Phylogenetic Comparative Analysis of Single-Cell Transcriptomes Reveals Constrained Accumulation of Gene Expression Heterogeneity during Clonal Expansion.

In the same way that a phylogeny summarizes the evolutionary history of species, a cell lineage tree describes the process of clonal expansion, in which gene expression differences between cells naturally accrue as a result of stochastic partitioning and imperfect expression control. How is functional homeostasis, a key factor in the biological function of any population of cells, maintained in the face of such continuous accumulation of transcriptomic heterogeneity remains largely unresolved. To answer this question, we experimentally determined the single-cell transcriptomes and lineage relationships of up to 50% cells in single-HEK293-seeded colonies. Phylogenetic comparative analyses of the single-cell transcriptomes on the cell lineage tree revealed three lines of evidence for the constrained accumulation of transcriptome heterogeneity among cells, including rapid saturation of transcriptomic heterogeneity upon four cell divisions, reduced expression differences within subtrees closer to expression boundaries, and cofluctuations among genes. Our analyses showcased the applicability of phylogenetic comparative methods in cell lineage trees, demonstrated the constrained accumulation of transcriptomic heterogeneity, and provided novel insight into the functional homeostasis of cell populations.

Inhibiting ferroptosis in brain microvascular endothelial cells: A potential strategy to mitigate polystyrene nanoplastics‒induced blood‒brain barrier dysfunction.

Polystyrene nanoplastics (PS-NPs), a group of ubiquitous pollutants, may injure the central nervous system through the blood‒brain barrier (BBB). However, whether exposure to PS-NPs contributes to BBB disruption and the underlying mechanisms are still unclear. In vivo, we found that PS-NPs (25 mg/kg BW) could significantly increase BBB permeability in mice and downregulate the distribution of the tight junction-associated protein zona occludens 1 (ZO-1) in brain microvascular endothelial cells (BMECs). Using an in vitro BBB model, exposure to PS-NPs significantly reduced the transendothelial electrical resistance and altered ZO-1 expression and distribution in a dose-dependent manner. RNA-seq analysis and functional investigations were used to investigate the molecular pathways involved in the response to PS-NPs. The results revealed that the ferroptosis and glutathione metabolism signaling pathways were related to the disruption of the BBB model caused by the PS-NPs. PS-NPs treatment promoted ferroptosis in bEnd.3 cells by inducing disordered glutathione metabolism in addition to Fe2+ and lipid peroxide accumulation, while suppressing ferroptosis with ferrostatin-1 (Fer-1) suppressed ferroptosis-related changes in bEnd.3 cells subjected to PS-NPs. Importantly, Fer-1 alleviated the decrease in ZO-1 expression in bEnd.3 cells and the exacerbation of BBB damage induced by PS-NPs. Collectively, our findings suggest that inhibiting ferroptosis in BMECs may serve as a potential therapeutic target against BBB disruption induced by PS-NPs exposure.

Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase.

The antibiotic resistance crisis continues to threaten human health. Better predictions of the evolution of antibiotic resistance genes could contribute to the design of more sustainable treatment strategies. However, comprehensive prediction of antibiotic resistance gene evolution via laboratory approaches remains challenging. By combining site-specific integration and high-throughput sequencing, we quantified relative growth under the respective selection of cefotaxime or ceftazidime selection in ∼23,000 Escherichia coli MG1655 strains that each carried a unique, single-copy variant of the extended-spectrum ß-lactamase gene blaCTX-M-14 at the chromosomal att HK022 site. Significant synergistic pleiotropy was observed within four subgenic regions, suggesting key regions for the evolution of resistance to both antibiotics. Moreover, we propose PEARP and PEARR, two deep-learning models with strong clinical correlations, for the prospective and retrospective prediction of blaCTX-M-14 evolution, respectively. Single to quintuple mutations of blaCTX-M-14 predicted to confer resistance by PEARP were significantly enriched among the clinical isolates harboring blaCTX-M-14 variants, and the PEARR scores matched the minimal inhibitory concentrations obtained for the 31 intermediates in all hypothetical trajectories. Altogether, we conclude that the measurement of local fitness landscape enables prediction of the evolutionary trajectories of antibiotic resistance genes, which could be useful for a broad range of clinical applications, from resistance prediction to designing novel treatment strategies.

