NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource

The National Collection of Type Cultures (NCTC) was founded on 1 January 1920 in order to fulfil a recognized need for a centralized repository for bacterial and fungal strains within the UK. It is among the longest-established collections of its kind anywhere in the world and today holds approximately 6000 type and reference bacterial strains - many of medical, scientific and veterinary importance - available to academic, health, food and veterinary institutions worldwide. Recently, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute established the NCTC3000 project to long-read sequence and assemble the genomes of up to 3000 NCTC strains. Here, at the beginning of the collection's second century, we introduce the resulting NCTC3000 sequence read datasets, genome assemblies and annotations as a unique, historically and scientifically relevant resource for the benefit of the international bacterial research community.

Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease diagnostics, as well as references for future studies and applications within the genus Streptococcus.

The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One

The sixth global cholera pandemic lasted from 1899 to 1923. However, despite widespread fear of the disease and of its negative effects on troop morale, very few soldiers in the British Expeditionary Forces contracted cholera between 1914 and 1918. Here, we have revived and sequenced the genome of NCTC 30, a 102-year-old Vibrio cholerae isolate, which we believe is the oldest publicly available live V. cholerae strain in existence. NCTC 30 was isolated in 1916 from a British soldier convalescent in Egypt. We found that this strain does not encode cholera toxin, thought to be necessary to cause cholera, and is not part of V. cholerae lineages responsible for the pandemic disease. We also show that NCTC 30, which predates the introduction of penicillin-based antibiotics, harbours a functional β-lactamase antibiotic resistance gene. Our data corroborate and provide molecular explanations for previous phenotypic studies of NCTC 30 and provide a new high-quality genome sequence for historical, non-pandemic V. cholerae.

Mycobacterial biomaterials and resources for researchers

There are many resources available to mycobacterial researchers, including culture collections around the world that distribute biomaterials to the general scientific community, genomic and clinical databases, and powerful bioinformatics tools. However, many of these resources may be unknown to the research community. This review article aims to summarize and publicize many of these resources, thus strengthening the quality and reproducibility of mycobacterial research by providing the scientific community access to authenticated and quality-controlled biomaterials and a wealth of information, analytical tools and research opportunities.

A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control.

Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.

Genome-based characterization of hospital-adapted Enterococcus faecalis lineages

Vancomycin-resistant Enterococcus faecalis (VREfs) is an important nosocomial pathogen1,2. We undertook whole genome sequencing of E. faecalis associated with bloodstream infection in the UK and Ireland over more than a decade to determine the population structure and genetic associations with hospital adaptation. Three lineages predominated in the population, two of which (L1 and L2) were nationally distributed, and one (L3) geographically restricted. Genome comparison with a global collection identified that L1 and L3 were also present in the USA, but were genetically distinct. Over 90% of VREfs belonged to L1-L3, with resistance acquired and lost multiple times in L1 and L2, but only once followed by clonal expansion in L3. Putative virulence and antibiotic resistance genes were over-represented in L1, L2 and L3 isolates combined, versus the remainder. Each of the three main lineages contained a mixture of vancomycin-resistant and -susceptible E. faecalis (VSEfs), which has important implications for infection control and antibiotic stewardship.

The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource

Studies of historical isolates inform on the evolution and emergence of important pathogens and phenotypes, including antimicrobial resistance. Crucial to studying antimicrobial resistance are isolates that predate the widespread clinical use of antimicrobials. The Murray collection of several hundred bacterial strains of pre-antibiotic era Enterobacteriaceae is an invaluable resource of historical strains from important pathogen groups. Studies performed on the Collection to date merely exemplify its potential, which will only be realised through the continued effort of many scientific groups. To enable that aim, we announce the public availability of the Murray collection through the National Collection of Type Cultures, and present associated metadata with whole genome sequence data for over half of the strains. Using this information we verify the metadata for the collection with regard to subgroup designations, equivalence groupings and plasmid content. We also present genomic analyses of population structure and determinants of mobilisable antimicrobial resistance to aid strain selection in future studies. This represents an invaluable public resource for the study of these important pathogen groups and the emergence and evolution of antimicrobial resistance.

The extant World War 1 dysentery bacillus NCTC1: a genomic analysis

BACKGROUND

Shigellosis (previously bacillary dysentery) was the primary diarrhoeal disease of World War 1, but outbreaks still occur in military operations, and shigellosis causes hundreds of thousands of deaths per year in developing nations. We aimed to generate a high-quality reference genome of the historical Shigella flexneri isolate NCTC1 and to examine the isolate for resistance to antimicrobials.

METHODS

In this genomic analysis, we sequenced the oldest extant Shigella flexneri serotype 2a isolate using single-molecule real-time (SMRT) sequencing technology. Isolated from a soldier with dysentery from the British forces fighting on the Western Front in World War 1, this bacterium, NCTC1, was the first isolate accessioned into the National Collection of Type Cultures. We created a reference sequence for NCTC1, investigated the isolate for antimicrobial resistance, and undertook comparative genetics with S flexneri reference strains isolated during the 100 years since World War 1.

FINDINGS

We discovered that NCTC1 belonged to a 2a lineage of S flexneri, with which it shares common characteristics and a large core genome. NCTC1 was resistant to penicillin and erythromycin, and contained a complement of chromosomal antimicrobial resistance genes similar to that of more recent isolates. Genomic islands gained in the S flexneri 2a lineage over time were predominately associated with additional antimicrobial resistances, virulence, and serotype conversion.

