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Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P.vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.

Benthic bioaccumulation of hazardous materials has been a great challenge to the health of lake ecosystems. As representative benthic macroinvertebrates, freshwater mussels and their accumulation characteristics have been regarded as effective indicators for assessing potential risks induced by sedimentary metal(loid)s in lakes. Here we profile organ-specific accumulation of 35 metal(loid)s in a freshwater mussel (Hyriopsis cumingii) and their correlations to metal speciation in sediments of Poyang Lake, the largest lake of China. Significant organ-specific characteristics of metal accumulation were found in gills, though higher thallium (Tl) and selenium (Se) were found in the hepatopancreas, and greater arsenic (As) mostly accumulated in gonads. Pearson correlation analysis revealed that the bioaccumulation of silver (Ag), cobalt (Co), and rare earth elements (ΣREE) in gills and As in gonads were closely associated with those in bioavailable fraction of sediments. Based on the biochemical analysis in the major organs, gills exhibited the highest enzymatic activity compared with hepatopancreas and gonads. Sedimentary metals, particularly for available Ag, Co, and ΣREE, play key roles in causing lipid peroxidation in gills and significantly promote the activities of superoxide dismutase (SOD)/glutathione reductase (GR), while many metals (e.g., cadmium, manganese, Se) inhibit the glutathione (GSH) content in gonads and hepatopancreas. Our study indicates a high physiological sensitivity of mussels to these target metals, which highlights the significance of organ-specific accumulation of metal(loid)s in understanding the potential ecological risks of sedimentary metal(loid)s in lake ecosystems.

Per-and polyfluoroalkyl substances (PFASs) are manmade chemicals that have wide industrial and commercial application. However, little research has been carried out on PFASs pollution in groundwater from a previously contaminated site. Here, we investigated 43 PFASs in a monitoring campaign from two different aquifers in the North China Plain. Our results revealed that total PFASs concentrations (∑

Anthropogenic activities are intensively affecting the structure and function of biological communities in river ecosystems. The effects of anthropogenic pollution on single-trophic community have been widely explored, but their effects on the structures and co-occurrence patterns of multitrophic communities remain largely unknown. In this study, we collected 13 water samples from the Neijiang River in Chengdu City of China, and identified totally 2352 bacterial, 207 algal, 204 macroinvertebrate, and 33 fish species based on the eDNA metabarcoding to systematically investigate the responses of multitrophic communities to environmental stressors. We observed significant variations in bacterial, algal, and macroinvertebrate community structures (except fish) with the pollution levels in the river. Network analyses indicated a more intensive interspecific co-occurrence pattern at high pollution level. Although taxonomic diversity of the multitrophic communities varied insignificantly, phylogenetic diversities of fish and algae showed significantly positive and negative associations with the pollution levels, respectively. We demonstrated the primary role of environmental filtering in driving the structures of bacteria, algae, and macroinvertebrates, while the fish was more controlled by dispersal limitation. Nitrogen was identified as the most important factor impacting the multitrophic community, where bacterial composition was mostly associated with NO

The recent discovery of comammox Nitrospira performing complete ammonia oxidation to nitrate has overturned the long-held dogma of two-step nitrification on Earth, yet little is known about the effect of urbanization interference on their distribution. Using gene-centric metagenomics, we provided the first blueprints about comammox community, biogeography, and environmental drivers along a high-elevation (2000 m) river flowing through the largest city on the vulnerable Qinghai-Tibetan Plateau. Our study confirmed a wide presence and diversity of yet-uncultured comammox clade B across wet and dry seasons, with average 3.0 and 2.0 times as abundant as clade-A amoA genes in water and sediments, respectively. Species identified from freshwater and drinking water treatment plants dominated the comammox guilds (58∼100%), suggesting this plateau river shared a similar comammox assemblage with the above habitat types. Compared with the urban area harboring more abundant canonical Nitrospira identified in wastewater (average 24%), the upstream suburban reach had a smaller human population but larger proportions of comammox in ammonia-oxidizing prokaryotes (24∼72% of abundances) and Nitrospira sublineages I/II. Higher contents of nitrate and nitrite in water, and antibiotics in water and sediments, may restrain comammox niches in nitrifiers over the urban area. Further random forest analysis revealed that lincosamides and quinolones were the most important antibiotic predictors for the niche differentiations between comammox and canonical nitrifiers in water, while macrolides for those in sediments. Finally, by incubation experiments, we demonstrated higher activity contributions of benthic comammox in the suburban area (36.2∼92.8% of potential ammonia-oxidation rates) than in the urban reach, and that the contribution variation had significant negative relations with macrolides and their major components. Overall, this study highlighted that anthropogenic activities hampered the advantage of riverine complete nitrifiers over the canonical two-step ones.

