Technical note: False catastrophic age‐at‐death profiles in commingled bone deposits

Age‐at‐death profiles obtained using the minimum number of individuals (MNI) for mass deposits of commingled human remains may be biased by over‐representation of subadult individuals. A computer simulation designed in the R environment has shown that this effect may lead to misinterpretation of such samples even in cases where the completeness rate is relatively high. The simulation demonstrates that the use of the Most Likely Number of Individuals (MLNI) substantially reduces this bias. Am J Phys Anthropol 152:554–557, 2013. © 2013 Wiley Periodicals, Inc.     

Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed

Brassica napus (AACC, 2n = 38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large‐scale introgression events on this young tetraploid. In this study, we reported the de novo assembly of the genome sequences of an Asian rapeseed (B. napus), Ningyou 7, and its four progenitors and compared these genomes with other available genomic data from diverse European and Asian cultivars. Our results showed that Asian rapeseed originally derived from European rapeseed but subsequently significantly diverged, with rapid genome differentiation after hybridization and intensive local selective breeding. The first historical introgression of B. rapa dramatically broadened the allelic pool but decreased the deleterious variations of Asian rapeseed. The second historical introgression of the double‐low traits of European rapeseed (canola) has reshaped Asian rapeseed into two groups (double‐low and double‐high), accompanied by an increase in genetic load in the double‐low group. This study demonstrates distinctive genomic footprints and deleterious SNP (single nucleotide polymorphism) variants for local adaptation by recent intra‐ and interspecies introgression events and provides novel insights for understanding the rapid genome evolution of a young allopolyploid crop.     

基于土地利用变化的四川省碳排放与碳足迹效应及时空格局

土地利用变化的碳排放与碳足迹研究对了解人类活动对生态环境的扰动程度及其机理、制定有效的碳排放政策具有重要意义。采用1990—2010年四川省能源消费数据和土地利用数据,通过构建碳排放模型、碳足迹及其压力指数模型,对研究区20年来土地利用的碳排放及碳足迹进行了定量分析。结果表明:(1)土地利用变化的碳排放和能源消费碳的足迹呈显著增加趋势。碳排放增加5407.839×10~4t,增长率达143%;能源消费的碳足迹增加1566.622×10~4hm~2,四川全省的生态赤字达1563.598×10~4hm~2。(2)建设用地和林地分别为四川省最大的碳源与碳汇。20年间建设用地的碳排放增加5407.072×10~4t,增长率达126.27%,占碳排放总量的88%以上;林地的碳汇减少10.351×10~4t,但仍占四川省碳汇的96%以上。(3)土地利用碳排放、碳足迹和生态赤字存在明显区域差异。成都平原区碳排放、碳足迹压力最大,生态赤字严重,西部高山高原区和盆周山区碳排放、碳足迹最小,未出现生态赤字;成都、德阳、资阳和内江等地的碳排放、碳足迹压力最大,生态赤字最严重,甘孜、阿坝等地的碳排放、碳足迹最小,未出现生态赤字。(4)土地利用结构与碳排放、碳足迹存在一定的相互关系,趋高的碳源、碳汇比导致土地利用的碳源效应远大于碳汇效应。因此,四川省减排的重点应该在保持或增加现有的林地的同时,主要以降低建设用地的碳排放、碳足迹为主。     

First evidence of stegosaurian Deltapodus footprints in North Africa (Iouaridène Formation, Upper Jurassic, Morocco)

Abstract:  New findings of dinosaur footprints are described from the Upper Jurassic Iouaridène ichnosite of Morocco. On the top of two surfaces, stratigraphically close to that bearing the famous Breviparopus taghbaloutensis trackways, two footprints were excavated and assigned to the ichnogenus Deltapodus . This ichnogenus is well known from the Middle Jurassic of Yorkshire and also occurs in Upper Jurassic deposits from Iberia and the United States. This finding represents the first record of Deltapodus from Africa. These footprints, probably produced by stegosaurian dinosaurs, add new data on the distribution of this type of dinosaur and on the connection between the northern and southern margin of Tethys. 3D models have been generated to allow more detailed studies and to record these unique footprints.     

