Computer simulations of Template-Directed RNA Synthesis driven by temperature cycling in diverse sequence mixtures.

We present simulations of non-enzymatic template-directed RNA synthesis that incorporate primer extension, ligation, melting, and reannealing. Strand growth occurs over multiple heating/cooling cycles, producing strands of several hundred nucleotides in length, starting with random oligomers of 4 to 10 nucleotides. A strand typically grows by only 1 or 2 nucleotides in each cycle. Therefore, a strand is copied from many different templates, not from one specific complementary strand. A diverse sequence mixture is produced, and there is no exact copying of sequences, even if single base additions are fully accurate (no mutational errors). It has been proposed that RNA systems may contain a virtual circular genome, in which sequences partially overlap in a way that is mutually catalytic. We show that virtual circles do not emerge naturally in our simulations, and that a system initiated with a virtual circle can only maintain itself if there are no mutational errors and there is no input of new sequences formed by random polymerization. Furthermore, if a virtual sequence and its complement contain repeated short words, new sequences can be produced that were not on the original virtual circle. Therefore the virtual circle sequence cannot maintain itself. Functional sequences with secondary structures contain complementary words on opposite sides of stem regions. Both these words are repeated in the complementary sequence; hence, functional sequences cannot be encoded on a virtual circle. Additionally, we consider sequence replication in populations of protocells. We suppose that functional ribozymes benefit the cell which contains them. Nevertheless, scrambling of sequences occurs, and the functional sequence is not maintained, even when under positive selection.

Can the RNA World Still Function without Cytidine?

Most scenarios for the origin of life assume that RNA played a key role in both catalysis and information storage. The A, U, G, and C nucleobases in modern RNA all participate in secondary structure formation and replication. However, the rapid deamination of C to U and the absence of C in meteorite samples suggest that prebiotic RNA may have been deficient in cytosine. Here, we assess the ability of RNA sequences formed from a three-letter AUG alphabet to perform both structural and genetic roles in comparison to sequences formed from the AUGC alphabet. Despite forming less thermodynamically stable helices, the AUG alphabet can find a broad range of structures and thus appears sufficient for catalysis in the RNA World. However, in the AUG case, longer sequences are required to form structures with an equivalent complexity. Replication in the AUG alphabet requires GU pairing. Sequence fidelity in the AUG alphabet is low whenever G's are present in the sequence. We find that AUG sequences evolve to AU sequences if GU pairing is rare, and to RU sequences if GU pairing is common (R denotes A or G). It is not possible to conserve a G at a specific site in either case. These problems do not rule out the possibility of an RNA World based on AUG, but they show that it wouldbe significantly more difficult than with a four-base alphabet.

Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life.

It is likely that RNA replication began non-enzymatically, and that polymerases were later selected to speed up the process. We consider replication mechanisms in modern viruses and ask which of these is possible non-enzymatically, using mathematical models and experimental data found in the literature to estimate rates of RNA synthesis and replication. Replication via alternating plus and minus strands is found in some single-stranded RNA viruses. However, if this occurred non-enzymatically it would lead to double-stranded RNA that would not separate. With some form of environmental cycling, such as temperature, salinity, or pH cycling, double-stranded RNA can be melted to form single-stranded RNA, although re-annealing of existing strands would then occur much faster than synthesis of new strands. We show that re-annealing blocks this form of replication at a very low concentration of strands. Other kinds of viruses synthesize linear double strands from single strands and then make new single strands from double strands via strand-displacement. This does not require environmental cycling and is not blocked by re-annealing. However, under non-enzymatic conditions, if strand-displacement occurs from a linear template, we expect the incomplete new strand to be almost always displaced by the tail end of the old strand through toehold-mediated displacement. A third kind of replication in viruses and viroids is rolling-circle replication which occurs via strand-displacement on a circular template. Rolling-circle replication does not require environmental cycling and is not prevented by toehold-mediated displacement. Rolling-circle replication is therefore expected to occur non-enzymatically and is a likely starting point for the evolution of polymerase-catalysed replication.

The RNA World: molecular cooperation at the origins of life.

The RNA World concept posits that there was a period of time in primitive Earth's history - about 4 billion years ago - when the primary living substance was RNA or something chemically similar. In the past 50 years, this idea has gone from speculation to a prevailing idea. In this Review, we summarize the key logic behind the RNA World and describe some of the most important recent advances that have been made to support and expand this logic. We also discuss the ways in which molecular cooperation involving RNAs would facilitate the emergence and early evolution of life. The immediate future of RNA World research should be a very dynamic one.

Diseases associated with hypercobalaminemia in dogs in United Kingdom: A retrospective study of 47 dogs.