INTERPRETATION

This S flexneri 2a lineage is a well adapted pathogen that has continued to respond to selective pressures. We have created a valuable historical benchmark for shigellae in the form of a high-quality reference sequence for a publicly available isolate.

FUNDING

The Wellcome Trust.

Development of verbal control over bizarre gestures of retardates through imitative and nonimitative reinforcement procedures

Two retardates, manifesting hand gestures and minimal instructional control, were trained by imitative reinforcement procedures to imitate a response that was in contrast to gesturing. Next, with the contrast response continuing to be imitatively reinforced, gesturing was reduced by nonimitative reinforcement procedures; while providing facial and gesture cues, the adult said, "Do not do this". Imitative and nonimitative procedures were found to have the same effects on the contrast response as on the gesturing response, such that imitative procedures increased both responses, whereas nonimitative procedures decreased both. Nonperformance of gesturing was further maintained when (1) explicit verbal directions for nongesturing were superimposed upon the demonstrational-facial-verbal cues as these collective stimuli were faded out and (2) food reinforcers for nongesturing were gradually removed while social consequences continued to be administered.

Assessment of the stability of cell-surface components of microorganisms by MALDI-TOF-MS following preservation on lenticule discs

Strains representing the species Campylobacter coli, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella enterica, and Staphylococcus aureus were randomly selected to assess the consistency of cells preserved on lenticule discs to those archived in traditional freeze-dried ampoules. Each matched pair was cultured using identical conditions and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS) to profile the surface-associated molecules of the cells. In addition, the cytosolic/membrane-bound proteins of C. coli and S. aureus strains were further analysed by surface-enhanced laser desorption/ionization time-of-flight MS. The mass spectral profiles in all cases showed a high degree of concordance between cells preserved by both methods and suggest that the properties of cells preserved on lenticule disc are consistent with those archived by the traditional method of freeze-drying.

LENTICULE discs provide a homogenous format for external quality assessment samples: a comparison with freeze-dried samples for shellfish microbiology

AIMS

The aim was to compare the variability in Escherichia coli enumeration data and detection of Salmonella spp. between four samples of LENTICULE discs and freeze-dried samples for the Health Protection Agency's External Quality Assessment (EQA) scheme for shellfish microbiology.

METHODS AND RESULTS

Four samples of known but undisclosed microbiological content were dispatched in both freeze-dried and LENTICULE disc formats to 57 participating laboratories in 20 countries. Participants examined samples using their routine methods for the most probable number (MPN) of E. coli per 100 g and the presence/absence of Salmonella spp. There was no significant difference between the Food and Environmental Proficiency Testing Unit and participating laboratories for E. coli and Salmonella spp. results. There were significantly less outlying results using the LENTICULE discs than freeze-dried sample format and equivalent or less variance for the former for E. coli MPN. There was no significant difference between LENTICULE discs and freeze-dried samples for the presence/absence of Salmonella spp.

CONCLUSIONS

Overall the results indicated that there was equivalent or less variance in results for the LENTICULE discs than for freeze-dried samples, therefore LENTICULE discs are a homogenous and stable matrix for EQA samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides validation data for the replacement of freeze-dried samples by LENTICULE discs for the Health Protection Agency Shellfish EQA Scheme.

A microsatellite genetic linkage map for Xiphophorus

Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between "male" and "female" maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent experiments.

The role of beta chains in the control of the hemoglobin oxygen binding function: chimeric human/mouse proteins, structure, and function

By using transgenic methodologies, we have produced a number of mouse/human chimeric hemoglobins containing adult mouse and human embryonic globin chains. A detailed analysis of the oxygen binding properties of these proteins identifies the dominant role played by the specific beta-type globin chains in the control of the oxygen binding characteristics. Further analysis traces the origins of these effects to alterations in the properties of the T states of these proteins. The human zeta/mouse beta chimeric protein has been crystallized, and its structure has been determined by X-ray diffraction to a resolution of 2.1 A with R (R(free)) values of 21.6% (24.9%). Close examination of the structure indicates that the subunit interfaces contain contacts which, although different from those present in either the parent human or the parent mouse proteins, retain the overall stabilizing interactions seen in other R state hemoglobins.

Structural and functional analysis of an mRNP complex that mediates the high stability of human beta-globin mRNA

Human globins are encoded by mRNAs exhibiting high stabilities in transcriptionally silenced erythrocyte progenitors. Unlike alpha-globin mRNA, whose stability is enhanced by assembly of a specific messenger RNP (mRNP) alpha complex on its 3' untranslated region (UTR), neither the structure(s) nor the mechanism(s) that effects the high-level stability of human beta-globin mRNA has been identified. The present work describes an mRNP complex assembling on the 3' UTR of the beta-globin mRNA that exhibits many of the properties of the stability-enhancing alpha complex. The beta-globin mRNP complex is shown to contain one or more factors homologous to alphaCP, a 39-kDa RNA-binding protein that is integral to alpha-complex assembly. Sequence analysis implicates a specific 14-nucleotide pyrimidine-rich track within its 3' UTR as the site of beta-globin mRNP assembly. The importance of this track to mRNA stability is subsequently verified in vivo using mice expressing human beta-globin transgenes that contain informative mutations in this region. In combination, the in vitro and in vivo analyses indicate that the high stabilities of the alpha- and beta-globin mRNAs are maintained through related mRNP complexes that may share a common regulatory pathway.

