Phage DNA Extraction, Genome Assembly, and Genome Closure

Bacteriophages, or more simply phages, are currently experiencing a renaissance in life science research for their roles in natural microbial communities, their potential use as antimicrobials, and biotechnological applications. In the modern era, one of the primary steps in phage characterization is obtaining the sequence of the complete genome; this information can be used to determine the relationship of the phage to known phages, predict phage lifestyle, and is a prerequisite for many downstream applications. This protocol describes methods for determining the complete sequence of a double-stranded DNA bacteriophage genome, including DNA extraction from a phage lysate, sending the DNA out to a sequencing service, assembly of the sequence raw reads, and completion of the genome sequence.

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology

Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.

Improved Neutron Lifetime Measurement with UCNτ

We report an improved measurement of the free neutron lifetime τ_{n} using the UCNτ apparatus at the Los Alamos Neutron Science Center. We count a total of approximately 38×10^{6} surviving ultracold neutrons (UCNs) after storing in UCNτ's magnetogravitational trap over two data acquisition campaigns in 2017 and 2018. We extract τ_{n} from three blinded, independent analyses by both pairing long and short storage time runs to find a set of replicate τ_{n} measurements and by performing a global likelihood fit to all data while self-consistently incorporating the β-decay lifetime. Both techniques achieve consistent results and find a value τ_{n}=877.75±0.28_{stat}+0.22/-0.16_{syst}  s. With this sensitivity, neutron lifetime experiments now directly address the impact of recent refinements in our understanding of the standard model for neutron decay.

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage

The Gram-negative bacterium Proteus mirabilis causes a large proportion of catheter-associated urinary tract infections, which are among the world's most common nosocomial infections. Here, we characterize P. mirabilis bacteriophage Privateer, a prolate podophage of the C3 morphotype isolated from Texas wastewater treatment plant activated sludge. Basic characterization assays demonstrated Privateer has a latent period of ~40 min and average burst size around 140. In the 90.7 kb Privateer genome, 43 functions were assigned for the 144 predicted protein-coding genes. Genes encoding DNA replication proteins, DNA modification proteins, four tRNAs, lysis proteins, and structural proteins were identified. Cesium-gradient purified Privateer particles analyzed via LC-MS/MS verified the presence of several predicted structural proteins, including a longer, minor capsid protein apparently produced by translational frameshift. Comparative analysis demonstrated Privateer shares 83% nucleotide similarity with Cronobacter phage vB_CsaP_009, but low nucleotide similarity with other known phages. Predicted structural proteins in Privateer appear to have evolutionary relationships with other prolate podophages, in particular the Kuraviruses.

Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation

In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.

The Nab experiment: A precision measurement of unpolarized neutron beta decay

Neutron beta decay is one of the most fundamental processes in nuclear physics and provides sensitive means to uncover the details of the weak interaction. Neutron beta decay can evaluate the ratio of axial-vector to vector coupling constants in the standard model, λ = gA/gV, through multiple decay correlations. The Nab experiment will carry out measurements of the electron-neutrino correlation parameter a with a precision of δa/a = 10−3 and the Fierz interference term b to δb = 3 × 10−3 in unpolarized free neutron beta decay. These results, along with a more precise measurement of the neutron lifetime, aim to deliver an independent determination of the ratio λ with a precision of δλ/λ = 0.03% that will allow an evaluation of Vud and sensitively test CKM unitarity, independent of nuclear models. Nab utilizes a novel, long asymmetric spectrometer that guides the decay electron and proton to two large area silicon detectors in order to precisely determine the electron energy and an estimation of the proton momentum from the proton time of flight. The Nab spectrometer is being commissioned at the Fundamental Neutron Physics Beamline at the Spallation Neutron Source at Oak Ridge National Lab. We present an overview of the Nab experiment and recent updates on the spectrometer, analysis, and systematic effects.