Comprehensive Transcriptome and Metabolome Analyses Reveal Primary Molecular Regulation Pathways Involved in Peanut under Water and Nitrogen Co-Limitation.

The yield and quality of peanut (Arachis hypogaea L.), an oil crop planted worldwide, are often limited by drought stress (DS) and nitrogen (N) deficiency. To investigate the molecular mechanism by which peanut counteracts DS and N deficiency, we conducted comprehensive transcriptomic and metabolomic analyses of peanut leaves. Herein, 829 known differentially accumulated metabolites, 324 differentially expressed transcription factors, and 5294 differentially expressed genes (DEGs) were identified under different water and N conditions. The transcriptome analysis demonstrated that drought-related DEGs were predominantly expressed in "glycolysis/gluconeogenesis" and "glycerolipid metabolism", while N-deficiency-related DEGs were mainly expressed in starch and sucrose metabolism, as well as in the biosynthesis of amino acid pathways. The biosynthesis, transport, and catabolism of secondary metabolites accounted for a large proportion of the 1317 DEGs present in water and N co-limitation. Metabolomic analysis showed that the metabolic accumulation of these pathways was significantly dependent on the stress conditions. Additionally, the roles of metabolites and genes in these pathways, such as the biosynthesis of amino acids and phenylpropanoid biosynthesis under different stress conditions, were discussed. The results demonstrated that different genes, metabolic pathways, and metabolites were related to DS and N deficiency. Thus, this study elucidates the metabolic pathways and functional genes that can be used for the improvement of peanut resistance to abiotic stress.

Bidirectional Genetic Control of Phenotypic Heterogeneity and Its Implication for Cancer Drug Resistance.

Negative genetic regulators of phenotypic heterogeneity, or phenotypic capacitors/stabilizers, elevate population average fitness by limiting deviation from the optimal phenotype and increase the efficacy of natural selection by enhancing the phenotypic differences among genotypes. Stabilizers can presumably be switched off to release phenotypic heterogeneity in the face of extreme or fluctuating environments to ensure population survival. This task could, however, also be achieved by positive genetic regulators of phenotypic heterogeneity, or "phenotypic diversifiers," as shown by recently reported evidence that a bacterial divisome factor enhances antibiotic resistance. We hypothesized that such active creation of phenotypic heterogeneity by diversifiers, which is functionally independent of stabilizers, is more common than previously recognized. Using morphological phenotypic data from 4,718 single-gene knockout strains of Saccharomyces cerevisiae, we systematically identified 324 stabilizers and 160 diversifiers and constructed a bipartite network between these genes and the morphological traits they control. Further analyses showed that, compared with stabilizers, diversifiers tended to be weaker and more promiscuous (regulating more traits) regulators targeting traits unrelated to fitness. Moreover, there is a general division of labor between stabilizers and diversifiers. Finally, by incorporating NCI-60 human cancer cell line anticancer drug screening data, we found that human one-to-one orthologs of yeast diversifiers/stabilizers likely regulate the anticancer drug resistance of human cancer cell lines, suggesting that these orthologs are potential targets for auxiliary treatments. Our study therefore highlights stabilizers and diversifiers as the genetic regulators for the bidirectional control of phenotypic heterogeneity as well as their distinct evolutionary roles and functional independence.

Transcriptome Analysis in Yeast Reveals the Externality of Position Effects.

