Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic.

The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

Microbial Danger Signals Control Transcriptional Induction of Distinct MHC Class I L Lineage Genes in Atlantic Salmon.

Antigen processing and presentation by major histocompatibility complex (MHC) molecules is a cornerstone in vertebrate immunity. Like mammals, teleosts possess both classical MHC class I and multiple families of divergent MHC class I genes. However, while certain mammalian MHC class I-like molecules have proven to be integral in immune regulation against a broad array of pathogens, the biological relevance of the different MHC class I lineages in fish remains elusive. This work focuses on MHC class I L lineage genes and reveals unique regulatory patterns of six genes (Sasa-lia, Sasa-lda, Sasa-lca, Sasa-lga, Sasa-lha, and Sasa-lfa) in antimicrobial immunity of Atlantic salmon (Salmo salar L.). Using two separate in vivo challenge models with different kinetics and immune pathologies combined with in vitro stimulation using viral and bacterial TLR ligands, we show that de novo synthesis of different L lineage genes is distinctly regulated in response to various microbial stimuli. Prior to the onset of classical MHC class I gene expression, lia was rapidly and systemically induced in vivo by the single-stranded (ss) RNA virus salmonid alpha virus 3 (SAV3) but not in response to the intracellular bacterium Piscirickettsia salmonis. In contrast, lga expression was upregulated in response to both viral and bacterial stimuli. A role for distinct MHC class I L-lineage genes in anti-microbial immunity in salmon was further substantiated by a marked upregulation of lia and lga gene expression in response to type I IFNa stimulation in vitro. Comparably, lha showed no transcriptional induction in response to IFNa stimulation but was strongly induced in response to a variety of viral and bacterial TLR ligands. In sharp contrast, lda showed no response to viral or bacterial challenge. Similarly, induction of lca, which is predominantly expressed in primary and secondary lymphoid tissues, was marginal with the exception of a strong and transient upregulation in pancreas following SAV3 challenge Together, these findings suggest that certain Atlantic salmon MHC class I L lineage genes play important and divergent roles in early anti-microbial response and that their regulation, in response to different activation signals, represents a system for selectively promoting the expression of distinct non-classical MHC class I genes in response to different types of immune challenges.

Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland.

The importance of the Atlantic walrus ivory trade for the colonization, peak, and collapse of the medieval Norse colonies on Greenland has been extensively debated. Nevertheless, no studies have directly traced medieval European ivory back to distinct Arctic populations of walrus. Analysing the entire mitogenomes of 37 archaeological specimens from Europe, Svalbard, and Greenland, we here discover that Atlantic walrus comprises two monophyletic mitochondrial (MT) clades, which diverged between 23 400 and 251 120 years ago. Our improved genomic resolution allows us to reinterpret the geographical distribution of partial MT data from 306 modern and nineteenth-century specimens, finding that one of these clades was exclusively accessible to Greenlanders. With this discovery, we ascertain the biological origin of 23 archaeological specimens from Europe (most dated between 900 and 1400 CE). These results reveal a significant shift in trade from an early, predominantly eastern source towards a near exclusive representation of Greenland ivory. Our study provides empirical evidence for how this remote Arctic resource was progressively integrated into a medieval pan-European trade network, contributing to both the resilience and vulnerability of Norse Greenland society.

A stainless-steel mortar, pestle and sleeve design for the efficient fragmentation of ancient bone.

Different types of milling equipment - such as oscillating ball mills, freezer mills, mortar and pestle - can be used to fragment ancient bone prior to DNA extraction. However, each of these tools is associated with practical drawbacks. Here, we present the design for a stainless-steel mortar and pestle, with a removable sleeve to contain bone material. The tool is easy to clean, practical and its simplicity allows university workshops equipped with a lathe, boring tools and a milling machine to make these components at local expense. This design allows for the efficient fragmentation of ancient bone and improves sample throughput. This design is recommended as a useful, economical addition to existing laboratory equipment for the handling of ancient bone.

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

Combining bleach and mild predigestion improves ancient DNA recovery from bones.

The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.

Long Absence from Work Due to Sickness among Psychiatric Outpatients in Japan, with Reference to a Recent Trend for Perfectionism.

