Saving Our Planet's Flora, the Contribution of the French National Natural History Museum to the Implementation of the Global Strategy for Plant Conservation

The National Natural History Museum plays a key role in the implementation of the GSPC through its botanical gardens,the Conservatoire Botanique National du Bassin Parisien,the Herbarium,and also by providing expertise on all areas of the Strategy(botany,conservation,ethonobotany,article 8j,substainable use),etc.For 2 of the goals of GSPC(conserving plant diversity,Understanding and Documenting Plant Diversity),the Muséum has developed activities all over the world,including compilation of various flora and...     

《昆明-蒙特利尔全球生物多样性框架》核心目标与我国的保护行动建议

在中国作为主席国的引领下,联合国《生物多样性公约》(以下简称《公约》)第十五次缔约方大会(以下简称COP15)第二阶段会议通过了62项决定,特别是达成了以变革理论为基础的《昆明-蒙特利尔全球生物多样性框架》(以下简称《昆蒙框架》),为全球生物多样性治理擘画了新的蓝图。该文就《昆蒙框架》的三个核心目标——保护地“3030目标”、资源调动、遗传资源数字序列信息进行解读,对保障《昆蒙框架》落地的相关决议进行简要介绍,并就我国未来的保护行动提出了相关建议:(1)加强生物多样性保护的主流化;(2)进一步制定详细的保护计划,明确保护区域的范围、目的和管理措施,并落实实施计划的责任部门和具体措施;(3)根据框架目标的监测要求,制定可操作的指标体系和监测计划;(4)继续加强生物多样性保护的意识和教育,提高公众对生物多样性保护的认识和重视程度,促进全社会的可持续生产和可持续消费;(5)大力推进国际合作,在更大尺度上探索和促进基于自然的解决方案,寻找对自然产生正面、积极效果的经济和社会发展路径。     

稻属中一个高度保守和组成型表达酪氨酸／丝氨酸－酸酸双特性蛋白激酶基因的克隆与分析

从水稻中克隆了一个在稻属植物中高度保守和组成型表达的丝氨酸／苏氨酸蛋白激酶基因（OsSTK）。该基因包含两个外显子和一个114bp的小内含子序列,预测编码一个419个氨基酸的蛋白质。该基因推导的氨基酸序列与其它已知序列的一致性均低于52％。利用从不同种和类型的野生稻克隆的部分该基因序列构建的系统树与野生稻的分类和进化关系相一致。OSPKN-端拥有一段富含丝氨酸、碱性氨基酸和带电荷氨基酸的特异性导肽序列,其中包含“GDGDGDGDG”短重复序列。由于该基因蛋白激酶结构域中的VIb,VIII和XI亚结构域中同时具有酪氨酸蛋白激酶和丝氨酸／苏氨酸蛋白激酶的特性,推测该基因可能同时具有催化酪氨酸和丝氨酸、苏氨酸磷酸化的双重功能。     

Conformational changes in a Vernier zone region: Implications for antibody dual specificity

Understanding the determinants of antibody specificity is one of the challenging tasks in antibody development. Monospecific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase the overall therapeutic effect. Dual-specific or “Two-in-One” antibodies can bind to two different antigens separately with the same antigen-binding site as opposed to bispecifics, which simultaneously bind to two different antigens through separate antigen-binding units. These nonstandard dual-specific antibodies were recently shown to be promising for new antibody-based therapeutics. Here, we physicochemically and structurally analyzed six different antibodies of which two are monospecific and four are dual-specific antibodies derived from monospecific templates to gain insight about dual-specificity determinants. These dual-specific antibodies can target both human epidermal growth factor receptor 2 and vascular endothelial growth factor at different binding affinities. We showed that a particular region of clustered Vernier zone residues might play key roles in gaining dual specificity. While there are minimal intramolecular interactions between a certain Vernier zone region, namely LV4 and LCDR1 of monospecific template, there is a significant structural change and consequently close contact formation between LV4-LCDR1 loops of derived dual-specific antibodies. Although Vernier zone residues were previously shown to be important for humanization applications, they are mostly underestimated in the literature. Here, we also aim to resurrect Vernier zone residues for antibody engineering efforts.     