The activity of a gene newly integrated into a chromosome depends on the genomic context of the integration site. This "position effect" has been widely reported, although the other side of the coin, that is, how integration affects the local chromosomal environment, has remained largely unexplored, as have the mechanism and phenotypic consequences of this "externality" of the position effect. Here, we examined the transcriptome profiles of approximately 250 Saccharomyces cerevisiae strains, each with GFP integrated into a different locus of the wild-type strain. We found that in genomic regions enriched in essential genes, GFP expression tended to be lower, and the genes near the integration site tended to show greater expression reduction. Further joint analysis with public genome-wide histone modification profiles indicated that this effect was associated with H3K4me2. More importantly, we found that changes in the expression of neighboring genes, but not GFP expression, significantly altered the cellular growth rate. As a result, genomic loci that showed high GFP expression immediately after integration were associated with growth disadvantages caused by elevated expression of neighboring genes, ultimately leading to a low total yield of GFP in the long run. Our results were consistent with competition for transcriptional resources among neighboring genes and revealed a previously unappreciated facet of position effects. This study highlights the impact of position effects on the fate of exogenous gene integration and has significant implications for biological engineering and the pathology of viral integration into the host genome.

miRNA-34c-5p targets Fra-1 to inhibit pulmonary fibrosis induced by silica through p53 and PTEN/PI3K/Akt signaling pathway.

Silica dust particles are representative of air pollution and long-term inhalation of silicon-containing dust through the respiratory tract can cause pulmonary fibrosis. Epithelial-mesenchymal transformation (EMT) plays an important role in the development of fibrosis. This process can relax cell-cell adhesion complexes and enhance cell migration and invasion properties of these cells. Dysregulation of microRNA-34c (miR-34c) is highly correlated with organ fibrosis including pulmonary fibrosis. In this study, we found that miR-34c-5p could alleviate the occurrence and development of silica-mediated EMT. Fos-related antigen 1 was identified as a functional target of miR-34c-5p by bioinformatics analysis and the dual luciferase gene reporting assay. Importantly, chemically induced up-regulation of hsa-miR-34c-5p correlated inversely with the expression of Fra-1 and further exploration found that the miR-34c-5p/Fra-1 axis inhibits the activation of the phosphatase and tensin homolog deleted on chromosome 10/phosphatidylinositol-4,5-bisphosphate3-kinase/protein kinase B (PTEN/PI3K/AKT) signaling pathway. In addition, through interaction with PTEN/p53 it inhibits the proliferation and migration of human bronchial epithelial cells stimulated by silica, and promotes cell apoptosis, thereby preventing EMT. This finding provides a promising biomarker for the diagnosis and prognosis of pulmonary fibrosis. Furthermore, overexpression of miR-34c-5p represents a potential therapeutic approach.

Reference equations for the six-minute walking distance in obese Chinese subjects more than 40 years old.

BACKGROUND: Studies have shown that the reference equations for the six-minute walking distance (6MWD), which were mainly derived from healthy, normal-weight people, are not suitable for individuals with obesity. The main purpose of this study was to establish reference equations for the 6MWD in obese Chinese subjects. METHODS: In our study, a total of 214 individuals with obesity performed the six-minute walking tests (6MWTs) according to the American thoracic society (ATS) guidelines, and the longer 6MWD was used for further analysis. The reference equations for the 6MWD were developed using stepwise multiple regression analysis. The newly established equations for the 6MWD were compared to the existing prediction equations. RESULTS: The mean 6MWD for the cohort was 523 ± 56 m. We found that the reliability of two 6MWTs was good. Age and BMI were identified as independent factors, and explained 31% and 27% of the variance in the 6MWD for the male and female participants, respectively. Thus, the reference equations reported in the previous studies did not accurately predict the 6MWD in our subjects. CONCLUSION: Our study was the first to describe the 6MWD in obese Chinese subjects and to propose new predictive equations. These established equations can improve the assessment of the health of obese Chinese patients whose exercise capacity is affected by the disease. LEVEL OF EVIDENCE: III, Cohort study.

The Origin of Additive Genetic Variance Driven by Positive Selection.