The neutron electric dipole moment experiment at the Spallation Neutron Source

Novel experimental techniques are required to make the next big leap in neutron electric dipole moment experimental sensitivity, both in terms of statistics and systematic error control. The nEDM experiment at the Spallation Neutron Source (nEDM@SNS) will implement the scheme of Golub & Lamoreaux [Phys. Rep., 237, 1 (1994)]. The unique properties of combining polarized ultracold neutrons, polarized 3He, and superfluid 4He will be exploited to provide a sensitivity to ∼ 10−28 e · cm. Our cryogenic apparatus will deploy two small (3 L) measurement cells with a high density of ultracold neutrons produced and spin analyzed in situ. The electric field strength, precession time, magnetic shielding, and detected UCN number will all be enhanced compared to previous room temperature Ramsey measurements. Our 3He co-magnetometer offers unique control of systematic effects, in particular the Bloch-Siegert induced false EDM. Furthermore, there will be two distinct measurement modes: free precession and dressed spin. This will provide an important self-check of our results. Following five years of “critical component demonstration,” our collaboration transitioned to a “large scale integration” phase in 2018. An overview of our measurement techniques, experimental design, and brief updates are described in these proceedings.

First Measurement of the Total Neutron Cross Section on Argon between 100 and 800 MeV

We report the first measurement of the neutron cross section on argon in the energy range of 100-800 MeV. The measurement was obtained with a 4.3-h exposure of the Mini-CAPTAIN detector to the WNR/LANSCE beam at LANL. The total cross section is measured from the attenuation coefficient of the neutron flux as it traverses the liquid argon volume. A set of 2631 candidate interactions is divided in bins of the neutron kinetic energy calculated from time-of-flight measurements. These interactions are reconstructed with custom-made algorithms specifically designed for the data in a time projection chamber the size of the Mini-CAPTAIN detector. The energy averaged cross section is 0.91±0.10(stat)±0.09(syst)  b. A comparison of the measured cross section is made to the GEANT4 and FLUKA event generator packages, where the energy averaged cross sections in this range are 0.60 and 0.68 b, respectively.

Measurement of the neutron lifetime using a magneto-gravitational trap and in situ detection

The precise value of the mean neutron lifetime, τ_n, plays an important role in nuclear and particle physics and cosmology. It is used to predict the ratio of protons to helium atoms in the primordial universe and to search for physics beyond the Standard Model of particle physics. We eliminated loss mechanisms present in previous trap experiments by levitating polarized ultracold neutrons above the surface of an asymmetric storage trap using a repulsive magnetic field gradient so that the stored neutrons do not interact with material trap walls. As a result of this approach and the use of an in situ neutron detector, the lifetime reported here [877.7 ± 0.7 (stat) +0.4/-0.2 (sys) seconds] does not require corrections larger than the quoted uncertainties.

Measurement of the neutron lifetime using a magneto-gravitational trap and in situ detection

The precise value of the mean neutron lifetime, τ_n, plays an important role in nuclear and particle physics and cosmology. It is used to predict the ratio of protons to helium atoms in the primordial universe and to search for physics beyond the Standard Model of particle physics. We eliminated loss mechanisms present in previous trap experiments by levitating polarized ultracold neutrons above the surface of an asymmetric storage trap using a repulsive magnetic field gradient so that the stored neutrons do not interact with material trap walls. As a result of this approach and the use of an in situ neutron detector, the lifetime reported here [877.7 ± 0.7 (stat) +0.4/-0.2 (sys) seconds] does not require corrections larger than the quoted uncertainties.

Alphavirus Purification Using Low-speed Spin Centrifugation

Chemical and sedimentation procedures are used to purify virus particles. While these approaches are successful for wild-type viruses, they are often not feasible for purifying mutant viruses with assembly defects. We combined two published methods ( Atasheva et al., 2013 ; Moller- Tank et al., 2013 ), to generate a protocol that uses low-speed centrifugation to purify both wildtype and mutant enveloped virus particles at high yield with minimal handling steps. This protocol has successfully been used to purify alphavirus particles for imaging and structural studies ( Wang et al., 2015 ; Ramsey et al., 2017 ).

Disentangling the Frames, the State of Research on the Alphavirus 6K and TF Proteins

For 30 years it was thought the alphavirus 6K gene encoded a single 6 kDa protein. However, through a bioinformatics search 10 years ago, it was discovered that there is a frameshifting event and two proteins, 6K and transframe (TF), are translated from the 6K gene. Thus, many functions attributed to the 6K protein needed reevaluation to determine if they properly belong to 6K, TF, or both proteins. In this mini-review, we reevaluate the past research on 6K and put those results in context where there are two proteins, 6K and TF, instead of one. Additionally, we discuss the most cogent outstanding questions for 6K and TF research, including their collective importance in alphavirus budding and their potential importance in disease based on the latest virulence data.