Cobalamin concentration is often assessed in clinical practice but little is known about the significance of hypercobalaminemia. The objective of this retrospective study was to identify the conditions associated with hypercobalaminemia in dogs and to investigate association with clinicopathological variables. Medical records of dogs having serum cobalamin measured between 2016 and 2018 were reviewed. One hundred sixty dogs were included and 47 (29%) showed hypercobalaminemia. Dogs with hypercobalaminemia had gastrointestinal (57%), hepatic (11%), neurological (11%), endocrine (9%), renal (4%), pancreatic (2%), and miscellaneous (6%) diseases. Overall, 11% had neoplasia. This distribution was not significantly different from that for hypocobalaminemic and normocobalaminemic dogs. There were significantly more dogs with hyperfolatemia in the hypercobalaminemia group. These results suggest that in clinical practice hypercobalaminemia is commonly identified in gastrointestinal and hepatic disease in dogs, but can also be seen with endocrine and neurological conditions. The frequency of hyperfolatemia alongside hypercobalaminemia may reflect common metabolic pathways.

Maladies associées à l'hypercobalaminémie chez des chiens au Royaume-Uni : étude rétrospective de 47 chiens. La concentration de cobalamine est souvent évaluée dans la pratique clinique, mais on en sait peu sur l'importance de l'hypercobalaminémie. L'objectif de cette étude rétrospective était d'identifier les conditions associées à l'hypercobalaminémie chez le chien et d'étudier l'association avec des variables clinicopathologiques. Les dossiers médicaux des chiens eu ayant une cobalamine sérique mesurée entre 2016 et 2018 ont été examinés. Cent soixante chiens ont été inclus et 47 (29%) ont présenté une hypercobalaminémie. Les chiens atteints d'hypercobalaminémie avaient des maladies gastro-intestinales (57%), hépatiques (11%), neurologiques (11%), endocriniennes (9%), rénales (4%), pancréatiques (2%) et diverses (6%). Dans l'ensemble, 11% avaient une néoplasie. Cette distribution n'était pas significativement différente de celle des chiens hypocobalaminémiques et normocobalaminémiques. Il y avait significativement plus de chiens atteints d'hyperfolatémie dans le groupe hypercobalaminémie. Ces résultats suggèrent qu'en pratique clinique, l'hypercobalaminémie est couramment identifiée dans les maladies gastro-intestinales et hépatiques chez le chien, mais peut également être observée avec des conditions endocriniennes et neurologiques. La fréquence de l'hyperfolatémie associée à l'hypercobalaminémie peut refléter des voies métaboliques communes.(Traduit par Dr Serge Messier).

"Falling through the cracks"; Stakeholders' views around the concept and diagnosis of mild cognitive impairment and their understanding of dementia prevention.

OBJECTIVES: Many people live with an awareness of mild cognitive changes that increase their dementia risk. Previous authors describe the uncertainties of this liminal state, between cognitive health and dementia, where being "at risk" can itself be an illness. We ask how services respond to people with memory concerns currently, and how a future, effective and inclusive dementia prevention intervention might be structured for people with memory concerns. METHODS/DESIGN: We conducted qualitative interviews with 18 people aged 60+ years with subjective or objective memory problems, six family members, 10 health and social care professionals and 11 third sector workers. Interviews were audio-recorded, transcribed and analysed using an inductive thematic approach. RESULTS: Three main themes were identified: (1) acknowledging the liminal state, compounded by current, discordant health service responses: medicalising memory concerns yet situating responsibilities for their management with patients and families; (2) enabling change in challenging contexts of physical and cognitive frailty and social disengagement and (3) building on existing values, cultures and routines. CONCLUSIONS: Effective dementia prevention must empower individuals to make lifestyle changes within challenging contexts. Programmes must be evidence based yet sufficiently flexible to allow new activities to be fitted into people's current lives; and mindful of the risks of pathologising memory concerns. Most current memory services are neither commissioned, financially or clinically resourced to support people with memory concerns without dementia. Effective, large scale dementia prevention will require a broad societal response.

APPLE-Tree (Active Prevention in People at risk of dementia: Lifestyle, bEhaviour change and Technology to REducE cognitive and functional decline) programme: Protocol.

