PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework. Users can submit sequences for classification to families and functional subfamilies. PhyloFacts is available as a worldwide web resource from

Caffeine stabilises fission yeast Wee1 in a Rad24-dependent manner but attenuates its expression in response to DNA damage identifying a putative role for TORC1 in mediating its effects on cell cycle progression

The widely consumed neuroactive compound caffeine has generated much interest due to its ability to override the DNA damage and replication checkpoints. Previously Rad3 and its homologues was thought to be the target of caffeine’s inhibitory activity. Later findings indicate that the Target of Rapamycin Complex 1 (TORC1) is the preferred target of caffeine. Effective Cdc2 inhibition requires both the activation of the Wee1 kinase and inhibition of the Cdc25 phosphatase. The TORC1, DNA damage, and environmental stress response pathways all converge on Cdc25 and Wee1. We previously demonstrated that caffeine overrides DNA damage checkpoints by modulating Cdc25 stability. The effect of caffeine on cell cycle progression resembles that of TORC1 inhibition. Furthermore, caffeine activates the Sty1 regulated environmental stress response. Caffeine may thus modulate multiple signalling pathways that regulate Cdc25 and Wee1 levels, localisation and activity. Here we show that the activity of caffeine stabilises both Cdc25 and Wee1. The stabilising effect of caffeine and genotoxic agents on Wee1 was dependent on the Rad24 chaperone. Interestingly, caffeine inhibited the accumulation of Wee1 in response to DNA damage. Caffeine therefore modulates cell cycle progression contextually through increased Cdc25 activity and Wee1 repression following DNA damage via TORC1 inhibition

Automated Protein Subfamily Identification and Classification

Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics) algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley.edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to provide their own subfamily definitions can do so. Source code is available on the Web page. The Berkeley Phylogenomics Group PhyloFacts resource contains pre-calculated subfamily predictions and subfamily HMMs for more than 40,000 protein families and domains at http://phylogenomics.berkeley.edu/phylofacts/

Caffeine Stabilises Fission Yeast Wee1 in a Rad24-Dependent Manner but Attenuates Its Expression in Response to DNA Damage

The widely consumed neuroactive compound caffeine has generated much interest due to its ability to override the DNA damage and replication checkpoints. Previously Rad3 and its homologues was thought to be the target of caffeine’s inhibitory activity. Later findings indicate that the Target of Rapamycin Complex 1 (TORC1) is the preferred target of caffeine. Effective Cdc2 inhibition requires both the activation of the Wee1 kinase and inhibition of the Cdc25 phosphatase. The TORC1, DNA damage, and environmental stress response pathways all converge on Cdc25 and Wee1. We previously demonstrated that caffeine overrides DNA damage checkpoints by modulating Cdc25 stability. The effect of caffeine on cell cycle progression resembles that of TORC1 inhibition. Furthermore, caffeine activates the Sty1 regulated environmental stress response. Caffeine may thus modulate multiple signalling pathways that regulate Cdc25 and Wee1 levels, localisation and activity. Here we show that the activity of caffeine stabilises both Cdc25 and Wee1. The stabilising effect of caffeine and genotoxic agents on Wee1 was dependent on the Rad24 chaperone. Interestingly, caffeine inhibited the accumulation of Wee1 in response to DNA damage. Caffeine may modulate cell cycle progression through increased Cdc25 activity and Wee1 repression following DNA damage via TORC1 inhibition, as TORC1 inhibition increased DNA damage sensitivity

Mother tongue classes : A parental choice, but does choice equate with parental involvement and engagement in learning?

Peer reviewedPublisher PD

What is known about the health and living conditions of the indigenous people of northern Scandinavia, the Sami?

