In this manuscript we describe Proteogenomics Viewer, a web‐based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of (...) both genomics and proteomics data, culminating with the release of the two human proteome drafts. It is now clear that mass spectrometry‐based peptide identification of uncharacterized sequences, such as those resulting from unpredicted exon joints or non‐coding regions, is still prone to a higher than expected false discovery rate. Therefore, proper visualization of the raw data and the corresponding genome alignments are fundamental for further data validation and interpretation. (shrink)

In late 1912, Fritz Goos at the Hamburg Physikalisches Staatslaboratorium discovered a systematic dependency of arc-spectra wavelengths on the length of the electric arc used and on its electric parameters, such as, for instance, the current employed. In early 1913, at Heinrich Kayser's better-equipped physical laboratory in Bonn, Goos was able to confirm these effects using a large concave Rowland grating. He was able to establish that variations of between 3 mm and 10 mm in the length of the arc (...) produced wavelength differences of up to 0.02 Å violet shift and -0.007 Å redshift respectively. Further inquiry also revealed a dependency of the wavelength on the region of the arc selected for spectrometric observation. All these surprising effects were soon collectively named ‘pole effect’.As is shown in this paper, the pole effect threatened the validity of the results of the entire research tradition of high-precision spectroscopy which, around 1910, had excelled in establishing several internally coherent systems of wavelength assignments. These wavelength catalogues had been established by spectroscopists such as Heinrich Kayser, Paul Eversheim and their co-workers in Bonn, by August Herman Pfund in Baltimore, and by Charles Fabry and Henri Buisson in Marseille under the aegis of the ‘International Union for Co-Operation in Solar Research’. They had all produced locally consistent, “homogeneous” systems of wavelengths with estimated errors sometimes smaller than 0.001 Å. However, long before 1913, strange non-local inconsistencies had emerged between these systems that were of much greater magnitude than the estimated error. The discovery of the pole effect opened up the possibility that variations in the arc parameters used in the measurements, which the different teams had hitherto not specified, were responsible for the systematic differences, in their respective sets of measurements, coming to up to 0.025 Å.This paper explores the interrelations between local knowledge production, the strategies for the establishment of local coherence, and the ways in which the community of physicists and spectroscopists handled a possible threat to this coherence after 1913. Around 1930, a general agreement was reached about the physical cause of the pole effect, namely Stark effects, caused in turn by intermolecular electric fields of ions in the arc. Much before 1930, however, the community had already succeeded in standardizing the instrumentation used in high-precision spectrometry and had conformed its research practice to such an extent that from 1917 on the pole effect could be routinely circumvented in high-precision spectrometry and interferometry. Thus, experimentation along with its instrumentation, indeed had ‘a life of its own’, independent of the many unsuccessful efforts to explain the pole effect theoretically. (shrink)

Cells are the fundamental building blocks of organisms and their organization holds the key to our understanding of the processes that control Development and Physiology as well as the mechanisms that underlie disease. Traditional methods of analysis of subcellular structure have relied on the purification of organelles and the painstaking biochemical description of their components. The arrival of high‐throughput genomic and, more significantly, proteomic technologies has opened hereto unforeseen possibilities for this task. Recently two reports(1,2) show how much can be (...) gleaned from the combination of analytical centrifugation, mass spectrometry and advanced statistical techniques focused on a high‐throughput analysis of the content and organization of plant and animal cells. The results reveal intriguing possibilities for the future and the possibility of mapping much of the known proteome onto our current map of the cell. BioEssays 28: 780–784, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

We demonstrate how different normalization techniques in GC‐MS analysis impart unique properties to the data, influencing any biological inference. Using simulations, and empirical data, we compare the most commonly used techniques (Total Sum Normalization ‘TSN’; Median Normalization ‘MN’; Probabilistic Quotient Normalization ‘PQN’; Internal Standard Normalization ‘ISN’; External Standard Normalization ‘ESN’; and a compositional data approach ‘CODA’). When differences between biological classes are pronounced, ESN and ISN provides good results, but are less reliable for more subtly differentiated groups. MN, TSN, and (...) CODA approaches produced variable results dependent on the structure of the data, and are prone to false positive biomarker identification. In contrast, PQN exhibits the lowest false positive rate, though with occasionally poor model performance. Because ESN requires extensive pre‐planning, and offers only mixed reliability, and ISN, TSN, MN, and CODA approaches are prone to introducing artefactual differences, we recommend the use of PQN in GC–MS research. (shrink)