BACKGROUND: Observational studies indicate that approximately a third of dementia cases are attributable to modifiable cardiometabolic, physical and mental health, and social and lifestyle risk factors. There is evidence that intensive behaviour change interventions targeting these factors can reduce cognitive decline. [Figure: see text] METHODS AND ANALYSIS: We will design and test a low intensity, secondary dementia-prevention programme (Active Prevention in People at risk of dementia: Lifestyle, bEhaviour change and Technology to REducE cognitive and functional decline, "APPLE-Tree") to slow cognitive decline in people with subjective cognitive decline with or without objective cognitive impairment. We will embed our work within social science research to understand how dementia prevention is currently delivered and structured. We will carry out systematic reviews and around 50 qualitative interviews with stakeholders, using findings to coproduce the APPLE-Tree intervention. We plan a 10-session group intervention, involving personalised goal-setting, with individual sessions for those unable or unwilling to attend groups, delivered by psychology assistants who will be trained and supervised by clinical psychologists. The coproduction group (including public and patient involvement [PPI], academic and clinical/third-sector professional representatives) will use the Behaviour Change Wheel theoretical framework to develop it. We will recruit and randomly allocate 704 participants, 1:1 to the intervention: informational control group. This sample size is sufficient to detect a between-group difference at 2 years of 0.15 on the primary outcome (cognition: modified neuropsychological test battery; 90% power, 5% significance, effect size 0.25, SD 0.6). DISSEMINATION: We will work with Public Health England and third-sector partners to produce an effective national implementation approach, so that if our intervention works, it is used in practice.

Relational experiences of people seeking help and assessment for subjective cognitive concern and memory loss.

Objective: To understand the experience of people who seek help for subjective cognitive concern and memory loss, including people not referred for further assessment. To understand the patients' perspective of the medical process of receiving a cognitive assessment. This work is situated within the context of policy priorities for dementia diagnosis.Methods: Participants with and without dementia were recruited through NHS trusts and community organisations in four regional areas in England. Data were collected using longitudinal qualitative interviews. Transcript data were thematically analysed.Results: Sample of 41 people (mean 75 years, 25 dementia diagnoses). Interpretative thematic analyses focused on the presence or absence of trust in relational experiences. There were three transition points where trust could be specifically developed or undermined: (1) deciding to seek help; (2) healthcare practitioners' response to help-seeking; (3) process and outcome of assessment. Triggers for help-seeking for subjective cognitive concern were being prompted by family and knowing a relative with dementia. When participants perceived healthcare practitioners' behaviour as dismissive, they had less trust in the outcome of the healthcare encounter. Misunderstandings and absence of trust in assessment processes led to participants stating they did not fully agree with the outcomes of the assessment.Conclusions: Healthcare practitioners have an important role in supporting people with subjective cognitive concern ensuring patients have trust in assessment outcomes. Where the validity of the assessment process is seen as ambiguous, people can be left dealing with uncertainty, rather than being clear about ways they can manage their condition, situation or status.

Maintaining Social Connections in Dementia: A Qualitative Synthesis.

The clinical symptoms of dementia include difficulty with speech, poor short-term memory, and changes in behavior. These symptoms can affect how the person with dementia understands and performs in social interactions. This qualitative review investigated how people with mild to moderate dementia managed social connections. A systematic search of social science databases retrieved 13 articles; data were synthesized using thematic analysis. Results established the work undertaken by people with dementia to maintain and present a social persona seen as socially acceptable. Interpretations are contextualized within Goffman and Sabat's theories on "self." People with dementia were agentic in impression management: undertaking work to maintain recognized social roles, while being aware of when their illness led to others discrediting them. Wider recognition of strategies used to maintain a social self could inform interventions designed to increase capability and confidence in co-managing social connections following dementia diagnosis.

Evolution of protein interfaces in multimers and fibrils.

A majority of cellular proteins function as part of multimeric complexes of two or more subunits. Multimer formation requires interactions between protein surfaces that lead to closed structures, such as dimers and tetramers. If proteins interact in an open-ended way, uncontrolled growth of fibrils can occur, which is likely to be detrimental in most cases. We present a statistical physics model that allows aggregation of proteins as either closed dimers or open fibrils of all lengths. We use pairwise amino-acid contact energies to calculate the energies of interacting protein surfaces. The probabilities of all possible aggregate configurations can be calculated for any given sequence of surface amino acids. We link the statistical physics model to a population genetics model that describes the evolution of the surface residues. When proteins evolve neutrally, without selection for or against multimer formation, we find that a majority of proteins remain as monomers at moderate concentrations, but strong dimer-forming or fibril-forming sequences are also possible. If selection is applied in favor of dimers or in favor of fibrils, then it is easy to select either dimer-forming or fibril-forming sequences. It is also possible to select for oriented fibrils with protein subunits all aligned in the same direction. We measure the propensities of amino acids to occur at interfaces relative to noninteracting surfaces and show that the propensities in our model are strongly correlated with those that have been measured in real protein structures. We also show that there are significant differences between amino acid frequencies at isologous and heterologous interfaces in our model, and we observe that similar effects occur in real protein structures.