Fisher's fundamental theorem of natural selection predicts no additive variance of fitness in a natural population. Consistently, studies in a variety of wild populations show virtually no narrow-sense heritability (h2) for traits important to fitness. However, counterexamples are occasionally reported, calling for a deeper understanding on the evolution of additive variance. In this study, we propose adaptive divergence followed by population admixture as a source of the additive genetic variance of evolutionarily important traits. We experimentally tested the hypothesis by examining a panel of ∼1,000 yeast segregants produced by a hybrid of two yeast strains that experienced adaptive divergence. We measured >400 yeast cell morphological traits and found a strong positive correlation between h2 and evolutionary importance. Because adaptive divergence followed by population admixture could happen constantly, particularly in species with wide geographic distribution and strong migratory capacity (e.g., humans), the finding reconciles the observation of abundant additive variances in evolutionarily important traits with Fisher's fundamental theorem of natural selection. Importantly, the revealed role of positive selection in promoting rather than depleting additive variance suggests a simple explanation for why additive genetic variance can be dominant in a population despite the ubiquitous between-gene epistasis observed in functional assays.

Protective mechanism of SIRT1 on Hcy-induced atrial fibrosis mediated by TRPC3.

High plasma levels of homocysteine (Hcy) are regarded as a risk factor for atrial fibrillation (AF), which is closely associated with the pathological consequence of atrial fibrosis and can lead to heart failure with a high mortality rate; here, we show that atrial fibrosis is mediated by the relationship between canonical transient receptor potential 3 (TRPC3) channels and sirtuin type 1 (SIRT1) under the stimulation of Hcy. The left atrial appendage was obtained from patients with either sinus rhythm (SR) or AF and used to evaluate the relationship between the concentration of Hcy and a potential mechanism of cardiac fibrosis mediated by TRPC3 and SIRT1. We next performed transverse aortic constriction (TAC) in mouse to investigate the relationship. The mechanisms underlying atrial fibrosis involving TRPC3 and SIRT1 proteins were explored by co-IP, BLI and lentivirus transfection experiments. qPCR and WB were performed to analyse gene and protein expression, respectively. The higher level of atrial fibrosis was observed in the HH mouse group with a high Hcy diet. Such results suggest that AF patients may be more susceptible to atrial fibrosis and possess a high probability of progressing to hyperhomocysteinemia. Moreover, our findings are consistent with the hypothesis that TRPC3 channel up-regulation leads to abnormal accumulation of collagen, with the down-regulation of SIRT1 as an aetiological factor of high Hcy, which in turn predisposes to atrial fibrosis and strongly enhances the possibility of AF.

Six-minute walking distance in healthy Chinese people older than 60 years.

BACKGROUND: The six-minute walking test (6MWT) is a tool that plays a key role in evaluating the functional exercise capacity, prognosis and evaluation of treatment response of patients with various cardiopulmonary diseases. However, standard reference equations are currently unavailable for the six-minute walking distance (6MWD) for people aged 60-85 years in China. The purpose of this study was to 1) measure the 6MWD of healthy Chinese people aged 60-85 years, 2) establish reference equations for predicting the 6MWD, and 3) compare our reference equations with equations reported in previously published studies. METHOD: We obtained informed consent from each participant prior to the test, and the research design was approved by the Ethics Committee of Wenzhou People's Hospital. The demographic and anthropometric data and the 6MWD of healthy Chinese subjects aged 60-85 years old were measured using a standardized protocol. Every subject completed two 6MWTs, and the longest 6MWD further analyzed. RESULTS: Two hundred sixty-six subjects (128 males and 138 females) completed the 6MWT, and the mean walking distance was 518 ± 72 m. Males achieved a longer walking distance than females (518 ± 72 m vs. 487 ± 70 m; p < 0.0001), and active subjects achieved a longer walking distance than nonactive subjects (512 ± 76 m vs. 485 ± 63 m; p < 0.0001). According to the univariate analysis, the 6MWD was significantly associated with age, height, body mass index (BMI), heart rate and blood pressure after exercise and changes in heart rate before and after exercise. The stepwise multivariate regression analysis identified age, height and BMI as independent predictors of the 6MWD. The reference equations for Caucasians and South Americans tended to overestimate the 6MWD of our subjects, while the equations for Asian and African populations tended to underestimate the 6MWD. CONCLUSIONS: This study is the first to describe the 6MWD of healthy Chinese people aged 60-85 years, and reference prediction equations were proposed. These findings will help to improve the evaluation of Chinese patients with diseases that affect exercise capacity.