Copy number variation associates with mortality in long‐lived individuals: a genome‐wide assessment

Copy number variants (CNVs) represent a significant source of genetic variation in the human genome and have been implicated in numerous diseases and complex traits. To date, only a few studies have investigated the role of CNVs in human lifespan. To investigate the impact of CNVs on prospective mortality at the extreme end of life, where the genetic component of lifespan appears most profound, we analyzed genomewide CNV data in 603 Danish nonagenarians and centenarians (mean age 96.9 years, range 90.0–102.5 years). Replication was performed in 500 long‐lived individuals from the Leiden Longevity Study (mean age 93.2 years, range 88.9–103.4 years). First, we assessed the association between the CNV burden of each individual (the number of CNVs, the average CNV length, and the total CNV length) and mortality and found a significant increase in mortality per 10 kb increase in the average CNV length, both for all CNVs (hazard ratio (HR) = 1.024, P = 0.002) and for duplications (HR = 1.011, P = 0.005), as well as per 100 kb increase in the total length of deletions (HR = 1.009, P = 0.0005). Next, we assessed the relation between specific deletions and duplications and mortality. Although no genome–wide significant associations were discovered, we identified six deletions and one duplication that showed consistent association with mortality in both or either of the sexes across both study populations. These results indicate that the genome–wide CNV burden, specifically the average CNV length and the total CNV length, associates with higher mortality in long‐lived individuals.     

Niche construction,human behavior,and the adaptive‐lag hypothesis

Niche construction is the process whereby organisms modify selective environments, thereby affecting evolution. The niche‐construction perspective is particularly relevant to researchers using evolutionary methods to interpret human behavior and society. On the basis of niche‐construction theory, we argue against the hypothesis that modern humans experience an atypically large adaptive lag. We stress that humans construct their world largely to suit themselves and frequently buffer adaptive lag through cultural niche construction. Where they are unable to do that, natural selection of genes rapidly ensues. Our argument has implications for evolutionary psychology and human behavioral ecology, and suggests that the methods of the latter are potentially applicable to all human societies, even postindustrial ones.     

Comparative proteomic analysis in children with idiopathic short stature (ISS) before and after short‐term recombinant human growth hormone (rhGH) therapy

This study was undertaken to identify growth hormone (GH) responsive proteins and protein expression patterns by short‐term recombinant human growth hormone (rhGH) therapy in patients with idiopathic short stature (ISS) using proteomic analysis. Seventeen children (14 males and three females) with ISS were included. They were treated with rhGH at a dose of 0.31 ± 0.078 mg/kg/week for 3 months. Immunodepletion of six highly‐abundant serum proteins followed by 2D DIGE analysis, and subsequent MALDI TOF MS, were employed to generate a panel of proteins differentially expressed after short‐term rhGH therapy and verify the differences in serum levels of specific proteins by rhGH therapy. Fourteen spots were differentially expressed after rhGH treatment. Among them, apo E and apo L‐1 expression were consistently enhanced, whereas serum amyloid A was reduced after rhGH therapy. The differential expressions of these proteins were subsequently verified by Western blot analysis using sera of the before and after rhGH treatment. This study suggests that rhGH therapy influences lipoprotein metabolism and enhances apo L‐1 protein expression in ISS patients.     