While mass spectrometry (MS)‐based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. In the backdrop of the genomic era reaching its zenith, certain questions arise: is (...) the proteomic era about to come? If we are at the beginning of a new future for protein quantification, are we prepared to incorporate targeted proteomics at the benchside for basic research and at the bedside for the good of patients? Here, an overview of the knowledge required to perform targeted proteomics as well as its applications is provided. A special emphasis is placed on upcoming areas such as peptidomics, proteoform research, and mass spectrometry imaging, where the utilization of targeted proteomics is expected to bring forth new avenues. The limitations associated with the acceptance of this technique for mainstream usage are also highlighted. (shrink)

Novel methods such as mass‐spectrometry enable a view of the proteomes of cells in unprecedented detail. Recently, these efforts have culminated in quantitative measurements of the number of copies per cell for most expressed proteins in organisms ranging from bacteria to mammalian cells. Here, we estimate the expected total number of proteins per unit of cell volume using known parameters related to the composition of cells such as the fraction of cell mass that is protein, and the average protein (...) length. Using simple arguments, we estimate a range of 2–4 million proteins per cubic micron (i.e. 1 fL) in bacteria, yeast, and mammalian cells. Interestingly, we find that measured values that are reported for fission yeast and mammalian cells are often about 3–10 times lower. We discuss this apparent discrepancy and how to use the estimate as benchmark to recalibrate proteome‐wide quantitative censuses or to revisit assumptions about cell composition. (shrink)

The emerging field of lipidomics has identified lipids as key players in disease physiology. Their physicochemical diversity allows precise control of cell structure and signaling events through modulation of membrane properties and trafficking of proteins. As such, lipids are important regulators of brain function and have been implicated in neurodegenerative and mood disorders. Importantly, environmental chronic stress has been associated with anxiety and depression and its exposure in rodents has been extensively used as a model to study these diseases. With (...) the accessibility to modern mass‐spectrometry lipidomic platforms, it is now possible to snapshot the extensively interconnected lipid network. Here, we review the fundamentals of lipid biology and outline a framework for the interpretation of lipidomic studies as a new approach to study brain pathophysiology. Thus, lipid profiling provides an exciting avenue for the identification of disease signatures with important implications for diagnosis and treatment of mood disorders. (shrink)

Mitochondria have been fundamental to the eco‐physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We (...) explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories. (shrink)

The primary transcripts, pre‐mRNAs, of almost all protein‐coding genes in higher eukaryotes contain multiple non‐coding intervening sequences, introns, which must be precisely removed to yield translatable mRNAs. The process of intron excision, splicing, takes place in a massive ribonucleoprotein complex known as the spliceosome. Extensive studies, both genetic and biochemical, in a variety of systems have revealed that essential components of the spliceosome include five small RNAs–U1, U2, U4, U5 and U6, each of which functions as a RNA, protein complex (...) called an snRNP (small nuclear ribonucleoprotein). In addition to snRNPs, splicing requires many non‐snRNP protein factors, the exact nature and number of which has been unclear. Technical advances, including new affinity purification methods and improved mass spectrometry techniques, coupled with the completion of many genome sequences, have now permitted a number of proteomic analyses of purified spliceosomes. These studies, recently reviewed by Jurica and Moore,1 reveal that the spliceosome is composed of as many as 300 distinct proteins and five RNAs, making it among the most complex macromolecular machines known. BioEssays 25:1147–1149, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Présentation de la méthode LA‑ICP‑MS appliquée aux objets d’orfèvrerie rhodiens La méthode LA‑ICP‑MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry ou spectrométrie de masse à plasma avec micro-prélèvement par ablation laser) est une méthode d’analyse multi-élémentaire séquentielle qui permet de déterminer la concentration des trois principaux éléments constitutifs des alliages à base d’or (or, argent, cuivre), ainsi que celle de la plupart des impuretés de ces métaux dont la te...

