Ultrafast Non-Volatile Floating-Gate Memory Based on All-2D Materials

The explosive growth of massive-data storage and the demand for ultrafast data processing require innovative memory devices with exceptional performance. 2D materials and their van der Waal heterostructures with atomically sharp interfaces hold great promise for innovations in memory devices. Here, this work presents non-volatile, floating-gate memory devices with all functional layers made of 2D materials, achieving ultrafast programming/erasing speeds (20 ns), high extinction ratios (up to 108), and multi-bit storage capability. These devices also exhibit long-term data retention exceeding 10 years, facilitated by a high gate-coupling ratio (GCR) and atomically sharp interfaces between functional layers. Additionally, this work demonstrates the realization of an "OR" logic gate on a single-device unit by synergistic electrical and optical operations. The present results provide a solid foundation for next-generation ultrahigh-speed, ultralong lifespan, non-volatile memory devices, with a potential for scale-up manufacturing and flexible electronics applications.

Machine learning-derived identification of prognostic signature for improving prognosis and drug response in patients with ovarian cancer

Clinical assessments relying on pathology classification demonstrate limited effectiveness in predicting clinical outcomes and providing optimal treatment for patients with ovarian cancer (OV). Consequently, there is an urgent requirement for an ideal biomarker to facilitate precision medicine. To address this issue, we selected 15 multicentre cohorts, comprising 12 OV cohorts and 3 immunotherapy cohorts. Initially, we identified a set of robust prognostic risk genes using data from the 12 OV cohorts. Subsequently, we employed a consensus cluster analysis to identify distinct clusters based on the expression profiles of the risk genes. Finally, a machine learning-derived prognostic signature (MLDPS) was developed based on differentially expressed genes and univariate Cox regression genes between the clusters by using 10 machine-learning algorithms (101 combinations). Patients with high MLDPS had unfavourable survival rates and have good prediction performance in all cohorts and in-house cohorts. The MLDPS exhibited robust and dramatically superior capability than 21 published signatures. Of note, low MLDIS have a positive prognostic impact on patients treated with anti-PD-1 immunotherapy by driving changes in the level of infiltration of immune cells. Additionally, patients suffering from OV with low MLDIS were more sensitive to immunotherapy. Meanwhile, patients with low MLDIS might benefit from chemotherapy, and 19 compounds that may be potential agents for patients with low MLDIS were identified. MLDIS presents an appealing instrument for the identification of patients at high/low risk. This could enhance the precision treatment, ultimately guiding the clinical management of OV.

Metabolism-associated molecular classification of cervical cancer

OBJECTIVE

This study aimed to explore metabolic abnormalities in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) for metabolism-related genes.

METHODS

We downloaded expression data for metabolism-related genes, performed differential expression analysis, and applied weighted gene co-expression network analysis (WGCNA) to identify metabolism-related functional modules. We obtained normalised miRNA expression data and identified master methylation regulators for metabolism-related genes. Cox regression of data on metabolism-related genes was performed to screen for genes that affect the prognosis of patients with CESC. Furthermore, we selected key genes for validation.

RESULTS

Our results identified 3620 metabolism-related genes in CESC, 2493 of which contained related mutations. The co-occurrence of CUBN, KALRN, and HERC1 was related to the prognosis of CESC. The fraction of genome altered (FGA) closely correlated with overall survival. In expression analysis, 374 genes were related to the occurrence and prognosis of CESC. We then identified four metabolic pathway modules in WGCNA. Further analysis revealed that glycolysis/gluconeogenesis was related to endothelial cells and that arachidonic acid metabolism was related to cell proliferation. These four modules were also related to the prognosis of CESC. Among CESC-related metabolic genes, two genes were found to be regulated by microRNAs (miRNAs) and methylation, whereas another two genes were coregulated by miRNAs and mutations.

CONCLUSIONS

Among metabolism-related genes, 15 genes were related to the prognosis of CESC. The co-occurrence of CUBN/KALRN/HERC1 was associated with CESC prognosis. Glycolysis/gluconeogenesis was related to endothelial cells, and arachidonic acid metabolism was related to cell proliferation.