Expression, purification, and characterization of human hemoglobins Gower-1 (zeta(2)epsilon(2)), Gower-2 (alpha(2)epsilon(2)), and Portland-2 (zeta(2)beta(2)) assembled in complex transgenic-knockout mice

Embryonic zeta- and epsilon-globin subunits assemble with each other and with adult alpha- and beta-globin subunits into hemoglobin heterotetramers in both primitive and definitive erythrocytes. The properties of these hemoglobins-Hbs Gower-1 (zeta(2)epsilon(2)), Gower-2 (alpha(2)epsilon(2)), and Portland-2 (zeta(2)beta(2))-have been incompletely described as they are difficult to obtain in quantity from either primary human tissue or conventional expression systems. The generation of complex transgenic-knockout mice that express these hemoglobins at levels between 24% and 70% is described, as are efficient methods for their purification from mouse hemolysates. Key physiological characteristics-including P(50), Hill coefficient, Bohr effect, and affinity for 2,3-BPG-were established for each of the 3 human hemoglobins. The stability of each hemoglobin in the face of mechanical, thermal, and chemical stresses was also determined. Analyses indicate that the zeta-for-alpha exchange distinguishing Hb Portland-2 and Hb A alters hemoglobin O(2)-transport capacity by increasing its P(50) and decreasing its Bohr effect. By comparison, the epsilon-for-beta exchange distinguishing Hb Gower-2 and Hb A has little impact on these same functional parameters. Hb Gower-1, assembled entirely from embryonic subunits, displays an elevated P(50) level, a reduced Bohr effect, and increased 2,3-BPG binding compared to Hb A. The data support the hypothesis that Hb Gower-2, assembled from reactivated epsilon globin in individuals with defined hemoglobinopathies and thalassemias, would serve as a physiologically acceptable substitute for deficient or dysfunctional Hb A. In addition, the unexpected properties of Hb Gower-1 call into question a common hypothesis for its primary role in embryonic development.

Functional effects of replacing human alpha- and beta-globins with their embryonic globin homologues in defined haemoglobin heterotetramers

Embryonic- and adult-stage globin subunits assemble into haemoglobin (Hb) heterotetramers that are expressed at low levels throughout human intrauterine development. These haemoglobins differ from adult Hb A (alpha2beta2) by the substitution of embryonic zeta for adult alpha globin (Hb zeta2beta2), or embryonic epsilon for adult beta globin (Hb alpha2epsilon2). Several key physiological properties of these 'semiembryonic' haemoglobins remain undefined, as ethical and methodological considerations have limited their availability from both human sources and conventional expression systems. The current study attempts to estimate how the physiological properties of semiembryonic and adult haemoglobins may differ, by determining whether the O2-binding characteristics of hybrid human/mouse haemoglobins change when human alpha- or beta-globin subunits are replaced by human embryonic zeta- or epsilon-globin subunits respectively. Each of the four human globins is expressed in transgenic mice that are nullizygous for either the endogenous mouse alpha- or beta-globin genes, resulting in the high-level expression of haemoglobins that can be studied either in situ in intact erythrocytes or in vitro. We showed that the exchange of human zeta-globin for human alpha-globin chains increased haemoglobin O2 affinity, both in the presence and in the absence of 2, 3-bisphosphoglycerate (2,3-BPG), and reduced the pH-dependent shift in its oxygen equilibrium curve (Bohr effect). By comparison, hybrid haemoglobins containing either human epsilon-globin or human beta-globin exhibited nearly identical O2-binding properties, both in situ and in vitro, regardless of 2,3-BPG levels or ambient pH. Neither the zeta-for-alpha nor the epsilon-for-beta substitutions substantially altered binding affinity for 2,3-BPG or cooperativity between globin subunits. These studies suggest that semiembryonic haemoglobins that assemble entirely from human subunits may exhibit properties that are similar to those of human Hb A.

Multilocus sequence typing and antigen gene sequencing in the investigation of a meningococcal disease outbreak

Multilocus sequence typing and antigen gene sequencing were used to investigate an outbreak of meningococcal disease in a university in the United Kingdom. The data obtained showed that five distinct Neisseria meningitidis strains belonging to the ET-37 complex were present in the student population during the outbreak. Three of these strains were not associated with invasive disease, and two distinct strains caused invasive disease, including several fatalities. The initial case of the disease cluster was caused by a strain distinct from that responsible for at least two subsequent cases and two cases remote from the university, which were epidemiologically linked to the outbreak. These observations were consistent with pulsed-field gel electrophoresis data, but the sequence data alone were sufficient to resolve the strains involved in the disease cluster. Interpretation of the nucleotide sequence data was more straightforward than interpretation of the fingerprint patterns, and the sequence data provided information on the genetic differences among the isolates.