The accumulation of potentially toxic elements (PTEs) has raised public awareness due to harmful contamination to both human and marine creatures. This study was designed to determine the concentration of copper (Cu), zinc (Zn), cadmium (Cd), and nickel (Ni) in the intestine, kidney, muscle, gill, and liver tissues of local commercial edible fish, fourfinger threadfin (Eleutheronema tetradactylum), and black pomfret (Parastromateus niger) collected from Morib (M) and Kuala Selangor (KS). Among the studied PTEs, Cu and Zn were essential elements to (...) regulate body metabolism with certain dosages required while Cd and Ni were considered as non-essential elements that posed chronic and carcinogenic risk. The concentration of PTEs in fish tissue samples was analyzed using flame atomic absorption spectrometry (F-AAS). By comparing the concentration of PTEs in fish tissues as a bioindicator, the environmental risk of Morib was more serious than Kuala Selangor because both fish species collected from Morib resulted in a higher PTEs concentration. For an average 62 kg adult with a fish ingestion rate (FIR) of 0.16 kg/person/day in Malaysia, the estimated weekly intake (EWI) of Cd from the consumption of E. tetradactylum (M: 0.0135 mg/kg; KS: 0.0134 mg/kg) and P. niger (M: 0.0140 mg/kg; KS: 0.0132 mg/kg) had exceeded the provisional tolerable weekly intake (Cd: 0.007 mg/kg) established by the Joint FAO/WHO Expert Committee on Food Additives (JECFA) and oral reference dose (ORD) values of Cd (0.001 mg/kg/day) as provided by the United States Environmental Protection Agency (USEPA) regional screening level, thus it posed chronic risks for daily basis consumption. Besides, the value of the carcinogenic risk of Cd (0.7−3 to 0.8−3) and Ni (0.5−3 to 0.6−3) were in between the acceptable range (10−6 to 10−4) of the health index that indicates a relatively low possibility cancer occurrence to the consumers in both Morib and Kuala Selangor. This study recommended FIR to be 0.80 kg/person/day to reduce the possibility of posing chronic and carcinogenic risks while at the same time obtaining the essential nutrients from the fish. (shrink)

Earlier investigations of the hormonal control of vitellogenin (egg‐yolk protein) synthesis in mosquitoes relied on microsurgical manipulations to identify organs that secrete the various hormones that stimulate or inhibit vitellogenesis. Advances in the last 10 years, using radioimmunoassays, HPLC, mass spectrometry and tissue‐culture incubations, have shown that the control mechanism involves a complex interaction between ecdysteroids, juvenile hormones and peptide hormones.

Intensive research and development of electrophoresis methodology and instrumentation during past decades has resulted in unique methods widely implemented in bioanalysis. While two‐dimensional electrophoresis and denaturing polyacrylamide gel electrophoresis in sodium dodecylsulfate are still the most frequently used electrophoretic methods applied to analyses of proteins, new miniaturized capillary and microfluidic versions of electromigrational methods have been developed. High‐throughput electrophoretic instruments with hundreds of capillaries for parallel separations and laser‐induced fluorescence detection of labeled DNA strands have been of key importance for (...) the scientific and commercial success of the Human Genome Project. Another powerful method, capillary isoelectric focusing with pressurized and pH‐driven mobilization, provides efficient separations and on‐line sensitive detection of proteins, bacteria and viruses. Electrophoretic microfluidic devices can integrate single‐cell injection, cell lysis, separation of its components and fluorescence or mass spectrometry detection. These miniaturized devices also proved the capability of single‐molecule detection. (shrink)

RésuméLe dosage de traces de molécules organiques dans les matrices biologiques fait appel à des techniques analytiques physico‐chimiques dont la chromatographie en phase gazeuse couplée à la spectrumétrie de masse est une des plus puissantes. Des possibilityés nouvelles pour augmenter la sensibilityé de la détection de ces substances sont presentees et mises en relation avec la signification physiologique des résultats obtenus.SummaryGas chromatography‐mass spectrometry is the method of choice for the quantitative determination of organic traces in biological systems. New technical (...) developments allow higher sensitivity and greater specificity which are discussed together with the physiological meaning of the data thus obtained.ZusammenfassungDie Dosierung der Spuren von organischen Molekülen in den biologischen Matrizen erfordert physico‐chemische analytische Techniken, deren Chromatographie in gasförmiger Phase ver‐bunden mit der Massenspektrometrie eine der mächtigsten ist. Es werden neue Möglichkeiten zur Steigerung der Empfindlichkeit der Aufweisung dieser Substanzen vorgelegt, und mit der physio‐logischen Bedeutung der erhaltenen Ergebnisse in Beziehung gesetzt. (shrink)

