Differentiation: A Central Topic in Developmental and Cell Biology

MyoD/myogenin   genes and neural key genes (e.g., achaete scute-C, neurogenin), are switched on which control entire sets of subordinate effector genes. In multiplying cells "cell heredity" based on an epigenetic cellular memory enables transmission of the cell type determining program from parental to daughter cells. This memory can be based on autocatalytic self-activation of cell type specific selector genes and on the enduring action of gene groups such as the Polycomb and thrithorax complexes that code for proteins which bind to DNA sequences called cellular memory modules. These modules confer permanent accessibility (potentiation) or inaccessibility (silencing) upon many different gene loci on the chromosomes.     

Design and Application of Nucleic Acid Standards for Quantitative Detection of Enteric Viruses by Real-Time PCR

Synthetic multiple-target RNA and DNA oligonucleotides were constructed for use as quantification standards for nucleic acid amplification assays for human norovirus genogroup I and II, hepatitis E virus, murine norovirus, human adenovirus, porcine adenovirus and bovine polyomavirus. This approach overcomes the problems related to the difficulty of obtaining practical quantities of viral RNA and DNA from these viruses. The quantification capacity of assays using the standards was excellent in each case (R ² > 0.998 and PCR efficiency > 0.89). The copy numbers of the standards were equivalent to the genome equivalents of representative viruses (murine norovirus and human adenovirus), ensuring an accurate determination of virus presence. The availability of these standards should facilitate the implementation of nucleic acid amplification-based methods for quantitative virus detection.     

Factors inducing the intense burrowing activity of the red-swamp crayfish,<Emphasis Type="Italic"> Procambarus clarkii</Emphasis>, an invasive species

The burrowing activity of the invasive red-swamp crayfish, Procambarus clarkii, was studied along a 25-m-long transect in an irrigation ditch system in Italy. Our objective was to understand the factors inducing this species intense digging, which can result in bank collapse and consequently in severe damage to both agricultural fields and natural ecosystems. Burrow morphology and position, together with their occupancy by crayfish and digging, were recorded once every 6 h for 10 consecutive days. The majority of burrows were simple, although a few had a chimney and were constructed at a farther distance from the water surface than simple burrows. Burrow occupancy and digging, together with their plugged/unplugged status, were constant throughout a 24-h cycle and were not related to any abiotic parameter of the habitat. Crayfish occupied and dug a burrow for a relatively short time (6 h on average). Once abandoned, old burrows were rarely reoccupied and often collapsed, while crayfish excavated new ones. As a result, the overall number of burrows increased. This massive use of banks by P. clarkii seems to be related to soil composition and humidity, which favour crayfish digging but also cause the easy collapse of burrows.     

RNAi-mediated silencing of vitellogenin gene function turns honeybee (Apis mellifera) workers into extremely precocious foragers

The switch from within-hive activities to foraging behavior is a major transition in the life cycle of a honeybee (Apis mellifera) worker. A prominent regulatory role in this switch has long been attributed to juvenile hormone (JH), but recent evidence also points to the yolk precursor protein vitellogenin as a major player in behavioral development. In the present study, we injected vitellogenin double-stranded RNA (dsVg) into newly emerged worker bees of Africanized genetic origin and introduced them together with controls into observation hives to record flight behavior. RNA interference-mediated silencing of vitellogenin gene function shifted the onset of long-duration flights (>10 min) to earlier in life (by 3–4 days) when compared with sham and untreated control bees. In fact, dsVg bees were observed conducting such flights extremely precociously, when only 3 days old. Short-duration flights (<10 min), which bees usually perform for orientation and cleaning, were not affected. Additionally, we found that the JH titer in dsVg bees collected after 7 days was not significantly different from the controls. The finding that depletion of the vitellogenin titer can drive young bees to become extremely precocious foragers could imply that vitellogenin is the primary switch signal. At this young age, downregulation of vitellogenin gene activity apparently had little effect on the JH titer. As this unexpected finding stands in contrast with previous results on the vitellogenin/JH interaction at a later age, when bees normally become foragers, we propose a three-step sequence in the constellation of physiological parameters underlying behavioral development. David Santos Marco Antonio and Karina Rosa Guidugli-Lazzarini contributed equally to the present study.     

