Conserved intron positions in ancient protein modules

BACKGROUND: The timing of the origin of introns is of crucial importance for an understanding of early genome architecture. The Exon theory of genes proposed a role for introns in the formation of multi-exon proteins by exon shuffling and predicts the presence of conserved splice sites in ancient genes. In this study, large-scale analysis of potential conserved splice sites was performed using an intron-exon database (ExInt) derived from GenBank. RESULTS: A set of conserved intron positions was found by matching identical splice sites sequences from distantly-related eukaryotic kingdoms. Most amino acid sequences with conserved introns were homologous to consensus sequences of functional domains from conserved proteins including kinases, phosphatases, small GTPases, transporters and matrix proteins. These included ancient proteins that originated before the eukaryote-prokaryote split, for instance the catalytic domain of protein phosphatase 2A where a total of eleven conserved introns were found. Using an experimental setup in which the relation between a splice site and the ancientness of its surrounding sequence could be studied, it was found that the presence of an intron was positively correlated to the ancientness of its surrounding sequence. Intron phase conservation was linked to the conservation of the gene sequence and not to the splice site sequence itself. However, no apparent differences in phase distribution were found between introns in conserved versus non-conserved sequences. CONCLUSION: The data confirm an origin of introns deep in the eukaryotic branch and is in concordance with the presence of introns in the first functional protein modules in an 'Exon theory of genes' scenario. A model is proposed in which shuffling of primordial short exonic sequences led to the formation of the first functional protein modules, in line with hypotheses that see the formation of introns integral to the origins of genome evolution. REVIEWERS: This article was reviewed by Scott Roy (nominated by Anthony Poole), Sandro de Souza (nominated by Manyuan Long), and Gáspár Jékely

Modelling evolution on design-by-contract predicts an origin of Life through an abiotic double-stranded RNA world

BACKGROUND: It is generally believed that life first evolved from single-stranded RNA (ssRNA) that both stored genetic information and catalyzed the reactions required for self-replication. PRESENTATION OF THE HYPOTHESIS: By modeling early genome evolution on the engineering paradigm design-by-contract, an alternative scenario is presented in which life started with the appearance of double-stranded RNA (dsRNA) as an informational storage molecule while catalytic single-stranded RNA was derived from this dsRNA template later in evolution. TESTING THE HYPOTHESIS: It was investigated whether this scenario could be implemented mechanistically by starting with abiotic processes. Double-stranded RNA could be formed abiotically by hybridization of oligoribonucleotides that are subsequently non-enzymatically ligated into a double-stranded chain. Thermal cycling driven by the diurnal temperature cycles could then replicate this dsRNA when strands of dsRNA separate and later rehybridize and ligate to reform dsRNA. A temperature-dependent partial replication of specific regions of dsRNA could produce the first template-based generation of catalytic ssRNA, similar to the developmental gene transcription process. Replacement of these abiotic processes by enzymatic processes would guarantee functional continuity. Further transition from a dsRNA to a dsDNA world could be based on minor mutations in template and substrate recognition sites of an RNA polymerase and would leave all existing processes intact. IMPLICATIONS OF THE HYPOTHESIS: Modeling evolution on a design pattern, the 'dsRNA first' hypothesis can provide an alternative mechanistic evolutionary scenario for the origin of our genome that preserves functional continuity. REVIEWERS: This article was reviewed by Anthony Poole, Eugene Koonin and Eugene Shakhnovic

Do study circles and a nutritional care policy improve nutritional care in a short- and long-term perspective in special accommodations?