Pregnancy outcomes of intrauterine insemination in young patients with diminished ovarian reserve: a multicenter cohort study

BACKGROUND

To date, there is no consensus on whether intrauterine insemination (IUI) treatment is required in young patients with diminished ovarian reserve (DOR). Pregnancy outcomes in young DOR patients undergoing IUI are controversial. The existing studies are all single-center studies, with no existing multicenter cohort studies. The purpose of this multicenter study was to investigate the pregnancy outcomes of young DOR patients undergoing IUI.

METHODS

This multicenter cohort study included a total of 4600 cycles in 2204 infertile patients who underwent IUI treatment in three reproductive medical centers between September 2018 and January 2022. The research subjects were divided into two groups according to their serum anti-Müllerian hormone (AMH) levels. Propensity score matching (PSM) was used to match the research subjects at a ratio of 1:4. The pregnancy outcomes in the two groups were compared.

RESULTS

There was no significant difference in the clinical pregnancy rates (CPR), biochemical rates, and ectopic pregnancy rates between the two groups (P > 0.05). There were, however, significant differences in the miscarriage rates between the groups (P < 0.05). The live birth rates (LBR) were 6.6 vs. 9.9 between the two groups. The multivariable logistic regression models reveal that body mass index, AMH were significantly correlated with CPR; AMH were significantly correlated with LBR; BMI, follicle stimulating hormone were significantly correlated with miscarriage rate.

CONCLUSIONS

The clinical pregnancy rate of DOR patients was not significantly different from that of NOR patients; however, the miscarriage rates were significantly different from those of NOR patients.

Development of a cryogen-free sub-3 K low-temperature scanning probe microscope by remote liquefaction scheme

We developed a new scheme for cryogen-free cooling down to sub-3 K temperature range and ultra-low vibration level. An ultra-high-vacuum cryogen-free scanning probe microscope (SPM) system was built based on the new scheme. Instead of mounting a below-decoupled cryocooler directly onto the system, the new design was realized by integrating a Gifford-McMahon cryocooler into a separate liquefying chamber, providing two-stage heat exchangers in a remote way. About 10 L of helium gas inside the gas handling system was cooled, liquefied in the liquefying chamber, and then transferred to a continuous-flow cryostat on the SPM chamber through an ∼2 m flexible helium transfer line. The exhausted helium gas from the continuous-flow cryostat was then returned to the liquefying chamber for reliquefaction. A base temperature of ∼2.84 K at the scanner sample stage and a temperature fluctuation of almost within ±0.1 mK at 4 K were achieved. The cooling curves, tunneling current noise, variable-temperature test, scanning tunneling microscopy and non-contact atomic force microscopy imaging, and first and second derivatives of I(V) spectra are characterized to verify that the performance of our cryogen-free SPM system is comparable to the bath cryostat-based low-temperature SPM system. This remote liquefaction close-cycle scheme shows conveniency to upgrade the existing bath cryostat-based SPM system, upgradeability of realizing even lower temperature down to sub-1 K range, and great compatibility of other physical environments, such as high magnetic field and optical accesses. We believe that the new scheme could also pave a way for other cryogenic applications requiring low temperature but sensitive to vibration.

Ultrafast-Programmable 2D Homojunctions Based on van der Waals Heterostructures on a Silicon Substrate

The development of electrically ultrafast-programmable semiconductor homojunctions can lead to transformative multifunctional electronic devices. However, silicon-based homojunctions are not programmable so that alternative materials need to be explored. Here 2D, multi-functional, lateral homojunctions made of van der Waals heterostructures with a semi-floating-gate configuration on a p++ Si substrate feature atomically sharp interfaces and can be electrostatically programmed in nanoseconds, more than seven orders of magnitude faster than other 2D-based homojunctions. By applying voltage pulses with different polarities, lateral p-n, n+ -n and other types of homojunctions can be formed, varied, and reversed. The p-n homojunctions possess a high rectification ratio of up to ≈105 and can be dynamically switched between four distinct conduction states with the current spanning over nine orders of magnitude, enabling them to function as logic rectifiers, memories, and multi-valued logic inverters. Built on a p++ Si substrate, which acts as the control gate, the devices are compatible with Si technology.

