Neoarchean and Paleoproterozoic K-rich granites in the Phan Si Pan Complex, north Vietnam : constraints on the early crustal evolution of the Yangtze Block

This study was financially supported by projects from the China Natural Science Foundation (41672222) and State Key Laboratory of Geological Process and Mineral Resources, China University of Geosciences, Wuhan (MSFGPMR201802). PAC acknowledges support from Australian Research Council grant FL160100168. This study was also supported by the Ministry of Natural Resources and Environment of Vietnam, Project BĐKH.29/16-20 to Dung My Tran.Precambrian igneous and metamorphic rocks of the Phan Si Pan Complex, North Vietnam, constitute the southern extension of the Yangtze Block, and provide a valuable record of the early evolution of the continental crust. We present results of U-Pb zircon geochronology and geochemistry for Precambrian granites in this complex to constrain their emplacement age and genesis. Granites from three plutonic bodies yielded ages of 2848 ± 15 Ma, 2768 ± 19 Ma and 1869 ± 30 Ma, which represent newly-recognized late Archean to Paleoproterozoic potassic granite plutonism in the southern Yangtze Block. The average εHf(t) values range from −6.2 to 0.1 for the 2.85–2.77 Ga granitic rocks and -13.1 to -9.2 for the ca. 1.86 Ga granitic rocks, with two-stage model ages of 3.64 to 3.20 Ga and 3.31 to 3.07 Ga, respectively, suggesting derivation from partial melting of Paleoarchean and Mesoarchean crust. The late Archean potassic granites exhibit high K2O, and high Sr/Y and (La/Yb)N ratios with negligible Eu anomalies, indicating derivation from melting of the thickened lower crust, which is inferred to have occurred in an active margin setting. The late Paleoproterozoic alkali feldspar granites are characterized by high FeOT/(FeOT + MgO)(0.96–0.99) and 10000∗Ga/Al (2.75–2.94) ratios, showing an affinity of A-type granite. These A-type granites exhibit flat chondrite-normalized HREE patterns and strong negative Eu anomalies, and low Sr/Y and (La/Yb)N ratios, corresponding to melting at a shallow depth, probably in a post-collisional extension setting. Comparison of the rock units and events recorded by the Phan Si Pan complex with other Archean to Paleoproterozoic complexes (Houhe, Dongchuan, Yudongzi, Douling, Zhongxiang and Kongling complexes) in the Yangtze Block indicate spatially distinct histories of crustal growth, and thus may reflect independent terranes. The ca. 1.86 Ga post-collisional magmatism, which succeeds a 2.0–1.9 Ga metamorphic event, is distributed throughout the Yangtze Block, including the Phan Si Pan Complex, suggesting assembly of the disparate terranes and final cratonization of the Yangtze Block overlaps with, and may be related to, assembly of the Nuna supercontinent.PostprintPeer reviewe

Early Paleoproterozoic magmatism in the Yangtze Block : evidence from zircon U-Pb ages, Sr-Nd-Hf isotopes and geochemistry of ca. 2.3 Ga and 2.1 Ga granitic rocks in the Phan Si Pan Complex, north Vietnam