Background: Disease-related malnutrition is a major health problem in the elderly population and management issues are under-explored. Objectives: What is the prevalence of undernutrition-risk (UN-risk), underweight, and overweight in special accommodations (SAs)? Do study circles and a nutritional care policy (NCP) improve the precision in nutritional care (NC) and decrease the prevalence of under- and overweight in a short- and/or long-term perspective?Design: Quasi-experimental pre- and post-intervention design with three experimental groups and one control group (CG). Setting: SAs. Participants: In 2005 (Time 1 – T1), 1726 (90.4%) residents agreed to participate; in 2007 (Time 2 – T2), 1,526 (81.8%); and in 2009 (Time 3 – T3), 1,459 (81.3%) residents participated. Interventions: Experimental groups: between T1 and T2 the first period of study circles was conducted in one municipality; between T2 and T3 a second period of study circles in another municipality was conducted; after T1 a NCP was implemented in one municipality. CG: residents in three municipalities. Measurements: Under- and overweight were defined based on BMI. Risk of undernutrition was defined as involving any of: involuntary weight loss, low BMI, and/or eating difficulties. The ‘precision in NC’ describes the relationship between nutritional treatment (protein- and energy-enriched food (PE-food) and/or oral supplements) and UN-risk. Results: The prevalence of UN-risk varied between 64 and 66%, underweight between 25 and 30%, and overweight between 30 and 33% in T1–T3. At T2 the prevalence of underweight was significantly lower in the first period study circle municipality, and at T3 in the second period study circle municipality compared to in the CG. The precision in NC was higher in a short-term perspective in the study circle municipalities and both in a short- and long-term perspective in the NCP municipality. At T3 between 54 and 70% of residents at UN-risk did not receive PE-food or oral supplements. Conclusions: Study circles give positive short-term effects and a NCP gives positive short- and long-term effects on NC. Whether a combination of study circles and the implementation of a NCP can give even better results is an area for future studies

Predicting synthetic rescues in metabolic networks

An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with compensatory function. Here, we propose an alternative, network-based strategy that aims to restore biological function by forcing the cell to either bypass the functions affected by the defective gene, or to compensate for the lost function. Focusing on the metabolism of single-cell organisms, we computationally study mutants that lack an essential enzyme, and thus are unable to grow or have a significantly reduced growth rate. We show that several of these mutants can be turned into viable organisms through additional gene deletions that restore their growth rate. In a rather counterintuitive fashion, this is achieved via additional damage to the metabolic network. Using flux balance-based approaches, we identify a number of synthetically viable gene pairs, in which the removal of one enzyme-encoding gene results in a nonviable phenotype, while the deletion of a second enzyme-encoding gene rescues the organism. The systematic network-based identification of compensatory rescue effects may open new avenues for genetic interventions.Comment: Supplementary Information is available at the Molecular Systems Biology website: http://www.nature.com/msb/journal/v4/n1/full/msb20081.htm

Multi-Timescale Perceptual History Resolves Visual Ambiguity

When visual input is inconclusive, does previous experience aid the visual system in attaining an accurate perceptual interpretation? Prolonged viewing of a visually ambiguous stimulus causes perception to alternate between conflicting interpretations. When viewed intermittently, however, ambiguous stimuli tend to evoke the same percept on many consecutive presentations. This perceptual stabilization has been suggested to reflect persistence of the most recent percept throughout the blank that separates two presentations. Here we show that the memory trace that causes stabilization reflects not just the latest percept, but perception during a much longer period. That is, the choice between competing percepts at stimulus reappearance is determined by an elaborate history of prior perception. Specifically, we demonstrate a seconds-long influence of the latest percept, as well as a more persistent influence based on the relative proportion of dominance during a preceding period of at least one minute. In case short-term perceptual history and long-term perceptual history are opposed (because perception has recently switched after prolonged stabilization), the long-term influence recovers after the effect of the latest percept has worn off, indicating independence between time scales. We accommodate these results by adding two positive adaptation terms, one with a short time constant and one with a long time constant, to a standard model of perceptual switching

Next-generation sequencing reveals substantial genetic contribution to dementia with Lewy bodies

Dementia with Lewy bodies (DLB) is the second most common neurodegenerative dementia after Alzheimer's disease. Although an increasing number of genetic factors have been connected to this debilitating condition, the proportion of cases that can be attributed to distinct genetic defects is unknown. To provide a comprehensive analysis of the frequency and spectrum of pathogenic missense mutations and coding risk variants in nine genes previously implicated in DLB, we performed exome sequencing in 111 pathologically confirmed DLB patients. All patients were Caucasian individuals from North America. Allele frequencies of identified missense mutations were compared to 222 control exomes. Remarkably, ~ 25% of cases were found to carry a pathogenic mutation or risk variant in APP, GBA or PSEN1, highlighting that genetic defects play a central role in the pathogenesis of this common neurodegenerative disorder. In total, 13% of our cohort carried a pathogenic mutation in GBA, 10% of cases carried a risk variant or mutation in PSEN1, and 2% were found to carry an APP mutation. The APOE ε4 risk allele was significantly overrepresented in DLB patients (p-value < 0.001). Our results conclusively show that mutations in GBA, PSEN1, and APP are common in DLB and consideration should be given to offer genetic testing to patients diagnosed with Lewy body dementia

Analysing and Recommending Options for Maintaining Universal Coverage with Long-Lasting Insecticidal Nets: The Case of Tanzania in 2011.