SNO spectral counting (SNOSC), a label-free proteomic method for quantification of changes in levels of protein S-nitrosation

Abstract

S-Nitrosation plays an important role in regulation of protein function and signal transduction. Discovering S-nitrosated targets is a prerequisite for further functional study. However, current proteomic methods used to quantify S-nitrosation are limited in their applicability to certain types of samples, or by the need for special reagents and complex procedures to obtain the results. Here we devised a label-free proteomic method for quantification of changes in the level of protein S-nitrosation on the basis of a spectral counting strategy, called S-nitrosothiol (SNO) spectral counting (SNOSC). With this method, samples can be from any source (cells, tissues); there is no need for labelling reagents or procedures, and the results yield quantitative information. Moreover, as it is based on the irreversible biotinylation procedure (IBP) for S-nitrosation protein enrichment, false positive targets caused by the interference of intermolecular disulphide bonds are ruled out. Using SNOSC we studied S-nitrosation in the cell line RAW264.7 induced exogenously with S-nitrosoglutathione (GSNO), or induced endogenously by lipopolysaccharides/interferon-gamma (LPS/IFN-γ). We detected a significant increase in S-nitrosation of 50 proteins after exogenous induction and 17 proteins after endogenous induction. We thus demonstrate that SNOSC is a widely applicable proteomic method for fast screening of SNO proteins.     

sampbias,a method for quantifying geographic sampling biases in species distribution data

Geo‐referenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a factor limiting the usefulness of such data for understanding species diversity and distribution. In particular, differences in sampling intensity across a landscape due to differences in human accessibility are ubiquitous but may differ in strength among taxonomic groups and data sets. Although several factors have been described to influence human access (such as presence of roads, rivers, airports and cities), quantifying their specific and combined effects on recorded occurrence data remains challenging. Here we present sampbias, an algorithm and software for quantifying the effect of accessibility biases in species occurrence data sets. sampbias uses a Bayesian approach to estimate how sampling rates vary as a function of proximity to one or multiple bias factors. The results are comparable among bias factors and data sets. We demonstrate the use of sampbias on a data set of mammal occurrences from the island of Borneo, showing a high biasing effect of cities and a moderate effect of roads and airports. sampbias is implemented as a well‐documented, open‐access and user‐friendly R package that we hope will become a standard tool for anyone working with species occurrences in ecology, evolution, conservation and related fields.     

Allometry of Prosopis glandulosa var. torreyana along a topographic gradient in the Chihuahuan desert

Abstract. The allometric relationships of trees in temperate and tropical forests are relatively well known, but not those of woody shrubs or transitional (shrub/tree) life forms. We explored the transition of Prosopis glandulosa var. torreyana from tree to shrub along a semi‐arid topographic sequence comprising of six landforms (hillslope, footslope, upper and lower bajada, playa and dune) with varying soil texture and water availability. In each landform, we measured P. glandulosa shoot pre‐dawn water potentials (Ψ) in one ‘dry’ and one ‘wet’ year. We also measured plant height, widest basal stem diameter, crown area and number of basal branches. Total basal stem area was calculated. We used simple (Model II linear regression) and expanded (incorporating an asymptote to height or crown area) allometry models to compare height with widest basal stem diameter and crown area with total basal stem area. There were significant correlations between maximum plant size and inter‐year Ψ means suggesting that soil water availability decreased down the topographical sequence. The height asymptote was statistically significant in all landforms and lower toward finer‐textured soils. On the other hand, crown area was a linear function of total basal stem area and was also site specific. Our results suggest that more basal branches are produced as plant height decreases in more stressful environments, effectively increasing crown area with a minimum investment in supporting tissues. The polymorphic characteristics of Prosopis may partly explain their occurrence in many arid and semi‐arid environments.     

A strategy to accelerate protein production from a pool of clones in Chinese hamster ovary cells for toxicology studies