Though metal resistance genes (MRGs) are of global concern in aquatic ecosystems, the underlying factors responsible for MRGs dissemination, especially in urban rivers on the vulnerable Qinghai-Tibet Plateau, are rarely known. Here, we collected 64 samples including water and sediments during the wet and dry seasons and effluents from six wastewater treatment plants (WWTPs) during the dry season and measured 50 metal(loid)s, 60 bacterial phyla, and 259 MRGs. We observed the distinct difference of metal(loid)s, bacterial communities, and MRGs between water and sediments and the great seasonal changes in metal(loid)s and bacterial communities instead of MRGs. Thirty-one metal(loid)s were detectable in the water, with relatively low concentrations and no significant effects on the planktonic bacterial communities and MRGs. Interestingly, the WWTPs effluent partially promoted the prevalence of dissolved metal(loid)s, bacterial communities, and MRGs along the river. In the sediments, the average concentrations of 17 metal(loid)s exceeded their corresponding background levels in this region and strongly influenced the bacterial communities and the MRGs. Sedimentary Hg and Cd, mainly sourced from the intensive animal husbandry, were the major pollutants causing ecological risks and largely shaped their corresponding resistomes. Moreover, we found that bacterial communities predominantly determined the variation of MRGs in both water and sediments. Metagenome-assembled genomes further reveals the widespread co-occurrence of MRGs and antibiotic resistance genes (ARGs) in MRG hosts. Our study highlighted the concern of effluents discharged from WWTPs and emphasized the importance of controlling the anthropogenic inputs of sedimentary metal(loid)s in the plateau river ecosystems.

Despite the known heritable nature of autism spectrum disorder (ASD), studies have primarily identified risk genes with de novo variants (DNVs). To capture the full spectrum of ASD genetic risk, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 ASD cases, including 35,130 new cases recruited online by SPARK. In the first stage, we analyzed 19,843 cases with one or both biological parents and found that known ASD or neurodevelopmental disorder (NDD) risk genes explain nearly 70% of the genetic burden conferred by DNVs. In contrast, less than 20% of genetic risk conferred by rare inherited loss-of-function (LoF) variants are explained by known ASD/NDD genes. We selected 404 genes based on the first stage of analysis and performed a meta-analysis with an additional 22,764 cases and 236,000 population controls. We identified 60 genes with exome-wide significance (p < 2.5e-6), including five new risk genes (NAV3, ITSN1, MARK2, SCAF1, and HNRNPUL2). The association of NAV3 with ASD risk is entirely driven by rare inherited LoFs variants, with an average relative risk of 4, consistent with moderate effect. ASD individuals with LoF variants in the four moderate risk genes (NAV3, ITSN1, SCAF1, and HNRNPUL2, n = 95) have less cognitive impairment compared to 129 ASD individuals with LoF variants in well-established, highly penetrant ASD risk genes (CHD8, SCN2A, ADNP, FOXP1, SHANK3) (59% vs. 88%, p= 1.9e-06). These findings will guide future gene discovery efforts and suggest that much larger numbers of ASD cases and controls are needed to identify additional genes that confer moderate risk of ASD through rare, inherited variants.