Long‐term variability of Abies alba in NW Romania: implications for its conservation management

Aim Although Abies alba is not yet prioritized for conservation in many European countries, its importance is acknowledged under the EU Directive on the marketing for forest reproductive material. The Apuseni National Park contains one of the largest areas of remnant native A. alba in central eastern Europe. Here, we examine the antiquity of the present A. alba communities in the forests of NW Romania and the drivers behind their variability over the last 6000 years leading to current distribution pattern. Location The Apuseni National Park (ANP), NW Romania. Methods We use fossil pollen, microscopic and macroscopic charcoal and AMS¹⁴C dating on four sedimentary sites in the west‐central ANP. Results The results reveal that stands of A. alba have been growing in NW Romania from at least 5700 yr bp and occurred in low abundance until 4200 yr bp . A. alba expanded thereafter and it thrived in multispecies forest stands with Fagus, Picea, Carpinus, Tilia, Quercus and Ulmus between 4200 and 1200 yr bp . The initial expansion occurred during an independently documented period of high moisture and cooler temperature as inferred from isotope data from cave stalagmites within this region. The final decline in A. alba abundance and distribution started from about 1200 yr bp and reached an unprecedently low value over the last 300 years, which was primarily caused by the increase in human activities in the region through deforestation, forest browsing and burning, and commercial forestry. Main conclusion Different management strategies ranging from restriction on harvesting and browsing need to be implemented in this region if A. alba is going to survive the forecasted decrease in precipitation and increase in temperature, which will further reduce its spatial distribution.     

miRNA‐940 reduction contributes to human Tetralogy of Fallot development

Tetralogy of Fallot (TOF) is a complex congenital heart defect and the microRNAs regulation in TOF development is largely unknown. Herein, we explored the role of miRNAs in TOF. Among 75 dysregulated miRNAs identified from human heart tissues, miRNA‐940 was the most down‐regulated one. Interestingly, miRNA‐940 was most highly expressed in normal human right ventricular out‐flow tract comparing to other heart chambers. As TOF is caused by altered proliferation, migration and/or differentiation of the progenitor cells of the secondary heart field, we isolated Sca‐1⁺ human cardiomyocyte progenitor cells (hCMPC) for miRNA‐940 function analysis. miRNA‐940 reduction significantly promoted hCMPCs proliferation and inhibited hCMPCs migration. We found that JARID2 is an endogenous target regulated by miRNA‐940. Functional analyses showed that JARID2 also affected hCMPCs proliferation and migration. Thus, decreased miRNA‐940 affects the proliferation and migration of the progenitor cells of the secondary heart field by targeting JARID2 and potentially leads to TOF development.     

Why specific anti‐integrase antibodies from HIV‐infected patients can efficiently hydrolyze 21‐mer oligopeptide corresponding to antigenic determinant of human myelin basic protein

Human immunodeficiency virus‐infected patients possess anti‐integrase (IN) catalytic IgGs and IgMs (abzymes), which, unlike canonical proteases, specifically hydrolyze only intact globular IN. Anti‐myelin MBP abzymes from patients with multiple sclerosis and systemic lupus erythematosus efficiently hydrolyze only intact MBP. Anti‐MBP and anti‐IN abzymes do not hydrolyze several other tested control globular proteins. Here, we show that anti‐IN abzymes efficiently hydrolyze a 21‐mer oligopeptide (OP21) corresponding to one antigenic determinant (AGD) of MBP, whereas anti‐MBP abzymes extremely poorly cleave oligopeptides corresponding to AGDs of IN. All sites of IgG‐mediated and IgM‐mediated proteolysis of OP21 by anti‐IN abzymes were found for the first time by a combination of reverse phase and thin layer chromatography and mass spectrometry. Several clustered sites of OP21 cleavage were revealed and compared with the cleavage sites within the complete IN. Several fragments of OP21 had good homology with many fragments of the IN sequence. The active sites of anti‐IN abzymes are known to be located on their light chains, whereas heavy chains are responsible for the affinity for protein substrates. Interactions of intact IN with both light and heavy chains of the abzymes provide high affinity for IN and the specificity of its hydrolysis. Our data suggest that OP21 interacts mainly with the light chains of polyclonal anti‐IN abzymes, which possess lower affinity and specificity for substrate. The hydrolysis of the non‐cognate OP21 oligopeptide may be also less specific than the hydrolysis of the globular IN because in contrast to previously described serine protease‐like abzymes against different proteins, anti‐IN abzymes possess serine, thiol, acidic, and metal‐dependent protease activities. Copyright © 2013 John Wiley & Sons, Ltd.     