In the biopharmaceutical industry, a clonally derived cell line is typically used to generate material for investigational new drug (IND)‐enabling toxicology studies. The same cell line is then used to generate material for clinical studies. If a pool of clones can be used to produce material for IND‐enabling toxicology studies (Pool for Tox (PFT) strategy) during the time a lead clone is being selected for clinical material production, the toxicology studies can be accelerated significantly (approximately 4 months at Genentech), leading to a potential acceleration of 4 months for the IND submission. We explored the feasibility of the PFT strategy with three antibodies—mAb1, mAb2, and mAb3—at the 2 L scale. For each antibody, two lead cell lines were identified that generated material with similar product quality to the material generated from the associated pool. For two antibody molecules, mAb1 and mAb2, the material generated by the lead cell lines from 2 L bioreactors was tested in an accelerated stability study and was shown to have stability comparable to the material generated by the associated pool. Additionally, we used this approach for two antibody molecules, mAb4 and mAb5, at Tox and GMP production. The materials from the Tox batch at 400 L scale and three GMP batches at 2000 L scale have comparable product quality attributes for both molecules. Our results demonstrate the feasibility of using a pool of clonally derived cell lines to generate material of similar product quality and stability for use in IND‐enabling toxicology studies as was derived from the final production clone, which enabled significant acceleration of timelines into clinical development. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1449–1455, 2017     

Transferrin response in normal and iron-deficient mice heterozygotic for hypotransferrinemia; effects on iron and manganese accumulation

Hypotransferrinemia is a genetic defect in mice resultingin 1% of normal plasma transferrin (Tf) concen-trations;heterozygotes for thismutation (+/hpx) have low circulating Tf concentrations. These mice providea unique opportunity toexamine the developmental pattern and response of Tf to iron-deficient diets, andfurthermore,to address the controversial role of Tf in Mn transport. Twenty-three weanling +/hpx miceandforty-five wild-type BALB/cJ mice were either killed at weaning or fed diets containing either13 or 72 mgkg Fe, and killed after four or eight weeks. Plasma Tfconcentrations were lower in +/hpx mice, plasmaTf nearly doubled and liver Tf was only 50% of normalin response to iron deficiency. Brain iron concen-trationdid not correlate significantlywith either plasma Tf or TIBC. However, iron accumulation into braincontinued with irondeficiency whereas most other organs had less iron. These results imply that eitherthereis a selected targeting of iron to the brain by plasma Tf or there is an alternative irondelivery system tothe brain. Furthermore, we observed no differences in tissuedistribution of Mn despite the differences incirculating Tf concentrationsand body iron stores; this suggests that there are non-Tf dependent mecha-nismsfor Mntransport.     

Development of a Simple PCR-based Marker for the Determination of Growth Habit in Vicia faba L. using a Candidate Gene Approach

We have developed the first molecular marker suitable for the selection of determinate growth habit in faba bean using the candidate gene approach. We obtained the sequences of TFL1/CEN like genes from public databases and designed primers on conserved domains. We used three cultivars with determinate growth habit and four accessions (two cultivars and two lines) with indeterminate growth habit. All these genotypes are used in our faba bean breeding program. A single monomorphic PCR fragment was obtained. A set of restriction enzymes was assayed. The enzyme Hind1II produced a clear polymorphism between determinate and indeterminate genotypes. This new cleaved amplified polymorphism (CAP) marker was tested using an F₂ population contrasting for growth habit derived from the cross ‘Verde Bonita’ × 2N52. This marker showed 100% efficiency in discriminating both types of genotypes. Moreover, the codominancy of this marker allows the detection of heterozygous individuals facilitating the breeding process when pyramiding different genes. The perfect cosegregation of the marker with the trait indicates that an orthologue of TFL1/CEN controls the growth habit in faba bean. This marker has been tested in all the genotypes used in our faba bean breeding program as donors of the determinate growth habit. Therefore, it is expected to work well in all the crosses performed with these parental lines as happens in the F₂ tested. The CAPS marker developed in this work will be useful for Marker Assisted Selection programs. In addition, this marker is useful for quality control to determinate the percentage of outsider seeds in commercial seed lots. Moreover, it is a valuable tool to breeders when submitting new faba bean varieties for registration since the method allows guaranteeing that outsider plants remains under the requested limit for registration.     

Liquid chromatographic and tandem mass spectrometric assay for evaluation of in vivo inhibition of rat brain monoamine oxidases (MAO) A and B following a single dose of MAO inhibitors: application of biomarkers in drug discovery