A new method for measuring the neutron lifetime using an in situ neutron detector

In this paper, we describe a new method for measuring surviving neutrons in neutron lifetime measurements using bottled ultracold neutrons (UCN), which provides better characterization of systematic uncertainties and enables higher precision than previous measurement techniques. An active detector that can be lowered into the trap has been used to measure the neutron distribution as a function of height and measure the influence of marginally trapped UCN on the neutron lifetime measurement. In addition, measurements have demonstrated phase-space evolution and its effect on the lifetime measurement.

Proximal Left Subclavian Artery Aneurysms: A Case Report and Review of the Literature

Aneurysms of the proximal subclavian artery are extremely rare. A 39-year-old female with an incidental finding of a small proximal left subclavian artery aneurysm at its origin from the aortic arch is described. This was an incidental finding during workup for chest pain. No other vascular abnormalities were found and no obvious etiology was identified. The workup, plan for conservative treatment, and close follow-up are described. Although larger aneurysms and those in the middle and distal subclavian arteries, symptomatic or asymptomatic, are generally considered for surgical treatment, very little is known about the natural history of small proximal subclavian aneurysms.

Regulating Surrogacy—A Contravention of Human Rights?

On the 2nd of October 2000, The Human Rights Act 1998 came into full force, signalling the incorporation of The European Convention on Human Rights into U.K. law. Areas of law believed to be inconsistent with the Convention may now be challenged in both The European Court of Human Rights and domestic courts. This article considers whether existing laws on the regulation of access to infertility services, in particular surrogacy, will be deemed incompatible with the ECHR. Human rights as enshrined within Articles 8 and 12 will be examined in light of recent suggestions that there may arise legal challenges by those who have had access to reproductive services restricted or denied. It will be shown that, although existing and potential future controls may arguably infringe these rights, it is nevertheless unlikely that they will be held to be in contravention of The Human Rights Act 1998.

The impact of a diagnosis of personality disorder on service usage in an adult Community Mental Health Team

PURPOSE

Patients with a diagnosis of personality disorder (PD) have multiple and diverse needs. It has been noted that individuals with personality disorder are high users of health care resources, especially psychiatric services, ambulance services and emergency departments. In addition PD has been shown to be a significant predictor of disability and mental health consultations independent of Axis I disorders and physical conditions. This study aimed to compare the patterns of service usage, clinical ratings of symptoms and functioning, as well as demographic and clinically relevant historical variables between a group of patients with PD and a random sample of all other patients registered with a South London Community Mental Health Team.

METHODS

A case–control design was used to examine service usage patterns over a one-year period for 73 cases and 96 controls. Diagnoses were established by clinician discussion. Clinical outcomes were measured with Health of the Nation Outcome Scales and Global Assessment of Functioning, while service use was recorded using ten variables obtained from case note review.

RESULTS

People with a diagnosis of PD were more often white and had a history of abuse, particularly childhood emotional abuse. They were higher users of some aspects of the service as compared to controls, and had significantly higher severity of symptoms and poorer functioning on clinician-rated measures.

CONCLUSION

This study confirms previous findings that people with PD have more severe symptomatology and greater degrees of functional impairment when compared to those without. Community clinicians should routinely screen attenders to predict likely difficulties that might arise and to make provision for these difficulties in the treatment and management of clients.

Monitoring trends in recreational drug use from the analysis of the contents of amnesty bins in gay dance clubs

BACKGROUND

In 2011/12, 8.9% of the UK population reported use of recreational drugs. Problems related to drug use is a major financial burden to society and a common reason for attendance to hospital.

AIM

The aim of this study was to establish current trends in recreational drug use amongst individuals attending gay-friendly nightclubs in South London.

METHOD

Contents of drug amnesty bins located at two night clubs were documented and categorized into powders, herbal products, liquids, tablets and capsules. These were then sent to a Home Office licensed laboratory for identification through a pre-existing database of almost 25 000 substances. If required, further qualitative analysis was performed.

RESULTS

A total of 544 samples were obtained. Of them, 240 (44.1%) were liquids, 220 (40.4%) powders, 42 (7.7%) herbal and 41 (7.5%) tablets or capsules. Gamma-butyrolactone (GBL) was the most common liquid drug (n = 160, 66.7%) followed by poppers (n = 72, 30.0%). Powders provided the widest range of drugs with mephedrone being the most common (n = 105, 47.7%) followed by ketamine (n = 28, 12.7%), 3,4-methylenedioxy-N-methylamphetamine (MDMA) (n = 26, 11.8%), and cocaine (n = 21, 9.5%). Tablets and capsules included medicinal drugs, recreational drugs and plaster of Paris tablets that mimicked the appearance of 'ecstasy' tablets.

