Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and proteobacteria autochthonous to commercial cucumber fermentation

We report 36 whole-genome sequences, along with annotations, of fermentative (n = 12) and spoilage associated (n = 6) lactic acid bacteria, Lysinibacillus (n = 3), Streptococcus (n = 1), and Proteobacteria (n = 14) isolated from commercial cucumber fermentations. Fifty-three percent of the genome sequence assemblies consist of 1-4 contigs, and the remainder have fewer than 16.

Observation of an exotic insulator to insulator transition upon electron doping the Mott insulator CeMnAsO

A promising route to discover exotic electronic states in correlated electron systems is to vary the hole or electron doping away from a Mott insulating state. Important examples include quantum criticality and high-temperature superconductivity in cuprates. Here, we report the surprising discovery of a quantum insulating state upon electron doping the Mott insulator CeMnAsO, which emerges below a distinct critical transition temperature, TII. The insulator-insulator transition is accompanied by a significant reduction in electron mobility as well as a colossal Seebeck effect and slow dynamics due to decoupling of the electrons from the lattice phonons. The origin of the transition is tentatively interpreted in terms of many-body localization, which has not been observed previously in a solid-state material.

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions

BACKGROUND

Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F₁ hybrids can be produced through artificial spawning. F₁ hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences.

RESULTS

We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as double crossovers, are extremely low among backcross progenies (progenies of channel catfish female × F₁ hybrid male), suggesting that the pericentric inversions interrupt postzygotic recombination or survival of recombinants. Identification of channel catfish- and blue catfish-specific genes, along with expansions of immunoglobulin genes and centromeric Xba elements, provides insights into genomic hallmarks of these species.

CONCLUSIONS

We generated high-quality reference genome sequences for both blue catfish and channel catfish and identified major chromosomal inversions on chromosomes 6, 11, and 24. These perimetric inversions were validated by additional sequencing analysis, genetic linkage mapping, and PCR analysis across the inversion junctions. The reference genome sequences, as well as the contrasted chromosomal architecture should provide guidance for the interspecific breeding programs.

Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture

Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.

A metagenomic-based study of two sites from the Barbadian reef system

We study the microbiome of sea water collected from two locations of the Barbadian coral reefs. The two sites differ in several environmental and ecological variables including their endogenous benthic community and their proximity to urban development and runoffs from inland watersheds. The composition of the microbial communities was estimated using whole genome DNA shotgun sequencing with adjuvant measurements of chemical and environmental qualities. Although both sites exhibit a similar degree of richness, the less urbanized site (Maycocks reef at Hangman's Bay) has a strong concentration of phototrophs whereas the more urbanized location (Bellairs reef at Folkstone) is enriched for copiotrophs, macroalgal symbionts and marine-related disease-bearing organisms from taxa scattered across the tree of life. Our results are concordant with previous profiles of warm ocean surface waters, suggesting our approach captures the state of each coral reef site, setting the stage for longitudinal studies of marine microbiome dynamics in Barbados.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00338-022-02330-y.

The Scottish Brain Health Service Model: Rationale and Scientific Basis for a National Care Pathway of Brain Health Services in Scotland

In order to address the oft-cited societal, economic, and health and social care impacts of neurodegenerative diseases, such as Alzheimer's disease, we must move decisively from reactive to proactive clinical practice and to embed evidence-based brain health education throughout society. Most disease processes can be at least partially prevented, slowed, or reversed. We have long neglected to intervene in neurodegenerative disease processes, largely due to a misconception that their predominant symptom - cognitive decline - is a normal, age-related process, but also due to a lack of multi-disciplinary collaboration. We now understand that there are modifiable risk factors for neurodegenerative diseases, that successful management of common comorbidities (such as diabetes and hypertension) can reduce the incidence of neurodegenerative disease, and that disease processes begin (and, crucially, can be detected, reduced, and delayed, prevented, or treated) decades earlier in life than had previously been appreciated. Brain Health Scotland, established by Scottish Government and working in partnership with Alzheimer Scotland, propose far-reaching public health and clinical practice approaches to reduce neurodegenerative disease incidence. Focusing here on Brain Health Scotland's clinical offerings, we present the Scottish Model for Brain Health Services. To our knowledge, the Scottish Model for Brain Health, built on foundations of personalised risk profiling, targeted risk reduction and prevention, early disease detection, equity of access, and harnessing comprehensive data to assist in clinical decision-making, marks the first example of a nationwide approach to overhauling clinical, societal, and political approaches to the prevention, assessment, and treatment of neurodegenerative disease.

Introduction to the complex intervention concept and the research perspectives

 

Few interventions are truly simple; complexity can arise from various sources, e.g.:

Aspects of the intervention itself, such as the number of intervention components, the number of groups targeted, how dynamic the intervention is permitted to be. The context in which the intervention is developed and delivered, such as the social, political, economic, and geographical context.

Complex intervention research should be approached with an awareness of these sources of complexity. Systems thinking can be helpful to understanding the dynamic interaction between interventions and their context. This presentation will introduce concepts of complex adaptive systems, e.g. feedback loops, adaptation, emergence, that should be considered when developing and evaluating complex interventions. It will then introduce participants to the research perspectives set out in the new framework: efficacy, effectiveness, theory-based, and systems perspectives. Each perspective is associated with a different type of research question, and therefore appropriate in different circumstances. The presentation will provide information to support participants to consider the research perspective(s) most suited to the research challenge that they are aiming to address.