BACKGROUND: Sick leave from work due to psychiatric disorders is a major public health problem, not only in Japan but also worldwide. As males and females in Japan tend to differ in their approach to work, a gender difference in perfectionism might be expected. We investigated the background factors leading to long-term absence from work due to sickness among psychiatric outpatients in Japan. METHODS: We surveyed 73 psychiatric outpatients who were absent from work for a long time (POAWs) and 228 employees without long-term sickness absence as controls. GHQ-30, NEO-FFI, MPS, RSS and questionnaires inquiring about background factors, including relationships with others, was used, and the data were compared between males and females. RESULTS: Male POAWs had a significantly higher tendency for depression and perfectionism than the controls, but in females this difference was not significant. With regard to personal relationships of POAWs, males had worse relationships with superiors and colleagues, whereas females had worse relationships with superiors, colleagues, and family. CONCLUSIONS: The data suggested that male workers exhibiting perfectionism tend to undertake too much work and become exhausted when trying to cope with complex human relationships in the workplace. Female workers having the double burden of family commitment and perfectionism tend to be isolated in terms of personal relationships, leading to exhaustion both in and outside the workplace.

Blindness and laser photocoagulation in patients with childhood-onset type 1 diabetes in Japan.

AIM: The aim of the study was to investigate trends in the incidence of blindness and the association with laser photocoagulation in patients with type 1 diabetes in Japan. METHODS: Patients diagnosed between 1965 and 1979 aged under 18 years old were studied. The status of blindness and laser photocoagulation was identified as of 1 January 1995. To examine the time trend, we divided the cohort into two groups: 285 patients diagnosed between 1965 and 1969 (65-69 cohort) and 769 patients diagnosed between 1975 and 1979 (75-79 cohort). Survival analysis was performed using the Kaplan-Meier method. Cox proportional hazard models were used to assess the demographic characteristics. RESULTS: Blindness developed in 60 subjects in the 65-69 cohort and 15 subjects in the 75-79 cohort. The incidence of blindness in the 75-79 cohort was significantly lower than that in the 65-69 cohort (p<0.0001). In spite of no change in the use of laser photocoagulation in the 75-79 cohort compared with the 65-69 cohort, the hazard ratio for the blindness in those who received laser photocoagulation in the 75-79 cohort decreased significantly to 0.55 (p<0.01) compared with those in the 65-69 cohort when adjusted for the age of onset, sex, and time of diagnosis. CONCLUSION: The incidence of blindness decreased significantly for the subjects diagnosed more recently. The change in quality and the earlier introduction of laser photocoagulation might have contributed to the decreased incidence of blindness observed over time.

Msh1p counteracts oxidative lesion-induced instability of mtDNA and stimulates mitochondrial recombination in Saccharomyces cerevisiae.

The proximity of the mitochondrial genome to the respiratory chain, a major source of ROS (radical oxygen species), makes mtDNA more vulnerable to oxidative damage than nuclear DNA. Mitochondrial BER (base excision repair) is generally considered to be the main pathway involved in the prevention of oxidative lesion-induced mutations in mtDNA. However, we previously demonstrated that the increased frequency of mitochondrial Oli(r) mutants in an ogg1Delta strain, lacking the activity of a crucial mtBER glycosylase, is reduced in the presence of plasmids encoding Msh1p, the mitochondrial homologue of the bacterial mismatch protein MutS. This finding suggested that Msh1p might be involved in the prevention of mitochondrial mutagenesis induced by oxidative stress. Here we show that a double mutant carrying the msh1-R813W allele, encoding a variant of the protein defective in the ATP hydrolysis activity, combined with deletion of SOD2, encoding the mitochondrial superoxide dismutase, displays a synergistic effect on the frequency of Oli(r) mutants, indicating that Msh1p prevents generation of oxidative lesion-induced mitochondrial mutations. We also show that double mutants carrying the msh1-R813W allele, combined with deletion of either OGG1 or APN1, the latter resulting in deficiency of the Apn1 endonuclease, exhibit a synergistic effect on the frequency of respiration-defective mutants having gross rearrangements of the mitochondrial genome. This suggests that Msh1p, Ogg1p and Apn1p play overlapping functions in maintaining the stability of mtDNA. In addition, we demonstrate, using a novel ARG8(m) recombination assay, that a surplus of Msh1p results in enhanced mitochondrial recombination. Interestingly, the mutant forms of the protein, msh1p-R813W and msh1p-G776D, fail to stimulate recombination. We postulate that the Msh1p-enhanced homologous recombination may play an important role in the prevention of oxidative lesion-induced rearrangements of the mitochondrial genome.

Balance between transcription and RNA degradation is vital for Saccharomyces cerevisiae mitochondria: reduced transcription rescues the phenotype of deficient RNA degradation.