Dosage sensitivity of X-linked genes in human embryonic single cells.

BACKGROUND: During the evolution of mammalian sex chromosomes, the degeneration of Y-linked homologs has led to a dosage imbalance between X-linked and autosomal genes. The evolutionary resolution to such dosage imbalance, as hypothesized by Susumu Ohno fifty years ago, should be doubling the expression of X-linked genes. Recent studies have nevertheless shown that the X to autosome expression ratio equals ~ 1 in haploid human parthenogenetic embryonic stem (pES) cells and ~ 0.5 in diploid pES cells, suggesting no doubled expression for X-linked genes and refuting Ohno's hypothesis. RESULTS: Here, by reanalyzing an RNA-seq-based single-cell transcriptome dataset of human embryos, we found that from the 8-cell stage until the time-point just prior to implantation, the expression levels of X-linked genes are not two-fold upregulated in male cells and gradually decrease from two-fold in female cells. Additional analyses of gene expression noise further suggest that the dosage sensitivity of X-linked genes is weaker than that of autosomal genes in differentiated female cells, which contradicts a key assumption in Ohno's hypothesis, that most X-linked genes are dosage sensitive. Moreover, the dosage-sensitive housekeeping genes are preferentially located on autosomes, implying selection against X-linkage for dosage-sensitive genes. CONCLUSIONS: We observed dosage imbalance between X-linked and autosomal genes, as well as relatively high expression noise from X-linked genes. These results collectively suggest that X-linked genes are less dosage sensitive than autosomal genes, putting one primary assumption of Ohno's hypothesis in question.

Nascent RNA folding mitigates transcription-associated mutagenesis.

Transcription is mutagenic, in part because the R-loop formed by the binding of the nascent RNA with its DNA template exposes the nontemplate DNA strand to mutagens and primes unscheduled error-prone DNA synthesis. We hypothesize that strong folding of nascent RNA weakens R-loops and hence decreases mutagenesis. By a yeast forward mutation assay, we show that strengthening RNA folding and reducing R-loop formation by synonymous changes in a reporter gene can lower mutation rate by >80%. This effect is diminished after the overexpression of the gene encoding RNase H1 that degrades the RNA in a DNA-RNA hybrid, indicating that the effect is R-loop-dependent. Analysis of genomic data of yeast mutation accumulation lines and human neutral polymorphisms confirms the generality of these findings. This mechanism for local protection of genome integrity is of special importance to highly expressed genes because of their frequent transcription and strong RNA folding, the latter also improves translational fidelity. As a result, strengthening RNA folding simultaneously curtails genotypic and phenotypic mutations.

Impacts of conservation and human development policy across stakeholders and scales.

Ideally, both ecosystem service and human development policies should improve human well-being through the conservation of ecosystems that provide valuable services. However, program costs and benefits to multiple stakeholders, and how they change through time, are rarely carefully analyzed. We examine one of China's new ecosystem service protection and human development policies: the Relocation and Settlement Program of Southern Shaanxi Province (RSP), which pays households who opt voluntarily to resettle from mountainous areas. The RSP aims to reduce disaster risk, restore important ecosystem services, and improve human well-being. We use household surveys and biophysical data in an integrated economic cost-benefit analysis for multiple stakeholders. We project that the RSP will result in positive net benefits to the municipal government, and to cross-region and global beneficiaries over the long run along with environment improvement, including improved water quality, soil erosion control, and carbon sequestration. However, there are significant short-run relocation costs for local residents so that poor households may have difficulty participating because they lack the resources to pay the initial costs of relocation. Greater subsidies and subsequent supports after relocation are necessary to reduce the payback period of resettled households in the long run. Compensation from downstream beneficiaries for improved water and from carbon trades could be channeled into reducing relocation costs for the poor and sharing the burden of RSP implementation. The effectiveness of the RSP could also be greatly strengthened by early investment in developing human capital and environment-friendly jobs and establishing long-term mechanisms for securing program goals. These challenges and potential solutions pervade ecosystem service efforts globally.