Main messages

There are multiple sources of complexity, each of which can affect how the intervention works or contributes to change. Complex intervention research can take an efficacy, effectiveness, theory-based, or systems perspective, the choice of which is based on what is known already and what further evidence would be most useful.

The new Framework and the Core Elements of complex intervention research

 

The new framework will be presented. The main phases of intervention research: development or identification, feasibility, evaluation and implementation are connected to 6 core elements:

Context: any feature of the circumstances in which an intervention is conceived, developed, evaluated and implemented Programme theory: how an intervention is expected to lead to its effects and under what conditions. Programme theory should be tested and refined at all stages and used to guide the identification of uncertainties and research questions Stakeholders: those who are targeted by the intervention, involved in its development or delivery, or more broadly those whose personal or professional interests are affected, that is who have a stake in the topic. This includes patients, the public, and professionals Refinement: the process of ‘fine tuning' or making changes to the intervention once a preliminary version has been developed Uncertainties: identifying key uncertainties that exist given what is already known and what the programme theory, researchers and stakeholders identify as being most important to find out. These judgements inform the framing of research questions that, in turn, govern research perspective choice Economic considerations: exploring the comparative resource and outcome consequences of the interventions for those people and organisations affected

The presentation will discuss how to use the framework, highlighting that complex intervention research can be an iterative process. Repeating of phases is preferable to automatic progression to the next phase if uncertainties remain unresolved.

Main messages

Complex intervention research may begin at any phase, depending on what is appropriate for the intervention in question, and does not necessarily move sequentially through the phases. The core elements should be considered early and revisited continually throughout, as this will make it most likely that the intervention will be implementable in practice.

Genome-wide surveillance of transcription errors in response to genotoxic stress

Mutagenic compounds are a potent source of human disease. By inducing genetic instability, they can accelerate the evolution of human cancers or lead to the development of genetically inherited diseases. Here, we show that in addition to genetic mutations, mutagens are also a powerful source of transcription errors. These errors arise in dividing and nondividing cells alike, affect every class of transcripts inside cells, and, in certain cases, greatly exceed the number of mutations that arise in the genome. In addition, we reveal the kinetics of transcription errors in response to mutagen exposure and find that DNA repair is required to mitigate transcriptional mutagenesis after exposure. Together, these observations have far-reaching consequences for our understanding of mutagenesis in human aging and disease, and suggest that the impact of DNA damage on human physiology has been greatly underestimated.

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N⁶-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.

Sequencing and genomic diversification of five allopolyploid cotton species provide insights into polyploid genome evolution and epigenetic landscapes for cotton improvement.

Mastery is associated with greater physical and mental health-related quality of life in two international cohorts of people with multiple sclerosis

BACKGROUND

Mastery is the sense of being in control of one's life and improvement in mastery may help to enhance quality of life. Little research has explored mastery in people with multiple sclerosis (MS), including its association with quality of life.

OBJECTIVE

To explore the association between mastery and health-related quality of life (HRQOL) in people with MS.

METHOD

Two cross-sectional cohorts of adults with MS (n = 1401 and n = 573), recruited through convenience sampling, completed an online survey which measured mastery using the Pearlin Mastery Scale, physical and mental HRQOL via physical and mental health composite scores of MSQOL-54, along with other covariates, including demographics, clinical characteristics and lifestyle factors. Linear regression assessed associations between mastery and physical HRQOL adjusting for age, sex, education, disability and depression, and between mastery and mental HRQOL adjusting for age, sex, education, disability and clinically significant fatigue.

RESULTS

Greater mastery score was associated with higher physical and mental HRQOL in both cohorts, such that a one-point increase in the PMS was associated with an increase of 2.9 (95% Confidence Interval (CI): 2.6, 3.1) and 2.8 points (95% CI: 2.4, 3.2) in the means of physical HRQOL score in the first and second cohorts respectively, and a 2.9-point (95% CI: 2.7, 3.1) and 3.1-point (95% CI: 2.7, 3.4) increase in the means of mental HRQOL score. A dose-dependent relationship was demonstrated between a quartile categorical mastery variable and both physical and mental HRQOL in both cohorts. Mastery was associated with all subscores of both physical and mental HRQOL.

CONCLUSIONS

Greater mastery is associated with better physical and mental quality of life. Efforts to improve the sense of self control and agency of people with MS may have benefits for their quality of life, even despite clinical features of the illness.

Severe Dehydration and Acute Renal Failure Associated with External Ventricular Drainage of Cerebrospinal Fluid in Children

We report three paediatric cases of severe dehydration and hyponatraemia with circulatory compromise associated with the use of external ventricular drainage of cerebrospinal fluid. Two of the children had cardiac arrests. All were successfully resuscitated. While there were additional factors that contributed to other fluid losses, and fluid balance data are incomplete, these cases highlight a need for increased vigilance when managing children with external ventricular drains.

Patient-reported outcomes are worse for progressive-onset multiple sclerosis than relapse-onset multiple sclerosis, particularly early in the disease process

BACKGROUND AND PURPOSE

Treatments for progressive-onset multiple sclerosis (MS) are lacking. To improve the disease management for progressive-onset MS, the differences between relapse-onset MS and progressive-onset MS in patient-reported disability, progression and symptoms were examined.

METHODS

A total of 1985 participants of the Australian Multiple Sclerosis Longitudinal Study were included. Associations between onset type and outcomes were assessed with negative binomial regression.