Structure of 6‐diazo‐5‐oxo‐norleucine‐bound human gamma‐glutamyl transpeptidase 1, a novel mechanism of inactivation

Intense efforts are underway to identify inhibitors of the enzyme gamma‐glutamyl transpeptidase 1 (GGT1) which cleaves extracellular gamma‐glutamyl compounds and contributes to the pathology of asthma, reperfusion injury and cancer. The glutamate analog, 6‐diazo‐5‐oxo‐norleucine (DON), inhibits GGT1. DON also inhibits many essential glutamine metabolizing enzymes rendering it too toxic for use in the clinic as a GGT1 inhibitor. We investigated the molecular mechanism of human GGT1 (hGGT1) inhibition by DON to determine possible strategies for increasing its specificity for hGGT1. DON is an irreversible inhibitor of hGGT1. The second order rate constant of inactivation was 0.052 mM ^?1 min^?1 and the K _i was 2.7 ± 0.7 mM . The crystal structure of DON‐inactivated hGGT1 contained a molecule of DON without the diazo‐nitrogen atoms in the active site. The overall structure of the hGGT1‐DON complex resembled the structure of the apo‐enzyme; however, shifts were detected in the loop forming the oxyanion hole and elements of the main chain that form the entrance to the active site. The structure of hGGT1‐DON complex revealed two covalent bonds between the enzyme and inhibitor which were part of a six membered ring. The ring included the OG atom of Thr381, the reactive nucleophile of hGGT1 and the α‐amine of Thr381. The structure of DON‐bound hGGT1 has led to the discovery of a new mechanism of inactivation by DON that differs from its inactivation of other glutamine metabolizing enzymes, and insight into the activation of the catalytic nucleophile that initiates the hGGT1 reaction.     

Occupational Status,Cortisol Secretory Pattern,and Visceral Obesity in Middle‐aged Men

Objective: Despite several studies indicating that social gradients are predictive of cardiovascular mortality, the pathogenetic mechanisms remain incompletely understood. Research Methods and Procedures: A population sample of 51‐year‐old men (N = 284) was divided into a socioeconomic gradient with manual laborers, civil servants, and university graduates. Anthropometric measurements were registered. Cortisol concentrations were measured in saliva, collected repeatedly during an ordinary working day, and a low‐dose dexamethasone suppression test was performed. Results: Lower socioeconomic status was associated with visceral obesity and higher cortisol values in relation to perceived stress. However, total cortisol secretion over the day of study was not elevated. The regulation of cortisol secretion showed less plasticity and dexamethasone inhibition was less efficient in the men in the lower socioeconomic status group than in those with a higher socioeconomic status. These are known consequences of long term stress. Longer duration in low socioeconomic conditions seemed to worsen these phenomena. Discussion: It was concluded that a low socioeconomic status is associated with perturbed cortisol secretion, which is elevated in relation to perceived stress. When the hypothalamic‐pituitary‐adrenal axis is subjected to prolonged increases in cortisol elicited by chronic stress, the regulation of cortisol secretion is affected, indicating neuroendocrine dysregulations. These observations may provide a means for understanding the association of socioeconomic impairments with visceral obesity and the social inequality in risk for prevalent and serious diseases.     