The study of intrinsic phosphorylation dynamics and kinetics in the context of complex protein architecture in vivo has been challenging: Method limitations have prevented significant advances in the understanding of the highly variable turnover of phosphate groups, synergy, and cooperativity between P‐sites. However, over the last decade, powerful analytical technologies have been developed to determine the full catalog of the phosphoproteome for many species. The curated databases of phospho sites found by mass spectrometry analysis and the computationally predicted sites (...) based on the linear sequence of kinase motifs are valuable tools. They allow investigation of the complexity of phosphorylation in vivo, albeit with strong discrepancies between different methods. A series of hypothetical scenarios on combinatorial processive phosphorylation is proposed that are likely unverifiable with current methodologies. These proposed a priori postulates could be considered as possible extensions of the known schemes of the activation/inhibition signaling process in vivo. (shrink)

Integrated developmental and elemental information in teeth provide a unique framework for documenting breastfeeding histories, physiological disruptions, and neurotoxicant exposure in humans and our primate relatives, including ancient hominins. Here we detail our method for detecting the consumption of mothers’ milk and exploring health history through the use of laser ablation‐inductively coupled plasma‐mass spectrometry (LA‐ICP‐MS) mapping of sectioned nonhuman primate teeth. Calcium‐normalized barium and lead concentrations in tooth enamel and dentine may reflect milk and formula consumption with minimal modification (...) during subsequent tooth mineralization, particularly in dentine. However, skeletal resorption during severe illness, and bioavailable metals in nonmilk foods, can complicate interpretations of nursing behavior. We show that explorations of the patterning of multiple elements may aid in the distinction of these important etiologies. Targeted studies of skeletal chemistry, gastrointestinal maturation, and the dietary bioavailability of metals are needed to optimize these unique records of human health and behavior. (shrink)

For over four decades, knowledge that symptoms of some inherited diseases can be prevented or reduced via early detection and treatment in newborns has underpinned state-funded screening programs in most developed countries. Conditions for which newborn screening is now a recognized preventative public health initiative include phenylketonuria, congenital hypothyroidism, and, more recently, cystic fibrosis and sickle cell disorder. The use of tandem mass spectrometry to detect conditions such as amino-acidopathies and fatty-acid oxidation defects is also becoming increasingly prevalent. a.

The human genome contains about 30,000 genes, each creating several transcripts per gene. Transcript structures and expression are studied by high‐throughput transcriptomic techniques using microarrays. Generally, transcripts are not directly operating molecules, but are translated into functional proteins, post‐translationally modified by proteolysis, glycosylation, phosphorylation, etc., sometimes with great functional impact. Proteins need to be analyzed by proteomic techniques, less suited for high‐throughput. Two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE), separating thousands of proteins has developed slowly over the past quarter of a century. (...) This technique is now quite reproducible and suitable for differential proteomics, comparing normal and diseased cells/tissues revealing differentially regulated proteins. 2D‐PAGE is combined with protein‐identification methods, currently mass spectrometry (MS), which has been significantly improved over the last decade. Other proteomic techniques studying protein–protein interactions are now either established or still being developed, such as peptide or protein arrays, phage display, and the yeast two‐hybrid system. The strengths and weaknesses of these techniques are discussed. BioEssays 26:901–915, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

In the present work, the microstructure of the melt-spun Al 90 Ce 10 alloy has been characterized using X-ray diffraction and transmission electron microscopy together with energy-dispersive spectrometry. It has been found that the microstructure of the melt-spun Al 90 Ce 10 alloy is composed of the amorphous phase, f -Al, f -Al 11 Ce 3 , Al 3 Ce and unidentified phases, quite different from that of the ingot-like alloy consisting of coarse primary f -Al- f -Al 11 (...) Ce 3 dendrites embedded in the f -Al- f -Al 11 Ce 3 eutectic matrix. Moreover, the amorphous phase is dominant in the melt-spun Al 90 Ce 10 alloy according to the XRD and TEM results. Al 3 Ce particles, less than 100 nm in size, are dispersed in the partial amorphous phase. Polygonal f -Al 11 Ce 3 crystals embedded in the f -Al matrix are also observed. The presence of the hexagonal, kite-like and petal-like intermetallic particles surrounded by the amorphous phase indicates that there exist micro-inhomogeneous structures in the Al 90 Ce 10 melt. These results demonstrate that the overheating of the melt has a significant effect on the amorphization of the Al 90 Ce 10 alloy. (shrink)