CONCLUSION

This study has provided a snapshot of the pattern of drug use in the gay community which compliments findings of the self-reported surveys and other studies from the same population. The information obtained will be helpful in guiding in designing harm reduction interventions in this community and for monitoring the impact of changes in legislation.

Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly

Prp8 stands out among hundreds of splicing factors as a protein that is intimately involved in spliceosomal activation and the catalytic reaction. Here, we present the first comprehensive in vivo RNA footprints for Prp8 in budding yeast obtained using CLIP (cross-linking and immunoprecipitation)/CRAC (cross-linking and analyses of cDNAs) and next-generation DNA sequencing. These footprints encompass known direct Prp8-binding sites on U5, U6 snRNA and intron-containing pre-mRNAs identified using site-directed cross-linking with in vitro assembled small nuclear ribonucleoproteins (snRNPs) or spliceosome. Furthermore, our results revealed novel Prp8-binding sites on U1 and U2 snRNAs. We demonstrate that Prp8 directly cross-links with U2, U5 and U6 snRNAs and pre-mRNA in purified activated spliceosomes, placing Prp8 in position to bring the components of the active site together. In addition, disruption of the Prp8 and U1 snRNA interaction reduces tri-snRNP level in the spliceosome, suggesting a previously unknown role of Prp8 in spliceosomal assembly through its interaction with U1 snRNA.

Performance of the Los Alamos National Laboratory spallation-driven solid-deuterium ultra-cold neutron source

In this paper, we describe the performance of the Los Alamos spallation-driven solid-deuterium ultra-cold neutron (UCN) source. Measurements of the cold neutron flux, the very low energy neutron production rate, and the UCN rates and density at the exit from the biological shield are presented and compared to Monte Carlo predictions. The cold neutron rates compare well with predictions from the Monte Carlo code MCNPX and the UCN rates agree with our custom UCN Monte Carlo code. The source is shown to perform as modeled. The maximum delivered UCN density at the exit from the biological shield is 52(9) UCN/cc with a solid deuterium volume of ~1500 cm(3).

Buying 'legal' recreational drugs does not mean that you are not breaking the law

BACKGROUND

Recreational drug use in the UK is common; sources of recreational drugs are changing, with increasing purchase of legal highs from the Internet. Previous studies have shown that there is not consistency of active ingredient(s) in legal highs purchased from the Internet.

AIM

The aim of this study was to determine the impact of the 16 April 2010 change to the Misuse of Drugs Act (1971) on the content of 'legal highs' purchased over the Internet and supplied within the UK.

METHODS

Legal highs were purchased from a number of different Internet suppliers and the active ingredients determined by analysis undertaken within a Home Office approved and licensed laboratory set in a UK academic institution. The active ingredient(s) detected on screening were then compared to the UK legislation in force at the time of purchase to determine whether each individual 'legal' high was in fact legal or not.

RESULTS

All 18 products purchased prior to the change in the UK legislation contained active ingredients that were legal under the Misuse of Drugs Act (1971) in force at that time. Six products were purchased and analysed after the changes to the UK Misuse of Drugs Act (1971) on the 16 April 2010. Five of the products contained information, either on the Internet site or the packaging, stating that the product contained legal substances; the final product did not specify the active ingredient and so purchasers would be unable to determine if this was truly a legal product. Five of the six products contained an active ingredient that is a Class B drug under the Misuse of Drugs Act (1971); the other product contained an unlicensed medicine not controlled under the Misuse of Drugs Act (1971).

CONCLUSION

We have shown in this study that some drugs sold as 'legal' highs contain drugs that are controlled under the Misuse of Drugs Act (1971). Under current UK legislation, individuals purchasing legal highs that contained controlled drugs would be subject to the same penalties as if they had knowingly purchased a controlled drug. Dissemination of information on the harm associated with the use of legal highs should also inform individuals that they may be purchasing controlled substances and the potential legal consequences of this.

Purchasing 'legal highs' on the Internet--is there consistency in what you get?

BACKGROUND

The supply of recreational drugs has changed and users increasingly buy 'legal highs' over the Internet. Use of these is common and there is a potential for significant toxicity associated with their use.

AIM

To determine the content of legal highs available for purchase in the UK and whether the content of these remains consistent.

METHODS

Twenty-six legal highs were purchased monthly from five different Internet sites over 6 months. These were analysed to determine the drugs in the products and whether there were any changes in their content over this time period.