Characterization and high‐yield production of non‐N‐glycosylated recombinant human BCMA‐Fc in Pichia pastoris

B‐cell maturation antigen (BCMA) fused at the C‐terminus to the Fc portion of human IgG1 (BCMA‐Fc) blocks B‐cell activating factor (BAFF) and proliferation‐inducing ligand (APRIL)‐mediated B‐cell activation, leading to immune disorders. The fusion protein has been cloned and produced by several engineering cell lines. To reduce cost and enhance production, we attempted to express recombinant human BCMA‐Fc (rhBCMA‐Fc) in Pichia pastoris under the control of the AOX1 methanol‐inducible promoter. To produce the target protein with uniform molecular weight and reduced immunogenicity, we mutated two predicted N‐linked glycosylation sites. The secretory yield was improved by codon optimization of the target gene sequence. After fed‐batch fermentation under optimized conditions, the highest yield (207 mg/L) of rhBCMA‐Fc was obtained with high productivity (3.45 mg/L/h). The purified functional rhBCMA‐Fc possessed high‐binding affinity to APRIL and dose‐dependent inhibition of APRIL‐induced proliferative activity in vitro through three‐step purification. Thus, this yeast‐derived expression method could be a low‐cost and effective alternative to the production of rhBCMA‐Fc in mammalian cell lines.     

4‐alkoxyethoxy‐N‐octadecyl‐1,8‐naphthalimide fluorescent sensor for human serum albumin and other major blood proteins: design,synthesis and solvent effect

A series of 4‐alkoxyethoxy‐N‐octadecyl‐1,8‐naphthalimides with intense blue fluorescence were designed and synthesized as polarity and spectrofluorimetric probes for the determination of proteins. In solvents of different polarities, the Stokes shifts of two dyes increased with increasing solvent polarity and fluorescence quantum yields decreased significantly, suggesting that electronic transiting from ground to excited states was π–π^* in character. Dipole moment changes were estimated from solvent‐dependent Stokes shift data using a solvatochromic method based on bulk solvent polarity functions and the microscopic solvent polarity parameter (). These results were generally consistent with semi‐empirical molecular orbital calculations and were found to be quite reliable based on the fact that the correlation of the solvatochromic Stokes shifts with was superior to that obtained using bulk solvent polarity functions. Fluorescence data revealed that the fluorescence quenching of human serum albumin (HSA) by dyes was the result of the formation of a Dye–HSA complex. The method was applied to the determination of total proteins (HSA + immunoglobulins) in human serum samples and results were in good agreement with those reported by the research institute. Copyright © 2012 John Wiley & Sons, Ltd.     

The evaluation of acute toxicity,antimicrobial activity of 1‐phenyl‐5‐p‐tolyl‐1H‐1, 2, 3‐triazole,and binding to human serum albumin

1‐Phenyl‐5‐p‐tolyl‐1H‐1, 2, 3‐triazole (PPTA) was a synthesized compound. The result of acute toxicities to mice of PPTA by intragastric administration indicated that PPTA did not produce any significant acute toxic effect on Kunming strain mice. It exhibited the various potent inhibitory activities against two kinds of bananas pathogenic bacteria, black sigatoka and freckle, when compared with that of control drugs and the inhibitory rates were up to 64.14% and 43.46%, respectively, with the same concentration of 7.06 mM. The interaction of PPTA with human serum albumin (HSA) was studied using fluorescence polarization, absorption spectra, 3D fluorescence, and synchronous spectra in combination with quantum chemistry and molecular modeling. Multiple modes of interaction between PPTA and HSA were suggested to stabilize the PPTA–HSA complex, based on thermodynamic data and molecular modeling. Binding of PPTA to HSA induced perturbation in the microenvironment around HSA as well as secondary structural changes in the protein.     

Automated,scalable culture of human embryonic stem cells in feeder‐free conditions

Large‐scale manufacture of human embryonic stem cells (hESCs) is prerequisite to their widespread use in biomedical applications. However, current hESC culture strategies are labor‐intensive and employ highly variable processes, presenting challenges for scaled production and commercial development. Here we demonstrate that passaging of the hESC lines, HUES7, and NOTT1, with trypsin in feeder‐free conditions, is compatible with complete automation on the CompacT SelecT, a commercially available and industrially relevant robotic platform. Pluripotency was successfully retained, as evidenced by consistent proliferation during serial passage, expression of stem cell markers (OCT4, NANOG, TRA1‐81, and SSEA‐4), stable karyotype, and multi‐germlayer differentiation in vitro, including to pharmacologically responsive cardiomyocytes. Automation of hESC culture will expedite cell‐use in clinical, scientific, and industrial applications. Biotechnol. Bioeng. 2009;102: 1636–1644. © 2008 Wiley Periodicals, Inc.     