To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance (P 2.5 × 10

Pharmaceuticals and personal care products (PPCPs) are a group of emerging anthropogenic pollutants. Here we investigated the occurrence and concentrations of 35 typical PPCPs in water, sediment, and freshwater mollusks (Hyriopsis cumingii, Unio douglasiae, Sinanodonta woodiana, Lamprotula leai and Corbicula fluminea) of the Dongting Lake downstream of the Three Gorges Dam. As results, 33 PPCPs were detected in water and sediment of the lake. Ketoprofen (not detected (ND)-292.8 ng/L, mean 91.1 ng/L) and roxithromycin (13.7-141.9 ng/L, mean 30.4 ng/L) were the primary PPCPs measured in lake water, while ibuprofen (ND-105.0 ng/g, mean 30.0 ng/g) and ketoprofen (ND-142.9 ng/g, mean 27.6 ng/g) were dominant in the sediment. Distinct seasonal difference in PPCP compositions was observed in both water and sediment of the Dongting Lake, potentially associated with the water-level fluctuations driven by the Three Gorges Dam operations. Ketoprofen and ibuprofen were also frequently detected in the soft tissues of freshwater mollusks, with concentrations of 42.5-1206.6 and 44.9-992.7 ng/g, respectively. Significant species-specific accumulation characteristics of PPCPs in mollusks were observed, with the highest total contents being reported for Corbicula fluminea (3.18 ± 1.13 μg/g). Moreover, gonads of mollusks were identified as the target organ to accumulate these compounds. Correlation analysis further revealed the strong associations of PPCP concentrations in mollusks with those in water and sediment, suggesting the importance of controlling dissolved and sedimentary bioavailability of PPCPs for ecological risk management in this freshwater lake ecosystems.

Phytoplankton play an important role in nutrient cycling and energy conversion. However, phytoplankton community is poorly understood in large river ecosystems. Based on the large-scale samplings conducted in spring and autumn of 2017, a systematic study has been made on seasonal and spatial distributions of phytoplankton community along the mainstream of the Yangtze River. As results, 6 phyla were identified and 59 phytoplankton species were detected using microscopy, including Bacillariophyta (29 species), Chlorophyta (13 species) and Cyanophyta (8 species) as the dominant group. Moreover, the density of phytoplankton was ranged 0.05 × 106−1.90 × 106 cells/L and the biomass was 0.01–1.01 mg/L, both reaching their maximum in the middle reach from Yichang to Wuhan. Significant seasonal difference of phytoplankton community was observed and spatial dissimilarity in spring was revealed. The cell abundance and biomass of phytoplankton could be fairly estimated by chlorophyll-a, and redundancy analysis indicated that water temperature, dissolved oxygen, biochemical oxygen demand, nitrite, and ammonia nitrogen were the most important explanatory environmental factors for phytoplankton compositions in the Yangtze River.

The fragrant rice breeding has become an important direction for hybrid rice breeding program. The selection and utilization of parent materials with ideal plant type, fine grain quality, strong resistance and other excellent agronomic characteristics with strong fragrance, especially the utilization and cultivation of the fragrant rice restorer lines, is of great significance to further promote the fragrant hybrid rice breeding. Taiguoxiaoxiangzhan is a restorer line with excellent grain quality, strong resistance and fragrance, which has been widely used in fragrant rice breeding in China. In order to trace the fragrance in Taiguoxiaoxiangzhan, we identified the type of the fragrance gene in Taiguoxiaoxiangzhan was badh2-E7 which has an 8 bp deletion and three single nucleotide polymorphisms (SNPs) in exon 7, and this gene is a non-functional badh2 allele and that the functional Badh2 allele encoding betaine aldehyde dehydrogenase (BADH2) could render rice non-fragrant. Furthermore, we found that the Taiguoxiaoxiangzhan increased 2-acetyl-1-pyrroline (2-AP) content (0.108 mg/kg) compared with the non-fragrant rice varieties of Nipponbare and 9311 (