Lower plasma levels of high-density lipoproteins in adolescents with type 2 diabetes have been associated with a higher pulse wave velocity, a marker of arterial stiffness. Evidence suggests that HDL proteins or particle subspecies are altered in T2D and these may drive these relationships. In this work, we set out to reveal any specific proteins and subspecies that are related to arterial stiffness in youth with T2D from proteomics data. Plasma and PWV measurements were previously acquired from lean and T2D (...) adolescents. Each plasma sample was separated into 18 fractions and evaluated by mass spectrometry. Then, we applied a validated network-based computational approach to reveal HDL subspecies associated with PWV. Among 68 detected phospholipid-associated proteins, we found that seven were negatively correlated with PWV, indicating that they may be atheroprotective. Conversely, nine proteins show positive correlation with PWV, suggesting that they may be related to arterial stiffness. Intriguingly, our results demonstrate that apoA-I and histidine-rich glycoprotein may reverse their protective roles and become antagonistic in the setting of T2D. Furthermore, we revealed two arterial stiffness-associated HDL subspecies, each of which contains multiple PWV-related proteins. Correlation and disease association analyses suggest that these HDL subspecies might link T2D to its cardiovascular-related complications. (shrink)

Tropical grasses are fast growing and often used for phytoremediation. Three different types of tropical grasses: Vetiver (V. zizanoides), Imperata (I. cylindrical) and Pennisetum (P. purpureum) tested in different growth media of spiked heavy metal contents under the glasshouse environment of RimbaIlmu for 60-day. The growth performance, metals tolerance and phyto-assessment of cadmium (Cd), lead (Pb), zinc (Zn) and copper (Cu) in shoots and roots were assessed using flame atomic absorption spectrometry (FAAS).Tolerance index (TI), translocation factor (TF), biological accumulation (...) coefficient (BAC), biological concentration factor (BCF), and uptake efficacy was applied to evaluate the metal translocation ability among all three grasses. All three grasses showed significantly higher (p<0.05) accumulation of the total heavy metals in the spiked metal treatment compared with other tested treatments. Vetiver accumulated remarkably higher total concentration of Cd (93.08 ± 3.81 mg/kg) and Zn (1284.00 ± 234.83 mg/kg) than both Imperata and Pennisetum. The overall trend of heavy metals accumulation for all three grasses followed the order of Zn>Pb>Cd>Cu. The results of study suggested that both Imperata and Pennisetum are commendable and potential phytoextractors for Zn as well as phytostabilizers for Cd, Pb and Cu, respectively. (shrink)

The growth response, metal tolerance and phytoaccumulation properties of water spinach (Ipomoea aquatica) and okra (Abelmoschus esculentus) were assessed under different contaminated spiked metals: control, 50 mg Pb/kg soil, 50 mg Zn/kg soil and 50 mg Cu/kg soil. The availability of Pb, Zn and Cu metals in both soil and plants were detected using flame atomic absorption spectrometry. The concentration and accumulation of heavy metals from soil to roots and shoots (edible parts) were evaluated in terms of translocation factor, (...) accumulation factor and tolerance index. Okra recorded the highest accumulation of Pb (80.20 mg/kg) in its root followed by Zn in roots (35.70 mg/kg) and shoots (34.80 mg/kg) of water spinach, respectively. Different accumulation trends were observed with, Pb > Zn > Cu in okra and Zn > Pb > Cu in water spinach. Significant differences (p < 0.01) of Pb, Zn and Cu accumulation were found in both water spinach and okra cultivated among tested treatments. However, only the accumulation of Pb metal in the shoots of water spinach and okra exceeded the maximum permissible levels of the national Malaysian Food Act 1983 and Food Regulations 1985 ([2006]) as well as the international Codex Alimentarius Commission limits. This study has shown that both water spinach and okra have good potential as Pb and Zn phytoremediators. (shrink)

