from flood-prone land on industrial river catchments was conducted. In August 2008 samples of cows' milk, along with grass and soil were taken from 5 pairs of flood-prone and control farms on the River Trent (Central UK). The sum of 7 BDE congeners (28, 47, 99, 100, 153, 154, and 183) was calculated. Higher PBDE levels occurred in soil on flood-prone compared to control farms (median 770 vs 280 ng/kg dry weight). These higher levels were not reflected in the grass samples indicating that PBDE contamination on soils is not transferred efficiently to grass. This observation alongside the fact that cows on flood-prone farms spend time on non-flood-prone land and are fed substantial quantities of commercial feed are reasons why higher PBDE levels were not found in milk from flood-prone farms (median 300 vs 250 ng/kg fat weight). Similar BDE47/BDE99 ratios were observed in soil and grass samples compared to the PBDE product commonly used in the UK, indicating few differences in source-pathway transfer efficiencies between congeners. The BDE47/BDE99 ratio in the milk samples was greater than those in the grass and feed indicating differential food to milk transfer efficiencies between congeners.

Genome of Geobacter sulfurreducens: metal reduction in subsurface environments

The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.

Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae

The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens.

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.

Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.

Tolerance or immunity to a tumor antigen expressed in somatic cells can be determined by systemic proinflammatory signals at the time of first antigen exposure

Mice transgenic for the E7 tumor Ag of human papillomavirus type 16, driven from a keratin 14 promoter, express E7 in keratinocytes but not dendritic cells. Grafted E7-transgenic skin is not rejected by E7-immunized mice that reject E7-transduced transplantable tumors. Rejection of recently transplanted E7-transgenic skin grafts, but not of control nontransgenic grafts or of established E7-transgenic grafts, is induced by systemic administration of live or killed Listeria monocytogenes or of endotoxin. Graft recipients that reject an E7 graft reject a subsequent E7 graft more rapidly and without further L. monocytogenes exposure, whereas recipients of an E7 graft given without L. monocytogenes do not reject a second graft, even if given with L. monocytogenes. Thus, cross-presentation of E7 from keratinocytes to the adaptive immune system occurs with or without a proinflammatory stimulus, but proinflammatory stimuli at the time of first cross-presentation of Ag can determine the nature of the immune response to the Ag. Furthermore, immune effector mechanisms responsible for rejection of epithelium expressing a tumor Ag in keratinocytes are different from those that reject an E7-expressing transplantable tumor. These observations have implications for immunotherapy for epithelial cancers.

Complete genome sequence of a virulent isolate of Streptococcus pneumoniae

The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.

Comparison of Sensory Profile scores of young children with and without autism spectrum disorders

OBJECTIVES

The purpose of this study was to describe the sensory-based behaviors of young children with autism as reported by their parents on the Sensory Profile. Factor scores of children with autism were compared with those of children without autism.

METHOD

The Sensory Profile questionnaire was completed by parents of 40 children with autism 3 through 6 years of age and parents of 40 children without autism 3 through 6 years of age.

RESULTS

The performance of children with autism was significantly different from that of children without autism on 8 of 10 factors. Factors where differences were found included Sensory Seeking, Emotionally Reactive, Low Endurance/Tone, Oral Sensitivity, Inattention/Distractibility, Poor Registration, Fine Motor/Perceptual, and Other.

CONCLUSION

Findings from the study suggest that young children with autism have deficits in a variety of sensory processing abilities as measured by the Sensory Profile. Further research is needed to replicate these findings, to examine the possibility of subgroups on the basis of sensory processing, and to contrast the sensory processing abilities of children with other disabilities to those of children with autism.

Microbial genes in the human genome: lateral transfer or gene loss?

The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.