Body mass estimations for <Emphasis Type="Italic">Plateosaurus engelhardti</Emphasis> using laser scanning and 3D reconstruction methods

Both body mass and surface area are factors determining the essence of any living organism. This should also hold true for an extinct organism such as a dinosaur. The present report discusses the use of a new 3D laser scanner method to establish body masses and surface areas of an Asian elephant (Zoological Museum of Copenhagen, Denmark) and of Plateosaurus engelhardti, a prosauropod from the Upper Triassic, exhibited at the Paleontological Museum in Tübingen (Germany). This method was used to study the effect that slight changes in body shape had on body mass for P. engelhardti. It was established that body volumes varied between 0.79 m³ (slim version) and 1.14 m³ (robust version), resulting in a presumable body mass of 630 and 912 kg, respectively. The total body surface areas ranged between 8.8 and 10.2 m², of which, in both reconstructions of P. engelhardti, ∼33% account for the thorax area alone. The main difference between the two models is in the tail and hind limb reconstruction. The tail of the slim version has a surface area of 1.98 m², whereas that of the robust version has a surface area of 2.73 m². The body volumes calculated for the slim version were as follows: head 0.006 m³, neck 0.016 m³, fore limbs 0.020 m³, hind limbs 0.08 m³, thoracic cavity 0.533 m³, and tail 0.136 m³. For the robust model, the following volumes were established: 0.01 m³ head, neck 0.026 m³, fore limbs 0.025 m³, hind limbs 0.18 m³, thoracic cavity 0.616 m³, and finally, tail 0.28 m³. Based on these body volumes, scaling equations were used to assess the size that the organs of this extinct dinosaur have.     

The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes

This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. It is emphasized that varying inheritance patterns and copy numbers among different types of genomes, and the potential advantage achieved through the transfer of many cytoplasmic genes to the nucleus, have important implications for the evolution of nuclear, mitochondrial and chloroplast genomes. Cytoplasmic genes transferred to the nucleus have joined the more strictly controlled genetic system of the nuclear genome, including also sexual recombination, while genes retained within the cytoplasmic organelles can be involved in selection and drift processes both within and among individuals. Within-individual processes can be either intra- or intercellular. In the case of heteroplasmy, which is attributed to mutations or biparental inheritance, within-individual selection on cytoplasmic DNA may provide a mechanism by which the organism can adapt rapidly. The inheritance of cytoplasmic genomes is not universally maternal. The presence of a range of inheritance patterns indicates that different strategies have been adopted by different organisms. On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution.     

An E. coli SOS-EGFP biosensor for fast and sensitive detection of DNA damaging agents

An E. coli SOS-EGFP biosensor which expresses enhanced green fluorescent protein as a reporter protein under the control of recA gene promoter in SOS response was constructed for detection of DNA damage and evaluation of DNA damaging chemicals. The chemicals that may cause substantial DNA damage will trigger SOS response in the constructed bacterial biosensor, and then the reporter egfp gene under the control of recA promoter is stimulated to express as a fluorescent protein, allowing fast and sensitive fluorescence detection. Interestingly, this biosensor can be simultaneously applied for evaluation of genotoxicity and cytotoxicity. The SOS-EGFP bacterial biosensor provides a sensitive, specific and simple method for detecting known and potential DNA damaging chemicals.     

Cytochrome P450 BM3 of Bacillus megaterium—A possible endosulfan biotransforming gene

Computing chemistry was applied to understand biotransforrnation mechanism of an organochlorine pesticide, endosulfan. The stereo specific metabolic activity of human CYP-2B6 （cytochrome P450） on endosulfan has been well demonstrated. Sequence and structural similarity search revealed that the bacterium Bacillus megaterium encodes CYP-BM3, which is similar to CYP-2B6. The functional similarity was studied at organism level by batch-scale studies and it was proved that B. megaterium could metabolize endosulfan to endosulfan sulfate, as CYP-2B6 does in human system. The gene expression analyses also confirmed the possible role of CYP-BM3 in endosulfan metabolism. Thus, our results show that the protein structure based in-silico approach can help us to understand and identify microbes for remediation strategy development. To the best of our knowledge this is the first report which has extrapolated the bacterial gene for endosulfan biotransformation through in silico prediction approach for metabolic gene identification.     