Agency in dementia care: systematic review and meta-ethnography.

ABSTRACTObjectives:Dementia often limits the agency of the person to such an extent that there is need for external support in making daily life decisions. This support is usually provided by family members who are sometimes legally empowered to engage in decision-making on behalf of the person for whom they care. However, such family carers receive little or no information on how to best provide support when there is a lack of capacity. This may have an impact on the agency of the person with dementia. This review explores the experience of agency in people living with dementia. DESIGN: A systematic search was conducted on IBSS, MedLine, PsychINFO, EMBASE, and CINAHL. Two independent researchers screened the studies and conducted the quality appraisal. We used meta-ethnography for data analysis. As part of the synthesis, we identified behavioral mechanisms underlying the process of decision-making and looked at how the support of carers comes into play in making deliberate choices. RESULTS: The meta-ethnography involved 20 studies. Three levels of third-order constructs were identified, each describing a decision-making pathway and reflecting the degree of autonomy of the person with dementia: autonomous decision-making, shared decision-making, and pseudo decision-making. Findings highlight those inter-relational processes that promote or negatively impact on the agency of people with dementia. CONCLUSIONS: Our review will provide health and social care personnel with an understanding of the role of the carer in the decision-making process, and therefore which mechanisms need to be promoted or discouraged through training.

Topographies of 'care pathways' and 'healthscapes': reconsidering the multiple journeys of people with a brain tumour.

People diagnosed with brain tumours enter new and unfamiliar worlds in which they must make complex and previously unimaginable decisions about care, treatment and how to live their lives. While decisions are increasingly based around care pathways, these are embedded in values that often fail to accord with those of patients. In this article, we examine the cases of people with a brain tumour and how they, their families and healthcare professionals navigate and intervene in the course of life-threatening disease. We use ethnographic data (2014-16) and modified social theory to highlight: (1) patients' interpretations of disease and care and how they might differ from dominant biomedical logics; (2) complexity and contingency in care decisions; (3) rapid and unanticipated change owing to disease and bodily change; and (4) how people find ways through a world that is continually in motion and which comes into being through the combined action of human and non-human agencies. Our modified 'healthscapes' approach provides an analytic that emphasises the constant precariousness of life with a brain tumour. It helps to explain the times when patients' feel bumped off the pathway and moments when they themselves step away to make new spaces for choice.

Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss.

We analyze patterns of gene presence and absence in a maximum likelihood framework with rate parameters for gene gain and loss. Standard methods allow independent gains and losses in different parts of a tree. While losses of the same gene are likely to be frequent, multiple gains need to be considered carefully. A gene gain could occur by horizontal transfer or by origin of a gene within the lineage being studied. If a gene is gained more than once, then at least one of these gains must be a horizontal transfer. A key parameter is the ratio of gain to loss rates, a/v We consider the limiting case known as the infinitely many genes model, where a/v tends to zero and a gene cannot be gained more than once. The infinitely many genes model is used as a null model in comparison to models that allow multiple gains. Using genome data from cyanobacteria and archaea, it is found that the likelihood is significantly improved by allowing for multiple gains, but the average a/v is very small. The fraction of genes whose presence/absence pattern is best explained by multiple gains is only 15% in the cyanobacteria and 20% and 39% in two data sets of archaea. The distribution of rates of gene loss is very broad, which explains why many genes follow a treelike pattern of vertical inheritance, despite the presence of a significant minority of genes that undergo horizontal transfer.

Chemical Evolution and the Evolutionary Definition of Life.

Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding. Chemical evolution applies to short oligonucleotides that can be generated by random polymerization, as well as by template-directed replication, and which may be too short to encode a specific function. Chemical evolution is an important stage on the pathway to life, between the stage of "just chemistry" and the stage of full biological evolution. A mathematical model is presented here that illustrates the differences between these three stages. Chemical evolution leads to much larger differences in molecular concentrations than can be achieved by selection without replication. However, chemical evolution is not open-ended, unlike biological evolution. The ability to undergo Darwinian evolution is often considered to be a defining feature of life. Here, I argue that chemical evolution, although Darwinian, does not quite constitute life, and that a good place to put the conceptual boundary between non-life and life is between chemical and biological evolution.

Error thresholds for RNA replication in the presence of both point mutations and premature termination errors.