Sequence and analysis of the Arabidopsis genome

The comprehensive analysis of the genome sequence of the plant Arabidopsis thaliana has been completed recently. The genome sequence and associated analyses provide the foundations for rapid progress in many fields of plant research, such as the exploitation of genetic variation in Arabidopsis ecotypes, the assessment of the transcriptome and proteome, and the association of genome changes at the sequence level with evolutionary processes. Nevertheless, genome sequencing and analysis are only the first steps towards a new plant biology. Much remains to be done to refine the analysis of encoded genes, to define the functions of encoded proteins systematically, and to establish new generations of databases to capture and relate diverse data sets generated in widely distributed laboratories.

Complete genome sequence of Caulobacter crescentus

The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.

Prediction of operons in microbial genomes

Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P: >/= 0.98) to belong to the same operon. The sensitivity of our method is 30-50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi.

TIGRFAMs: a protein family resource for the functional identification of proteins

TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification of proteins by sequence homology. We introduce the term 'equivalog' to describe members of a set of homologous proteins that are conserved with respect to function since their last common ancestor. Related proteins are grouped into equivalog families where possible, and otherwise into protein families with other hierarchically defined homology types. TIGRFAMs currently contains over 800 protein families, available for searching or downloading at www.tigr.org/TIGRFAMs. Classification by equivalog family, where achievable, complements classification by orthology, superfamily, domain or motif. It provides the information best suited for automatic assignment of specific functions to proteins from large-scale genome sequencing projects.

The Comprehensive Microbial Resource

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.

Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana

The genome of the flowering plant Arabidopsis thaliana has five chromosomes. Here we report the sequence of the largest, chromosome 1, in two contigs of around 14.2 and 14.6 megabases. The contigs extend from the telomeres to the centromeric borders, regions rich in transposons, retrotransposons and repetitive elements such as the 180-base-pair repeat. The chromosome represents 25% of the genome and contains about 6,850 open reading frames, 236 transfer RNAs (tRNAs) and 12 small nuclear RNAs. There are two clusters of tRNA genes at different places on the chromosome. One consists of 27 tRNA(Pro) genes and the other contains 27 tandem repeats of tRNA(Tyr)-tRNA(Tyr)-tRNA(Ser) genes. Chromosome 1 contains about 300 gene families with clustered duplications. There are also many repeat elements, representing 8% of the sequence.

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.

Prediction of transcription terminators in bacterial genomes

This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energy-scoring function that reflects hairpin stability, and a tail-scoring function based on the number of U nucleotides and their proximity to the stem, are computed. A confidence value can be assigned to each terminator by analyzing candidate terminators found both within and between genes, and taking into account the energy and tail scores. The confidence is an empirical estimate of the probability that the sequence is a true terminator. The algorithm was used to conduct a comprehensive analysis of 12 bacterial genomes to identify likely candidates for rho-independent transcription terminators. Four of these genomes (Deinococcus radiodurans, Escherichia coli, Haemophilus influenzae and Vibrio cholerae) were found to have large numbers of rho-independent terminators. Among the other genomes, most appear to have no transcription terminators of this type, with the exception of Thermotoga maritima. A set of 131 experimentally determined E. coli terminators was used to evaluate the sensitivity of the method, which ranges from 89 % to 98 %, with corresponding false positive rates of 2 % and 18 %.

Children with burn injuries: purposeful activity versus rote exercise

OBJECTIVE

This study was designed to compare measures of pain when children with burn injuries were engaged in a purposeful activity, specifically a play activity, versus rote exercise.

METHOD

Two 6-year-old children participated in a study using a single-subject, randomized multiple treatment design to compare two conditions: purposeful activity and rote exercise. Data were gathered for each session on four dependent measures: number of repetitions of therapeutic exercise completed, number and type of overt distress behaviors displayed, scores on self-report scales of pain intensity, and overall enjoyment of the activity.

RESULTS

Visual inspection of the graphed data suggested that, early in the rehabilitation process, the use of a play activity in comparison to rote exercise yielded better outcomes in terms of all four dependent measures. Additionally, the data implied that there may be a point later in the rehabilitation of a child with a burn injury when rote exercise may be as effective as play activities in meeting therapeutic goals.