Development of marginal emission factors for N losses from agricultural soils with the DNDC–CAPRI meta-model

The article discusses marginal emission factors for N losses from agricultural soils, with rape and wheat as examples, and presents results for EU15 as high-resolution maps and aggregated to Member State level. The results are generated by linking the economic model for the agricultural sector CAPRI (Common Agricultural Policy Regional Impact) with spatial down-scaling, and a statistical meta-model for the bio-physical model DNDC (DeNitrification–DeComposition). For a given agro-economic scenario, CAPRI supplies for each crop the crop share, yield and fertilizer application rate spatially downscaled to clusters of 1 km × 1 km grid cells. The results from CAPRI are processed by a meta-model of DNDC to estimate the local greenhouse gas emissions from the soil. DNDC is a dynamic process-oriented model, which estimates trace gas fluxes and nutrient turnover in agricultural soils. The fit of the regressions is typically very good (0.95R² for the majority of the regressions), and all coefficients are significant at 99% probability. The meta-model allows a seamless integration between the economic and the bio-physical models, offering additional benefit such as the site-specific calibration of the bio-physical model ensuring the match between simulated and observed yield at the grid-level.The meta-model is used to calculate marginal emission factors for a 1 kg ha⁻¹ increase of mineral N and manure fertilizer rates for rape and wheat, at different levels of fertilization. They show that for Western European farming practice, only a small fraction of extra nitrogen fertilizer would go into increased yields: most of it would be emitted to the environment. The largest spatial variability is observed for N₂O emissions. The derivation of marginal emission factors is just one of the many possible uses for the linked regionalized agro-economic and soil chemistry model, which exploits to a large extent both geo-referenced and regionally available statistical information at European scale.     

紫外线和次氯酸钠对Escherichia coli和Poliovirus的消毒作用

本研究选用大肠杆菌(Escherichia coli)和脊髓灰质炎病毒(poliovirus)分别作为典型的细菌和病毒,利用培养和定量PCR的检测技术,对比研究紫外线消毒和次氯酸钠消毒对细菌和病毒的作用特点.结果表明:脊髓灰质炎病毒比大肠杆菌更难被灭活,达到1-log所需的氯剂量分别为19.2 mg·L~(-1)·min和10.14 mg·L~(-1)·min;所需的紫外线剂量分别为6.37 m J·cm~(-2)和1.81 m J·cm~(-2).定量PCR方法检测大肠杆菌和脊髓灰质炎病毒达到1-log的核酸损伤所需的紫外线剂量和氯剂量要比培养法高出1~2数量级,紫外线消毒对脊髓灰质炎病毒的RNA损伤量明显大于对大肠杆菌的DNA损伤,病毒的单链RNA对紫外线的敏感性更强,该结果与培养法正好相反.达到1-log核酸损伤脊髓灰质炎病毒所需的紫外线剂量为135 m J·cm~(-2),大肠杆菌所需的剂量为270.3 m J·cm~(-2),核酸损伤需要更多的消毒剂量,可能由于消毒过程微生物进入活性但处于非可培养状态(VBNC),以及灭活对微生物其他分子的损伤和微生物死后核酸的持续性.     

Prenatal diagnosis of CLCN4-related neurodevelopmental disorder in fetuses with congenital brain anomalies

We report two male fetuses born to a healthy unrelated couple, with agenesis of the corpus callosum identified on detailed 20-week ultrasound scans and confirmed by in-utero MRI. Whole-genome sequencing identified a likely pathogenic missense variant in the CLCN4 gene, establishing this as the causative gene in the family. Pathogenic variants in the CLCN4 gene cause a neurodevelopmental disorder (also called Raynaud-Claes syndrome) inherited in an X-linked pattern. The disorder is characterised by developmental delay, intellectual disability, autism spectrum disorder, epilepsy, mental health conditions, and significant feeding difficulties, predominantly, but not exclusively, affecting males. This is the first report of a prenatal phenotype associated with variants in the CLCN4 gene. The diagnosis of the CLCN4-related neurodevelopmental disorder in this family allowed accurate genetic counseling and discussion of reproductive choices. This leaves uncertainty about the possibility of a postnatal neurodevelopmental phenotype in heterozygous females, which we discuss.     

