Redundancy analysis,genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.     

Nuclear DNA changes within Helianthus annum L.: changes within single progenies and their relationships with plant development

Summary The variations in the basic nuclear DNA content, which previous results indicated to occur within one and the same progeny of Helianthus annuus, were studied in detail and correlated with certain developmental features of the plants. The size and organization of the genome of seedlings obtained from seeds (achenes) collected at the periphery (P-seedlings) or in the middle (M-seedlings) of the flowering heads of plants belonging to a line selfed for 10 years were compared. Cytophotometric determinations indicated that the nuclear DNA content of P-seedlings is 14.7% higher than that of M-seedlings. Thermal denaturation and reassociation kinetics of extracted DNAs showed that variations in the redundancy of repetitive DNA, in particular of a family of medium repeated sequences with a Cot range of 2–100, account for the differences in genome size. These findings were confirmed by the results of molecular hybridizations (slot blots), which also indicated a higher amount of ribosomal DNA in the P-seedlings than in the M-seedlings. Cell proliferation is affected by DNA content, and mitotic cycle time is 1h30 longer in the P-seedlings. By studying mature plants, positive correlations were also found between genome size and both the surface area of leaf epidermal cells (P0.01) and flowering time (P0.001). It is suggested that the variations of nuclear DNA content and organization observed play a role in determining developmental variability in plant populations, which may be of importance in buffering the effects of changing environmental conditions.     

The effect of temperature on the pattern of torpor in a marsupial hibernator

Physiological variables of torpor are strongly temperature dependent in placental hibernators. This study investigated how changes in air temperature affect the duration of torpor bouts, metabolic rate, body temperature and weight loss of the marsupial hibernator Burramys parvus (50 g) in comparison to a control group held at a constant air temperature of 2°C. The duration of torpor bouts was longest (14.0±1.0 days) and metabolic rate was lowest (0.033±0.001 ml O₂·g^-1·h^-1) at2°C. At higher air temperatures torpor bouts were significantly shorter and the metabolic rate was higher. When air temperature was reduced to 0°C, torpor bouts also shortened to 6.4±2.9 days, metabolic rate increased to about eight-fold the values at 2°C, and body temperature was maintained at the regulated minimum of 2.1±0.2°C. Because air temperature had such a strong effect on hibernation, and in particular energy expenditure, a change in climate would most likely increase winter mortality of this endangered species.Abbreviationst STP standard temperature and pressure - T _a air temperature - T _b body temperature - VO₂ rate of oxygen consumption     

Citrate metabolism in lactic acid bacteria

Abstract: Citrate metabolism plays an important role in many food fermentations involving lactic acid bacteria. Since citrate is a highly oxidized substrate, no reducing equivalents are produced during its degradation, resulting in the formation of metabolic end products other than lactic acid. Some of these end products, such as diacetyl and acetaldehyde, have very distinct aroma properties and contribute significantly to the quality of the fermented foods. In this review the metabolic pathways involved in product formation from citrate are described, the bioenergetic consequences of this metabolism for the lactic acid bacteria are discussed and detailed information on some key enzymes in the citrate metabolism is presented. The combined knowledge is used for devising strategies to avoid, control or improve product formation from citrate.     

Metabolic capacity of muscle fibers from high-altitude natives

We evaluate the effects of chronic hypoxia on the metabolic phenotype of the muscle fiber types of humans. The subjects were three Quechua natives residing in the Peruvian Andes at an altitude greater than 3300 m, and three lowlanders from below 700 m. Biopsy specimens were obtained from the vastus lateralis muscles of volunteers. Muscle fibers were identified histochemically as type 1 (oxidative), 2a (oxidativeglycolytic) or 2b (glycolytic). The relative contribution of each fiber type to the total cross-sectional area of each biopsy sample was determined. In individual fibers, the activities of malate dehydrogenase (MDH, citric acid cycle), lactate dehydrogenase (LDH, glycolysis) and adenylokinase (high-energy phosphate) were quantified. The cross-sectional area of the muscle occupied by each fiber type is comparable between Quechuas and lowlanders. Type 1 fibers are the only fiber type to demonstrate statistically significant (P 50.05) differences in enzyme activities between Quechuas and lowlanders. MDH activity is, on average, 19.6% less (P 0.0001) and LDH activity 28.1% more (P 0.0001) in the type 1 fibers of the Quechuas. Chronic hypoxia appears to produce a shift from oxidative to glycolytic metabolism in those fibers which are typically the, most aerobic in human muscle.     