RESULTS

The severity of 17 of the 19 outcomes was significantly higher for progressive-onset MS patients than relapse-onset MS patients, including perspectives from disability, progression over the last year, fatigue, sensory, walking difficulties, pain, balance, spasticity, sexual dysfunction, bladder, bowel, anxiety, depression and the European quality of life (EQ-5D) (P < 0.05; adjusted mean ratio ranged from 1.11 to 1.52). The differences between the two onset types were most pronounced early in the disease process and reduced with increasing MS duration, and the interaction was significant for disability, progression over the last year, walking difficulties, bladder problems, bowel problems and spasticity.

CONCLUSION

Participants with progressive-onset MS were significantly worse off on nearly all patient-reported outcomes than relapse-onset MS participants, and the differences were most pronounced early in the disease course, highlighting the importance of early intervention for those with progressive-onset MS.

Self-reported cognitive function in a large international cohort of people with multiple sclerosis: associations with lifestyle and other factors

Background and purpose

We aimed to estimate the prevalence of perceived cognitive impairment (PCI) and explore its associations with lifestyle and disease characteristics in a large international cohort of people with multiple sclerosis (MS).

Methods

This study was a cross‐sectional analysis. Participants rated their cognitive function over the preceding 4 weeks using four questions in a subscale within the Multiple Sclerosis Quality of Life questionnaire (MSQOL‐54). These questions assessed perceived concentration, attention and memory by the patient and family/friends. Four definitions of PCI were derived, ranging from lowest to highest specificity. Associations with PCI were assessed by log‐binomial regression.

Results

The prevalence of PCI in our sample ranged from 41.0% (95% confidence interval, 39.0–43.0) using the least‐specific definition to 11.6% (95% confidence interval, 10.3–12.9) using the most specific definition. A number of factors were associated with PCI, increasing in magnitude as the definition specificity increased, including positive associations for smoking and body mass index, whereas physical activity, dietary quality and use of vitamin D/omega‐3 supplements were inversely associated with PCI.

Conclusions

Our study reports associations between healthy lifestyle behaviours and PCI in people with MS. Although reverse causality is a potential explanation for our findings, previous studies have shown comparable associations with healthy lifestyle and MS onset and progression. Subject to external validation, these results suggest benefits realized from a healthy lifestyle in people with MS.

Should old age psychiatry develop memory clinics? A comparison with domiciliary work

Aims and Method

Memory clinics have become very popular in old age psychiatry and there is some pressure for them to be developed in old age services. However, there is little evidence to suggest that they are more advantageous over the traditional domiciliary visits or who should be seen in clinic. This was a naturalistic comparison of 76 consecutive new referrals to a memory clinic, with 74 consecutive new domiciliary requests within the same service over the same period of time. A retrospective case note review collected the clinical features and an 18-month prospective follow-up examined the subsequent clinical management.

Clinical Implications

The two groups were characterised more by their similarities than their differences. However, the domiciliary group had greater behavioural and psychological complications. The memory clinic patients were less likely to receive psychotropic medication and here more likely to be followed up.

Results

We conclude that memory clinics might be less suitable for patients with prominent psychiatric complications. Memory clinics could complement the domiciliary model by providing early psychosocial/neuropsychiatric approaches, although this is likely to lead to an increased clinical case-load.

Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historical cultivation

PREMISE OF THE STUDY

Qat (Catha edulis, Celastraceae) is a woody plant species cultivated for its stimulant alkaloids. Qat is important to the economy and culture in large regions of Ethiopia, Kenya, and Yemen. Despite the importance of this species, the wild origins and dispersal of cultivars have only been described in often contradictory historical documents. We examined the wild origins, human-mediated dispersal, and genetic divergence of cultivated qat compared to wild qat.

METHODS

We sampled 17 SSR markers and 1561 wild and cultivated individuals across the historical areas of qat cultivation.

KEY RESULTS

On the basis of genetic structure inferred using Bayesian and nonparametric methods, two centers of origin in Kenya and one in Ethiopia were found for cultivated qat. The centers of origin in Ethiopia and northeast of Mt. Kenya are the primary sources of cultivated qat genotypes. Qat cultivated in Yemen is derived from Ethiopian genotypes rather than Yemeni wild populations. Cultivated qat with a wild Kenyan origin has not spread to Ethiopia or Yemen, whereas a small minority of qat cultivated in Kenya originated in Ethiopia. Hybrid genotypes with both Ethiopian and Kenyan parentage are present in northern Kenya.

CONCLUSIONS

Ethiopian cultivars have diverged from their wild relatives, whereas Kenyan qat has diverged less. This pattern of divergence could be caused by the extinction of the wild-source qat populations in Ethiopia due to deforestation, undersampling, and/or artificial selection for agronomically important traits.

Anxiety, depression and fatigue at 5-year review following CNS demyelination

BACKGROUND

Anxiety and depression are common in multiple sclerosis (MS). We evaluated the prevalence and factors associated with anxiety, depression and fatigue at the 5-year review of a longitudinal cohort study following a first clinical diagnosis of CNS demyelination (FCD).

METHODS

Cases with a FCD were recruited soon after diagnosis and followed annually thereafter. A variety of environmental, behavioural and clinical covariates were measured at five-year review. Anxiety and depression were measured using the Hospital Anxiety & Depression Scale (HADS), and fatigue by the Fatigue Severity Scale (FSS).