Atlantic sturgeons (<Emphasis Type="Italic">Acipenser sturio</Emphasis>, <Emphasis Type="Italic">Acipenser oxyrinchus</Emphasis>): American females successful in Europe

Recent molecular data on the maternally inherited mitochondrial (mt) DNA have challenged the traditional view that the now extinct Baltic sturgeon population belonged to the European sturgeon Acipenser sturio. Instead, there is evidence that American sea sturgeon Acipenser oxyrinchus historically immigrated into the Baltic Sea. In this study, we test the hypothesis that A. oxyrinchus introgressed into, rather than replaced, the A. sturio population in the Baltic. We established four single nucleotide polymorphisms (SNPs) in the nuclear MHC II antigen gene with a species-specific SNP pattern. Using an ancient DNA approach and two independent lines of molecular evidence (sequencing of allele-specific clones, SNaPshot), we detected both A. sturio and A. oxyrinchus alleles in the available museum material of the now extinct Baltic sturgeon population. The hybrid nature of the Baltic population was further confirmed by very high levels of heterozygosity. It had been previously postulated that the immigration of the cold-adapted A. oxyrinchus into the Baltic occurred during the Medieval Little Ice Age, when temperature likely dropped below the degree inducing spawning in A. sturio. Under this scenario, our new findings suggest that the genetic mosaic pattern in the Baltic sturgeon population (oxyrinchus mtDNA, sturio and oxyrinchus MHC alleles) is possibly caused by sex-biased introgression where spawning was largely restricted to immigrating American females, while fertilization was predominantly achieved by abundant local European males. The hybrid nature of the former Baltic sturgeon population should be taken into account in the current reintroduction measures. Electronic supplementary material  Supplementary material is available in the online version of this article at and is accessible for authorized users.     

N and P dynamics in the litter layer and soil of Mexican semi-arid forests, state of Morelos

In central Mexico, it is common for farmers to retain useful trees in abandoned lands after maize cultivation, creating a park-like landscape of scattered trees for extensive livestock grazing, among other land uses (mature forests, secondary forests, and livestock grazing in secondary forests). Among these trees Acacia cochliancantha and Ipomoea arborescens are the most common species associated with this land use in the region. The objective of this study was to assess the effects of both tree species on soil N and P recycling. To this end, we measured N and P concentrations in leaves of both species; and the seasonal N and P (total and dissolved) content in the litter, and total N and P, inorganic N, and bicarbonate-extractable-P concentrations, and the N transformations in the soil, in samples collected under crown of Acacia and Ipomoea and in open areas. Trees of different species varied in their capacity to cycle N. The leaves of Acacia were richer in N than those of Ipomoea (29.7 and 25.0 mg N g⁻¹, respectively), and nutrient resorption was higher in leguminous trees than in Ipomoea (by 20% in the case of N, and 35% in the case of P). Acacia trees had higher effects on soils than Ipomoea trees, like consistent increases of N concentrations (by 30% in the case of total N, and by 50% in the case of inorganic N) and transformations (N mineralization and nitrification in rainy season increases by a factor of 20 and 36, respectively). On the other hand, Ipomoea produced senescent leaves and accumulated forest litter with less P concentration (0.8 and 0.7 mg P g⁻¹, respectively) in relation to Acacia (senescent leaves: 1.3 mg P g⁻¹; litter: 1.1 mg P g⁻¹), reflecting the lower availability of the nutrient in the soil. The total litter N and P pools decreased in the rainy season under crown of both species, as the dissolved P pool did. The total soil N and P concentrations did not change with sampling season. However, potential N transformations and bicarbonate P under both species were higher in dry season than in rainy season samples. Comparison with other land uses in the region suggests that the Acacia–Ipomoea system cycles low quantity of nutrients, but there are no notable differences in the availability of P in the soils. These results demonstrate that scattered trees improve the N and P cycling following the discontinuation of agricultural practices, and the effects will vary depending on the tree species.     