Both antibiotics and sediments can affect the denitrification in aquatic systems. However, little is known how antibiotics influence the denitrification in the presence of sediments. Here, the effects of antibiotics (sulfamethoxazole, tetracycline and ofloxacin) on denitrification in the absence and presence of sediments were investigated. The influencing mechanisms were revealed by quantifying the denitrification functional genes (DNGs), 16S-seq of bacteria, and antibiotic resistance genes (ARGs). The results showed that the presence of antibiotics inhibited NO3-N reduction by decreasing the abundances of narG, nirK, nosZ, total DNGs, and denitrifying bacteria. However, the inhibition effect was alleviated by sediments, which promoted the growth of bacteria and decreased the selective pressure of antibiotics as the vector of bacteria and antibiotics, thus increasing the abundances of denitrifying bacteria and all the DNGs. Partial least-squares path model disclosed that antibiotics had negative effects on bacteria, ARGs and DNGs, while sediments had negative effects on ARGs but positive effects on bacteria and DNGs. The network analysis further revealed the close relation of the genera Bacillus, Acinetobacter, and Enterobacter with the ARGs and DNGs. The findings are helpful to understand the denitrification in antibiotic-polluted natural waters.

The molecular self-assembly of deoxyribonucleic acid (DNA) plays an important role in understanding how nucleic acids form and can be exploited to construct nanostructures. In this study, scanning tunneling microscopy (STM) was used to observe nanostructures that form from co-adsorption of the guanine (G) and cytosine (C) complementary DNA bases on a highly oriented pyrolytic graphite surface. The high-resolution STM images show that the well-ordered co-adsorption structures are attributed to the rows formed from Watson–Crick G–C pairs, which are distinct from the structures observed for individual G–C components. The observed co-adsorption structure was modeled by density functional theory calculations, which provide information on the intermolecular interactions underlying its formation.

Gerbera hybrida is one of the top five cut flowers across the world, it is host for the root rot causing parasite called Phytophthora cryptogea. In this study, plantlets of healthy and root-rot pathogen-infected G. hybrida were used as plant materials for transcriptome analyis using high-throughput Illumina sequencing technique. A total 108,135 unigenes were generated with an average length of 727 nt and N50 equal to 1274 nt out of which 611 genes were identified as DEGs by DESeq analyses. Among DEGs, 228 genes were up-regulated and 383 were down-regulated. Through this annotated data and Kyoto encyclopedia of genes and genomes (KEGG), molecular interaction network, transcripts accompanying with tyrosine metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, phenylpropanoid and flavonoid biosynthesis, and plant hormone signal transduction pathways were thoroughly observed considering expression pattern. The involvement of DEGs in tyrosine metabolism pathway was validated by real-time qPCR. We found that genes related with tyrosine metabolism were activated and up-regulated against stress response. The expression of GhTAT, GhAAT, GhHPD, GhHGD and GhFAH genes was significantly increased in the leaves and petioles at four and six dpi (days post inoculation) as compared with control. The study predicts the gene sequences responsible for the tyrosine metabolism pathway and its responses against root-rot resistance in gerbera plant. In future, identification of such genes is necessary for the better understanding of rot resistance mechanism and to develop a root rot resistance strategy for ornamental plants.

The identification and utilization of broad-spectrum resistance genes is the most effective and economical strategy of controlling rice blast disease. Kangfeng B (KFB), an elite Chinese rice cultivar, has been shown to exhibit broad-spectrum resistance to 53 isolates of Magnaporthe oryzae, the rice blast causative agent, from different regions of China. In this study, we identified a dominant blast-resistance gene at the Pi2/Pi9 locus from cultivar KFB, through genetic analysis and physical mapping. Allele-specific marker-based assessment revealed that Pi2, Pi9, and Piz-t are not the blast-resistance genes in KFB. By combining bulked segregation analysis (BSA) and recessive class analysis (RCA), the blast-resistance gene was fine-mapped to an approximately 249-kb interval between markers InDel-22 and Rm7213 on chromosome 6. Three bacterial artificial chromosome (BAC) clones spanning the region were identified. This region contains 19 predicted genes, including 7 nucleotide binding site–leucine-rich repeat (NBS-LRR) genes at the Pi2/Pi9 locus in japonica cv. Nipponbare genome. Further sequence comparison of the four functional NBS-LRR genes revealed that NBS-LRR2 and NBS-LRR4, as evidenced by their allelic/orthologous to Pi9 or Pi2, had significant differences of 9 to 43 and 14 to 48 amino acids in KFB, respectively, unlike the other known Pi2/Pi9 alleles, suggesting that KFB carries a hitherto undocumented member of the Pi2/Pi9 multigene family. It was tentatively designated as Pi-kf2(t). Our results provide essential information for the isolation of the Pi-kf2(t) gene and will facilitate both map-based cloning and marker-assisted selection of this gene for rice blast-resistance breeding.