Tanzania achieved universal coverage with long-lasting insecticidal nets (LLINs) in October 2011, after three years of free mass net distribution campaigns and is now faced with the challenge of maintaining high coverage as nets wear out and the population grows. A process of exploring options for a continuous or "Keep-Up" distribution system was initiated in early 2011. This paper presents for the first time a comprehensive national process to review the major considerations, findings and recommendations for the implementation of a new strategy. Stakeholder meetings and site visits were conducted in five locations in Tanzania to garner stakeholder input on the proposed distribution systems. Coverage levels for LLINs and their decline over time were modelled using NetCALC software, taking realistic net decay rates, current demographic profiles and other relevant parameters into consideration. Costs of the different distribution systems were estimated using local data. LLIN delivery was considered via mass campaigns, Antenatal Care-Expanded Programme on Immunization (ANC/EPI), community-based distribution, schools, the commercial sector and different combinations of the above. Most approaches appeared unlikely to maintain universal coverage when used alone. Mass campaigns, even when combined with a continuation of the Tanzania National Voucher Scheme (TNVS), would produce large temporal fluctuations in coverage levels; over 10 years this strategy would require 63.3 million LLINs and a total cost of $444 million USD. Community mechanisms, while able to deliver the required numbers of LLINs, would require a massive scale-up in monitoring, evaluation and supervision systems to ensure accurate application of identification criteria at the community level. School-based approaches combined with the existing TNVS would reach most Tanzanian households and deliver 65.4 million LLINs over 10 years at a total cost of$449 million USD and ensure continuous coverage. The cost of each strategy was largely driven by the number of LLINs delivered. The most cost-efficient strategy to maintain universal coverage is one that best optimizes the numbers of LLINs needed over time. A school-based approach using vouchers targeting all students in Standards 1, 3, 5, 7 and Forms 1 and 2 in combination with the TNVS appears to meet best the criteria of effectiveness, equity and efficiency

Predicting the peak growth velocity in the individual child: validation of a new growth model

Predicting the peak growth velocity in an individual patient with adolescent idiopathic scoliosis is essential or determining the prognosis of the disorder and timing of the (surgical) treatment. Until the present time, no accurate method has been found to predict the timing and magnitude of the pubertal growth spurt in the individual child. A mathematical model was developed in which the partial individual growth velocity curve was linked to the generic growth velocity curve. The generic curve was shifted and stretched or shrunk, both along the age axis and the height velocity axis. The individual age and magnitude of the PGV were obtained from the new predicted complete growth velocity curve. Predictions were made using 2, 1.5, 1 and 0.5 years of the available longitudinal data of the individual child, starting at different ages. The predicted values of 210 boys and 162 girls were compared to the child’s own original values of the PGV. The individual differences were compared to differences obtained when using the generic growth velocity curve as a standard. Using 2 years of data as input for the model, all predictions of the age of the PGV in boys and girls were significantly better in comparison to using the generic values. Using only 0.5 years of data as input, the predictions with a starting age from 13 to 15.5 years in boys and from 9.5 to 14.5 years in girls were significantly better. Similar results were found for the predictions of the magnitude of the PGV. This model showed highly accurate results in predicting the individual age and magnitude of the PGV, which can be used in the treatment of patients with adolescent idiopathic scoliosis

Kidney growth curves in healthy children from the third trimester of pregnancy until the age of two years. The Generation R Study

Information about growth of kidney structures in early life is limited. In a population-based prospective cohort study, from foetal life onwards, we constructed reference curves for kidney growth from the third trimester of pregnancy until early childhood, using data from 1,158 healthy children. Kidney size, defined as length, width, depth and volume, was measured in the third trimester of pregnancy and at the postnatal ages of 6 months and 24 months. Analyses were based on more than 2,500 kidney measurements. In the third trimester of pregnancy and at 6 months of age all kidney measurements were larger in boys than in girls. At 24 months of age, these gender differences were only significant for left kidney structures and right kidney length. Both groups showed trends towards smaller left kidney measurements than right kidney measurements at all ages. Gender-specific reference curves based on post-conceptional and postnatal ages were constructed for left and right kidney length, width, depth and volume. We concluded that kidney size is influenced by age and gender. Left kidney size tended to be smaller than right kidney size, except for kidney length. The reference curves can be used for assessing kidney structures by ultrasound in foetal life and early childhood