兼性CAM植物NAD—苹果酸酶的行为研究

以土三七（Ｓｅｄｕｍ ａｉｚｏｏｎ）和露花（Ｍｅｓｅｍ ｂｒｙａｎｔｈｅｍ ｕｍ ｃｏｒｄｉｆｏｌｉｕｍ ）为材料,对兼性景天酸代谢（ＣＡＭ）植物的ＮＡＤ－苹果酸酶作了初步研究。当有５ ｍ ｍ ｏｌ／ＬＭｎＣｌ２、６ ｍ ｍ ｏｌ／ＬＭａｌ和５０ μｍ ｏｌ／ＬＣｏＡ 存在时,其最适ｐＨ 为７,且在低ｐＨ（７ 以下）范围内活性较高,而在高ｐＨ（７以上）范围内活性较低。该酶活性有季节性的变化,在７ 月份酶活性达最高峰,这与羧化系统的磷酸烯醇式丙酮酸（ＰＥＰＣ）活性变化趋势基本一致。同时,其活性也有昼夜变化,白天活性高,夜间活性低。经水分胁迫诱导出ＣＡＭ 后,ＮＡＤ－ＭＥ活性增加了２—３ 倍。我们认为,ＣＡＭ的调节是由羧化系统的ＰＥＰＣ和脱羧系统的ＮＡＤ－ＭＥ协调作用的结果     

Biology of L-lysine overproduction byCorynebacterium glutamicum

Summary The Gram positive bacteriumCorynebacterium glutamicum is used for the production of L-lysine. This review focuses on the progress achieved in the past five years for a deeper understanding of lysine overproduction. This period also coincides with decisive progress in the use of genetic engineering techniques for analysing and increasing the metabolite flux inC. glutamicum. It was thus demonstrated that thein vivo activity of the allosterically controlled aspartate kinase is important for flux control, but in addition also the amount of the dihydrodipicolinate synthase. An outstanding feature ofC. glutamicum is the split lysine biosynthesis pathway. NMR investigations have clearly shown that both pathways are simultaneously usedin vivo and that the flux ratio depends on nitrogen availability. The cellular synthesized lysine is eventually exported into the external medium through a specific carrier. Interestingly lysine producers have other export characteristics so that the carrier properties also seem to be important for increased metabolite flux.     

Characteristics and culture of osteoblasts derived from avian long bone

Summary A method is presented for isolating primary osteoblasts from the periosteal surface of chick tibia. The culture system identified supports both cell proliferation and phenotype retention. Cell numbers increased 8-fold in Week 1 and 20-fold over a total of 12 days. Well-established osteoblast markers, alkaline phosphatase staining,γ-carboxyglutamic acid, osteocalcin, type I collagen, and parathyroid hormone binding were detected. Osteocalcin,γ-carboxyglutamic acid, and type I collagen were present on culture Day 4, and were increased in amount by Day 8, but were similar to the earlier level on Day 12, suggesting that the phenotype may revert to a less differentiated state by 12 days in culture. Alkaline phosphatase staining was intense at all three assay times, however. During the last 4 days of the 12-day culture period, proliferation rates were higher than in the previous 8 days.     

Plasmodium yoelii: blood oxygen and brain function in the infected mouse

The carriage of oxygen by the blood and the in vivo response of the brain were investigated in mice infected with a lethal strain of Plasmodium yoelii. All mice with parasitaemia exceeding 70% were severely anaemic (Hb 3.5 +/- 1.8 g/dl; mean +/- 1 SD), acidotic (blood pH 7.04 +/- 0.06) and hypoglycaemic (blood glucose 0.6 +/- 0.76 mumol/ml). The oxyhaemoglobin dissociation curve (ODC) of blood from heavily infected mice was shifted right as compared to controls, but the increase in p50 was less than expected from the accompanying acidosis. The reduced shift right was due to a decrease in the 2,3-DPG/Hb ratio in infected animals (0.72 +/- 0.12, n = 17 vs 1.10 +/- 0.09, n = 12 in controls). Despite the severity of terminal infection, the cerebral pH and the relative steady-state concentrations of PCr, ATP and Pi measured in vivo by nuclear magnetic resonance (31P NMR) were normal. Alterations in brain energy status and pH cannot account for cerebral signs or death in this proposed mouse model of cerebral malaria.