A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean

Although root nodules are essential for biological nitrogen fixation in legumes, the cell types and molecular regulatory mechanisms contributing to nodule development and nitrogen fixation in determinate nodule legumes, such as soybean (Glycine max), remain incompletely understood. Here, we generated a single-nucleus resolution transcriptomic atlas of soybean roots and nodules at 14 days post inoculation (dpi) and annotated 17 major cell types, including six that are specific to nodules. We identified the specific cell types responsible for each step in the ureides synthesis pathway, which enables spatial compartmentalization of biochemical reactions during soybean nitrogen fixation. By utilizing RNA velocity analysis, we reconstructed the differentiation dynamics of soybean nodules, which is differed from those of indeterminate nodules in Medicago truncatula. Moreover, we identified several putative regulators of soybean nodulation and two of these genes, GmbHLH93 and GmSCL1, were as-of-yet uncharacterized in soybean. Overexpression of each gene in soybean hairy root systems validated their respective roles in nodulation. Notably, enrichment for cytokinin-related genes in soybean nodules led to identification of the cytokinin receptor, GmCRE1, as a prominent component of nodulation pathway. GmCRE1 knockout in soybean resulted in a striking nodule phenotype with decreased nitrogen fixation zone and markedly fewer symbionts, accompanied by downregulation of nodule-specific gene expression, as well as almost complete abrogation of biological nitrogen fixation. In summary, this study provides a comprehensive perspective of the cellular landscape during soybean nodulation, shedding light on the underlying metabolic and developmental mechanisms of soybean nodule formation. This article is protected by copyright. All rights reserved.

Experimental Realization of Atomic Monolayer Si9 C15

Monolayer Si_x C_y constitutes an important family of 2D materials that is predicted to feature a honeycomb structure and appreciable bandgaps. However, due to its binary chemical nature and the lack of bulk polymorphs with a layered structure, the fabrication of such materials has so far been challenging. Here, the synthesis of atomic monolayer Si₉ C₁₅ on Ru (0001) and Rh(111) substrates is reported. A combination of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), scanning transmission electron microscopy (STEM), and density functional theory (DFT) calculations is used to infer that the 2D lattice of Si₉ C₁₅ is a buckled honeycomb structure. Monolayer Si₉ C₁₅ shows semiconducting behavior with a bandgap of ≈1.9 eV. Remarkably, the Si₉ C₁₅ lattice remains intact after exposure to ambient conditions, indicating good air stability. The present work expands the 2D-materials library and provides a promising platform for future studies in nanoelectronics and nanophotonics.

[Safety and efficacy of left atrial appendage closure combined with patent foramen ovale closure for atrial fibrillation patients with patent foramen ovale]

Objective: To analyze the safety and efficacy of combined left atrial appendage (LAA) and patent foramen ovale (PFO) closure in adult atrial fibrillation (AF) patients complicating with PFO. Methods: This study is a retrospective and cross-sectional study. Seven patients with AF complicated with PFO diagnosed by transesophageal echocardiography (TEE) in Zhoupu Hospital Affiliated to Shanghai University of Medicine & Health Sciences from June 2017 to October 2020 were selected. Basic data such as age, gender and medical history were collected. The atrial septal defect or PFO occluder and LAA occluder were selected according to the size of PFO, the ostia width and depth of LAA. Four patients underwent left atrial appendage closure(LAAC) and PFO closure at the same time. PFO closure was performed during a one-stop procedure of cryoablation combined with LAAC in 2 patients. One patient underwent PFO closure at 10 weeks after one-stop procedure because of recurrent transient ischemic attack (TIA). All patients continued to take oral anticoagulants. TEE was repeated 8-12 weeks after intervention. In case of device related thrombus(DRT), TEE shall be rechecked 6 months after adjusting anticoagulant and antiplatelet drug treatment. Patients were follow-up at 1, 3, 6, 12, 24 months by telephone call, and the occurrence of cardio-cerebrovascular events was recorded. Results: Among the 7 patients with AF, 2 were male, aged (68.0±9.4) years, and 3 had a history of recurrent cerebral infarction and TIA. Average PFO diameter was (3.5±0.8)mm. Three patients were implanted with Watchman LAA occluder (30, 30, 33 mm) and atrial septal defect occluder (8, 9, 16 mm). 2 patients were implanted with LAmbre LAA occluder (34/38, 18/32 mm) and PFO occluder (PF1825, PF2525). 2 patients were implanted with LACbes LAA occluder (24, 28 mm) and PFO occluder (PF2525, PF1825) respectively. The patients were followed up for 12 (11, 24) months after operation. TEE reexamination showed that the position of LAA occluder and atrial septal defect occluder or PFO occluder was normal in all patients. DRT was detected in 1 patient, and anticoagulant therapy was adjusted in this patient. 6 months later, TEE showed that DRT disappeared. No cardiovascular and cerebrovascular events occurred in all patients with AF during follow-up. Conclusions: In AF patients complicated with PFO, LAAC combined with PFO closure may have good safety and effectiveness.