The X to Autosome Expression Ratio in Haploid and Diploid Human Embryonic Stem Cells.

Ohno proposed that the expression levels of X-linked genes have been doubled to compensate the degeneration of Y-linked homologs during the evolution of mammalian sex chromosomes, but RNA sequencing in human somatic tissues showed no such upregulation for the vast majority of X-linked genes. Here we report that the X to autosome expression ratio equals ∼1 in haploid human parthenogenetic embryonic stem (pES) cells and ∼0.5 in diploidized pES cells, both with one active X chromosome. Although we confirmed the upregulation of ∼5% of X-linked genes encoding members of large protein complexes in diploids, these genes are also upregulated in haploids, breaking the otherwise balanced dosage. These findings argue against Ohno's hypothesis for both haploid and diploid cells and demonstrate that, at least in humans, precise gene regulation for dosage balance, even for members of large protein complexes, is much less critical than is commonly thought.

Codon-by-codon modulation of translational speed and accuracy via mRNA folding.

Rapid cell growth demands fast protein translational elongation to alleviate ribosome shortage. However, speedy elongation undermines translational accuracy because of a mechanistic tradeoff. Here we provide genomic evidence in budding yeast and mouse embryonic stem cells that the efficiency-accuracy conflict is alleviated by slowing down the elongation at structurally or functionally important residues to ensure their translational accuracies while sacrificing the accuracy for speed at other residues. Our computational analysis in yeast with codon resolution suggests that mRNA secondary structures serve as elongation brakes to control the speed and hence the fidelity of protein translation. The position-specific effect of mRNA folding on translational accuracy is further demonstrated experimentally by swapping synonymous codons in a yeast transgene. Our findings explain why highly expressed genes tend to have strong mRNA folding, slow translational elongation, and conserved protein sequences. The exquisite codon-by-codon translational modulation uncovered here is a testament to the power of natural selection in mitigating efficiency-accuracy conflicts, which are prevalent in biology.

Reference Equations for the Six-Minute Walk Distance in the Healthy Chinese Han Population, Aged 18-30 Years.

BACKGROUND: The six-minute walk test (6MWT) is a safe, simple, inexpensive tool for evaluating the functional exercise capacity. However, there is a lack of standard reference equations for the six-minute walk distance (6MWD) in the healthy Chinese Han population with an age of 18-30 years. The aims of the present study were as follows: 1) to measure the anthropometric data and the walking distance in a sample of healthy Chinese Han population, aged 18-30 years; 2) to construct reference equations for the 6MWD; 3) to compare the measured 6MWD of our cohort with previously published equations. METHODS: The anthropometric data, demographic, lung function and the walking distance of Chinese Han population, aged 18-30 years, were prospectively measured using a standardized protocol. Informed consent was obtained from each participant and the approval was obtained from the ethics committee of Wenzhou People's Hospital. The 6MWT was performed twice and the longer 6MWD was used for further analysis. RESULTS: A total of 355 subjects (176 female and 179 male) completed the 6MWT, and the average walking distance was 627.3 ± 52.88 m. The walking distance was achieved by females compared with males (607.4 ± 51.00 m vs. 646.9 ± 47.15 m; p < 0.0001) and active subjects compared with non-active subjects (646.1 ± 48.27 m vs. 611.6 ± 51.52 m; p < 0.0001). Univariate analysis showed age, height, body mass index, resting blood pressure, heart rate and blood pressure after the walk test and difference in heart rate before and after the walk test were significantly correlated with the 6MWD. Stepwise multiple regression analysis showed that height and difference in heart rate before and after the walk test were independent predictors associated with the 6MWD. The reference equations from Caucasian, Canadian and Chilean populations tend to overestimate the walking distance in our subjects, while Brazilian and Arabian equations tend to underestimate the walking distance. There was no significant difference in the walking distance between Korean equations and the current study. CONCLUSION: In summary, height and difference in heart rate before and after the walk test were the most significant predictors of the 6MWD, and the regression equations could explain approximately 38% and 31% of the distance variance in the female and male groups, respectively.