Background Anthurium andraeanum, an important ornamental flower, has to go through a growth-delaying period after transfer from tissue culture to soil, which requires time and extra costs. Furthermore, during this period, the plantlets are highly susceptible to bacterial infections, which results in impaired development and severe losses. Here, we aimed to address whether application of the endophytic fungus, Piriformospora indica protects the A. andraeanum root system during the critical propagation period, and whether P. indica reduce the mortality rate by stimulating the host’s resistance against diseases. Results We demonstrate that P. indica shortens the recovery period of Anthurium, promotes growth and confers disease resistance. The beneficial effect of P. indica results in faster elongation of Anthurium roots early in the interaction. P. indica-colonized plants absorb more phosphorus and exhibit higher photosynthesis rates than uncolonized control plants. Moreover, higher activities of stress-related enzymes, of jasmonic acid levels and mRNA levels of jasmonic acid-responsive genes suggest that the fungus prepares the plant to respond more efficiently to potentially upcoming threats, including bacterial wilt. Conclusion These results suggest that P. indica is a helpful symbiont for promoting Anthurium rooting and development. All our evidences are sufficient to support the disease resistance conferred by P. indica through the plant-fungal symbiosis. Furthermore, it implicates that P. indica has strong potential as bio-fertilizer for utilization in ornamental plant cultivation.

Additional file 2: Figure S2. P. indica colonization of Oncidium roots confers resistance against E. chrysanthemi. (PPTX 1961 kb)

INTRODUCTION The brain is responsible for cognition, behavior, and much of what makes us uniquely human. The development of the brain is a highly complex process, and this process is reliant on precise regulation of molecular and cellular events grounded in the spatiotemporal regulation of the transcriptome. Disruption of this regulation can lead to neuropsychiatric disorders. RATIONALE The regulatory, epigenomic, and transcriptomic features of the human brain have not been comprehensively compiled across time, regions, or cell types. Understanding the etiology of neuropsychiatric disorders requires knowledge not just of endpoint differences between healthy and diseased brains but also of the developmental and cellular contexts in which these differences arise. Moreover, an emerging body of research indicates that many aspects of the development and physiology of the human brain are not well recapitulated in model organisms, and therefore it is necessary that neuropsychiatric disorders be understood in the broader context of the developing and adult human brain. RESULTS Here we describe the generation and analysis of a variety of genomic data modalities at the tissue and single-cell levels, including transcriptome, DNA methylation, and histone modifications across multiple brain regions ranging in age from embryonic development through adulthood. We observed a widespread transcriptomic transition beginning during late fetal development and consisting of sharply decreased regional differences. This reduction coincided with increases in the transcriptional signatures of mature neurons and the expression of genes associated with dendrite development, synapse development, and neuronal activity, all of which were temporally synchronous across neocortical areas, as well as myelination and oligodendrocytes, which were asynchronous. Moreover, genes including MEF2C , SATB2 , and TCF4 , with genetic associations to multiple brain-related traits and disorders, converged in a small number of modules exhibiting spatial or spatiotemporal specificity. CONCLUSION We generated and applied our dataset to document transcriptomic and epigenetic changes across human development and then related those changes to major neuropsychiatric disorders. These data allowed us to identify genes, cell types, gene coexpression modules, and spatiotemporal loci where disease risk might converge, demonstrating the utility of the dataset and providing new insights into human development and disease. Spatiotemporal dynamics of human brain development and neuropsychiatric risks. Human brain development begins during embryonic development and continues through adulthood (top). Integrating data modalities (bottom left) revealed age- and cell type–specific properties and global patterns of transcriptional dynamics, including a late fetal transition (bottom middle). We related the variation in gene expression (brown, high; purple, low) to regulatory elements in the fetal and adult brains, cell type–specific signatures, and genetic loci associated with neuropsychiatric disorders (bottom right; gray circles indicate enrichment for corresponding features among module genes). Relationships depicted in this panel do not correspond to specific observations. CBC, cerebellar cortex; STR, striatum; HIP, hippocampus; MD, mediodorsal nucleus of thalamus; AMY, amygdala.