CONCLUSION

This study supports the belief that purposeful activity can yield results equal to or better than those achieved using rote exercise. Replication of this study is warranted, and the development is indicated of a measure of overt behavioral distress that is more appropriate than those currently available for children with burn injuries.

Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39

The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun strategy. The MoPn genome exhibited a general conservation of gene order and content with the previously sequenced C.trachomatis serovar D. Differences between C.trachomatis strains were focused on an approximately 50 kb 'plasticity zone' near the termination origins. In this region MoPn contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a predicted toxin from Escherichia coli O157:H7 but had apparently lost the tryptophan biosyntheis genes found in serovar D in this region. The C. pneumoniae AR39 chromosome was >99.9% identical to the previously sequenced C.pneumoniae CWL029 genome, however, comparative analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in different orientations in the two genomes. AR39 also contained a novel 4524 nt circular single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C. pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing differences in key nucleotide salvage pathways: C.pneumoniae has a uridine kinase gene for dUTP production, MoPn has a uracil phosphororibosyl transferase, while C.trachomatis serovar D contains neither gene. Chromosomal comparison revealed that there had been multiple large inversion events since the species divergence of C.trachomatis and C.pneumoniae, apparently oriented around the axis of the origin of replication and the termination region. The striking synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological isolation of the obligate intracellular parasites. In the absence of genetic analysis, comparative genomics will continue to provide insight into the virulence mechanisms of these important human pathogens.

Complete genome sequence of Neisseria meningitidis serogroup B strain MC58

The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.

A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi

We have determined that Borrelia burgdorferi strain B31 MI carries 21 extrachromosomal DNA elements, the largest number known for any bacterium. Among these are 12 linear and nine circular plasmids, whose sequences total 610 694 bp. We report here the nucleotide sequence of three linear and seven circular plasmids (comprising 290 546 bp) in this infectious isolate. This completes the genome sequencing project for this organism; its genome size is 1 521 419 bp (plus about 2000 bp of undetermined telomeric sequences). Analysis of the sequence implies that there has been extensive and sometimes rather recent DNA rearrangement among a number of the linear plasmids. Many of these events appear to have been mediated by recombinational processes that formed duplications. These many regions of similarity are reflected in the fact that most plasmid genes are members of one of the genome's 161 paralogous gene families; 107 of these gene families, which vary in size from two to 41 members, contain at least one plasmid gene. These rearrangements appear to have contributed to a surprisingly large number of apparently non-functional pseudogenes, a very unusual feature for a prokaryotic genome. The presence of these damaged genes suggests that some of the plasmids may be in a period of rapid evolution. The sequence predicts 535 plasmid genes >/=300 bp in length that may be intact and 167 apparently mutationally damaged and/or unexpressed genes (pseudogenes). The large majority, over 90%, of genes on these plasmids have no convincing similarity to genes outside Borrelia, suggesting that they perform specialized functions.

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037 genes, 49% of which have no predicted function. Roughly 250 tandem gene duplications were found in addition to large-scale duplications of about 0.5 and 4.5 Mb between chromosomes 2 and 1 and between chromosomes 2 and 4, respectively. Sequencing of nearly 2 Mb within the genetically defined centromere revealed a low density of recognizable genes, and a high density and diverse range of vestigial and presumably inactive mobile elements. More unexpected is what appears to be a recent insertion of a continuous stretch of 75% of the mitochondrial genome into chromosome 2.

Global transposon mutagenesis and a minimal Mycoplasma genome

Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently replicating cell so far identified. Global transposon mutagenesis was used to identify nonessential genes in an effort to learn whether the naturally occurring gene complement is a true minimal genome under laboratory growth conditions. The positions of 2209 transposon insertions in the completely sequenced genomes of M. genitalium and its close relative M. pneumoniae were determined by sequencing across the junction of the transposon and the genomic DNA. These junctions defined 1354 distinct sites of insertion that were not lethal. The analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including about 100 genes of unknown function.