The Sami are the indigenous ethnic population of northern Scandinavia. Their health condition is poorly known, although the knowledge has improved over the last decade.The aim was to review the current information on mortality, diseases, and risk factor exposure in the Swedish Sami population.Health-related research on Sami cohorts published in scientific journals and anthologies was used to compare the health condition among the Sami and the majority non-Sami population. When relevant, data from the Sami populations in Swedish were compared with corresponding data from Norwegian and Finnish Sami populations.Life expectancy and mortality patterns of the Sami are similar to those of the majority population. Small differences in incidences of cancer and cardiovascular diseases have been reported. The traditional Sami lifestyle seems to contain elements that reduce the risk to develop cancer and cardiovascular diseases, e.g. physical activity, diet rich in antioxidants and unsaturated fatty acids, and a strong cultural identity. Reindeer herding is an important cultural activity among the Sami and is associated with high risks for accidents. Pain in the lower back, neck, shoulders, elbows, and hands are frequent among both men and women in reindeer-herding families. For men, these symptoms are related to high exposure to terrain vehicles, particularly snowmobile, whereas for women psychosocial risk factors seem to more important, e.g. poor social support, high effort, low reward, and high economical responsibilities.Although the health condition of the Sami population appears to be rather similar to that of the general Swedish population, a number of specific health problems have been identified, especially among the reindeer-herding Sami. Most of these problems have their origin in marginalization and poor knowledge of the reindeer husbandry and the Sami culture in the majority population. It is suggested that the most sustainable measure to improve the health among the reindeer-herding Sami would be to improve the conditions of the reindeer husbandry and the Sami culture

Familial liability for eating disorders and suicide attempts : evidence from a population registry in Sweden

Importance: Suicide attempts are common in individuals with eating disorders. More precise understanding of the mechanisms underlying their co-occurrence is needed. Objective: To examine the association between eating disorders and suicide attempts and whether familial risk factors contribute to the association. Design: A cohort design following a Swedish birth cohort 1979-2001 from age 6 until 31/12/2009. Setting: Information was acquired from Swedish national registers. Participants: Individuals born 1979-2001 and living in Sweden before age 6 (N= 2,268,786) were eligible for the study. Each individual was linked to his/her biological full-siblings, maternal half-siblings, paternal half-siblings, full-cousins, and half-cousins. Eating disorders were captured by three variables: any eating disorder, anorexia nervosa (AN), and bulimia nervosa (BN), identified by any lifetime diagnoses recorded in the registers. Suicide attempts were defined as any suicide attempts, including death by suicide, recorded in the registers. We examined the association between eating disorders and death by suicide separately, but were underpowered to explore familial liability for this association. Results: Individuals with any eating disorder had increased risk of suicide attempts (OR=5.28, 95%CI [5.04, 5.54]) and death by suicide (OR=5.39, 95%CI [4.00, 7.25]). The risks attenuated but remained significant after adjusting for comorbid major depressive disorder, anxiety disorders, and substance use disorder. Similar results were found for AN and BN, except that adjusted OR of death by suicide in BN became insignificant, possibly due to insufficient power. Individuals (index) who had a full-sibling with any eating disorder had increased risk of suicide attempts (OR=1.41, 95%CI [1.29, 1.53]). The risk attenuated for any eating disorder in more distant relatives (maternal half-siblings, OR=1.10, 95%CI [0.90, 1.34]; paternal half-siblings, OR=1.21, 95%CI [0.98, 1.49]; full-cousins, OR=1.11, 95%CI [1.06, 1.18]; half-cousins, OR=0.90, 95%CI [0.78, 1.03]). This familial pattern remained stable after adjusting for the index individuals’ eating disorders. Similar patterns were found for AN and BN. Conclusions and Relevance: Our results suggest increased risk of suicide attempts in individuals with lifetime eating disorders and their relatives. The pattern of familial co-aggregation suggests familial liability for the association between eating disorders and suicide. Psychiatric comorbidities partially explain this association, suggesting particularly high-risk presentations.China Scholarship CouncilAmerican Foundation for Suicide PreventionSwedish Initiative for Research on Microdata in the Social and Medical Sciences framework, 340-2013-5867Swedish Research Council, 538-2013Global Foundation for Eating DisordersSwedish Research Council, 538-2013-8864Manuscrip

