The Earth BioGenome project: opportunities and challenges for plant genomics and conservation

Sequencing them all. That is the ambitious goal of the recently launched Earth BioGenome project (Proceedings of the National Academy of Sciences of the United States of America, 115, 4325–4333), which aims to produce reference genomes for all eukaryotic species within the next decade. In this perspective, we discuss the opportunities of this project with a plant focus, but highlight also potential limitations. This includes the question of how to best capture all plant diversity, as the green taxon is one of the most complex clades in the tree of life, with over 300 000 species. For this, we highlight four key points: (i) the unique biological insights that could be gained from studying plants, (ii) their apparent underrepresentation in sequencing efforts given the number of threatened species, (iii) the necessity of phylogenomic methods that are aware of differences in genome complexity and quality, and (iv) the accounting for within‐species genetic diversity and the historical aspect of conservation genetics.     

Comparative Anatomy of Chromosomal Domains with Imprinted and Non-Imprinted Allele-Specific DNA Methylation

Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.     

Overweight Is an Independent Risk Factor for Reduced Lung Volumes in Myotonic Dystrophy Type 1

Background

In this large observational study population of 105 myotonic dystrophy type 1 (DM1) patients, we investigate whether bodyweight is a contributor of total lung capacity (TLC) independent of the impaired inspiratory muscle strength.

Methods

Body composition was assessed using the combination of body mass index (BMI) and fat-free mass index. Pulmonary function tests and respiratory muscle strength measurements were performed on the same day. Patients were stratified into normal (BMI < 25 kg/m²) and overweight (BMI ≥ 25 kg/m²) groups. Multiple linear regression was used to find significant contributors for TLC.

Results

Overweight was present in 59% of patients, and body composition was abnormal in almost all patients. In overweight patients, TLC was significantly (p = 2.40×10⁻³) decreased, compared with normal-weight patients, while inspiratory muscle strength was similar in both groups. The decrease in TLC in overweight patients was mainly due to a decrease in expiratory reserve volume (ERV) further illustrated by a highly significant (p = 1.33×10⁻¹⁰) correlation between BMI and ERV. Multiple linear regression showed that TLC can be predicted using only BMI and the forced inspiratory volume in 1 second, as these were the only significant contributors.

Conclusions

This study shows that, in DM1 patients, overweight further reduces lung volumes, as does impaired inspiratory muscle strength. Additionally, body composition is abnormal in almost all DM1 patients.     

Enzyme activity of rat tibialis anterior muscle differs between treatment with triamcinolone and prednisolone and nutritional deprivation

The maximal activity of a selection of enzymes involved in muscle carbohydrate handling, citric acid cycle and fatty acyl beta-oxidation were studied after treatment with the fluorinated corticosteroid triamcinolone and compared to a similar treatment of the non-fluorinated corticosteroid prednisolone in an equipotent anti-inflammatory dose. Furthermore, because triamcinolone causes loss of body mass and muscle wasting, the effects of triamcinolone were investigated relative to a control group, with the same loss of body mass, due to nutritional deprivation. The study was performed in male Wistar rats in the following treatment groups: TR, triamcinolone treatment (0.25 mg x kg(-1) x day(-1) for 2 weeks), which resulted in a reduction of body mass (24%); ND, nutritional deprivation (30% of normal daily food intake for 2 weeks) resulting in a similar (24%) decrease of body mass as TR; PR, prednisolone treatment (0.31 mg x kg(-1) x day(-1) for 2 weeks), with a 10% increase in body mass; FF, free-fed control group, with a 12% increase in body mass in 2 weeks. Compared to FF, TR induced an increase in phosphofructokinase (PFK) activity (P < 0.01), glycogen synthase [GS(i + d)] activity (P < 0.05) and glycogen content (P < 0.01) in the tibialis anterior muscle. The PR and ND caused no alterations in PFK or citrate synthase (CS) activity compared to FF. Compared to PR, TR induced an increase in PFK (P < 0.01), CS (P < 0.05) and GS(i + d) activity (P < 0.01). Both TR and PR caused an increased muscle glycogen content, being more pronounced in TR (P < 0.05). Compared to ND, TR induced an increased CS (P < 0.05) and GS(i + d) activity (P < 0.01) and glycogen content (P < 0.01). The ND resulted in a decreased glycogen content compared to FF (P < 0.05). None of the treatments affected the activity of glycogen phosphorylase, beta-hydroxyacyl coenzyme A dehydrogenase and lactate dehydrogenase. It was concluded that corticosteroids led to an increased muscle glycogen content; however, the changes in the enzymes of carbohydrate metabolism were corticosteroid type specific and did not relate to undernutrition, which accompanied the triamcinolone treatment.     