Neural stem cells directly or indirectly generate all neurons and macroglial cells and guide migrating neurons by using a palisade-like scaffold made of their radial fibers. Here, we describe an unexpected role for the radial fiber scaffold in directing corticospinal and other axons at the junction between the striatum and globus pallidus. The maintenance of this scaffold, and consequently axon pathfinding, is dependent on the expression of an atypical RHO-GTPase, RND3/RHOE, together with its binding partner ARHGAP35/P190A, a RHO GTPase-activating protein, in the radial glia-like neural stem cells within the ventricular zone of the medial ganglionic eminence. This role is independent of RND3 and ARHGAP35 expression in corticospinal neurons, where they regulate dendritic spine formation, axon elongation, and pontine midline crossing in a FEZF2-dependent manner. The prevalence of neural stem cell scaffolds and their expression of RND3 and ARHGAP35 suggests that these observations might be broadly relevant for axon guidance and neural circuit formation., This work was supported by Labex LifeSenses grants ANR-10-LABX-65 and ANR-11-IDEX-0004-02 to A.C.; MINECO SAF2013-49176-C2-1-R and Programa Santander-FUSP to I.P.-R. and J.T.; NIH grants R01 MH115939, NS105640, and NS089662 to A.J.K.; and NIH grants MH103339, MH106934, MH110926, and MH109904 to N.S. Additional support was provided by the Kavli Foundation and the Simons Foundation.

The monolayer self-assembled porous supramolecular networks of p-terphenyl-3,5,3′′,5′′-tetra-carboxylic acid (TPTC) that stabilized by intermolecular hydrogen bonding between four carboxyl groups at nonanoic acid/graphite interface were constructed. Scanning tunneling microscopy (STM) demonstrates that the guest molecules coronene (COR) adsorption in the pores of TPTC monolayer network. Furthermore, TPTC molecules can form the bilayer supramolecular framework and the trapping of COR guest molecules in both layers.

The disappearance of fine motor control Manual skills are much better developed in primates than in rodents. This difference is in part due to species-specific differences in the control of motoneurons by the brain. Gu et al. used a range of approaches to evaluate potential corticospinal tract projections in neonatal mice. These projections exist immediately after birth but disappear within the first 2 postnatal weeks owing to the actions of plexin A, a member of the semaphorin receptor family. Targeted deletion of semaphorin receptors in mutant mice prevented elimination of corticospinal tract projection and loss of functional monosynaptic input to spinal motoneurons. Science , this issue p. 400