RESULTS

Of the 236 cases, 40.2% had clinical anxiety (median HADS-A: 6.0), 16.0% had clinical depression (median HADS-D: 3.0), and 41.3% had clinical fatigue (median FSS: 4.56). The co-occurrence of all three symptoms was 3.76 times greater than expectation. Younger age, higher disability, concussion or other disease diagnosis were independently associated with a higher anxiety score; male sex, higher disability, being unemployed, less physical activity, and antidepressant and/or anxiolytic-sedative medication use were independently associated with a higher depression score. Higher disability, immunomodulatory medication use, other disease diagnosis and anxiolytic-sedative medication use were independently associated with having fatigue, while female sex, higher BMI, having had a concussion, being unemployed and higher disability were associated with a higher fatigue score.

CONCLUSION

These results support previous findings of the commonality of anxiety, depression and fatigue in established MS and extend this to post-FCD and early MS cases. The clustering of the three symptoms indicates that they may share common antecedents.

Admission blood glucose predicts mortality and length of stay in patients admitted through the emergency department

BACKGROUND

Hyperglycaemia has been associated with adverse outcomes in several different hospital populations.

AIM

The aim of this study was to investigate the relationship between admission blood glucose level (BGL) and outcomes in all patients admitted through the emergency department.

METHODS

This study was a retrospective observational cohort study from an Australian tertiary referral hospital. Patients admitted in the first week of each month from April to October 2012 had demographic data, co-morbidities, BGL, intensive care unit admission, length of stay and dates of death recorded. Factors associated with outcomes were assessed by multi-level mixed-effects linear regression.

RESULTS

Admission BGL was recorded for 601 admissions with no diagnosis of diabetes and for 219 admissions diagnosed with type 2 diabetes (T2DM). In patients with no diagnosis of diabetes, admission BGL was associated with in-hospital and 90-day mortality (P < 0.001). After multivariate analysis, BGL greater than 11.5 mmol/L was significantly associated with increased mortality at 90 days (P < 0.05). In patients with T2DM increased BGL on admission was not associated with in-hospital or 90-day mortality but was associated with length of hospital stay (β: 0.22 days/mmol/L; 95% confidence interval 0.09-0.35; P < 0.001), although this association was lost on multivariable analysis. In patients with T2DM, increased coefficient of variation of BGL was also positively associated with length of hospital stay in an almost dose-dependent fashion (P < 0.001).

CONCLUSION

Admission BGL was independently associated with increased mortality in patients with no diagnosis of diabetes. Glycaemic variability was associated with increased length of hospital stay in patients with T2DM.

A protocol for management of blood loss in surgical treatment of peritoneal malignancy by cytoreductive surgery and hyperthermic intraperitoneal chemotherapy

BACKGROUND AND AIMS

The treatment of peritoneal malignancies with cytoreductive surgery (CRS) combined with hyperthermic intraperitoneal chemotherapy (HIPEC) has been shown to be associated with massive surgical blood loss. Maintaining high fibrinogen levels throughout surgery may reduce blood loss in these patients. The primary aim of the study was to see if Tranexamic Acid (TXA) and cryoprecipitate reduced surgical blood loss and hence red cell transfusions. A comparison was made with a cohort of patients treated with fresh frozen plasma (FFP) alone. The secondary aim was to measure the effect of both protocols on coagulation parameters and the incidence of arterial or venous thrombosis.

METHOD

We used prospectively collected data from 201 patients who had complete CRS with HIPEC for peritoneal malignancy using different protocols during two discrete 12-month time periods.

RESULTS

The new transfusion protocol led to a higher average fibrinogen level intra-operatively and post-operatively, with a significant reduction in average RBC, FFP and platelet transfusion intra-operatively per patient from 4·2 to 1·8 units, 6·2 to 0·2 units and 0·1 to 0 units, respectively. No significant difference in PT or APTT was seen between patients treated with the standard and new protocols. Venous thrombosis occurred in seven patients treated with the standard protocol and five with the new protocol. A single case of arterial thrombosis was seen in both groups.

CONCLUSION

Patients treated with upfront TXA and cryoprecipitate during CRS required less RBC transfusion than those treated with the standard protocol of early FFP.

27 AN IMPROVED LARGE ANIMAL MODEL FOR THE STUDY OF ADULT STEM CELLS

Murine models for the study of adult stem cell populations have broadened the understanding of previously uncharacterized stem cell niches. The development of murine reporter lines for the leucine-rich repeat-containing G-protein-coupled receptor-5 (Lgr5) has highlighted the importance of this gene as a stem cell marker in the stomach, intestine, hair follicle, liver, and kidney in mice. These models however have significant limitations in terms of translational applications because of anatomical and physiological differences between humans and mice. In order to overcome these limitations, we have sought to develop a porcine LGR5 reporter line. We report the generation of a porcine stem cell reporter line using the combination of transcription activator-like effector nucleases and somatic cell NT. Transcription activator-like effector nuclease-mediated homologous recombination was used to drive the integration of an internal ribosome entry site green fluorescent protein fusion into the 3′ untranslated region of the LGR5 locus in porcine fetal fibroblast cells. Multiple cell lines were developed and screened for the proper integration event. Upon confirmation of proper integration by genomic DNA sequencing, these lines were used as donors for somatic cell NT. Transfer of the somatic cell NT reconstructed embryos to a surrogate gilt resulted in 3 live births, and the establishment of a founder line of LGR5-green fluorescent protein reporter pigs. We have begun to characterise these lines, having observed fluorescent labelling of putative stem cell populations in the intestinal crypts and hair follicles from these animals. Many of these observations parallel the expression patterns observed in similar murine models. We have confirmed the fluorescent reporter signal by immunohistochemistry using an anti-green fluorescent protein antibody, and are working towards colocalization studies using anti-LGR5 antibodies and RNA in situ hybridization, as well as the characterisation of additional stem cell populations in the pig. The development of this line of transgenic pigs represents significant progress toward the study of adult stem cells, their progenitors, and the stem cell niche, using a large animal model with an anatomy, physiology, and ability to recapitulate human disease that overcomes the current limitations of rodent models. Funding was provided by NIH R21OD019738.