Population genetic and evolutionary approaches to analysis of Neisseria meningitidis isolates belonging to the ET-5 complex

Periodically, new disease-associated variants of the human pathogen Neisseria meningitidis arise. These meningococci diversify during spread, and related isolates recovered from different parts of the world have different genetic and antigenic characteristics. An example is the ET-5 complex, members of which were isolated globally from the mid-1970s onwards. Isolates from a hyperendemic outbreak of meningococcal disease in Worcester, England, during the late 1980s were characterized by multilocus sequence typing and sequence determination of antigen genes. These data established that the Worcester outbreak was caused by ET-5 complex meningococci which were not closely related to the ET-5 complex bacteria responsible for a hyperendemic outbreak in the nearby town of Stroud during the years preceding the Worcester outbreak. A comparison with other ET-5 complex meningococci established that there were at least three distinct globally distributed subpopulations within the ET-5 complex, characterized by particular housekeeping and antigen gene alleles. The Worcester isolates belonged to one of these subpopulations, the Stroud isolates belonged to another, and at least one representative of the third subpopulation identified in this work was isolated elsewhere in the United Kingdom. The sequence data demonstrated that ET-5 variants have arisen by multiple complex pathways involving the recombination of antigen and housekeeping genes and de novo mutation of antigen genes. The data further suggest that either the ET-5 complex has been in existence for many years, evolving and spreading relatively slowly until its disease-causing potential was recognized, or it has evolved and spread rapidly since its first identification in the 1970s, with each of the subpopulations attaining a distribution spanning several continents.

Reversal of lethal alpha- and beta-thalassemias in mice by expression of human embryonic globins

Genetic mutations that block alpha- or beta-globin gene expression in humans can result in severe and frequently lethal thalassemic phenotypes. Homozygous inactivation of the endogenous alpha- or beta-globin genes in mice results in corresponding thalassemic syndromes that are uniformly fatal in utero. In the current study, we show that the viability of these mice can be rescued by expression of human embryonic zeta- and -globins, respectively. The capacity of embryonic globins to fully substitute for their adult globin homologues is further demonstrated by showing that zeta- and -globins reverse the hemolytic anemia and abnormal erythrocyte morphology of mice with nonlethal forms of alpha- and beta-thalassemia. These results illustrate the potential therapeutic utility of embryonic globins as substitutes for deficient adult globins in thalassemic individuals. Moreover, the capacity of embryonic globins to functionally replace their adult homologues brings into question the physiologic basis for globin gene switching.

Modification of the standard method used in the United Kingdom for counting Escherichia coli in live bivalve molluscs

The standard method for counting Escherichia coli in live bivalve molluscs is labour intensive and takes three days to obtain a result. Modifications to the standard method were investigated in a collaborative trial conducted in five centres. No significant difference was found between results based on the presence of acid at 24 hours (h) in first stage tests and those based on the presence of acid and gas after 48 h (standard method). The use of the chromogenic medium BCIG (5-bromo-4-chloro-3-indolyl-beta-D glucuronide) agar incubated at 44 degrees C to confirm first stage tests was also found to give equivalent results to conventional confirmation tests. The preferred, modified method removes the presence of gas as a criterion of detection, uses a chromogenic agar medium to confirm the presence of E. coli, and gives results within 48 h. A distribution of simulated samples and selected strains of E. coli to other laboratories using the PHLS external quality assurance scheme for shellfish found no significant difference between results obtained by the standard and modified methods.

Expression and developmental control of the human alpha-globin gene cluster

The human alpha-globin gene cluster contains three functional genes zeta, alpha 2 and alpha 1. The zeta-globin gene is expressed exclusively in the primitive erythroblasts of the embryonic yolk sac and is selectively silenced during the transition from primitive to definitive erythropoesis. The two alpha-globin genes are expressed through development; they are expressed at equivalent levels in embryonic cells at a 2.6:1 ratio of alpha 2:alpha 1 in fetal and adult cells. The dominant contribution of the alpha 2-globin locus to overall expression of adult alpha-globin is reflected in the more severe phenotype resulting from mutations that affect this locus. Developmental silencing of the zeta-globin gene reflects both transcriptional and posttranscriptional mechanisms. Transcriptional silencing is mediated by an interaction between the zeta-globin gene promoter and a silencer located in the 3' flanking region. This transcriptional silencing is only partial, and residual levels of zeta-globin mRNA are subject to subsequent degredation. This instability of zeta-globin mRNA relative to that of alpha-globin mRNA reflects differences in their respective 3'UTR segments; the zeta-globin mRNA 3'UTR has a lower affinity for a sequence-specific mRNP stability complex which assembles at this site. The alpha-globin mRNA assembles this complex at a higher efficiency and mutations which interfere with 3'UTR function result in corresponding loss of alpha-globin gene expression. These data outline a developmental pathway for the alpha-globin gene cluster which reflects transcriptional and posttranscriptional controls.

Sequence divergence in the 3' untranslated regions of human zeta- and alpha-globin mRNAs mediates a difference in their stabilities and contributes to efficient alpha-to-zeta gene development switching

The developmental stage-specific expression of human globin proteins is characterized by a switch from the coexpression of zeta- and alpha-globin in the embryonic yolk sac to exclusive expression of alpha-globin during fetal and adult life. Recent studies with transgenic mice demonstrate that in addition to transcriptional control elements, full developmental silencing of the human zeta-globin gene requires elements encoded within the transcribed region. In the current work, we establish that these latter elements operate posttranscriptionally by reducing the relative stability of zeta-globin mRNA. Using a transgenic mouse model system, we demonstrate that human zeta-globin mRNA is unstable in adult erythroid cells relative to the highly stable human alpha-globin mRNA. A critical determinant of the difference between alpha- and zeta-globin mRNA stability is mapped by in vivo expression studies to their respective 3' untranslated regions (3'UTRs). In vitro messenger ribonucleoprotein (mRNP) assembly assays demonstrate that the alpha- and zeta-globin 3'UTRs assemble a previously described mRNP stability-determining complex, the alpha-complex, with distinctly different affinities. The diminished efficiency of alpha-complex assembly on the zeta 3'UTR results from a single C-->G nucleotide substitution in a crucial polypyrimidine tract contained by both the human alpha- and zeta-globin mRNA 3'UTRs. A potential pathway for accelerated zeta-globin mRNA decay is suggested by the observation that its 3'UTR encodes a shortened poly(A) tail. Based upon these data, we propose a model for zeta-globin gene silencing in fetal and adult erythroid cells in which posttranscriptional controls play a central role by providing for accelerated clearance of zeta-globin transcripts.

