Factors affecting the sleep of one-year-olds : a pilot study using objective monitoring of New Zealand infants : a thesis presented in partial fulfilment of the requirements of the degree of Master of Science in Psychology at Massey University, Wellington, New Zealand

Sleep takes time to mature and in infancy the structure and cycle of sleep differs greatly to that of adults. Data concerning normative sleep of infants is lacking due to few studies using objective measures. Factors affecting infants' sleep are both intrinsic and extrinsic in nature. The causes of problematic sleep are not well understood. This study aimed to pilot a methodology involving 1 week of actigraphy monitoring of 1-year-olds, as well as collecting normative data concerning sleep and sleep ecology through questionnaires and diaries. Potential factors contributing to sleep quantity, quality and maturation were investigated. Sleeping problems were reported in 35% of the sample of 52 Wellington infants. Current breastfeeding, time awake at night, and poor evening mood were all associated with problem sleep. Short sleep duration and more instances of being put to bed were also significant predictors of reporting problem sleep. Infants were typically rated in a poorer mood and exhibited more bedtime problems at the weekend. Longer sleep onset latencies and poorer sleep efficiency were identified by actigraphy on weekend evenings. The timing of sleep did not differ between genders or between week days and weekends, or childcare and non-childcare days. Mixed model analysis of variance indicated that the maturation and quality of sleep were significantly correlated with age and stages of cognitive and motor development. Sleep duration did not correlate with ponderal index, possibly due to the young age group as well as underrepresentation of short sleeping or overweight infants. Results support previous studies in western societies and autonomous sleeping is common. Potential mechanisms behind relationships between sleep and feeding, temperament and development are discussed. Strengths and limitations of methods and procedures are assessed. Actigraphic recording of 1-year-olds is demonstrated to be a useful and reliable tool for studying sleep of infants and the results contribute to normative data. Future studies in NZ should consider recruiting a more representative sample and incorporate a longitudinal design to further assess the relationships highlighted here and in previous research

Lipopolysaccharide Diversity Evolving in Helicobacter pylori Communities through Genetic Modifications in Fucosyltransferases

Helicobacter pylori persistently colonizes the gastric mucosa of half the human population. It is one of the most genetically diverse bacterial organisms and subvariants are continuously emerging within an H. pylori population. In this study we characterized a number of single-colony isolates from H. pylori communities in various environmental settings, namely persistent human gastric infection, in vitro bacterial subcultures on agar medium, and experimental in vivo infection in mice. The lipopolysaccharide (LPS) O-antigen chain revealed considerable phenotypic diversity between individual cells in the studied bacterial communities, as demonstrated by size variable O-antigen chains and different levels of Lewis glycosylation. Absence of high-molecular-weight O-antigen chains was notable in a number of experimentally passaged isolates in vitro and in vivo. This phenotype was not evident in bacteria obtained from a human gastric biopsy, where all cells expressed high-molecular-weight O-antigen chains, which thus may be the preferred phenotype for H. pylori colonizing human gastric mucosa. Genotypic variability was monitored in the two genes encoding α1,3-fucosyltransferases, futA and futB, that are involved in Lewis antigen expression. Genetic modifications that could be attributable to recombination events within and between the two genes were commonly detected and created a diversity, which together with phase variation, contributed to divergent LPS expression. Our data suggest that the surrounding environment imposes a selective pressure on H. pylori to express certain LPS phenotypes. Thus, the milieu in a host will select for bacterial variants with particular characteristics that facilitate adaptation and survival in the gastric mucosa of that individual, and will shape the bacterial community structure

Abstracts from the NIHR INVOLVE Conference 2017

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Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Understanding and managing dementia-related sleep problems : community-based research with older New Zealanders : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, Sleep/Wake Research Centre, Wellington, New Zealand

Listed in 2015 Dean's List of Exceptional ThesesSleep changes with ageing and people with dementia and their carers often have disturbed sleep, but information on the sleep of older New Zealanders is lacking. Four studies were conducted in order to address these factors. The first two used pre-existing survey data to understand the sleep health of older people, and to explore the relationship between caregiving and sleep. Sleep problems were reported by 20-32% of participants, prevalence decreased with increasing age. In those aged at least 79 years, sleep problems were associated more with health status rather than demographic factors. Older carers were more likely to report feeling tired than non-carers. Dementia-related sleep problems are challenging for individuals and their carers, and poor sleep may exacerbate waking dementia symptoms. However, there is limited research with community-dwelling dyads of people with dementia (PWD) and their carers. Studies 3 and 4 were conducted to understand and treat dementia-related sleep problems. Focus groups with 12 dyads revealed the multifaceted nature of their sleep problems. Normalisation of sleep problems was common. In the final study, a five-week trial was piloted involving sleep education, light therapy and an exercise programme. Sleep of the dyads was monitored using actigraphy and standardised questionnaires. Questionnaires also measured cognitive functioning, quality of life, and dementia-related disruption, as well as carers’ mental health and coping. Fifteen pairs participated, of whom nine completed the trial. Case studies revealed that five PWD had improvements to their subjective sleep ratings. These PWD also showed some improvements in wake time at night, cognitive functioning, and carer-rated quality of life. These changes did not always translate into improved sleep or mental health for carers. Many PWD’s health deteriorated across the trial, masking the effects of the intervention. Overall, these studies illustrate the importance and diverse nature of sleep with ageing, dementia, and caregiving. Non-pharmacological interventions can be used successfully by some community-dwelling dyads. It is recommended that these low-risk interventions are considered by healthcare professionals. Increased knowledge and options could empower individuals to manage their own symptoms, providing hope for improving the sleeping and waking experience of older people affected by dementia

Swarming behaviour in natural populations of Anopheles gambiae and An. coluzzii: review of 4 years survey in rural areas of sympatry, Burkina Faso (West Africa)

International audienceThe swarming behaviour of natural populations of Anopheles gambiae and An. coluzzii (formerly known as An. gambiae S and M forms, respectively) were investigated through longitudinal surveys conducted between July 2006 and October 2009 in two rural areas of south-western Burkina Faso where these forms are sympatric. In both sites, the majority of swarms were recorded above visual markers localised among houses. In Soumousso, a wooded area of savannah, 108 pairs caught in copula from 205 swarms were sampled; in VK7, a rice growing area, 491 couples from 250 swarms were sampled. If segregated swarms were the norm in both sites, many visual markers were shared by the two forms of An. gambiae. Furthermore, mixed swarms were collected annually in frequencies varying from one site to another, though no mixed inseminations were recorded, corroborating the low hybrid rate previously reported in the field. The occurrence of inter-specific mate-recognition mechanisms, which allow individuals to avoid hybridisation, is discussed