1 GENERATION OF A STABLE TRANSGENIC SWINE MODEL FOR CELL TRACKING AND CHROMOSOME DYNAMIC STUDIES

Transgenic pigs are an attractive research model in the field of translational research, regenerative medicine, and stem cell therapy due to their anatomic, genetic, and physiological similarities with humans. The development of a transgenic murine model with a fusion of green fluorescent protein (GFP) to histone 2B protein (H2B, protein of nucleosome core) resulted in an easier and more convenient method for tracking cell migration and engraftment levels after transplantation as well as a way to better understand the complexity of molecular regulation within cell cycle/division, cancer biology, and chromosome dynamics. Up to now the development of a stable transgenic large animal model expressing H2B-GFP has not been described. Our objective was to develop the first transgenic porcine H2B-GFP model via CRISPR-CAS9 mediated recombination and somatic cell nuclear transfer (SCNT). Porcine fetal fibroblasts were cotransfected with CRISPR-CAS9 designed to target the 3′ untranslated region of ACTB locus and a targeting vector containing 1Kb homology arms to ACTB flanking an IRES-H2B-GFP transgene. Four days after transfection GFP cells were fluorescence activated cell sorted. Single cell colonies were generated and analysed by PCR, and heterozygous colonies were used as donor cells for SCNT. The custom designed CRISPR-CAS9 knockin system demonstrated a 2.4% knockin efficiency. From positive cells, 119 SCNT embryos were generated and transferred to a recipient gilt resulting in three positive founder boars (P1 generation). Boars show normal fertility (pregnancies obtained via AI of wild type sows). Generated P1 clones were viable and fertile with a transgene transmission rate of 55.8% (in concordance with Mendel’s law upon chi-square test with P = 0.05). Intranuclear H2B-GFP expression was confirmed via fluorescence microscopy on 8-day in vitro cultured SCNT blastocysts and a variety of tissues (heart, kidney, brain, bladder, skeletal muscle, stomach, skin, and so on) and primary cultured cells (chondrocytes, bone marrow derived, adipocyte derived, neural stem cells, and so on) from P1 cloned boars and F1 42-day fetuses and viable piglets. In addition, chromosome segregation could be easily identified during cell cycle division in in vitro cultured stem cells. Custom designed CRISPR-CAS 9 are able to drive homologous recombination in the ACTB locus in porcine fetal fibroblasts, allowing the generation of the first described viable H2B-GFP porcine model via SCNT. Generated clones and F1 generation expressed H2B-GFP ubiquitously, and transgene transmission rates were with concordance of Mendel’s law. This novel large animal model represents an improved platform for regenerative medicine and chromosome dynamic and cancer biology studies.

The epidemiology of multiple sclerosis in the Isle of Man: 2006-2011

BACKGROUND

We sought to determine the prevalence of MS on the Isle of Man in 2006 and 2011, and the incidence and mortality rates over this interval.

METHODS

Cases were identified by hospital medical record review, General Practitioners and the local MS Society. The significance of the change in prevalence over time and the significance of differences in frequencies by sex and place of birth were assessed by Poisson regression.

RESULTS

The 2006 prevalence was 153.64 per 100,000 persons and the 2011 prevalence was 179.89. The prevalence was higher among females and persons born in the Isle of Man at both time points. The 2006-2011 incidence rate was 6.86 per 100,000 person-years, much higher among females and persons born in the Isle of Man. The prevalence sex ratios in 2006 and 2011, 2.77 and 2.59, respectively, and the incidence sex ratio, 2.19, are similar to others found in the region. The mortality rate over the study period was 2.84 per 100,000 person-years, this solely among persons born overseas.

CONCLUSIONS

This is the first study of MS epidemiology in the Isle of Man, finding this area to be of high prevalence and to have one of the highest incidence rates in the UK region.

Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

PREMISE OF THE STUDY

Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners.

METHODS AND RESULTS

Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy.

CONCLUSIONS

These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit.

Modulating effects of WT1 on interferon-β-vitamin D association in MS

OBJECTIVE

To investigate whether those genes involved in the vitamin D pathway modulate the relationship between 25-hydroxyvitamin D (25(OH)D) and IFN-β, the relationship between IFN-β and sun in predicting 25(OH)D, and the interaction between IFN-β and 25(OH)D in modulating relapse risk in patients with MS.

METHODS

Prospective cohort study of 169 participants with MS and genotype data followed 2002-2005. Gene-IFN-β and gene-IFN-β-sun interactions predicting 25(OH)D evaluated by multilevel mixed-effects linear regression. Gene-IFN-β interactions with 25(OH)D in modulating in relapse risk assessed using survival analysis.

RESULTS

The cohort was 71.6% female and of mean age 47.8. Two-independent intronic genotyped SNPs (rs10767935 and rs5030244) in WT1 significantly modified the IFN-β-25(OH)D association after adjustment (P(interaction) = 0.001, 0.0002; P(adj) = 0.003, 0.006, respectively). There was a marked difference in the interaction between self-reported sun exposure and IFN-β in predicting 25(OH)D by level of rs10767935, although this did not reach statistical significance. No SNPs modified the interaction between IFN-β and 25(OH)D in predicting relapse.