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

Destabilization of human alpha-globin mRNA by translation anti-termination is controlled during erythroid differentiation and is paralleled by phased shortening of the poly(A) tail

The extraordinary stability of globin mRNAs permits their accumulation to over 95% of total cellular mRNA during erythroid differentiation. The stability of human alpha-globin mRNA correlates with assembly of a sequence-specific ribonucleoprotein complex at its 3'-untranslated region. A naturally occurring anti-termination mutation, Constant Spring (CS), which permits ribosomes to enter the 3'-untranslated region of the alpha-globin mRNA, results in accelerated mRNA decay. To study the mechanism of this destabilization in vivo, we established transgenic mouse lines carrying the human alphaCS gene. Relative to wild-type human alpha-globin mRNA (alphawt), alphaCS mRNA is destabilized in marrow erythroid cells. The poly(A) tails of both the alphaCS and alphawt mRNAs show a periodicity of 20-25 nucleotides consistent with phased binding of poly(A) binding proteins. However, the mean size of poly(A) tails of the unstable alphaCS mRNA is significantly shorter than that of the alphawt mRNA. Unexpectedly, the alphawt and alphaCS mRNAs are of equal stability in peripheral reticulocytes, where their respective poly(A) tails shorten coordinately. These findings demonstrate a characteristic organization of the poly(A) tail on alpha-globin mRNA which is maintained during normal and accelerated decay, a correlation between poly(A) metabolism and anti-termination-mediated accelerated mRNA turnover, and a switch in the mechanism of mRNA decay during erythroid terminal differentiation.

The stability of human beta-globin mRNA is dependent on structural determinants positioned within its 3' untranslated region

Controls that act at both transcriptional and posttranscriptional levels assure that globin genes are highly expressed in developing erythroid cells. The extraordinary stabilities of alpha- and beta-globin mRNAs permit globin proteins to accumulate to substantial levels in these cells, even in the face of physiologic transcriptional silencing. Structural features that determine alpha-globin mRNA stability have recently been identified within its 3'UTR; in contrast, the structural features that determine beta-globin mRNA stability remain obscure. The current study begins to define the structural basis for beta-globin mRNA stability. Two tandem antitermination mutations are introduced into the wild-type human beta-globin gene that permit ribosomes to read into the 3'UTR of the encoded beta-globin mRNA. The readthrough beta-globin mRNA is destabilized in cultured erythroid cells, indicating that, as in human alpha-globin mRNA, an unperturbed 3'UTR is crucial to maintaining mRNA stability. Additional experiments show that the beta-globin and alpha-globin mRNA 3'UTRs provide equivalent levels of stability to a linked beta-globin mRNA coding region, suggesting a parallel in their functions. However, destabilization of the antiterminated beta-globin mRNA is independent of active translation into the 3'UTR, whereas translation into the alpha-globin mRNA 3'UTR destabilizes a linked beta-globin coding region in a translationally dependent manner. This indicates that the alpha- and beta-globin 3'UTRs may stabilize linked mRNAs through distinct mechanisms. Finally, it is shown that neither of the two mutations that, in combination, destabilize the beta-globin mRNA have any effect on beta-globin mRNA stability when present singly, suggesting potential redundancy of stabilizing elements. In sum, the current study shows that a functionally intact beta-globin mRNA 3'UTR is crucial to maintaining beta-globin mRNA stability and provides a level of stability that is functionally equivalent to, although potentially mechanistically distinct from, the previously characterized alpha-globin mRNA 3'UTR stability element.

Developmental silencing of the embryonic zeta-globin gene: concerted action of the promoter and the 3'-flanking region combined with stage-specific silencing by the transcribed segment

Globin gene switching is a well-described model of eucaryotic developmental control. In the case of the human alpha-globin gene cluster, migration of erythropoietic activity from the embryonic yolk sac to the fetal liver is parallaled by the zeta-globin gene silencing and enhanced expression of the alpha-globin genes. To map critical cis determinants of this switch, the human zeta-globin gene, the alpha-globin gene, and chimeric recombinants were introduced into the mouse genome. Consistent with previous studies, expression of the individual alpha- and zeta-globin transgenes was found to be developmentally appropriate. Contrary to current models, however, the alpha- and zeta-globin gene promoters were not sufficient to establish this control. Instead, full silencing of the zeta-globin gene required the combined activities of this promoter, transcribed region, and 3'-flanking sequences. Individually, the silencing activities of the zeta-globin gene promoter and 3'-flanking region were minimal but increased markedly when both regions were present. The zeta-globin transcribed region appeared to contribute to gene silencing by a mechanism specifically activated in definitive erythroblasts in the fetal liver. These data demonstrate that a complex set of controls, requiring at least three determinants and involving at least two independent mechanisms, is necessary for full developmental silencing of the human zeta-globin gene.

