Management objectives of Queensland fisheries: Putting the horse before the cart

A review of future management arrangements for the Queensland East Coast Trawl fishery was undertaken in 2010 to develop a management plan for the next 10 years. A key question raised at the start of the review process was: what should the management plan achieve? As with fisheries management in most countries, multiple management objectives were implicit in policy statements, but were poorly specified in some areas (particularly social objectives) and strongly identified in others (e.g., an objective of sustainability). As a start to the management review process, an analysis of what objectives the management system should aim to achieve was undertaken. A review of natural resource management objectives employed internationally was used to develop a candidate list, and the objectives most relevant to the fishery were short-listed by a scientific advisory group. Additional objectives specific to Queensland fisheries management, but not identified in the international review, were also identified and incorporated into the objective set. The relative importance of the different objectives to different stakeholder groups was assessed using the Analytic Hierarchy Process. As with other studies, the relative importance of the different objectives varied both within and between the different stakeholder groups, although general trends in preferences were observed

Online survey into the development of a model legal framework for a cannabis market in the United Kingdom

Background Despite rescheduling of cannabis to Schedule 2 and amendments to the law permitting legal availability of cannabis for the treatment of medical conditions, access to cannabis for medical use remains challenging for patients in the United Kingdom (UK). Recreational use is widespread despite laws stating users can be sentenced to prison for up to 5 years for possession. Objective The aim of the study was to develop a model for a legal cannabis market in the UK building upon the results of a preceding study in which a UK population sample determined that pharmacies are the most suitable primary legal vendor of cannabis as opposed to regulated shops or the black market. Methods An online survey was developed using Qualtrics software and advertised via the Multidisciplinary Association for Psychedelic Studies’ Facebook, Twitter and Instagram social media accounts and monthly newsletter. Results Three hundred and ninety seven individuals, a majority having used cannabis at least once, consented to participate in the study. The participants concluded that there is enough evidence for cannabis to be prescribed to treat a range of medical conditions. In addition to pharmacies providing cannabis to patients with a prescription, a majority of participants supported cannabis being sold in pharmacies for harm reduction purposes and allowing access to medicinal cannabis in cases where supporting evidence is insufficient to merit a prescription. Participants supported greater integration between dispensing pharmacies and mental health services. Overall, the participants did not oppose a consultation or screening for potential cannabis users prior to obtaining access from licensed vendors. UK participants were supportive of the concept of a cannabis card, which users can present to licensed vendors such as pharmacies, with specific recommendations (such as strains relevant to a patient’s medical condition) being coded into the card. A majority of participants supported the existence of shisha-type bars for the purchase and onsite consumption of cannabis and determined that such vendors should not be part of a pharmacy chain of stores or regulated by pharmacy regulators. The participants generally preferred that laws regarding public consumption are in line with existing smoking legislation. Participants determined that it should be legally permitted to grow cannabis at home for personal medical and non-medical purposes but not to sell for profit. Conclusion The results are suggestive of a regulatory system that medical and non-medical cannabis users can use which aims to maximise therapeutic applications, minimise harms and respect individual liberty

Bayesian identification of bacterial strains from sequencing data

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an environmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel pipeline for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence-based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at https://github.com/PROBIC/BIB.</p

Acute severe mitral regurgitation: consideration of papillary muscle architecture

We present a case of an individual who presented with acute severe mitral regurgitation in the setting of an inferior ST elevation myocardial infarction. Both transthoracic and transesophageal echocardiography demonstrated a posteriorly directed eccentric jet of severe mitral regurgitation with flail anterior mitral valve leaflet attached presumably to the anterior papillary muscle. Intraoperative findings demonstrated rupture of the postero-medial papillary muscle attached via chords to the anterior mitral valve leaflet. This case serves to remind us that both the anterior and posterior leaflets of the mitral valve are attached to both papillary muscle heads. The direction and eccentricity of the mitral regurgitant jet on echocardiography helps to locate the leaflet involved, but not necessarily the coexisting papillary muscle pathology

Bayesian identification of bacterial strains from sequencing data

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an environmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel pipeline for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence-based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at https://github.com/PROBIC/BIB.Peer reviewe

Quantifying bacterial evolution in the wild : A birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter colt (2.4 x 10(-6) s/s/y) and Campylobacter jejuni (3.4 x 10(-6) s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.Peer reviewe