A simple and selective assay for the evaluation of in vivo inhibition of rat brain monoamine oxidases (MAO) A and B following a single dose of MAO inhibitors was developed through the simultaneous determination of endogenous 5-hydroxy tryptamine, 5-hydroxyindole-3-acetic acid (5-HIAA), tryptophane, and 2-phenethylamine (PEA) in rat brain using liquid chromatography-tandem mass spectrometry (LC/MS/MS). These analytes were separated on a Zorbax SB-C18 column using a gradient elution with acetonitrile and 0.2% formic acid and detected on an electrospray ionization mass spectrometer in positive-ion multiple-reaction-monitoring mode. The susceptibility and variability of these analytes as potential biomarkers in response to MAO inhibition in vivo were evaluated after application to three MAO inhibitors, tranylcypromine, clorgyline, and pargyline. A dramatic increase (about 40-fold) in PEA brain level and a decrease in 5-HIAA by more than 90% were observed after administration of 15 mg/kg of the nonselective MAO inhibitor tranylcypromine. As expected, the brain level of PEA escalated to about 6-fold, while the 5-HIAA level remained unchanged following a dose of the MAO B inhibitor pargyline at 2mg/kg. In contrast, the brain level of 5-HIAA reduced by approximately 53%, but the PEA level was unaffected following the same dose of the MAO A inhibitor clorgyline. The results indicated that 5-HIAA and PEA were susceptible and effective biomarkers in the rat brain in response to MAO A and B inhibition, respectively. The LC/MS/MS method is useful not only for the determination of inhibitory potency but also for the differentiation of the selectivity of a MAO inhibitor against rat brain MAO A and B in vivo.     

Sleep Biological Rhythms in Normal Infants and those at High Risk for SIDS

The focus of this study was on daytime and nighttime sleep and wakefulness during the peak age for Sudden Infant Death Syndrome (SIDS), two to four months, to determine whether there are differences between at‐risk for SIDS (R) and control (C) infants. Such differences may provide insight on the frequent occurrence of SIDS in the early morning hours, when most babies are asleep. This is the only study in which R and C infants were continuously monitored for long periods of time (24–48 h) and then followed and recorded at monthly intervals until the age of 4–6 months. Data analyses indicate that ultradian REM/NREM cyclicity becomes stabilized into a regular pattern at three months of age. Infants at this age convert from a polyphasic sleep/wakefulness pattern to a circadian one. Among the changes that occur is a lengthening of short sleep periods that consolidate at night and wake periods that consolidate in the daytime. The most striking effects are related to sleep state and vary according to age and sex. The lengthening of single sleep and wakeful periods is coupled with the maturation of the brain. The development of the central nervous system facilitates the synchronization of sleeping patterns with external light input and social entrainment. One or more biological clocks or oscillators may be responsible for these REM/NREM patterns and circadian cycles. These differences during the early morning hours, when the occurrence of SIDS peaks, may have important implications for understanding the pathophysiological mechanism of SIDS.     

Sleep biological rhythms in normal infants and those at high risk for SIDS

The focus of this study was on daytime and nighttime sleep and wakefulness during the peak age for Sudden Infant Death Syndrome (SIDS), two to four months, to determine whether there are differences between at-risk for SIDS (R) and control (C) infants. Such differences may provide insight on the frequent occurrence of SIDS in the early morning hours, when most babies are asleep. This is the only study in which R and C infants were continuously monitored for long periods of time (24-48 h) and then followed and recorded at monthly intervals until the age of 4-6 months. Data analyses indicate that ultradian REM/NREM cyclicity becomes stabilized into a regular pattern at three months of age. Infants at this age convert from a polyphasic sleep/wakefulness pattern to a circadian one. Among the changes that occur is a lengthening of short sleep periods that consolidate at night and wake periods that consolidate in the daytime. The most striking effects are related to sleep state and vary according to age and sex. The lengthening of single sleep and wakeful periods is coupled with the maturation of the brain. The development of the central nervous system facilitates the synchronization of sleeping patterns with external light input and social entrainment. One or more biological clocks or oscillators may be responsible for these REM/NREM patterns and circadian cycles. These differences during the early morning hours, when the occurrence of SIDS peaks, may have important implications for understanding the pathophysiological mechanism of SIDS.     