Titanate nanotubes (TNTs) have been reported to show good adsorption performance for heavy metals, but researches on organic contaminants adsorption by TNTs are limited. In this study, co-adsorption of a heavy metal (Cu) and an emerging organic contaminant (ciprofloxacin, CIP) by TNTs was investigated in binary systems. TNTs could simultaneously remove the two contaminants, with a high adsorption capacity of 234.5 μmol/g for Cu(II) and 237.0 μmol/g for CIP at pH 4 in the binary system. pH greatly affected adsorption due to speciation variation of the contaminants and surface charge change of TNTs. Cu(II)-CIP complexes dominated adsorption capacity and mechanism. Adsorption of CIP was promoted by high concentration of Cu(II) at pH 3–8 due to formation of abundant Cu(CIP±)2+, while inhibited by low concentration of Cu(II) because of competitive adsorption. The adsorption affinity of CIP species to TNTs was ranked as: Cu(CIP±)2+ > CIP+ > CIP± > Cu(CIP±)2+ > Cu(CIP−·CIP±)+ > CIP−. In comparison, the co-existence of CIP slightly affected Cu(II) adsorption considering the strong affinity of Cu2+ to TNTs. X-ray photoelectron spectrometer (XPS) and Fourier transform infrared spectroscopy (FTIR) results further confirmed the formation of Cu(II)-CIP complexes through –NH2Cu/–COOCu linkages. This work not only proposed a feasible technology for co-removal of heavy metals and organics from water, but also presented insight into interaction mechanisms of different contaminants with nanomaterials during adsorption.

Connecting inner and surface propagation field in photonic crystal waveguides (PCWs) with an efficient method is critical to achieve flexible designs and applications in photonic integrated circuits. This letter realizes highly efficient coupling between inner and surface PCWs by modifying the structures of waveguides and interface. The aim of the modification is to achieve a good match of modal field profiles between different types of waveguide structures as well as suppress the reflected field at the interface. The numerical results based on finite difference time-domain simulations show that the bandwidth for coupling efficiency larger than 90% can be as broad as over 100 nm.

Dimension reduction methods are commonly applied to high-throughput biological datasets. However, the results can be hindered by confounding factors, either biologically or technically originated. In this study, we extend Principal Component Analysis to propose AC-PCA for simultaneous dimension reduction and adjustment for confounding variation. We show that AC-PCA can adjust for a) variations across individual donors present in a human brain exon array dataset, and b) variations of different species in a model organism ENCODE RNA-Seq dataset. Our approach is able to recover the anatomical structure of neocortical regions, and to capture the shared variation among species during embryonic development. For gene selection purposes, we extend AC-PCA with sparsity constraints, and propose and implement an efficient algorithm. The methods developed in this paper can also be applied to more general settings.

As a prominent component of the human fetal brain, the structure of the cerebral wall is characterized by its laminar organization which includes the radial glial scaffold during fetal development. Diffusion tensor imaging (DTI) is useful to quantitatively delineate the microstructure of the developing brain and to clearly identify transient fetal layers in the cerebral wall. In our study, the spatio-temporal microstructural changes in the developing human fetal cerebral wall were quantitatively characterized with high-resolution DTI data of postmortem fetal brains from 13 to 21 gestational weeks. Eleven regions of interest for each layer in the entire cerebral wall were included. Distinctive time courses of microstructural changes were revealed for 11 regions of the neocortical plate. A histological analysis was also integrated to elucidate the relationship between DTI fractional anisotropy (FA) and histology. High FA values correlated with organized radial architecture in histological image. Expression levels of 17565 genes were quantified for each of 11 regions of human fetal neocortex from 13 to 21 gestational weeks to identify transcripts showing significant correlation with FA change. These correlations suggest that the heterogeneous and regionally specific microstructural changes of the human neocortex are related to different gene expression patterns.

Recent research on disparate psychiatric disorders has implicated rare variants in genes involved in global gene regulation and chromatin modification, as well as many common variants located primarily in regulatory regions of the genome. Understanding precisely how these variants contribute to disease will require a deeper appreciation for the mechanisms of gene regulation in the developing and adult human brain. The PsychENCODE project aims to produce a public resource of multidimensional genomic data using tissue- and cell type–specific samples from approximately 1,000 phenotypically well-characterized, high-quality healthy and disease-affected human post-mortem brains, as well as functionally characterize disease-associated regulatory elements and variants in model systems. We are beginning with a focus on autism spectrum disorder, bipolar disorder and schizophrenia, and expect that this knowledge will apply to a wide variety of psychiatric disorders. This paper outlines the motivation and design of PsychENCODE.