RESULTS

All products were supplied initially, but there was a decline in supply of products month by month. The following drug classes were detected: piperazines, cathinones, caffeine/ephedrine or products in which no psychoactive drugs were detected. Of the products supplied on more than one occasion, 15 (75%) contained the same compounds on each occasion. In three products there was a change in the piperazine detected, with 1-benzylpiperazine being substituted for 1-methyl-4-benzylpiperazine or vice versa. In two other products there was a cathinone [4-fluorophenylpiperazine (pFPP) or 3-fluromethcathinone (3FMC)] detected in products purchased in Month 1 that was not present in the products purchased in subsequent months.

CONCLUSION

Whilst there was no variation in the composition of most legal highs supplied over 6 month, there was significant variation in the piperazine or cathinone content of one quarter of the products. This variation could be of clinical significance as the cathinone and piperazine products can be associated with significant toxicity.

What evidence is there that the UK should tackle the potential emerging threat of methamphetamine toxicity rather than established recreational drugs such as MDMA ('ecstasy')?

BACKGROUND

There is increasing interest in whether methamphetamine is an emerging recreational drug in the UK.

AIM

To determine what evidence is there that methamphetamine use is an emerging drug in the UK compared to established recreational drugs such as MDMA.

DESIGN AND METHODS

We undertook a retrospective study collating data on the number of enquiries to both our poisons centre and the UK National Poisons Information Service (NPIS) relating to all recreational drugs, methamphetamine and MDMA; presentations to our Emergency Department (ED) with acute methamphetamine toxicity and the frequency of positive urine tests for methamphetamine and MDMA in workplace drug screening programmes.

RESULTS

There was a small increase in the number of methamphetamine-related calls to our poisons centre, but it remained uncommon (0.1% of all recreational drugs cases in 2000 to 1.23% in 2006) compared to MDMA (17.3-42.7% of all recreational drugs cases). The number of 2005/6 enquiries to the UK NPIS for methamphetamine was 12, compared to 455 MDMA enquiries (0.014 and 0.52% of all enquiries, respectively). There were five presentations to our ED relating to methamphetamine over a 15-month period compared to 171 for MDMA. Of the 254 440 urine samples screened for the presence of drugs in the workplace (2000-06), three were positive for methamphetamine and 147 for MDMA.

CONCLUSION

There is no evidence of increasing use of methamphetamine or that acute methamphetamine poisoning is a significant clinical problem compared to established recreational drugs such as MDMA. In our opinion, healthcare, educational and law enforcement resources should be proportionally directed towards tackling drugs that pose an immediate and continuing healthcare risk to the population rather than emerging recreational drugs.

Medical and legal confusion surrounding gamma-hydroxybutyrate (GHB) and its precursors gamma-butyrolactone (GBL) and 1,4-butanediol (1,4BD)

BACKGROUND

Gamma-hydroxybutyrate (GHB) is used as a recreational drug, with significant associated morbidity and mortality; it is therefore a class C drug under the Misuse of Drugs Act (1971). However, its precursors gamma-butyrolactone (GBL) and 1,4-butanediol (1,4BD) remain legally available despite having similar clinical effects.

AIM

The aim of this study was to determine whether the relative proportions of self-reported ingestions of GHB or its precursors GBL and 1,4BD were similar to those seen in analysis of seized drugs.

DESIGN AND METHODS

Retrospective review of our clinical toxicology database to identify all cases of self-reported recreational GHB, GBL and 1,4BD use associated with ED presentation in 2006. Additionally all seized substances on people attending local club venues were analysed by a Home Office approved laboratory to identify any illicit substances present.

RESULTS

In 2006, there were a total of 158 ED presentations, of which 150 (94.9%) and 8 (5.1%) were GHB and GBL self-reported ingestions respectively; 96.8% (153) were recreational use. Of the 418 samples seized, 225 (53.8%) were in liquid form; 85 (37.8%) contained GHB and 140 (62.2%) contained GBL. None of the seized samples contained 1,4BD and there were no self-reported 1,4BD ingestions.

CONCLUSION

Self-reported GHB ingestion was much more common than GBL ingestion, whereas GBL was more commonly found in the seized samples. These differences suggest that GBL use may be more common than previously thought and we suggest that there should be further debate about the legal status of the precursors of GHB.