CONCLUSIONS

We have demonstrated that two-independent SNPs (rs10767935 and rs5030244) in WT1 modified the IFN-β-25(OH)D association in patients with MS. Some evidence was shown for a difference in the sun-IFN-β-25(OH)D association by level of rs10767935. These findings indicate that WT1 variants may play a role in altering the effects of IFN-β on vitamin D in MS.

Lung function in African infants: a pilot study

BACKGROUND

The burden of childhood respiratory illness is large in low and middle income countries (LMICs). Infant lung function (ILF) testing may provide useful information about lung growth and susceptibility to respiratory disease. However, ILF has not been widely available in LMICs settings where the greatest burden of childhood respiratory disease occurs.

AIM

To implement and evaluate a pilot study of ILF testing in a semi-rural setting in South Africa.

METHOD

Infant lung function testing was established at a community hospital in South Africa. All measures were done in unsedated infants during sleep. Measurements, made with the infant quietly breathing through a face mask and bacterial filter, included tidal breathing (TBFVL), exhaled nitric oxide (eNO), and sulphur hexafluoride multiple breath washout (MBW) measures using an ultrasonic flow meter and chemoluminescent NO analyzer.

RESULTS

Twenty infants, mean age of 7.7 (SD 2.9) weeks were tested; 8 (40%) were Black African and 12 (60%) were mixed race. Five (25%) infants were preterm. There were 19 (95%) successful TBFVL and NO tests and 18 (90%) successful MBW tests. The mean tidal volume was 30.5 ml (SD 5.9), respiratory rate 50.2 breaths per minute (SD 8.7), and eNO 10.4 ppb (SD 7.3). The mean MBW measures were: functional residual capacity 71 ml (SD 13) and the lung clearance index 7.6 (SD 0.5). The intra-subject coefficient of variations (CV) of lung function measures were similar to published normative data for Caucasian European infants.

CONCLUSION

In this study we demonstrate that unsedated infant lung function measures of tidal breathing, MBW, and eNO are feasible in a semi-rural African setting with rates comparable to those reported from high income countries.

EBV & HHV6 reactivation is infrequent and not associated with MS clinical course

BACKGROUND

Among the environmental factors associated with multiple sclerosis (MS) causation, some of the strongest associations are with Epstein-Barr virus (EBV), and to a lesser extent human herpesvirus 6 (HHV6). Associations with clinical course are less conclusive, however.

METHODS

We evaluated serum anti-EBV-EA-R IgG and anti-HHV6 IgM, and EBV and HHV6 viral load (VL) for their associations with relapse, disability, and progression in disability in a prospective cohort of 198 participants with clinically definite MS.

RESULTS

Anti-EBV-EA-R IgG was detected in 81.8% of cases at study entry, and titers remained essentially unchanged during the study. Anti-HHV6 IgM was detected in only one participant, and EBV-VL (29%) and HHV6-VL (1.8%) were detected in a minority of samples, and where detected levels were low. Our previously demonstrated association between anti-HHV6 IgG and relapse hazard was not affected by adjustment for parameters of reactivation. We found no evidence that any of the viral markers were associated with disability or progression in disability. In relation to relapse, only EBV-VL was positively associated, although this was strongly influenced by a single individual.

CONCLUSION

Using a prospective cohort design, we found no convincing evidence that reactivation parameters of EBV or HHV6 were associated with subsequent MS relapse hazard or progression in disability, confirming previous findings, and indicating that herpesvirus reactivation is not an important driver of relapse or disability in this established MS population.

Higher levels of reported sun exposure, and not vitamin D status, are associated with less depressive symptoms and fatigue in multiple sclerosis

OBJECTIVE

Insufficient sun exposure and vitamin D deficiency have both been associated with increased risk of multiple sclerosis (MS). Depressi on, anxiety, fatigue and cognitive impairment are prevalent and disabling symptoms in MS. Our objective was to examine the associations between personal sun exposure and serum 25-hydroxyvitamin D (25(OH)D), and depression, anxiety, fatigue and cognition.

METHODS

A total of 198 participants with multiple sclerosis were followed prospectively for an average of 2.3 years. Assessments of serum 25(OH)D, sun exposure, depression, anxiety and fatigue were carried out biannually; cognition was assessed annually.

RESULTS

Personal reported sun exposure was inversely associated with depression scores (β -0.26 (95%CI -0.40, -0.12);P ≤ 0.001) and fatigue scores (β -0.65 (95%CI -1.23, -0.07); P = 0.028). Only high levels of 25(OH)D (>80 nm) were inversely associated depression scores (β -0.64 (95%CI -1.15, -0.13); P = 0.015), but this was not significant after adjustment for reported sun exposure. No associations were seen between reported sun exposure or serum 25(OH)D levels and anxiety or cognition scores.

CONCLUSION

We found that higher levels reported sun exposure, rather than 25(OH)D levels, were associated with less depressive symptoms and levels of fatigue. The role of UV or light therapy will need to be evaluated in randomized controlled trials to confirm an effect on these symptoms in MS.

