Björn M. Hallström

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.

Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.

Determinants of Quality of Life in Stroke Survivors and Their Informal Caregivers

Background and Purpose— We examined longitudinal changes of quality of life (QOL) covering physical and mental factors in an unselected group of stroke patients and their informal caregivers. Our hypothesis was that informal caregivers would have better QOL than patients at both follow-ups, and that changes, if any, would be related to the patients’ status. Methods— QOL of 304 consecutive stroke patients and their 234 informal caregivers from the population-based Lund Stroke Register was assessed 4 months after stroke onset with the Short Form 36 (SF-36) questionnaire. SF-36 was repeated for both groups after 16 months together with Mini Mental State Examination (MMSE) and Geriatric Depression Scale (GDS-20) for patients. Results— The patients’ mean QOL scores improved between 4 and 16 months after stroke in the socio-emotional and mental SF-36 domains and decreased in the domain physical function. Multivariate analyses showed that the patients’ most important determinants of QOL after 16 months were GDS-20 score, functional status, age, and gender. Informal caregivers had better QOL than patients except for the domain role emotional and the mental component summary. The caregivers’ most important determinants of QOL were their own age and the patients’ functional status. Conclusions— Our study highlights depressive symptoms in determining QOL of stroke patients. Despite self-perceived deterioration in physical function over time, several other components of QOL improved, suggesting internal adaptation to changes in their life situations. Informal caregivers of stroke patients may be under considerable strain as suggested by their lower emotional–mental scores.

Prevalence and intensity of pain after stroke: a population based study focusing on patients’ perspectives

Objective: To determine prevalence and intensity of pain after stroke, focusing on patients’ perspectives. Methods: During a one year period, 416 first-ever stroke patients were included in the population based Lund Stroke Register. After 4 and 16 months (median), 297 patients (98% of survivors) were followed up. Worst pain intensity during the previous 48 hours was assessed on a visual analogue scale (VAS), range 0 to 100: a score of 0 to 30 was defined as no or mild pain; 40 to 100 as moderate to severe pain. NIH stroke scale (NIHSS) score and HbA1c were assessed at baseline. At 16 months, screening for depression was done using the geriatric depression scale (GDS-20), and cognition with the mini-mental state examination (MMSE). Predictors of pain were determined by multivariate analyses. Results: Moderate to severe pain was reported by 96 patients (32%) after four months (VAS median = 60). Predictors of pain were younger age (p = 0.01), female sex (p = 0.006), higher NIHSS score (p<0.001), and raised HbA1c (p = 0.001) at stroke onset. At 16 months, only 62 patients (21%) had moderate to severe pain, but pain intensity was more severe (median VAS score = 70; p<0.016). Higher pain intensity correlated with female sex, worse GDS-20 score, better MMSE score, and raised HbA1c. Pain was persistent in 47%, disturbed sleep in 58%, and required rest for relief in 40% of patients. Conclusions: Although prevalence of pain after stroke decreased with time, after 16 months 21% had moderate to severe pain. Late pain after stroke was on average more severe, and profoundly affected the patients’ wellbeing.

Altered sterol composition renders yeast thermotolerant

Tricks for boosting yeasts ethanol yields To become a widely used source of fuel, widespread industrial production of ethanol using yeast needs to be simple and efficient. However, two conditions ideal for boosting production—tolerance of higher temperatures and high concentrations of ethanol—have been limiting (see the Perspective by Cheng and Kao). Now, Caspeta et al. have used adaptive laboratory evolution to find yeast strains that can tolerate high temperatures and Lam et al. have identified a route to improve yeasts resistance to high concentrations of ethanol. Science, this issue p. 75, p. 71; see also p. 35 Adaptive laboratory evolution can select for increased production of ethanol by yeast above 40°C. [Also see Perspective by Cheng and Kao] Ethanol production for use as a biofuel is mainly achieved through simultaneous saccharification and fermentation by yeast. Operating at ≥40°C would be beneficial in terms of increasing efficiency of the process and reducing costs, but yeast does not grow efficiently at those temperatures. We used adaptive laboratory evolution to select yeast strains with improved growth and ethanol production at ≥40°C. Sequencing of the whole genome, genome-wide gene expression, and metabolic-flux analyses revealed a change in sterol composition, from ergosterol to fecosterol, caused by mutations in the C-5 sterol desaturase gene, and increased expression of genes involved in sterol biosynthesis. Additionally, large chromosome III rearrangements and mutations in genes associated with DNA damage and respiration were found, but contributed less to the thermotolerant phenotype.