This study was financially supported by projects from the China Natural Science Foundation (41672222) and State Key Laboratory of Geological Process and Mineral Resources, China University of Geosciences, Wuhan (MSFGPMR201802). PAC acknowledges support from Australian Research Council grant FL160100168. This study was also supported by the Ministry of Natural Resources and Environment of Viet Nam, Project BĐKH.29/16-20 to Dung My Tran.Our understanding of the early evolution of the Yangtze Block is limited by the sparsely dispersed nature of pre-Neoproterozoic exposures. New, integrated petrographic, zircon U-Pb age and Hf-Nd isotope analyses, and whole-rock geochemical data for early Paleoproterozoic granites in the Phan Si Pan Complex provides new insights into the evolution of the Yangtze Block as well as its role in the Pre-Nuna supercontinent. LA-ICP-MS zircon U-Pb dating of magmatic zircons from quartz monzonite and gneissic granite yielded 207Pb/206Pb ages of 2306 ± 12 Ma and 2096 ± 15 Ma, respectively. Zircons from the quartz monzonite have εHf(t) values ranging from -4.1 to -2.1, corresponding to TDM2 model ages of 3002–2890 Ma, whereas zircons in the gneissic granite have εHf(t) values between -0.95 and +1.72 and corresponding TDM2 model ages of 2660–2516 Ma, which are consistent with their whole-rock Nd isotope values. Geochemically, the quartz monzonites are I-type granites. Combined with their relatively high Sr/Y ratios and low Y concentrations, as well as fractionated REE patterns with relatively high LREE but low HREE concentrations, they were probably generated by partial melting of the thickened middle-lower crust under elevated temperature. Geochemical and isotopic signatures suggest that the ca. 2.1 Ga gneissic granites are high-K calc-alkaline, ferroan A-type granites formed by partial melting of juvenile crustal source at high temperature and low pressure with little involvement of ancient crustal material. The Phan Si Pan complex has a distinct early Paleoproterozoic crustal evolution history compared with the other crustal provinces of the Yangtze Block, suggesting independent histories that were not unified until the late Paleoproterozoic during the assembly of Nuna. Moreover, the magmatism and tectonic evolution of the north Vietnam region is broadly similar to that of the Arrowsmith Orogen of the Rae craton in Laurentia suggesting a potential spatial linkage. The geologic record of the Yangtze Block does not support an early Paleoproterozoic shutdown of plate tectonics.PostprintPeer reviewe

Robust Genetic Transformation System to Obtain Non-chimeric Transgenic Chickpea

Chickpea transformation is an important component for the genetic improvement of this crop, achieved through modern biotechnological approaches. However, recalcitrant tissue cultures and occasional chimerism, encountered during transformation, hinder the efficient generation of transgenic chickpeas. Two key parameters, namely micro-injury and light emitting diode (LED)-based lighting were used to increase transformation efficiency. Early PCR confirmation of positive in vitro transgenic shoots, together with efficient grafting and an extended acclimatization procedure contributed to the rapid generation of transgenic plants. High intensity LED light facilitate chickpea plants to complete their life cycle within 9 weeks thus enabling up to two generations of stable transgenic chickpea lines within 8 months. The method was validated with several genes from different sources, either as single or multi-gene cassettes. Stable transgenic chickpea lines containing GUS (uidA), stress tolerance (AtBAG4 and TlBAG), as well as Fe-biofortification (OsNAS2 and CaNAS2) genes have successfully been produced

Spatio-Temporal Dependence of the Signaling Response in Immune-Receptor Trafficking Networks Regulated by Cell Density: A Theoretical Model

Cell signaling processes involve receptor trafficking through highly connected networks of interacting components. The binding of surface receptors to their specific ligands is a key factor for the control and triggering of signaling pathways. In most experimental systems, ligand concentration and cell density vary within a wide range of values. Dependence of the signal response on cell density is related with the extracellular volume available per cell. This dependence has previously been studied using non-spatial models which assume that signaling components are well mixed and uniformly distributed in a single compartment. In this paper, a mathematical model that shows the influence exerted by cell density on the spatio-temporal evolution of ligands, cell surface receptors, and intracellular signaling molecules is developed. To this end, partial differential equations were used to model ligand and receptor trafficking dynamics through the different domains of the whole system. This enabled us to analyze several interesting features involved with these systems, namely: a) how the perturbation caused by the signaling response propagates through the system; b) receptor internalization dynamics and how cell density affects the robustness of dose-response curves upon variation of the binding affinity; and c) that enhanced correlations between ligand input and system response are obtained under conditions that result in larger perturbations of the equilibrium . Finally, the results are compared with those obtained by considering that the above components are well mixed in a single compartment

SnO2Nanowire Arrays and Electrical Properties Synthesized by Fast Heating a Mixture of SnO2and CNTs Waste Soot