5 DISRUPTION OF THE HIGH MOBILITY GROUP AT-HOOK 2 (HMGA2) GENE IN SWINE REDUCES POSTNATAL GROWTH

The high mobility group AT-hook 2 (HMGA2) protein has been shown to be a crucial gene for cell growth, proliferation, and apoptosis; HMGA2 is also a strong biological candidate for growth, because mutations in this gene alter body size in mice and humans. Compared with wild-type controls, adult mice lacking HMGA2 are 60% smaller, and adult heterozygous mutants are 20% smaller. In humans, HMGA2 has been associated with adult and childhood height without any other deleterious effect. Additionally, a microdeletion in the HMGA2 gene in a human patient resulted in short stature, with no dysmorphologies and normal puberty. In order to determine the effect of HMGA2 on fetal and adult growth in pigs, a transgenic pig line deficient in HMGA2 expression was generated by gene targeting in fetal fibroblasts (FF). Using a targeting vector carrying a reporter gene, and homology arms specific to HMGA2, heterozygous mutant cell lines were generated. The cell lines were then used to generate 6 heterozygous females by somatic cell nuclear transfer (SCNT). Bodyweights and lengths from snout to base of tail were measured every 2 weeks for a year for mutant (n = 6) and wild-type farm gilts (n = 6). Data were analysed by one-way ANOVA. As in mice, disruption of one allele of the HMGA2 gene resulted in 25% reduction in weight (P < 0.0001) and 14% reduction in length (P < 0.0001). Early in postnatal growth (2 months), weights of mutants were not different than wild-type. However, mutants were 20 to 35% lighter (P < 0.05) during mid stages (6 months) and 25 to 30% (P < 0.0001) in late stages (3 months). The same insertional mutation generated 8 heterozygous male clones by SCNT. In addition, 7 nontransgenic males from the same FF line were generated as SCNT controls. Bodyweights and lengths were measured every 2 weeks for 30 weeks for HMGA2 heterozygous mutants (n = 8), control SCNT (n = 7) and wild-type farm boars (n = 5). The weight curve of boars showed similar pattern as for mutant gilts. At 30-week postnatal stage, mutants were 17% (P < 0.05) and 16% (P < 0.05) lighter in weight compared with littermate and wild-type animals, respectively. We are presently developing homozygous HMGA2 mutant lines. Currently, 3 of 6 heterozygous gilts have been bred with heterozygous boars, with 1 confirmed pregnancy. The expectation is that the homozygous animals will, like mice, be 60% smaller than the wild-type animals. The approach described here will result not only in a valuable large-animal model of dwarfism, but also in a tool to reduce the size of existing transgenic and nontransgenic swine lines. This, in turn, will increase the receptivity of valuable transgenic lines by the biomedical community. Funding for this work was provided by NIH grant R21-OD010553 to JP.

Kagome-like lattice of π–π stacked 3-hydroxyphenalenone on Cu(111)

Three-dimensional arrangement of 3-HPLN on a 2D surface, involving π–π stacking and perpendicular molecule attachment, results in a Kagome lattice.

Meta-analyses to investigate gene-environment interactions in neuroepidemiology

BACKGROUND

Most chronic neurological diseases are caused by a combination of multiple genetic and environmental factors. Increasingly, gene-environment interactions (GxE) are being examined, providing opportunities to combine studies systematically using meta-analysis.

METHODS

Systematic review of the literature on how to examine GxE using observational study designs, and how to conduct a meta-analysis of studies on GxE.

RESULTS

Most methods and challenges related to a standard meta-analysis apply to a GxE meta-analysis. There are, however, some substantive differences. With GxE, there is the capability of using a case-only design. Research on GxE interactions may be more prone to publication bias, since interactions are usually not the primary hypothesis and only 'exciting' significant GxE findings are reported out of a range of secondary analyses. In disease aetiology research, there has been debate whether to measure interaction on a multiplicative or additive scale. There are some significant challenges associated with measuring interaction on an additive scale, and thus the uptake of the measures of additive interaction has been limited. As a result, the methods of analysing interaction have been less consistent and reporting has been highly variable. We suggest using the STROBE/STREGA reporting guidelines to allow evaluation of interaction on both scales.

CONCLUSIONS

We identified a number of differences of a GxE meta-analysis over a standard meta-analysis. Awareness of these issues is important. Using established reporting guidelines for GxE studies is recommended. The development of consortia for neurological disorders that include both genetic and environmental data might offer benefits for GxE meta-analyses in the future.

White matter microstructural abnormality in children with hydrocephalus detected by probabilistic diffusion tractography

BACKGROUND AND PURPOSE

Hydrocephalus is a severe pathologic condition in which WM damage is a major factor associated with poor outcomes. The goal of the study was to investigate tract-based WM connectivity and DTI measurements in children with hydrocephalus by using the probabilistic diffusion tractography method.

MATERIALS AND METHODS

Twelve children with hydrocephalus and 16 age-matched controls were included in the study. Probabilistic diffusion tractography was conducted to generate tract-based connectivity distribution and DTI measures for the genu of the corpus callosum and the connectivity index. Tract-based summary measurements, including the connectivity index and DTI measures (fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity), were calculated and compared between the 2 study groups.

RESULTS

Tract-based summary measurement showed a higher percentage of voxels with lower normalized connectivity index values in the WM tracts in children with hydrocephalus. In the genu of the corpus callosum, the left midsegment of the corticospinal tract, and the right midsegment of the corticospinal tract, the normalized connectivity index value in children with hydrocephalus was found to be significantly lower (P < .05, corrected). The tract-based DTI measures showed that the children with hydrocephalus had significantly higher mean diffusivity, axial diffusivity, and radial diffusivity in the genu of the corpus callosum, left midsegment of the corticospinal tract, and right midsegment of corticospinal tract and lower fractional anisotropy in the genu of the corpus callosum (P < .05, corrected).