Ultralow-Power Electronic Trapping of Nanoparticles with Sub-10 nm Gold Nanogap Electrodes.

We demonstrate nanogap electrodes for rapid, parallel, and ultralow-power trapping of nanoparticles. Our device pushes the limit of dielectrophoresis by shrinking the separation between gold electrodes to sub-10 nm, thereby creating strong trapping forces at biases as low as the 100 mV ranges. Using high-throughput atomic layer lithography, we manufacture sub-10 nm gaps between 0.8 mm long gold electrodes and pattern them into individually addressable parallel electronic traps. Unlike pointlike junctions made by electron-beam lithography or larger micron-gap electrodes that are used for conventional dielectrophoresis, our sub-10 nm gold nanogap electrodes provide strong trapping forces over a mm-scale trapping zone. Importantly, our technology solves the key challenges associated with traditional dielectrophoresis experiments, such as high voltages that cause heat generation, bubble formation, and unwanted electrochemical reactions. The strongly enhanced fields around the nanogap induce particle-transport speed exceeding 10 µm/s and enable the trapping of 30 nm polystyrene nanoparticles using an ultralow bias of 200 mV. We also demonstrate rapid electronic trapping of quantum dots and nanodiamond particles on arrays of parallel traps. Our sub-10 nm gold nanogap electrodes can be combined with plasmonic sensors or nanophotonic circuitry, and their low-power electronic operation can potentially enable high-density integration on a chip as well as portable biosensing.

Split-Wedge Antennas with Sub-5 nm Gaps for Plasmonic Nanofocusing.

We present a novel plasmonic antenna structure, a split-wedge antenna, created by splitting an ultrasharp metallic wedge with a nanogap perpendicular to its apex. The nanogap can tightly confine gap plasmons and boost the local optical field intensity in and around these opposing metallic wedge tips. This three-dimensional split-wedge antenna integrates the key features of nanogaps and sharp tips, i.e., tight field confinement and three-dimensional nanofocusing, respectively, into a single platform. We fabricate split-wedge antennas with gaps that are as small as 1 nm in width at the wafer scale by combining silicon V-grooves with template stripping and atomic layer lithography. Computer simulations show that the field enhancement and confinement are stronger at the tip-gap interface compared to what standalone tips or nanogaps produce, with electric field amplitude enhancement factors exceeding 50 when near-infrared light is focused on the tip-gap geometry. The resulting nanometric hotspot volume is on the order of λ3/106. Experimentally, Raman enhancement factors exceeding 107 are observed from a 2 nm gap split-wedge antenna, demonstrating its potential for sensing and spectroscopy applications.

No X-chromosome dosage compensation in human proteomes.

The X and Y chromosomes of placental and marsupial mammals originated from a pair of autosomes. Ohno proposed that the expression levels of X-linked genes must have been doubled in males to compensate for the degeneration of their Y homologs. Recent mRNA sequencing experiments, however, found at most weak or infrequent X-chromosome dosage compensation. Nonetheless, dosage compensation need not occur at the mRNA level, because ultimately it is the protein concentration that matters. Analyzing human proteomic data from 22 tissues, we here report that X upregulation is absent at the protein level, indicating that Ohno's hypothesis is also invalid at the protein level.