SnO2nanowire arrays were synthesized by fast heating a mixture of SnO2and the carbon nanotubes waste soot by high-frequency induction heating. The resultant SnO2nanowires possess diameters from 50 to 100 nm and lengths up to tens of mircrometers. The field-effect transistors based on single SnO2nanowire exhibit that as-synthesized nanowires have better transistor performance in terms of transconductance and on/off ratio. This work demonstrates a simple technique to the growth of nanomaterials for application in future nanoelectronic devices

Light Variability Illuminates Niche-Partitioning among Marine Picocyanobacteria

Prochlorococcus and Synechococcus picocyanobacteria are dominant contributors to marine primary production over large areas of the ocean. Phytoplankton cells are entrained in the water column and are thus often exposed to rapid changes in irradiance within the upper mixed layer of the ocean. An upward fluctuation in irradiance can result in photosystem II photoinactivation exceeding counteracting repair rates through protein turnover, thereby leading to net photoinhibition of primary productivity, and potentially cell death. Here we show that the effective cross-section for photosystem II photoinactivation is conserved across the picocyanobacteria, but that their photosystem II repair capacity and protein-specific photosystem II light capture are negatively correlated and vary widely across the strains. The differences in repair rate correspond to the light and nutrient conditions that characterize the site of origin of the Prochlorococcus and Synechococcus isolates, and determine the upward fluctuation in irradiance they can tolerate, indicating that photoinhibition due to transient high-light exposure influences their distribution in the ocean

Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella

Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

<p>Abstract</p> <p>Background</p> <p>A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been co-inherited during evolution.</p> <p>Results</p> <p>Our experimentation with <it>E. coli </it>and yeast proteins with 16 different carefully composed reference sets of genomes revealed that the phyletic patterns of proteins in prokaryotes alone could be adequate enough to make reasonably accurate functional linkage predictions. A slight improvement in performance is observed on adding few eukaryotes into the reference set, but a noticeable drop-off in performance is observed with increased number of eukaryotes. Inclusion of most parasitic, pathogenic or vertebrate genomes and multiple strains of the same species into the reference set do not necessarily contribute to an improved sensitivity or accuracy. Interestingly, we also found that evolutionary histories of individual pathways have a significant affect on the performance of the PPC approach with respect to a particular reference set. For example, to accurately predict functional links in carbohydrate or lipid metabolism, a reference set solely composed of prokaryotic (or bacterial) genomes performed among the best compared to one composed of genomes from all three super-kingdoms; this is in contrast to predicting functional links in translation for which a reference set composed of prokaryotic (or bacterial) genomes performed the worst. We also demonstrate that the widely used random null model to quantify the statistical significance of profile similarity is incomplete, which could result in an increased number of false-positives.</p> <p>Conclusion</p> <p>Contrary to previous proposals, it is not merely the number of genomes but a careful selection of informative genomes in the reference set that influences the prediction accuracy of the PPC approach. We note that the predictive power of the PPC approach, especially in eukaryotes, is heavily influenced by the primary endosymbiosis and subsequent bacterial contributions. The over-representation of parasitic unicellular eukaryotes and vertebrates additionally make eukaryotes less useful in the reference sets. Reference sets composed of highly non-redundant set of genomes from all three super-kingdoms fare better with pathways showing considerable vertical inheritance and strong conservation (e.g. translation apparatus), while reference sets solely composed of prokaryotic genomes fare better for more variable pathways like carbohydrate metabolism. Differential performance of the PPC approach on various pathways, and a weak positive correlation between functional and profile similarities suggest that caution should be exercised while interpreting functional linkages inferred from genome-wide large-scale profile comparisons using a single reference set.</p

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Description of a new Pselaphodes Westwood (Coleoptera: Staphylinidae: Pselaphinae) from Vietnam

A new species of the genus Pselaphodes Westwood, P. fansipanensis Bekchiev & Yin sp. n., is described from northern Vietnam. The unique modification of the antennomeres 9–10 of the male readily separates the new species from all known congeners. New Pselaphodes species from Vietna