Functional characterization of the alternatively spliced, placental human growth hormone receptor

The human growth hormone family of peptide hormones is encoded by five genes, pituitary growth hormone (hGH-N), and four placentally expressed genes, growth hormone variant (hGH-V), chorionic somatomammotropin A and B (hCS-A, hCS-B), and prolactin (hPrl). As part of an effort to define the local effects of the placentally expressed members of the GH/Prl family of hormones on the placenta, we have identified an isoform (hGHRd3) of the growth hormone receptor expressed in the placental villi. hGHRd3 mRNA differs from the liver GHR mRNA by the deletion of a 66-base pair segment encoding exon 3. In this study we show that hGHRd3 mRNA encodes a stable and functional receptor. hGHRd3 mRNA is efficiently translated and processed in a rabbit reticulocyte lysate translation system as well as in an in vivo Xenopus laevis oocyte expression system. In Xenopus oocytes hGHRd3 is stably integrated into the cell membrane and binds and internalizes ligand as efficiently as hGHR. hGHRd3 binds all three of the placentally expressed members of the GH/Prl gene family (hGH-V, hCS, and Prl) as well as both the 22 and 20 kDa isoforms of the pituitary hGH-N. The results of the present study strongly support the expression of a functional hGHRd3 isoreceptor in the placenta which may serve in autocrine, paracrine, and/or endocrine activation.

Double-stranded RNA triggers generalized translational arrest in Xenopus oocytes

Controls of gene expression which act at the translational level can be rapidly activated and readily reversed. The impact of double-stranded RNA on translational control is of significant interest as a number of studies point to its ability to directly activate generalized translational arrest. This activity is observed in in vitro systems stimulated by native double-stranded RNAs or synthetic homopolymers and is inferred in virally infected cells in tissue culture. Significantly, however, this activity has never been studied in an intact cell system using RNAs of known secondary structure. In this study we arrest total cellular translation in intact Xenopus oocytes by micro-injecting them with alpha-globin-derivative mRNAs containing defined double-stranded segments. The ability of these mRNAs to directly activate translational arrest in oocytes substantiates the potential role for this activity in vivo and establishes a well-characterized whole cell system for its further study.

Bone maturation and resorption by peritoneal macrophages in noninsulin-dependent streptozocin-induced diabetes in the rat

The existence of osteopenia in noninsulin-dependent diabetes mellitus (NIDDM) is controversial. In this regard rats with a diabetic condition that simulates NIDDM have normal bone mineral content. However, normal total mineral content in bones does not preclude abnormalities in more delicate functions in bones of rats with NIDDM (specifically, bone maturation and response of bone matrix to resorptive activity). To evaluate these functions, bone maturation was studied in tibias from 14-week old male and female rats with streptozocin-induced NIDDM and controls. The ability of macrophages to resorb bone was studied in bone particles that were obtained from femors of male rats with NIDDM and controls. The diabetic rats had the overt NIDDM condition for 8 weeks at the time of the study. We found that bone maturation/mineralization remained intact in the diabetic rats and that response of the bone particles that were obtained from their femors to the resorptive activity of macrophages was similar to that of the bone particles that were obtained from controls. These data suggest that in the rat, a diabetic condition that simulates NIDDM does not alter the physiologic functions of the bone matrix.

Effect of sodium fluoride on bone density in chickens

In addition to increasing bone volume, fluoride has been demonstrated to increase ash weight and mineral density. To determine whether newly formed or older bone is most affected by fluoride treatment, bone from chickens receiving fluoridated water was fractionated into lower density (recently formed) and higher density (more mature) specific gravity fractions. Fluoride was administered to the chickens for different lengths of time (4 or 13 weeks) or at varying doses for a 4-week period (0, 4.2, 16.8 mmol/liter drinking water). Fluoride treatment caused a shift in the mineral density profile, showing an increased proportion of mineral distribution in the more mature, higher density fractions. To determine whether this density gradient shift was due to increased maturation rate of bone or decreased resorption and mineralization rates, [3H]proline and 45Ca were injected 5 days and 24 hours prior to sacrifice, respectively. The distributions of both 3H or 45Ca, as percentages of total counts incorporated, were shifted by fluoride treatment into more mature, higher density fractions. Expressing the number of counts as a percent of the bone in each fraction (total hydroxyproline or Ca) revealed an increased incorporation of both 3H and 45Ca into the higher specific gravity fractions 2.0-2.2. These results suggest that fluoride treatment increases bone maturation and the rate of secondary mineralization in the cortical bone. Such changes in the quality of more mature, well-mineralized bone, in humans as well as animals, may have a significant influence on brittleness and strength.