Stroke Incidence and Survival in the Beginning of the 21st Century in Southern Sweden Comparisons With the Late 20th Century and Projections Into the Future

Background and Purpose— We report trends of stroke incidence and survival up to year 2001/2002 in Lund-Orup, Sweden, and projections of future stroke incidence in Sweden. Methods— Lund Stroke Register, a prospective population-based study, included all first-ever stroke patients, between March 1, 2001 and February 28, 2002, in the Lund-Orup health care district. Institution-based studies for 1983 to 1985 and 1993 to 1995 were used for comparison. We calculated age-standardized incidence and Cox proportional hazards analysis of survival (stroke subtype, sex, age group, and study period in the analysis). Minimum follow-up was 46 months. Based on our register’s stroke incidence and the official Swedish population projection, a projection for future stroke incidence on a national basis was calculated. Results— We included 456 patients with first-ever stroke in 2001/2002. The age-standardized incidence (to the European population) was 144 per 100 000 person-years (95%CI 130 to 158) in 2001/2002, 158 (95%CI 149 to 168) in 1993 to 1995, and 134 (95%CI 126 to 143) in 1983 to 1985. Cox proportional hazard analysis indicated decreased risk of death after stroke in 2001/2002 (hazard ratio 0.80; 95%CI 0.67 to 0.94) compared with 1993 to 1995. Up to year 2050, the annual number of new stroke patients in Sweden may increase by 59% based solely on demographic changes. Conclusions— Despite possible underestimation of stroke incidence during the previous institution-based studies, the increased stroke incidence between 1983 to 1985 and 1993 to 1995 did not continue in 2001/2002. The long-term survival after stroke continues to improve. As the elderly population is growing in Sweden, stable incidence and increasing survival will result in a rapidly increasing prevalence of stroke patients in Sweden.

Mammalian evolution may not be strictly bifurcating

The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide-long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1–4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago (Ma). Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100–80 Ma and with continental fragmentation. These global processes may have triggered the rapid diversification of placental mammals. However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression. These speciation-related processes led to a mosaic genome and conflicting phylogenetic signals. Split network methods are ideal for visualizing these problematic branches and can therefore depict data conflict and possibly the true evolutionary history better than strictly bifurcating trees. Given the timing of tectonics, of placental mammalian divergences, and the fossil record, a Laurasian rather than Gondwanan origin of placental mammals seems the most parsimonious explanation.

Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations

BackgroundA number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew), probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method.ResultsThe rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides) from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95–100 million years ago. Many of the following divergences occurred only a few (2–4) million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses.ConclusionThe narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in speciation processes such as lineage sorting, introgression from species hybridization or hybrid speciation. These processes obscure phylogenetic analysis, making some parts of the tree difficult to resolve even with genome data.

Gene-specific correlation of RNA and protein levels in human cells and tissues

An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non‐secreted proteins based on parallel reaction monitoring to measure, at steady‐state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene‐specific RNA‐to‐protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.

Lund Stroke Register: hospitalization pattern and yield of different screening methods for first-ever stroke

Objectives –  To explore case ascertainment, hospitalization, characteristics of both hospitalized and non‐hospitalized patients in a population‐based group of stroke patients.

Using Transcriptomics To Improve Butanol Tolerance of Synechocystis sp. Strain PCC 6803

ABSTRACT Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as n-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of Synechocystis sp. strain PCC 6803 to two concentrations of exogenous n-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solvent-tolerant cyanobacteria strains that could be the foundation for a more productive biofuel host.