We consider a spatial model of replication in the RNA World in which polymerase ribozymes use neighbouring strands as templates. Point mutation errors create parasites that have the same replication rate as the polymerase. We have shown previously that spatial clustering allows survival of the polymerases as long as the error rate is below a critical error threshold. Here, we additionally consider errors where a polymerase prematurely terminates replication before reaching the end of the template, creating shorter parasites that are replicated faster than the functional polymerase. In well-known experiments where Qß RNA is replicated by an RNA polymerase protein, the virus RNA is rapidly replaced by very short non-functional sequences. If the same thing were to occur when the polymerase is a ribozyme, this would mean that termination errors could potentially destroy the RNA World. In this paper, we show that this is not the case in the RNA replication model studied here. When there is continued generation of parasites of all lengths by termination errors, the system can survive up to a finite error threshold, due to the formation of travelling wave patterns; hence termination errors are important, but they do not lead to the inevitable destruction of the RNA World by short parasites. The simplest assumption is that parasite replication rate is inversely proportional to the strand length. In this worst-case scenario, the error threshold for termination errors is much lower than for point mutations. We also consider a more realistic model in which the time for replication of a strand is the sum of a time for binding of the polymerase, and a time for polymerization. When the binding step is considered, termination errors are less serious than in the worst case. In the limit where the binding time is dominant, replication rates are equal for all lengths, and the error threshold for termination is the same as for point mutations.

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World.

It is believed that life passed through an RNA World stage in which replication was sustained by catalytic RNAs (ribozymes). The two most obvious types of ribozymes are a polymerase, which uses a neighbouring strand as a template to make a complementary sequence to the template, and a nucleotide synthetase, which synthesizes monomers for use by the polymerase. When a chemical source of monomers is available, the polymerase can survive on its own. When the chemical supply of monomers is too low, nucleotide production by the synthetase is essential and the two ribozymes can only survive when they are together. Here we consider a computational model to investigate conditions under which coexistence and cooperation of these two types of ribozymes is possible. The model considers six types of strands: the two functional sequences, the complementary strands to these sequences (which are required as templates), and non-functional mutants of the two sequences (which act as parasites). Strands are distributed on a two-dimensional lattice. Polymerases replicate strands on neighbouring sites and synthetases produce monomers that diffuse in the local neighbourhood. We show that coexistence of unlinked polymerases and synthetases is possible in this spatial model under conditions in which neither sequence could survive alone; hence, there is a selective force for increasing complexity. Coexistence is dependent on the relative lengths of the two functional strands, the strand diffusion rate, the monomer diffusion rate, and the rate of deleterious mutations. The sensitivity of this two-ribozyme system suggests that evolution of a system of many types of ribozymes would be difficult in a purely spatial model with unlinked genes. We therefore speculate that linkage of genes onto mini-chromosomes and encapsulation of strands in protocells would have been important fairly early in the history of life as a means of enabling more complex systems to evolve.

Ageing, dementia and the social mind: past, present and future perspectives.

Accompanying the ageing of contemporary ageing societies is an increase in age associated morbidity, with dementia having an important impact. Mental frailty in later life is a source of fear for many and a major policy concern to all those concerned with health and welfare services. This introduction to the special issue on 'Ageing, dementia and the social mind' situates the selected papers within the context of debates about dementia and its social relations. In particular it draws attention to the importance of the social imaginary of the fourth age and what this means for the issue of personhood, care, social representations of dementia and its social contextualisation. The papers illuminating these themes draw on a variety of disciplines and approaches; from the social sciences to the humanities and from the theoretical to the empirical in order to help orientate future researchers to the complexities of dementia and the social and cultural matrix in which it exists. This paper provides an introduction to the potential for a more extended sociology of dementia; one which could combine the insights from medical sociology with the concerns of social gerontology.

Interrogating personhood and dementia.

OBJECTIVES: To interrogate the concept of personhood and its application to care practices for people with dementia. METHOD: We outline the work of Tom Kitwood on personhood and relate this to conceptualisations of personhood in metaphysics and in moral philosophy. RESULTS: The philosophical concept of personhood has a long history. The metaphysical tradition examines the necessary and sufficient qualities that make up personhood such as agency, consciousness, identity, rationality and second-order reflexivity. Alternative viewpoints treat personhood as a matter of degree rather than as a superordinate category. Within moral philosophy personhood is treated as a moral status applicable to some or to all human beings. CONCLUSION: In the light of the multiple meanings attached to the term in both metaphysics and moral philosophy, personhood is a relatively unhelpful concept to act as the foundation for developing models and standards of care for people with dementia. Care, we suggest, should concentrate less on ambiguous and somewhat abstract terms such as personhood and focus instead on supporting people's existing capabilities, while minimising the harmful consequences of their incapacities.