Unreduced gametes and neopolyploids in natural populations of Achillea borealis (Asteraceae)

Polyploidy is a major mechanism of speciation and adaptation, yet little is known about the origins of polyploids in natural species. I investigated gametic nonreduction and neopolyploid formation in natural tetraploid populations of Achillea borealis (Asteraceae), an autopolyploid complex consisting of tetraploid and hexaploid cytotypes. Cytological analyses of tetraploid populations revealed the occurrence of reduced (n=2x) as well as unreduced 'big' (2n=4x) and 'jumbo' (4n=8x) pollen grains, which were clearly distinguished by size. Production of unreduced pollen was monitored in two tetraploid populations in 1997 and 1998. Mean population-level frequencies of unreduced pollen ranged from 0.030 to 0.538%, with as few as one-third and as many as one-half of sampled plants producing unreduced grains. Eight individuals were found to produce >1% unreduced pollen, with highest observed frequencies of 7.0, 13.2 and 15.8%. Experimental crosses using high unreduced pollen producers as male parents generated viable seeds. However, the frequency of neohexaploids in the progeny of experimental crosses (0.388%) was similar to that observed in progeny of randomly selected, open-pollinated control parents (0.465%). These results suggest that unreduced eggs are the most likely source of new polyploids. In spite of the inefficiency of unreduced pollen in unilateral sexual polyploidization, the overall rate of neohexaploid formation (one in 233) was several orders of magnitude greater than estimates of genic mutation rates.

Chromosomal variation and genome size support existence of cryptic species of Triatoma dimidiata with different epidemiological importance as Chagas disease vectors

The wide geographical distribution of Triatoma dimidiata, one of the three major vectors of Chagas disease, ranges from Mexico to northern Peru. Since this species occupies a great diversity of artificial and natural ecotopes, its eradication is extremely difficult. In order to assist control efforts, we used chromosome analyses and DNA amount as taxonomic markers to study genetic variability in populations of T. dimidiata from Mexico, Guatemala, El Salvador and Colombia. We differentiated three groups or cytotypes defined by characteristic chromosome C-banding patterns and genome size measured by flow cytometry. The three cytotypes are restricted to different geographic locations. Cytotype 1 occurs in Mexico (excluding Yucatán), Guatemala (excluding Petén), El Salvador and Colombia. Cytotype 2 occurs in Yucatán and cytotype 3 occurs in Petén. Cytotype 1, commonly associated with domestic and peridomestic environments but also inhabiting sylvatic ecotopes, is the most widespread and with major epidemiological significance. In contrast, the Yucatán cytotype inhabits wild ecotopes but increasingly enters houses, while the Petén cytotype appears exclusively sylvatic. We suggest that these cytotypes represent cryptic species of T. dimidiata with different epidemiological relevance as Chagas disease vectors. Poor ability to colonize human dwellings, together with their restricted geographic distribution, indicate that the Yucatán and Petén putative species probably have much less epidemiological significance than cytotype 1. Thus, the genetic markers we describe are powerful tools to differentiate cryptic species in T. dimidiata with different epidemiological significance, contributing to planning the most effective control measures.

Cuticular hydrocarbon variability among Triatoma dimidiata (Hemiptera: Reduviidae) populations from Mexico and Guatemala

The geographic variation in the cuticular hydrocarbon pattern among 11 populations of Triatoma dimidiata Latreille (Hemiptera: Reduviidae: Triatominae) from different regions of Mexico and Guatemala, was studied using capillary gas chromatography. T. dimidiata populations were differentiated based on the relative amounts of 71 hydrocarbon components. Insect population classification was mostly in agreement with their geographical vicinity; Mexican populations from the Yucatan peninsula grouped together with those from northern Guatemala, insects from the Mexican Gulf coast states were closely related to those collected from northern Oaxaca, and to a lesser extent, to insects from Chiapas. Insects from southern Oaxaca were clustered together with those from southern Guatemala. All these populations were clearly separated from Guatemalan specimens collected in caves from Alta Verapaz.

The cost-effectiveness of a patient-sitter program in an acute care hospital: a test of the impact of sitters on the incidence of falls and patient satisfaction

This article analyzes the costs and benefits of a patient-sitter program in relation to patient falls and patient satisfaction. During these days of intense budgetary scrutiny, it is necessary to integrate methods of cost/benefit analysis into our loss prevention management programs, whether physical loss or loss patient base due to dissatisfied patients. This article presents the research we have conducted to analyze costs and benefits of our patient-sitter program in relation to patient falls and patient satisfaction.