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.Peer reviewe

Azetidines Kill Multidrug-Resistant <i>Mycobacterium tuberculosis</i> without Detectable Resistance by Blocking Mycolate Assembly

Tuberculosis (TB) is the leading cause of global morbidity and mortality resulting from infectious disease, with over 10.6 million new cases and 1.4 million deaths in 2021. This global emergency is exacerbated by the emergence of multidrug-resistant MDR-TB and extensively drug-resistant XDR-TB; therefore, new drugs and new drug targets are urgently required. From a whole cell phenotypic screen, a series of azetidines derivatives termed BGAz, which elicit potent bactericidal activity with MIC99 values &lt;10 μM against drug-sensitive Mycobacterium tuberculosis and MDR-TB, were identified. These compounds demonstrate no detectable drug resistance. The mode of action and target deconvolution studies suggest that these compounds inhibit mycobacterial growth by interfering with cell envelope biogenesis, specifically late-stage mycolic acid biosynthesis. Transcriptomic analysis demonstrates that the BGAz compounds tested display a mode of action distinct from the existing mycobacterial cell wall inhibitors. In addition, the compounds tested exhibit toxicological and PK/PD profiles that pave the way for their development as antitubercular chemotherapies. </p

Relative mobility determines the efficacy of MPAs in a two species mixed fishery with conflicting management objectives

Marine Protected Areas (MPAs) have been used to protect species in need of conservation and as a fisheries management tool. It has been suggested MPAs can benefit mobile stocks by protecting spawning grounds whilst also allowing yields to be maintained as mature fish move out of the protected areas. However, the robustness of this claim in mixed species fisheries has yet to be established. We use a simulation model to explore the efficacy of spatial closures and effort regulation when other forms of fishery control (e.g., Total Allowable Catches) are absent or non-enforced as ways of addressing management objectives that are difficult to reconcile due to the contrasting life-histories of a target and a bycatch, conservation species in a two-species fishery. The mobility of each stock in such a fishery affects the benefits conferred by an MPA. The differing management objectives of the two species can be partially met by effort regulations or closures when the species exhibit similar mobility. However, a more mobile conservation species prevents both sets of aims being met by either management tool. We use simulations to explore how spatial closures and effort regulation can be used to seek compromise between stakeholders when the mobility of one stock prevents conflicting management objectives to be fully met. Our results demonstrate that stock mobility is a key factor in considering whether an MPA can meet conflicting aims in a multispecies fishery compromised of stocks with differing life histories and mobilities

Association of Six Single Nucleotide Polymorphisms with Gestational Diabetes Mellitus in a Chinese Population

To investigate whether the candidate genes that confer susceptibility to type 2 diabetes mellitus are also correlated with gestational diabetes mellitus (GDM) in pregnant Chinese women.In this study, 1764 unrelated pregnant women were recruited, of which 725 women had GDM and 1039 served as controls. Six single nucleotide polymorphisms (rs7754840 in CDKAL1, rs391300 in SRR, rs2383208 in CDKN2A/2B, rs4402960 in IGF2BP2, rs10830963 in MTNR1B, rs4607517 in GCK) were genotyped using TaqMan allelic discrimination assays. The genotype and allele distributions of each SNP between the GDM cases and controls and the combined effects of alleles for the risk of developing GDM were analyzed. We found that the rs4402960, rs2383208 and rs391300 were statistically associated with GDM (OR = 1.207, 95%CI = 1.029-1.417, p = 0.021; OR = 1.242, 95%CI = 1.077-1.432, p = 0.003; OR = 1.202, 95%CI = 1.020-1.416, P = 0.028, respectively). In addition, the effect was greater under a recessive model in rs391300 (OR = 1.820, 95%CI = 1.226-2.701, p = 0.003). Meanwhile, the joint effect of these three loci indicated an additive effect of multiple alleles on the risk of developing GDM with an OR of 1.196 per allele (p = 1.08×10(-4)). We also found that the risk alleles of rs2383208 (b = -0.085, p = 0.003), rs4402960 (b = -0.057, p = 0.046) and rs10830963 (b = -0.096, p = 0.001) were associated with HOMA-B, while rs7754840 was associated with decrease in insulin AUC during a 100 g OGTT given at the time of GDM diagnosis (b = -0.080, p = 0.007).Several risk alleles of type 2 diabetes were associated with GDM in pregnant Chinese women. The effects of these SNPs on GDM might be through the impairment of beta cell function and these risk loci contributed additively to the disease