Complications during gestation in the cow

Uterine torsion and vaginal prolapse are accidents of gestation; this paper first reviews the predisposition, symptoms, diagnosis, and treatment of uterine torsion, and the predisposition, pathogenesis, symptoms, treatment, and prognosis of vaginal prolapse during late gestation in the cow. Other noninfectious complications of gestation are either fetal or placental in origin. Two relatively unusual fetal problems, mummification and maceration, are also discussed, followed by a comparison of two hydropic conditions (hydrallantois and hydramnios). Hydrops allantois, primarily a placental problem, occurs about nine times more frequently than hydrops amnii, which is a result of fetal anomalies. Abnormal offspring syndrome is a more recent phenomenon associated with the transfer of IVF or SCNT embryos. Finally, reference is made to teratology in general and a website of illustrations is cited.     

Entwicklung und Aufbau einer Population der Silberm?we,Larus argentatus argentatus

X. Zusammenfassung Die neben dem Institutsgebäude der Vogelwarte Helgoland in Wilhelmshaven gelegene Silbermöwenpopulation nahm ihren Anfang mit 2 Paaren im Jahre 1948, wuchs bis 1955 auf 51, 1956 auf über 100 Paare an und schwankte 1957–1959 zwischen 127 und 139 Paaren. 1960 waren es mindestens 150 Paare.Das rasche Anwachsen wurde durch Zuzug bewirkt; die Ansiedlung in der Kolonie Geborener — erstmals 1953 — macht nur 1,9 bis 5,4 % der Gesamtzahl jährlicher Brutvögel aus (Tab. 1a).Die Zugezogenen stammen wohl meist von benachbarten Brutstätten. Ein Zuzügler war auf der Insel Mellum, ein anderer auf der Insel Langeoog jung beringt worden.Ein Teil der Altvögel setzt für eine Brutperiode oder länger mit der Brut aus. Die vermutlichen Ursachen werden erörtert.Das Brutergebnis dieser Felsbrüter ist im Vergleich mit anderen Kolonien gut: aus 100 Eiern gingen 13–34, im Mittel 25,2 flügge Junge hervor. Ein Elternpaar hatte alljährlich 0,4–0,9, im Mittel 0,7 flügge Junge.Von 40 Silbermöwen, deren Geburtsjahr feststeht, brüteten im Kontrollgebiet zum erstenmal 8 3jährig, 9 und 1? 4jährig und 15 , 6 und 1? erst 5jährig.Zumindest viele junge Silbermöwen wählen ihre künftige Brutkolonie schon, ehe sie voll geschlechtsreif geworden sind. Erstbrüter besetzen ihr Nestrevier später als die Älteren. Ihr Bruterfolg ist im allgemeinen schlechter als der älterer Artgenossen, aber auch bei diesen ist er sehr verschieden gut; er wird mindestens z. T. beeinflußt durch die Gunst oder Ungunst der Nestlage und durch die unterschiedliche Reaktion der Individuen auf schlechte Erfahrungen.Die Ehen und ein Teil der Nachkommenschaft des A und des B konnten 13 Jahre lang erfaßt werden (Tab. 6a, 7a); von der Familie des B lebten im Sommer 1959 3 Generationen.Von 81 im Jahre 1956 alt beringten Brutvögeln kehrten ins Kontrollgebiet zurück nach 1, 2 und 3 Jahren: 75 %, 69 % und 62 % (Tab. 8).Nestplatzwechsel ist wesentlich seltener als Nestplatztreue. Partnertreue überwiegt vor Partnerwechsel im Verhältnis von etwa 4 : 1.Umherstreifende Angehörige unserer Population sind nachweislich nordwärts bis Sylt (165 km), südwestlich bis zur Scheldemündung (360 km) und landeinwärts bis Oldenburg und Bremen (bis 70 km) gelangt. Ein nicht unbeträchtlicher Teil hält sich auch in den Wintermonaten im Kontrollgebiet auf.Die als Brutvögel (seit 1948) beringten Angehörigen unserer Population waren 1959 im Mittel mehr als 7 Jahre alt.Es erlebten im Mittel etwa 90 % der altberingten Brutvögel den auf ihre Zählung folgenden Sommer (Tab. 13). Daraus folgt eine jährliche Sterblichkeit von etwa 10 % und vom Eintritt der Geschlechtsreife ab eine weitere Lebenserwartung von 9.5 Jahren. Im Mittel erreichen die adulten Silbermöwen demnach ein Alter von 4 Jahren + 9.5 Brutjahren = 13.5 Jahren.