Prolactin induces chitotriosidase expression in human macrophages through PTK,PI3‐K,and MAPK pathways

We previously reported that prolactin (PRL) induces chitotriosidase (CHIT‐1) mRNA expression in human macrophages. In this investigation we determined the signaling pathways involved in CHIT‐1 induction in response to PRL. The CHIT‐1 induction PRL‐mediated was reduced by wortmannin and LY‐294002, inhibitors of phosphatidylinositol 3‐kinase (PI3‐K) and by genistein an inhibitor of protein tyrosine kinase (PTK). Pre‐treatment of macrophages with SB203580, a specific inhibitor of the mitogen‐activated kinases (MAPK) p38, or with U0126, an inhibitor of MAPK p44/42, prevented both basal and exogenous PRL‐mediated CHIT‐1 expression. No significant effects on CHIT‐1 induction PRL‐mediated were observed with a protein kinase C inhibitor (PKC), rottlerin, or with an Src inhibitor, PP2, or with JAK2 inhibitor, AG490. In addition, PRL induced a phosphorylation of AKT that was prevented both by the two MAPK inhibitors SB203580 and U0126 and by the PI3‐K inhibitors wortmannin and LY‐294002. In conclusion, our results indicate that PRL up‐regulated CHIT‐1 expression via PTK, PI3‐K, MAPK, and signaling transduction components. J. Cell. Biochem. 107: 881–889, 2009. © 2009 Wiley‐Liss, Inc.     

Anti‐proliferative effect of rhein,an anthraquinone isolated from Cassia species,on Caco‐2 human adenocarcinoma cells

In recent years, the use of anthraquinone laxatives, in particular senna, has been associated with damage to the intestinal epithelial layer and an increased risk of developing colorectal cancer. In this study, we evaluated the cytotoxicity of rhein, the active metabolite of senna, on human colon adenocarcinoma cells (Caco‐2) and its effect on cell proliferation. Cytotoxicity studies were performed using 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT), neutral red (NR) and trans‐epithelial electrical resistance (TEER) assays whereas ³H‐thymidine incorporation and Western blot analysis were used to evaluate the effect of rhein on cell proliferation. Moreover, for genoprotection studies Comet assay and oxidative biomarkers measurement (malondialdehyde and reactive oxygen species) were used. Rhein (0.1–10 μg/ml) had no significant cytotoxic effect on proliferating and differentiated Caco‐2 cells. Rhein (0.1 and 1 μg/ml) significantly reduced cell proliferation as well as mitogen‐activated protein (MAP) kinase activation; by contrast, at high concentration (10 μg/ml) rhein significantly increased cell proliferation and extracellular‐signal‐related kinase (ERK) phosphorylation. Moreover, rhein (0.1–10 μg/ml): (i) did not adversely affect the integrity of tight junctions and hence epithelial barrier function; (ii) did not induce DNA damage, rather it was able to reduce H₂O₂‐induced DNA damage and (iii) significantly inhibited the increase in malondialdehyde and reactive oxygen species (ROS) levels induced by H₂O₂/Fe²⁺. Rhein was devoid of cytotoxic and genotoxic effects in colon adenocarcinoma cells. Moreover, at concentrations present in the colon after a human therapeutic dosage of senna, rhein inhibited cell proliferation via a mechanism that seems to involve directly the MAP kinase pathway. Finally, rhein prevents the DNA damage probably via an anti‐oxidant mechanism.