Ascorbic acid requirement for optimal flexor tendon repair in vitro

Numerous studies from our laboratory have defined aspects of the repair process in a lacerated flexor tendon model, both in vivo and in vitro. Inherent in the development of a viable tissue or cell culture model system is the definition of the optimal media environment. Since our laboratory investigations of in vitro flexor tendon repair encompass the formation of numerous extracellular matrix proteins, we have defined the optimal level of ascorbic acid with which to study the tendon wound healing process. The ascorbic acid requirement for proline and lysine hydroxylase activity during collagen biosynthesis is well known, and the importance of this vitamin for matrix proteoglycan synthesis more recently has been appreciated. This report describes the effect of several levels of ascorbic acid on 3H-thymidine incorporation, collagen and noncollagen protein synthesis, and glucose utilization and lactate production. Profundus flexor tendon segments were obtained from young adult New Zealand white rabbits and maintained in organ culture for periods of 1, 2, or 3 weeks. Ascorbic acid concentrations ranged from 50 to 300 micrograms/ml and were added fresh at each 48-h media change. Tendon protein synthesis, glucose metabolism, and cell permeability/viability were significantly correlated with the level of ascorbic acid in the culture medium. The results suggest that ascorbic acid levels in excess of the traditional 50 micrograms/ml are necessary to optimally maintain flexor tendons from adult animals in organ culture with 48-h media and ascorbate changes. Additionally, it may be necessary to determine the precise ascorbic acid requirement for individual tissues, since the specific tissue/cell and species requirement for ascorbate may vary.

A new method for measurement of airway occlusion pressure

Airway occlusion pressure correlates with central respiratory drive. The airway occlusion pressure (P0.1) may be an excellent predictor of the ability of patients with obstructive lung disease to wean from mechanical ventilation. We describe a new method for measuring P0.1 using digitized signals generated from standard respiratory equipment and a computer program to automatically determine P0.1 values. The accuracy of this new method was tested by comparison with standard analog recorder methods using a mechanical lung model, in ventilated patients in an intensive care unit, and in normal volunteers. In all settings, excellent correlation was obtained between P0.1 measurements by the digital Servo and standard analog methods (r = 0.99). This new method permits accurate and automatic determination of P0.1 in ventilated patients using standard respiratory equipment. The rapid response and ease of use of this method should enable evaluation of a number of physiologic variables involved in respiratory control in ventilated and nonventilated patients.

Analysis of individual variability among older adults on the Stroop Color Word Interference Test

The present study examines systematic variation in the pattern of response to the Stroop test among a sample of older adults (N = 41), as well as the extent to which various configural patterns of response are related to other individual difference factors. Pattern analysis identified four reasonably prototypic patterns of performance. Three significant discriminant functions, capable of differentiating the four response patterns, were significantly and uniquely related to age, level of cautiousness, and verbal intelligence, respectively. The analyses suggest that performance on the Stroop test is multidimensional with significant variation among older adults, and that different components of performance are differentially related to unique individual difference variables. The findings reinforce the importance of recognizing and understanding the nature of individual variation among elderly individuals in aging research.

Collagen synthesis during primate flexor tendon repair in vitro

The concept that flexor tendons have the intrinsic capacity to participate actively in the repair process following laceration has been developed in recent years as the result of experimental studies from numerous laboratories. However, the role of the outer/epitenon and inner/endotenon cell populations with regard to protein synthesis is still controversial. The purpose of this study was to investigate the respective participation of these tendon fibroblast populations in the synthesis of the collagen matrix during in vitro repair of the flexor tendon from nonhuman primates, utilizing immunohistochemical techniques and a Type I procollagen antibody. Zone II profundus flexor tendon segments were obtained from young adult Macaca nemestrina monkeys. One centimeter segments were cultured, either with or without a transverse laceration across 90% of the midsection of the tendon segment. Frozen sections of the cultured tendon segments were reacted with the (mouse monoclonal) Type I procollagen antisera. At all times of culture of the nonlacerated tendon segment, only a few of the epitenon cells along the surface of the tendon and distant from the cut end stained positively for active collagen synthesis. In the lacerated segments, and as early as 9 days of culture and repair, the procollagen reaction product was starting to appear in those cells of the outer epitenon cell layer. These studies support the concept that the inner fibroblasts do actively participate in collagen production. However, it now also appears that a significant degree of collagen synthesis during tendon repair resides in the outer/epitenon layer of cells enveloping the tendon segment, and that the repair response of the flexor tendon in vitro is proportional to the degree of injury.

Myeloperoxidase-positive acute megakaryoblastic leukemia

Acute megakaryoblastic leukemia (FABM7) is an unusual but well recognized form of acute myelogenous leukemia in which the bone marrow blast cells are phenotypically recognized by the demonstration of cytoplasmic platelet peroxidase or surface staining for the IIb/IIIa platelet-specific glycoprotein. Herein, the authors report a case of acute megakaryoblastic leukemia that satisfies the accepted French-American-British criteria and in which the blast cells also exhibit evidence of myeloid differentiation, including surface MY7 (CD13) by flow cytometry and immunocytochemical positivity for myeloperoxidase. These findings suggest that megakaryoblasts may be closely related to myelomonoblasts, that they have the potential to partially differentiate along multiple phenotypic lines, and that aberrant phenotypes can occur that do not correspond to known stages of normal maturation. The authors illustrate the difficulty in classification of these aberrant phenotypes by standard cytochemical and morphologic criteria.