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Summary The herring gull population near the building of the ornithological research institute at Wilhelmshaven developed out of 2 pairs in 1948; in 1955 the population numbered 51 pairs, in 1956 more than 100, and fluctuated between 127 and 139 during 1957–1959; in 1960 there were at least 150 pairs.The rapid increase was due to immigration; settling of birds born in the colony, which had taken place for the first time in 1953, makes up for only 1.9 to 5.4 % of the whole breeding population (table 1a).The immigrants came probably from breeding grounds in the neighbourhood. Two of them had been ringed as young birds on the island of Mellum and the island of Langeoog, respectively.Some of the mature adults fail to breed for one or more breeding seasons. The causes are discussed.The breeding success of this population, nesting on rocks, is as good as in other colonies: 100 eggs give rise to 13–34 fledglings, on the average up to 25. One breeding pair produces 0.4–0.9 fledglings per year, and on the average 0.7.Out of 40 herring gulls of known age 8 males nested for the first time at the age of 3 years, 9 males and 1? at 4 years, and 15 males, 6 females, and 1? at an age of 5.A considerable number of young herring gulls choose their prospective breeding ground already before maturity. Birds breeding for the first time establish territories later than the older ones and have a lower breeding success. But even in old birds the breeding success varies considerably and is influenced by the nest site and individual experience.The progeny of two birds, A and B, is shown in table 6 and 7 for a period of 13 years; in 1959 the family of male B consisted of birds belonging to 3 generations.Out of 81 birds ringed as adults in 1956 75 %, 69 %, and 62 % returned to the study area after 1, 2, and 3 years, respectively (table 8).Birds will adhere to the nest site from year to year more often than they will change it. The tendency to keep to the former mate is four times stronger than to pair up with a new one.Birds of the population studied have been found straggling toward north up to Sylt (165 km), to the southwest as far as the mouth of the river Schelde (360 km), and into the mainland up to Oldenburg and Bremen (70 km). During this time a considerable part stays in the study area.Birds ringed as breeding adults averaged more than 6.63 years in 1959.90% of the registered birds survived from one summer to the next (table 13). Hence, the annual mortality is 10%; after reaching sexual maturity further expectancy of life figures 9.5 years. Thus adult herring gulls reach an age, on the average, of 13.5 years, i. e. 4 years as immature birds + 9.5 years when mature.

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Mit Unterstützung der Deutschen Forschungsgemeinschaft.

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Herrn Prof. Dr. Erwin Stresemann zum 70. Geburtstag gewidmet.     

Reduced hexokinase II impairs muscle function 2 wk after ischemia-reperfusion through increased cell necrosis and fibrosis

We previously demonstrated that hexokinase (HK) II plays a key role in the pathophysiology of ischemia-reperfusion (I/R) injury of the heart (Smeele et al. Circ Res 108: 1165-1169, 2011; Wu et al. Circ Res 108: 60-69, 2011). However, it is unknown whether HKII also plays a key role in I/R injury and healing thereafter in skeletal muscle, and if so, through which mechanisms. We used male wild-type (WT) and heterozygous HKII knockout mice (HKII(+/-)) and performed in vivo unilateral skeletal muscle I/R, executed by 90 min hindlimb occlusion using orthodontic rubber bands followed by 1 h, 1 day, or 14 days reperfusion. The contralateral (CON) limb was used as internal control. No difference was observed in muscle glycogen turnover between genotypes at 1 h reperfusion. At 1 day reperfusion, the model resulted in 36% initial cell necrosis in WT gastrocnemius medialis (GM) muscle that was doubled (76% cell necrosis) in the HKII(+/-) mice. I/R-induced apoptosis (29%) was similar between genotypes. HKII reduction eliminated I/R-induced mitochondrial Bax translocation and oxidative stress at 1 day reperfusion. At 14 days recovery, the tetanic force deficit of the reperfused GM (relative to control GM) was 35% for WT, which was doubled (70%) in HKII(+/-) mice, mirroring the initial damage observed for these muscles. I/R increased muscle fatigue resistance equally in GM of both genotypes. The number of regenerating fibers in WT muscle (17%) was also approximately doubled in HKII(+/-) I/R muscle (44%), thus again mirroring the increased cell death in HKII(+/-) mice at day 1 and suggesting that HKII does not significantly affect muscle regeneration capacity. Reduced HKII was also associated with doubling of I/R-induced fibrosis. In conclusion, reduced muscle HKII protein content results in impaired muscle functionality during recovery from I/R. The impaired recovery seems to be mainly a result of a greater susceptibility of HKII(+/-) mice to the initial I/R-induced necrosis (not apoptosis), and not a HKII-related deficiency in muscle regeneration.     

Kurze Mitteilungen

Ohne Zusammenfassung     

Reconsidering environmental effects assessment of chemicals: Proposal for a dynamic testing strategy

Certain substances may be hazardous to ecosystems. To be able to preserve the structures and functions of ecosystems, knowledge is required to qualify and quantify such hazards. To this end, biotests are indispensable tools. For the development and/or choice of biotests, special attention has to be drawn to conflicts between scientific demands and practical constraints. From a purely scientific point of view, experiments should be designed to maximise the ecological relevance of the obtained results. However, this often collides with the limited resources (budget, time, manpower) available. Furthermore, societal issues (e.g. animal welfare) have to be taken into account. Thus, it is necessary to develop a scientifically sound testing approach that avoids unnecessary animal testing, keeps the costs low, and can be performed within a short timeframe. The different perspectives of ecology, environmental toxicology, and environmental chemistry should be integrated into a balanced ecotoxicological approach. Accordingly, we propose a dynamic testing strategy, which is adapted to the substance (or substance group) in question and its mode(s) of action.