CONCLUSIONS

The analysis of WM connectivity showed that the probabilistic diffusion tractography method is a sensitive tool to detect the decreased continuity in WM tracts that are under the direct influence of mechanical distortion and increased intracranial pressure in hydrocephalus. This voxel-based connectivity method can provide quantitative information complementary to the standard DTI summary measures.

Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species

PREMISE OF THE STUDY

Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. •

METHODS AND RESULTS

A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. •

CONCLUSIONS

These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

Comparative safety and effectiveness of sitagliptin in patients with type 2 diabetes: retrospective population based cohort study

OBJECTIVE

To determine if the use of sitagliptin in newly treated patients with type 2 diabetes is associated with any changes in clinical outcomes.

DESIGN

Retrospective population based cohort study.

SETTING

Large national commercially insured US claims and integrated laboratory database.

PARTICIPANTS

Inception cohort of new users of oral antidiabetic drugs between 2004 and 2009 followed until death, termination of medical insurance, or December 31 2010.

MAIN OUTCOME MEASURE

Composite endpoint of all cause hospital admission and all cause mortality, assessed with time varying Cox proportional hazards regression after adjustment for demographics, clinical and laboratory data, pharmacy claims data, healthcare use, and time varying propensity scores.

RESULTS

The cohort included 72,738 new users of oral antidiabetic drugs (8032 (11%) used sitagliptin; 7293 (91%) were taking it in combination with other agents) followed for a total of 182,409 patient years. The mean age was 52 (SD 9) years, 54% (39,573) were men, 11% (8111) had ischemic heart disease, and 9% (6378) had diabetes related complications at the time their first antidiabetic drug was prescribed. 14,215 (20%) patients met the combined endpoint. Sitagliptin users showed similar rates of all cause hospital admission or mortality to patients not using sitagliptin (adjusted hazard ratio 0.98, 95% confidence interval 0.91 to 1.06), including patients with a history of ischemic heart disease (adjusted hazard ratio 1.10, 0.94 to 1.28) and those with estimated glomerular filtration rate below 60 mL/min (1.11, 0.88 to 1.41).

CONCLUSIONS

Sitagliptin use was not associated with an excess risk of all cause hospital admission or death compared with other glucose lowering agents among newly treated patients with type 2 diabetes. Most patients prescribed sitagliptin in this cohort were concordant with clinical practice guidelines, in that it was used as add-on treatment.

Diffusion tensor imaging properties and neurobehavioral outcomes in children with hydrocephalus

BACKGROUND AND PURPOSE

White matter structural alterations and the correlation with neuropsychological deficits in children with hydrocephalus have not been well investigated. In this prospective study, the objectives were the following: 1) to apply DTI to detect in vivo white matter alterations based on diffusion properties in children with acute hydrocephalus, 2) to quantify early neuropsychological deficits, and 3) to explore the correlation between potential neuropsychological deficits and abnormalities in functionally related white matter.

MATERIALS AND METHODS

A total of 44 children, 24 with hydrocephalus and 20 controls, were enrolled in the study. DTI indices, FA, MD, AD, and RD, were evaluated in the gCC, sCC, PLIC, and ALIC. The ABAS-II was used as a broad screener of development, including conceptual, social, practical, and motor skills. The correlation between the Motor Scale and DTI indices in the PLIC was analyzed.

RESULTS

DTI analyses showed that the gCC and sCC in children with hydrocephalus had lower FA and higher MD, driven by the increased RD with statistical significance (P < .05) or trend-level significance (P = .06). The PLIC and ALIC had significantly higher AD in children with hydrocephalus (P < .05). On the ABAS-II, parent ratings of general adaptive skills, conceptual skills, and motor skills were significantly lower in children with hydrocephalus (all at P < .05). The MD and RD values in the PLIC were found to have trend-level or significant correlation with the Motor Scale (P = .057, .041, respectively).

CONCLUSIONS

DTI reveals alterations in the white matter structure in children with hydrocephalus with preliminary findings suggesting correlation with clinical motor deficits.

Exploring child maltreatment and its relationship to alcohol and cannabis use in selected Latin American and Caribbean countries

OBJECTIVES

Research from developed countries shows that child maltreatment increases the risk for substance use and problems. However, little evidence on this relationship is available from developing countries, and recognition of this relationship may have important implications for substance demand reduction strategies, including efforts to prevent and treat substance use and related problems. Latin America and the Caribbean is a rich and diverse region of the world with a large range of social and cultural influences. A working group constituted by the Inter-American Drug Abuse Control Commission and the Center for Addiction and Mental Health in June, 2010 identified research on this relationship as a priority area for a multinational research partnership.

METHODS

This paper examines the association between self-reported child maltreatment and use in the past 12 months of alcohol and cannabis in 2294 university students in seven participating universities in six participating countries: Colombia, El Salvador, Jamaica, Nicaragua, Panama and Uruguay. The research also considers the possible impact of religiosity and minimal psychological distress as factors contributing to resiliency in these samples.

RESULTS

The results showed that experience of maltreatment was associated with increased use of alcohol and cannabis. However, the effects differed depending on the type of maltreatment experienced. Higher levels of religiosity were consistently associated with lower levels of alcohol and cannabis use, but we found no evidence of an impact of minimal psychological distress on these measures.

CONCLUSIONS

This preliminary study shows that the experience of maltreatment may increase the risk of alcohol and cannabis use among university students in Latin American and Caribbean countries, but that higher levels of religiosity may reduce that risk. More work to determine the nature and significance of these relationships is needed.