Cet article présente les résultats des analyses radiochronologiques pratiquées sur sept échantillons d'ossements humains issus des fouilles de l'habitat mésohelladique de l'Aspis. Les analyses ont été réalisées au Centre de recherche sur les isotopes de l'université de Gröningen, par la méthode SMA (spectrométrie de masse par accélérateur). L'objectif principal des analyses est de dater plus précisément les phases d'occupation de l'habitat en comparant les dates absolues avec la chronologie relative fondée sur la stratigraphie complexe et la séquence céramique du site. (...) Les résultats suggèrent que le passage de l'HM III à l'HR I se situe aux alentours de 1700 av. J.-C. La méthode ne permet pas de dater avec précision le passage de l'HM II à l'HM III parce que ces deux phases sont de courte durée alors que la marge d'incertitude des datations par le radiocarbone est assez grande, étant donné la forme de la courbe de calibration pour cette période. (shrink)

Various types of plant species have been extensively used for heavy metals phyto-remediation without taking into consideration its tolerance threshold. In this study, Vetiver grass, Vetiveria zizanioides (Linn.) Nash was evaluated under five different sets of contaminated spiked cadmium (5Cd, 10Cd, 50Cd, 100Cd and 150Cd mg/kg) and lead (50Pb, 100Pb, 200Pb, 400Pb and 800Pb mg/kg) concentration levels in soil. The growth performance, metal tolerance and phyto-assessment of Cd and Pb in the roots and tillers were assessed using flame atomic absorption (...) spectrometry (FAAS). Tolerance index (TI), translocation factor (TF), biological transfer factor (BTF), biological accumulation coefficient (BAC) and metal uptake efficacy were used to determine the Cd and Pb translocation capability in Vetiver grass. Significantly higher (p<0.05) accumulation of Cd and Pb was recorded in the roots of all spiked treatments. Furthermore, strong and significantly positive correlations were exhibited between the increased levels of spiked heavy metal concentrations with both Cd (r=0.975) and Pb (r=0.952) accumulations. The results of this study showed Vetiver grass as an effective phyto-stabilizer for both Cd and Pb. Nevertheless, the growth of Vetiver grass was restricted when the tolerance threshold of 100 mg/kg (dry weight basis) Cd was exceeded in the contaminated soil. (shrink)

Most phyto-remediation studies have been conducted merely on a single type of contaminant element without consideration of the influence of other co-existent contaminants. In this study, Vetiveria zizanioides (Linn.) Nash was evaluated in both single and mixed heavy metal (Cd, Pb, Cu and Zn) spiked contaminated soil. The plant growth, metal accumulation and overall efficiency of metal uptake by different plant parts (lower root, upper root, lower tiller and upper tiller) were investigated in detail. The relative growth performance, metal tolerance (...) and phyto-assessment of heavy metal in roots and tillers of Vetiver grass were assessed. Metals in plants were measured using the flame atomic absorption spectrometry (F-AAS) after acid digestion. The root-tiller (R/T) ratio, tolerance index (TI), translocation factor (TF), biological concentration factor (BCF), biological accumulation coefficient (BAC) and metal uptake efficacy were estimated to examine the ability of metal accumulation and translocation in Vetiver grass. No significant difference (p > 0.05) of plant height was observed among all single and mixed heavy metal spiked soils compared with the control. However, significantly higher (p < 0.05) heavy metal (Cd, Pb, Cu and Zn) accumulations were found in roots, tillers and overall total accumulation of the individual spiked metal as compared with other treatments. Vetiver grass grown in the mixed Cd + Pb + Cu + Zn spiked soils accumulated the highest Zn (3322 ± 21.6 mg/kg) followed by Cu (430 ± 11.4 mg/kg), Pb (197 ± 13.5 mg/kg) and Cd (100 ± 0.7 mg/kg). Vetiver grass grown in mixed Cd + Pb, Cu + Zn and Cd + Pb + Cu + Zn spiked soils accumulated higher heavy metal concentrations than from the single spiked soil with the following order of metals: Zn > > Cu > Pb > Cd. Moreover, lower roots and lower tillers of Vetiver grass revealed a strong tendency for greater uptake and accumulation of all four heavy metals in both single and/or mixed spiked contaminated soils. -/- . (shrink)