Monitoring PCDD/Fs in Soil and Herbage Samples Collected Near a Hazardous Waste Incinerator: Health Risks for the Population Living Nearby

In 1998, we started a wide environmental surveillance program focused on evaluating the environmental impact of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) emitted by a new hazardous waste incinerator (HWI) (Tarragona County, Catalonia, Spain) and assessing the potential health risks for the population living nearby. The HWI began regular operations in 1999. Since then, periodical surveys have been performed. We report here the results concerning PCDD/F levels in 40 soil and 40 herbage samples collected in years 2004 and 2005, respectively, in the vicinity of the HWI. The human health risks derived from exposure to PCDD/Fs were also assessed. PCDD/F concentrations in soils ranged from 0.06 to 12.60 ng I-TEQ/kg, with median and mean values of 0.65 and 1.14 ng I-TEQ/kg, respectively. In herbage, PCDD/F concentrations ranged from 0.03 to 1.57 ng I-TEQ/kg, with median and mean values of 0.31 and 0.40 ng I-TEQ/kg, respectively. A comparison of these results with those from the baseline survey shows that, after six years of regular operation, the HWI did not significantly increase PCDD/F levels in soils and herbage in the surrounding environment. Moreover, PCDD/F emissions from the HWI do not mean additional significant risks for the health of the individuals living in the vicinity of the facility. The results of the current study together with those of recent investigations in municipal waste incinerators indicate that, when adequately controlled for PCDD/F emissions, modern waste incinerators should not portend any special concern for the populations living nearby.     

Lysyl-tRNA synthetase from Bacillus stearothermophilus: the Trp314 residue is shielded in a non-polar environment and is responsible for the fluorescence changes observed in the amino acid activation reaction

Three Trp variants of lysyl-tRNA synthetase from Bacillus stearothermophilus, in which either one or both of the two Trp residues within the enzyme (Trp314 and Trp332) were substituted by a Phe residue, were produced by site-directed mutagenesis without appreciable loss of catalytic activity. The following two phenomena were observed with W332F and with the wild-type enzyme, but not with W314F: (1) the addition of L-lysine alone decreased the protein fluorescence of the enzyme, but the addition of ATP alone did not; (2) the subsequent addition of ATP after the addition of excess L-lysine restored the fluorescence to its original level. Fluorometry under various conditions and UV-absorption spectroscopy revealed that Trp314, which was about 20A away from the lysine binding site and was shielded in a non-polar environment, was solely responsible for the fluorescence changes of the enzyme in the L-lysine activation reaction. Furthermore, the microenvironmental conditions around the residue were made more polar upon the binding of L-lysine, though its contact with the solvent was still restricted. It was suggested that Trp314 was located in a less polar environment than was Trp332, after comparison of the wavelengths at the peaks of fluorescence emission and of the relative fluorescence quantum yields. Trp332 was thought, based on the fluorescence quenching by some perturbants and the chemical modification with N-bromosuccinimide, to be on the surface of the enzyme, whereas Trp314 was buried inside. The UV absorption difference spectra induced by the L-lysine binding indicated that the state of Trp314, including its electrostatic environment, changed during the process, but Trp332 did not change. The increased fluorescence from Trp314 at acidic pH compared with that at neutral pH suggests that carboxylate(s) are in close proximity to the Trp314 residue.     

BCR-ABL Gene Expression Is Required for Its Mutations in a Novel KCL-22 Cell Culture Model for Acquired Resistance of Chronic Myelogenous Leukemia

Acquired resistance through genetic mutations is a common phenomenon in several cancer therapies using molecularly targeted drugs, best exemplified by the BCR-ABL inhibitor imatinib in treating chronic myelogenous leukemia (CML). Overcoming acquired resistance is a daunting therapeutic challenge, and little is known about how these mutations evolve. To facilitate understanding the resistance mechanisms, we developed a novel culture model for CML acquired resistance in which the CML cell line KCL-22, following initial response to imatinib, develops resistant T315I BCR-ABL mutation. We demonstrate that the emergence of BCR-ABL mutations do not require pre-existing BCR-ABL mutations derived from the original patient as the subclones of KCL-22 cells can form various BCR-ABL mutations upon imatinib treatment. BCR-ABL mutation rates vary from cell clone to clone and passages, in contrast to the relatively stable mutation rate of the hypoxanthine-guanine phosphoribosyltransferase gene. Strikingly, development of BCR-ABL mutations depends on its gene expression because BCR-ABL knockdown completely blocks KCL-22 cell relapse on imatinib and acquisition of mutations. We further show that the endogenous BCR-ABL locus has significantly higher mutagenesis potential than the transduced randomly integrated BCR-ABL cDNA. Our study suggests important roles of BCR-ABL gene expression and its native chromosomal locus for acquisition of BCR-ABL mutations and provides a new tool for further studying resistance mechanisms.