Interaction of photons with plasmas and liquid metals: photoabsorption and scattering

Formulas to describe the photoabsorption and the photon scattering by a plasma or a liquid metal are derived in a unified manner with each other. It is shown how the nuclear motion, the free-electron motion and the core-electron behaviour in each ion in the system determine the structure of photoabsorption and scattering in an electron-ion mixture. The absorption cross section in the dipole approximation consists of three terms which represent the absorption caused by the nuclear motion, the absorption owing to the free-electron motion producing optical conductivity or inverse Bremsstrahlung, and the absorption ascribed to the core-electron behaviour in each ion with the Doppler correction. Also, the photon scattering formula provides an analysis method for experiments observing the ion-ion dynamical structure factor (DSF), the electron-electron DSF giving plasma oscillations, and the core-electron DSF yielding the X-ray Raman (Compton) scattering with a clear definition of the background scattering for each experiment, in a unified manner. A formula for anomalous X-ray scattering is also derived for a liquid metal. At the same time, Thomson scattering in plasma physics is discussed from this general point of view.Comment: LaTeX file: 18 pages without figur

Quasiparticle Effective Mass for the Two- and Three-Dimensional Electron Gas

We calculate the quasiparticle effective mass for the electron gas in two and three dimensions in the metallic region. We employ the single particle scattering potential coming from the Sj\"{o}lander-Stott theory and enforce the Friedel sum rule by adjusting the effective electron mass in a scattering calculation. In 3D our effective mass is a monotonically decreasing function of $r_s$ throughout the whole metallic domain, as implied by the most recent numerical results. In 2D we obtain reasonable agreement with the experimental data, as well as with other calculations based on the Fermi liquid theory. We also present results of a variety of different treatments for the effective mass in 2D and 3D.Comment: 12 pages, 2 figure

Novel glucose-lowering drugs and the risk of acute kidney injury in routine care: the Stockholm CREAtinine Measurements (SCREAM) project

Introduction Little is known about the comparative effects of sodium glucose cotransporter-2 inhibitors (SGLT2i), glucagon-like peptide-1 receptor agonists (GLP1-RA), or dipeptidyl peptidase-4 inhibitors (DPP-4i) on the risk of acute kidney injury (AKI) in routine care, which may differ from the controlled setting of trials.Methods Observational study comparing risks of AKI among new users of SGLT2i, GLP1-RA or DPP-4i in the region of Stockholm, Sweden, during 2008-2018. AKI was defined by ICD-10 codes and creatinine-based KDIGO criteria. We used inverse probability of treatment weighting (IPTW) to adjust for 60 potential confounders, weighted Kaplan-Meier curves and Cox regression to estimate hazard ratios and absolute risks.Results We included 17,407 participants who newly initiated DPP-4i (N = 10,605), GLP1-RA (N = 4448) or SGLT2i (N = 2354). Mean age was 63 years (39% women) and median (IQR) eGFR was 89 (73-100) ml/min/1.73 m(2). During a median follow-up of 2.5 years, 1411 participants experienced AKI. SGLT2i users had the lowest incidence rate of AKI, 18.3 [CI 95% 14.1-23.4] per 1000 person years, followed by GLP1-RA (22.5; 19.9-25.3) and DPP-4i (26.6; 25-28.2). The weighted 3-year absolute risk for AKI was 5.79% [3.63-8.52] in the SGLT2i group, compared with 7.03% [5.69-8.69] and 7.00% [6.43-7.58] in the GLP1-RA and DPP-4i groups, respectively. The adjusted hazard ratio was 0.73 [CI 95% 0.45-1.16] for SGLT2i vs. DPP-4i, and 0.98 [CI 95% 0.82-1.18] for GLP1-RA vs. DPP-4i.Conclusion This study of routine care patients initiating novel glucose-lowering drugs showed similar occurrence of AKI between therapies, and suggests lower risk for SGLT2i.Clinical epidemiolog