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of host-jumping. The molecular spectrum of mutations (i.e., the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.

Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process

The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in RNA. Although the molecular spectrum of de novo mutations—the relative rates at which various base substitutions occur—are widely recognized as informative toward understanding the evolution of a viral genome, little attention has been paid to the possibility of using molecular spectra to infer the host origins of a virus. Here, we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines, enabled by the use of sporadic junctions formed during discontinuous transcription as molecular barcodes. We find that de novo mutations are generated in a replication-independent manner, typically on the genomic strand, and highly dependent on mutagenic mechanisms specific to the host cellular environment. De novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution, in an asymmetric manner favoring specific mutation types. Consequently, similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13, which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into humans. Collectively, our findings provide data-driven support for the natural origin of SARS-CoV-2.

•

The asymmetric de novo mutations in SARS-CoV-2 are induced by mutagenic mechanisms in the host cellular environment

•

De novo mutations determine the molecular spectrum of accumulated mutations during SARS-CoV-2 evolution

•

Molecular spectra of accumulated mutations in betacoronaviruses cluster according to the host species instead of the phylogenetic relationship

•

The mutations accumulated in SARS-CoV-2 prior to its transmission to humans are consistent with an evolutionary process in a bat host

A time-shared switching scheme designed for multi-probe scanning tunneling microscope

We report the design of a time-shared switching scheme, aiming to realize the manipulation and working modes (imaging mode and transport measurement mode) switching between multiple scanning tunneling microscope (STM) probes one by one with a shared STM control system (STM CS) and an electrical transport characterization system. This scheme comprises three types of switch units, switchable preamplifiers (SWPAs), high voltage amplifiers, and a main control unit. Together with the home-made software kit providing the graphical user interface, this scheme achieves a seamless switching process between different STM probes. Compared with the conventional scheme using multiple independent STM CSs, this scheme possesses more compatibility, flexibility, and expansibility for lower cost. The overall architecture and technique issues are discussed in detail. The performances of the system are demonstrated, including the millimeter scale moving range and atomic scale resolution of a single STM probe, safely approached multiple STM probes beyond the resolution of the optical microscope (1.1 µm), qualified STM imaging, and accurate electrical transport characterization. The combinational technique of imaging and transport characterization is also shown, which is supported by SWPA switches with ultra-high open circuit resistance (909 TΩ). These successful experiments prove the effectiveness and the usefulness of the scheme. In addition, the scheme can be easily upgraded with more different functions and numbers of probe arrays, thus opening a new way to build an extremely integrated and high throughput characterization platform.

Integrated global analysis reveals a vitamin E-vitamin K1 sub-network, downstream of COLD1, underlying rice chilling tolerance divergence

Rice, a staple food with tropical/subtropical origination, is susceptible to cold stress, one of the major constraints on its yield and distribution. Asian cultivated rice consists of two subspecies with diverged chilling tolerance to adapt to different environments. The mechanism underlying this divergence remains obscure with a few known factors, including membrane protein CHILLING-TOLERANCE DIVERGENCE 1 (COLD1). Here, we reveal a vitamin E-vitamin K1 sub-network responsible for chilling tolerance divergence through global analyses. Rice genome regions responsible for tolerance divergence are identified with chromosome segment substitution lines (CSSLs). Comparative transcriptomic and metabolomic analysis of chilling-tolerant CSSL4-1 and parent lines uncovered a vitamin E-vitamin K1 sub-network in chloroplast with tocopherol (vitamin E) mediating chloroplast-to-nucleus signaling. COLD1, located in the substitution segment in CSSL4-1, is confirmed as its upstream regulator by transgenic material analysis. Our work uncovers a pathway downstream of COLD1, through which rice modulates chilling tolerance for thermal adaptation, with potential utility in crop improvement.