Summary Here we report the generation and analysis of genome-wide exon-level transcriptome data from 16 brain regions comprising the cerebellar cortex, mediodorsal nucleus of the thalamus, striatum, amygdala, hippocampus, and 11 areas of the neocortex. The dataset was generated from 1,340 tissue samples collected from one or both hemispheres of 57 postmortem human brains, spanning from embryonic development to late adulthood and representing males and females of multiple ethnicities. We also performed genotyping of 2.5 million SNPs and assessed copy number variations for all donors. Approximately 86% of protein-coding genes were found to be expressed using stringent criteria, and over 90% of these were differentially regulated at the whole transcript or exon level across regions and/or time. The majority of these spatiotemporal differences occurred before birth, followed by an increase in the similarity among regional transcriptomes during postnatal lifespan. Genes were organized into functionally distinct co-expression networks, and sex differences were present in gene expression and exon usage. Finally, we demonstrate how these results can be used to profile trajectories of genes associated with neurodevelopmental processes, cell types, neurotransmitter systems, autism, and schizophrenia, as well as to discover associations between SNPs and spatiotemporal gene expression. This study provides a comprehensive, publicly available dataset on the spatiotemporal human brain transcriptome and new insights into the transcriptional foundations of human neurodevelopment.

The corticospinal (CS) tract is involved in controlling discrete voluntary skilled movements in mammals. The CS tract arises exclusively from layer (L) 5 projection neurons of the cerebral cortex, and its formation requires L5 activity of Fezf2 ( Fezl , Zfp312 ). How this L5-specific pattern of Fezf2 expression and CS axonal connectivity is established with such remarkable fidelity had remained elusive. Here we show that the transcription factor TBR1 directly binds the Fezf2 locus and represses its activity in L6 corticothalamic projection neurons to restrict the origin of the CS tract to L5. In Tbr1 null mutants, CS axons ectopically originate from L6 neurons in a Fezf2 -dependent manner. Consistently, misexpression of Tbr1 in L5 CS neurons suppresses Fezf2 expression and effectively abolishes the CS tract. Taken together, our findings show that TBR1 is a direct transcriptional repressor of Fezf2 and a negative regulator of CS tract formation that restricts the laminar origin of CS axons specifically to L5.

With a compact resonator, continuous-wave (cw) and Q-switched laser performances of Nd:LuVO4 crystal was investigated. The maximum cw output power was 5.19 W. The shortest pulse width, largest pulse repetition rate, and largest pulse energy were measured to be 3.3 ns, 24.8 kHz, and 92.8 μJ, respectively, by using Cr4+:YAG crystals as the saturable absorbers. To our knowledge, this is the shortest passively Q-switched pulse width with Nd:LuVO4 as the laser crystal. From the satellite pulse, the lifetime of the lower laser energy level of Nd:LuVO4 was determined to be about 20 ns.

Retina explants are widely used as a model of neural development. To define the molecular basis of differences between the development of retina in vivo and in vitro during the early postnatal period, we carried out a series of microarray comparisons using mouse retinas. About 75% of 8,880 expressed genes from retina explants kept the same expression volume and pattern as the retina in vivo. Fewer than 6% of the total gene population was changed at two consecutive time points, and only about 1% genes showed more than a threefold change at any time point studied. Functional Gene Ontology (GO) mapping for both changed and unchanged genes showed similar distribution patterns, except that more genes were changed in the GO clusters of response to stimuli and carbohydrate metabolism. Three distinct expression patterns of genes preferentially expressed in rod photoreceptors were observed in the retina explants. Some genes showed a lag in increased expression, some showed no change, and some continued to have a reduced level of expression. An early downregulation of cyclin D1 in the explanted retina might explain the reduction in numbers of precursors in explanted retina and suggests that external factors are required for maintenance of cyclin D1. The global view of gene profiles presented in this study will help define the molecular changes in retina explants over time and will provide criteria to define future changes that improve this model system. Electronic supplementary material The online version of this article (doi:10.1007/s12177-008-9009-z) contains supplementary material, which is available to authorized users.