The Saccharomyces cerevisiae SUV3 gene encodes the helicase component of the mitochondrial degradosome (mtEXO), the principal 3'-to-5' exoribonuclease of yeast mitochondria responsible for RNA turnover and surveillance. Inactivation of SUV3 (suv3Delta) causes multiple defects related to overaccumulation of aberrant transcripts and precursors, leading to a disruption of mitochondrial gene expression and loss of respiratory function. We isolated spontaneous suppressors that partially restore mitochondrial function in suv3Delta strains devoid of mitochondrial introns and found that they correspond to partial loss-of-function mutations in genes encoding the two subunits of the mitochondrial RNA polymerase (Rpo41p and Mtf1p) that severely reduce the transcription rate in mitochondria. These results show that reducing the transcription rate rescues defects in RNA turnover and demonstrates directly the vital importance of maintaining the balance between RNA synthesis and degradation.

[MRI of anterior cruciate ligament autografts].

The purpose of this study was to assess the usefulness of MRI in the evaluation of autografts after anterior cruciate ligament reconstruction. The subjects were 110 patients with anterior cruciate ligament reconstruction using patellar tendon autografts who underwent clinical examination, MRI, and arthroscopy of the knee. T1- and T2-weighted MR images were obtained in sagittal plane. Clinical findings were categorized into three groups: normal, borderline, and abnormal. The MRI appearances of the autografts were categorized into three types: straight continuous band (type I), interrupted band (type II) and generalized increased intensity band (type III). The clinical findings and MRI findings were compared with arthroscopic findings. Ninety-six percent of the type I showed no autograft tear on arthroscopy. In comparison with the clinical findings, MRI was found to be well correlated with arthroscopic findings. In conclusion, if the clinical findings are normal, patients are to be followed-up without MRI and arthroscopy. However, if clinical findings are either borderline or abnormal, MRI should be performed prior to arthroscopy.

A major improvement in the prognosis of individuals with IDDM in the past 30 years in Japan. The Diabetes Epidemiology Research International Study Group.

OBJECTIVE: To evaluate the time trends of mortality among individuals with IDDM in Japan. RESEARCH DESIGN AND METHODS: A historical prospective study of two independent population-based cohorts composed of individuals who were diagnosed between 1965 and 1969 (1960s cohort) and between 1975 and 1979 (1970s cohort), which included 286 IDDM patients (onset age < 18 years) for the 1960s cohort and 779 patients for the 1970s cohort, was performed. After 10 years of observation, mortality status and causes of deaths between the two cohorts were compared. RESULTS: The age-adjusted mortality rate per 100,000 person-years of the 1960s cohort was 754 (95% CI, 471-1,141); in contrast, that of the 1970s cohort was only 196 (95% CI, 107-329) (P < 0.001). The standardized mortality ratio of the 1960s cohort was 1,432 (95% CI, 898-2,161), and that of the 1970s cohort was 489 (95% CI, 267-821). Analyses of the causes of deaths revealed a marked decline in recent years in the number of deaths by acute complications and renal disease. CONCLUSIONS: A major decline in the mortality of diabetic children in Japan may be attributed to the dramatic changes in the quality of care and medical infrastructure that occurred after the mid-1970s.

Social and economic impact on youth-onset diabetes in Japan.

OBJECTIVE: To investigate the social and economic backgrounds of youth-onset insulin-treated diabetes mellitus in Japan. RESEARCH DESIGN AND METHODS: We conducted a case-control study on 35 diabetic patients with age at onset of 19.5 +/- 5.1 yr and duration of diabetes 14.9 +/- 6.7 yr. Sex- and age-matched (within 5 yr) siblings were selected as control subjects. Thirty-five matched pairs were asked to complete a questionnaire, including employment status and educational achievement. RESULTS: Overall, diabetic patients were more likely to encounter job refusal in their lives than sibling control subjects (20 vs. 0%), and most patients (6/7) who had an experience of job refusal told job interviewers about their diabetes. Although the full-time employment rate and unemployment rate did not differ significantly between patients and control subjects, income levels were lower among patients than in the sibling (1600 vs. 2500 thousand yen). A multivariate analysis indicated that patients had lower incomes than control subjects after adjusting for the effect of physical disability. Educational achievements in the patients were similar to those in the siblings. CONCLUSIONS: These results suggested that diabetic patients had several social and economic problems in Japan. Further studies in more subjects are required to grasp the social and economic impact on diabetes precisely, and minimize the social handicaps on diabetic patients.