LncRNA AFAP1-AS1 regulates proliferation and apoptosis of endometriosis through activating STAT3/TGF-β/Smad signaling via miR-424-5p

AIM

Endometriosis is a common gynecological disorder characterized by chronic pelvic pain and infertility, which negatively affects women's health worldwide. AFAP1-AS1 has been implicated in endometriosis lesions recently, but its mechanism of endometriosis progression remains unclear.

METHODS

Endometrial stromal cells (ESCs) were used to identify the role of AFAP1-AS1 in endometriosis. The migratory capability was determined by transwell. Gene and protein expressions were identified by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. Cell viability and apoptosis were detected by MTT assays and flow cytometry, respectively. Luciferase report assays were used to identify the interaction of AFAP1-AS1, miR-424-5p and signal transducer and activator of transcription 3 (STAT3).

RESULTS

AFAP1-AS1 knockdown or miR-424-5p overexpression inhibited proliferation and migration, and promoted apoptosis in ESCs. In addition, knockdown of AFAP1-AS1 repressed the expression of ki-67 and Bcl-2, and promoted the levels of cleaved caspase-3 and Bax. Furthermore, knockdown of AFAP1-AS1 inhibited the conversion of E-cadherin to N-cadherin and the expression of Snail. Moreover, AFAP1-AS1 activated the STAT3/transforming growth factor-β1 (TGF-β1)/Smad2 axis via directly targeting miR-424-5p. The regulatory effect of AFAP1-AS1 silencing in ESC migration, proliferation, and apoptosis was reversed by miR-424-5p inhibition or STAT3 overexpression.

CONCLUSIONS

AFAP1-AS1 silencing could inhibit cell proliferation and promote apoptosis by regulating STAT3/TGF-β/Smad signaling pathway via targeting miR-424-5p in ESCs. AFAP1-AS1 may be a potential therapeutic target of controlling the progression of endometriosis.

Single-cell transcriptome atlas of the leaf and root of rice seedlings

As a multicellular organism, rice flourishes relying on gene expression diversity among cells of various functions. However, cellular-resolution transcriptome features are yet to be fully recognized, let alone cell-specific transcriptional responses to environmental stimuli. In this study, we apply single-cell RNA sequencing to both shoot and root of rice seedlings growing in Kimura B nutrient solution or exposed to various abiotic stresses and characterize transcriptomes for a total of 237,431 individual cells. We identify 15 and nine cell types in the leaf and root, respectively, and observe that common transcriptome features are often shared between leaves and roots in the same tissue layer, except for endodermis or epidermis. Abiotic stress stimuli alter gene expression largely in a cell type-specific manner, but for a given cell type, different stresses often trigger transcriptional regulation of roughly the same set of genes. Besides, we detect proportional changes in cell populations in response to abiotic stress and investigate the underlying molecular mechanisms through single-cell reconstruction of the developmental trajectory. Collectively, our study represents a benchmark-setting data resource of single-cell transcriptome atlas for rice seedlings and an illustration of exploiting such resources to drive discoveries in plant biology.