Over the years, ethylene-diamine-tetra-acetate (EDTA) has been widely used for many purposes. However, there are inadequate phytoassessment studies conducted using EDTA in Vetiver grass. Hence, this study evaluates the phytoassessment (growth performance, accumulation trends, and proficiency of metal uptake) of Vetiver grass, Vetiveria zizanioides (Linn.) Nash in both single and mixed heavy metal (Cd, Pb, Cu, and Zn)—disodium EDTA-enhanced contaminated soil. The plant growth, metal accumulation, and overall efficiency of metal uptake by different plant parts (lower root, upper root, lower (...) tiller, and upper tiller) were thoroughly examined. The relative growth performance, metal tolerance, and phytoassessment of heavy metal in roots and tillers of Vetiver grass were examined. Metals in plants were measured using the flame atomic absorption spectrometry (F-AAS) after acid digestion. The root-tiller (R/T) ratio, biological concentration factor (BCF), biological accumulation coefficient (BAC), tolerance index (TI), translocation factor (TF), and metal uptake efficacy were used to estimate the potential of metal accumulation and translocation in Vetiver grass. All accumulation of heavy metals were significantly higher (p < 0.05) in both lower and upper roots and tillers of Vetiver grass for Cd + Pb + Cu + Zn + EDTA treatments as compared with the control. The single Zn + EDTA treatment accumulated the highest overall total amount of Zn (8068 ± 407 mg/kg) while the highest accumulation for Cu (1977 ± 293 mg/kg) and Pb (1096 ± 75 mg/kg) were recorded in the mixed Cd + Pb + Cu + Zn + EDTA treatment, respectively. Generally, the overall heavy metal accumulation trends of Vetiver grass were in the order of Zn >>> Cu > Pb >> Cd for all treatments. Furthermore, both upper roots and tillers of Vetiver grass recorded high tendency of accumulation for appreciably greater amounts of all heavy metals, regardless of single and/or mixed metal treatments. Thus, Vetiver grass can be recommended as a potential phytoextractor for all types of heavy metals, whereby its tillers will act as the sink for heavy metal accumulation in the presence of EDTA for all treatments. (shrink)

Sources of soil contamination can exist in various types of conditions including in the form of semifluids. In this study, 3 different types of tropical plants, Acacia (Acacia mangium Willd), Mucuna (Mucuna bracteata DC. ex Kurz) and Vetiver (Vetiveria zizanioides L. Nash), were tested under different levels of soil-leachate conditions. The relative growth rate, metal tolerance, and phytoassessment of cadmium (Cd) and lead (Pb) accumulation in the roots and shoots were determined using flame atomic absorption spectrometry. Tolerance index, translocation (...) factor, metal accumulation ratio, and percentage metal efficacy were applied to assess the metal translocation ability among all the 3 types of plants. Significantly higher (P < .05) accumulation of Cd and Pb was exhibited in the roots and shoots of all 3 plants growing under the soil-leachate conditions. However, negative growth performance and plant withering were observed in both Acacia and Mucuna with increased application of higher soil-leachate levels. Vetiver accumulated remarkably higher total concentration of Cd (116.16-141.51 mg/kg) and Pb (156.37-365.27 mg/kg) compared with both Acacia and Mucuna. The overall accumulation trend of Cd and Pb in the 3 plants growing under the soil-leachate conditions was in the order of Vetiver > Acacia > Mucuna. The findings of the study suggest that Vetiver has great potential as Cd and Pb phytoremediator in soil-leachate conditions. (shrink)

The cluster variation method has been applied to establish effective interaction potentials that describe both n '-Fe 4 N 1 m x - k -Fe 2 N 1 m z miscibility gaps in the Fe-N phase diagram. The calculated nitrogen distributions show that long-range order occurs in the n :'-Fe 4 N 1 m x phase and that short-range ordering as well as long-range ordering occurs in the k -Fe 2 N 1 m z phase. The calculated nitrogen distributions for (...) the k -Fe 2 N 1 m z , pertaining to temperatures and concentrations at the n '- k -phase boundaries, are compared with available data obtained by Mössbauer spectrometry. Preferential occupation of specific interstitial sites occurs from about 16 at.% N onwards; at the highest concentration considered, about 25 at.% N, the occupation is that of Fe 3 N as proposed in the literature on the basis of diffraction data. (shrink)

The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review (...) within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. Review articles for the individual volumes are invited by the volume editors. Readership: research chemists at universities or in industry, graduate students. (shrink)

Interpretation of experiments involving use of vacuum ultraviolet radiation to effect ionization of N 2 in terms of measurements of a molecular orbital is erroneous.

The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real‐time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of (...) research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic—to elicit a T cell response—has remained both enigmatic and a long sought‐after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead. (shrink)