Biochemical evaluation of organ cultures from primate flexor tendons

Recently our laboratory has reported, in a lacerated flexor tendon model, that the "early turnover" phase of the repair process extends for a longer period of time in vivo than previously documented. The extensive turnover of the collagenous matrix was consistent with the presence of collagenolytic activity in repairing tendon tissue and suggested a possible regulatory role for neutral metalloproteinases in flexor tendon repair. However, these in vivo observations could not distinguish the relative contribution by the tendon fibroblasts from that of the surrounding sheath and vascular tissue elements. To further define these interrelationships, the present study investigates the repair process of the flexor tendon in an in vitro tissue culture environment. The sequential changes in matrix formation were defined (i.e., proteoglycans/glycosaminoglycans, glycoproteins, and collagenous proteins). The concomitant production of neutral metalloproteinases as well as prostaglandin E2 was determined in relation to net tissue repair. Profundus flexor tendon segments were obtained from young adult Macaca nemestrina monkeys and maintained in organ culture for periods from 4 days through 9 weeks. Initially (at 2 wks) there was an increase in both sulfated and nonsulfated glycosaminoglycans, which preceded the onset of maximal collagen protein formation. By 6 and 9 weeks of in vitro repair, of the lacerated tendon segments, there was a significant increase in net collagen formation. Neutral metalloproteinase activity increased early in the repair period, from the 4th to 9th day, and decreased thereafter through the 9th week of culture. Functionally the enzyme appeared to be a gelatinase. The temporal pattern of in vitro collagen synthesis in relation to the gelatinase activity support the hypothesis that regulation of this enzyme(s) may be a critical factor in mediating the flexor tendon response to injury.

Bone cell populations and histomorphometric correlates to function

A circadian context has been used to develop information about the proliferative and functional behavior of the cell populations that function to model the long bones of growing rats. We asked: Are the proliferating cells in the growth cartilages and diaphyseal bone of young adult growing rats distributed within single or multiple populations? Can cytomorphometry (TEM-C) be used to determine ultrastructural correlates to the well-defined circadian rhythm of matrix formation displayed by functionally synchronous populations of metaphyseal osteoblasts? Can TEM-C reveal changes in osteoclast ultrastructure that could index a biological rhythm for osteoclastic bone mineralysis/resorption? Kinetic results derived from multiple radiothymidine labeling (DNA synthesis) support the single population model for chondrocytes and diaphyseal osteoprogenitor cells. TEM-C studies at the midpoints of the daily light and dark spans show that osteoblast RER-membrane development and cysternal volumes are maximal at the recorded daytime peak of net collagen synthesis. The extent of metaphyseal osteoclast surface ruffling (mineralysis) is also twofold greater during the day than the night--an observation supporting the concept that bone formation and resorption activities are coupled.

The effect of vascularization on avian flexor tendon repair. A biochemical study

Although it has been demonstrated in experimental animals that vascular perfusion functions less effectively than diffusion as a nutrient pathway to the uninjured flexor tendon, it is recognized that the nutritional requirements of an injured flexor tendon may be different. The present study examines several biochemical parameters of avian flexor tendon repair, during a six-week period, in the presence of an intact vinculum longum and with the vinculum longum ligated. Formation of collagen/noncollagen protein, glycosaminoglycan synthesis, and tissue levels of both DNA and hexosamine were quantified. The absence of the vincular blood supply did not affect the levels of total DNA and hexosamine, did not alter the pattern of either protein or glycosaminoglycan formation in the early healing phase, and did not impair the overall synthesis of collagen and noncollagen protein throughout the six-week study period. However, the pattern of collagen and noncollagen protein synthesis differed in lacerated tendons during the period of repair; noncollagen protein synthesis peaked at ten days, while collagen synthesis increased uniformly throughout the 42-day period of study. There was a notable decrease in total matrix hydroxyproline (collagen) during repair, which continued throughout the entire first three weeks after laceration. Thus, the actual percentage of collagen synthesis decreased during the first three weeks of repair and began to return to its normal uninjured level by the sixth week.(ABSTRACT TRUNCATED AT 250 WORDS)

Regional differences in matrix formation in the healing flexor tendon

In 20 white leghorn chickens, the effect of proximity (proximal vs. distal) to the repair site and the effect of sheath excision versus sheath repair on biochemical matrix formation in the healing zone 2 flexor tendon were studied. In 14 animals, the profundus tendon of the long toe on both feet was lacerated and repaired in zone 2. In the right foot, the sheath was repaired, and on the left foot, the sheath was excised. Segments proximal and distal to the laceration site were studied at six weeks postrepair compared to control segments. Sheath excision versus sheath repair had no effect on the net matrix formation of the healing flexor tendon. A higher DNA content and lower hydroxyproline and hexosamine contents were present in the healing tendons, indicating the healing process was not complete at six weeks. Sheath excision versus sheath repair had no effect on net matrix formation in the healing tendon. There is no difference in DNA content or glycosaminoglycan content in the proximal versus distal segments. There was a significantly greater net hydroxyproline content in the proximal segment versus the distal segment of the healing tendon, which was not present in similar control segments. These results support the concept that the zone 2 flexor tendon does not respond to injury as a homogeneous structure.

Cautiousness and visual selective attention performance among older adults

Cautiousness has been implicated in the literature as a possible factor responsible for observed performance decrements among older adults in a number of research paradigms. This study sought to assess whether the speed and accuracy of performance on a perceptual-cognitive task (the Stroop Color-Word Interference Test) differed significantly for more and less cautious older adults. The participants (N = 41), ranging from 55 to 81 years of age, were classified as either more cautious (n = 20) or less cautious (n = 21) on the basis of their responses on a personality test. Results indicated that cautiousness among older adults was manifested more in terms of the accuracy of response (fewer errors of commission) than in terms of the speed of response, and that level of cautiousness increased with increasing age.