Prenatal diagnosis of a lethal form of Netherton syndrome by SPINK5 mutation analysis

Netherton syndrome (NS) is a severe autosomal recessive ichthyosis with no specific treatment or prenatal diagnosis available at present. The recent identification of SPINK5, which encodes a serine protease inhibitor, as the defective gene enables DNA-based prenatal diagnosis to be carried out. Here we report the first direct molecular prenatal diagnosis of a lethal form due to a recurrent SPINK5 mutation in three consanguineous Turkish families. XmnI restriction enzyme digestion and DNA sequencing demonstrated that each deceased affected child was homozygous for mutation 153delT inherited from each parent. Analysis of fetal DNA from amniotic fluid cells in Family 1 and from a chorionic villus sampling in Family 3 showed that the fetus was heterozygous for 153delT in both cases. The pregnancies were carried to term and the newborns were unaffected. In Family 2, fetal DNA analysis from chorionic villus biopsy showed in a first pregnancy that the fetus was homozygous for 153delT. The pregnancy was terminated at 13 weeks and DNA analysis of fetal keratinocytes confirmed the prenatal prediction. In a second pregnancy in Family 2, fetal DNA analysis showed heterozygosity for 153delT, and the pregnancy was continued. Direct SPINK5 mutation analysis in families at risk for NS represents the first early, rapid and reliable method for prenatal diagnosis of this life-threatening form of ichthyosis. Copyright © 2002 John Wiley & Sons, Ltd.     

Prenatal exclusion of haemophilia a and carrier testing by direct detection of a disease lesion

A novel mutation was detected in the Factor VIII gene of a sporadic case of severe haemophilia A. The lesion, a CGA → TGA transition, converts Arg 795 to Term and adequately accounts for the severe phenotype observed. PCR/direct sequencing was used to confirm the carrier status in the mother. Exclusion of haemophilia A in an at-risk pregnancy was then achieved by demonstration of the absence of this lesion in fetal DNA from a chorionic villus sample. The mutation was also detectable by chemical cleavage of mismatch (CCM), which both confirmed the prenatal diagnosis and established the carrier status of the proband's sister. This example therefore serves to illustrate the potential of direct gene analysis in sporadic cases of haemophilia A and/or in families uninformative for known RFLPs.     

H_2O_2诱导拟南芥NIT2基因甲基化特征与转录水平改变

用外源H2O2处理拟南芥植株,亚硫酸氢盐修饰后测序法分析胁迫生理中NIT2基因启动子区甲基化特征变化,RT-PCR检测该基因的转录水平.结果显示:用100#mol·L-1的H2O2处理3 h后,NIT2启动子区胞嘧啶总甲基化水平与对照差异不大,但对照组CHG(H为C、A或T)和CG位点甲基化水平分别为35.0%和93.3%,H2O2处理组CHG和CG位点甲基化水平分别为50.0%和96.9%;H2O2处理组CHH位点则表现为甲基化水平升高、降低或去甲基化;H2O2胁迫组拟南芥地上组织中NIT2基因转录水平提高.研究结果表明:NIT2基因的转录应答和DNA甲基化修饰参与了植株的逆境生理过程;氧化胁迫与DNA甲基化改变、基因转录上调同时发生,说明胁迫诱发的活性氧增高可能参与胞嘧啶甲基化修饰和基因转录的调节.     

Rapid matching in Drosophila place learning

The level of conditioned behavior in animals is proportional to the intensity, amount, frequency, or probability of reinforcement. Interestingly, this matching can be dynamic, with performance levels following, for example, a switch in the probability of reinforcement with a short delay. We previously found that conditioned performance levels in Drosophila match reinforcement intensity in a place conditioning paradigm. Whether Drosophila can match conditioned behavior to a change in reinforcement intensity was an open question. In this study, we found that both conditioned behavior and memory levels match reinforcement intensity after a switch, and this rapid matching occurs within 2 min. Thus, fruit flies can dynamically match conditioned behavior and memory levels to a change in reinforcement intensity.