Synergistic construction of bifunctional and stable Pt/HZSM-5-based catalysts for efficient catalytic cracking of n-butane

Efficient conversion of light alkanes is of essential significance for enhancing the utilization efficiency of resources and exploring the activation and evolution regulation of C-C and C-H bonds in stable molecules. The processes are often executed with catalysts under harsh conditions. The olefin yield and metal stability have been the long-standing concerns. Herein, we report a facile strategy of constructing a bifunctional Pt/HZSM-5-based catalyst by two-step atomic layer deposition (ALD) to achieve a high light olefin formation rate of 0.48 mmol gcat-1·min-1 in the catalytic cracking of n-butane at 600 °C, which is ∼2.2 times higher than that of the conventional Pt/HZSM-5 catalyst (0.22 mmol gcat-1·min-1). Moreover, the bifunctional Pt/HZSM-5-based catalyst exhibited outstanding recyclability and excellent metal stability against sintering in comparison with conventional Pt/HZSM-5. Detailed microscopic and spectroscopic characterization studies demonstrate that the metal oxide (TiO2 or Al2O3) coating not only prevents the metal from high-temperature sintering, but also regulates the proportion of coordinately unsaturated platinum surface atoms. Theoretical calculations further confirm the preference of nucleation of TiO2 or Al2O3 on coordinately unsaturated platinum sites, which in turn modulates the bifunctional dehydrogenation-cracking pathway to improve the olefin formation rate.

Wrinkle-induced highly conductive channels in graphene on SiO2/Si substrates

A graphene wrinkle is a quasi-one-dimensional structure and can alter the intrinsic physical and chemical activity, modify the band structure and introduce transport anisotropy in graphene thin films. However, the quasi-one-dimensional electrical transport contribution of wrinkles to the whole graphene films compared to that of the two-dimensional flat graphene nearby has still been elusive. Here, we report measurements of relatively high conductivity in micrometer-wide graphene wrinkles on SiO2/Si substrates using an ultrahigh vacuum (UHV) four-probe scanning tunneling microscope. Combining the experimental results with resistor network simulations, the wrinkle conductivity at the charge neutrality point shows a much higher conductivity up to ∼33.6 times compared to that of the flat monolayer region. The high conductivity can be attributed not only to the wrinkled multilayer structure but also to the large strain gradients located mainly in the boundary area. This method can also be extended to evaluate the electrical-transport properties of wrinkled structures in other two-dimensional materials.

Direct Visualization of Hydrogen-Transfer Intermediate States by Scanning Tunneling Microscopy

Hydrogen atoms bonded within molecular cavities often undergo tunneling or thermal-transfer processes that play major roles in diverse physical phenomena. Such transfers may or may not entail intermediate states. The existence of such fleeting states is typically determined by indirect means, while their direct visualization has not been achieved, largely because their concentrations under equilibrium conditions are negligible. Here we use density-functional-theory calculations and scanning-tunneling-microscopy (STM) image simulations to predict that, under specially designed nonequilibrium conditions of voltage-enhanced high transfer rates, the cis-intermediate of the two-hydrogen transfer process in metal-free naphthalocyanine molecules adsorbed on Ag(111) surfaces would be visualizable in a composite image of double-C morphology. As guided by the theoretical predictions, at adjusted scanning temperature and bias, STM experiments achieve a direct visualization of the cis-intermediate. This work demonstrates a practical way to directly visualize elusive intermediates, which enhances understanding of the quantum dynamics of hydrogen atoms.

Combinatorial laser molecular beam epitaxy system integrated with specialized low-temperature scanning tunneling microscopy

We present a newly developed facility comprising a combinatorial laser molecular beam epitaxy system and an in situ scanning tunneling microscope (STM). This facility aims at accelerating the materials research in a highly efficient way by advanced high-throughput film synthesis techniques and subsequent fast characterization of surface morphology and electronic states. Compared with uniform films deposited by conventional methods, the so-called combinatorial thin films will be beneficial in determining the accurate phase diagrams of different materials due to the improved control of parameters such as chemical substitution and sample thickness resulting from a rotary-mask method. A specially designed STM working under low-temperature and ultrahigh vacuum conditions is optimized for the characterization of combinatorial thin films in an XY coarse motion range of 15 mm × 15 mm with submicrometer location precision. The overall configuration and some key aspects such as the sample holder design, scanner head, and sample/tip/target transfer mechanism are described in detail. The performance of the device is demonstrated by synthesizing high-quality superconducting FeSe thin films with gradient thickness and imaging surfaces of highly oriented pyrolytic graphite, Au (111), Bi₂Sr₂CaCu₂O_8+δ (BSCCO), and FeSe. In addition, we also have obtained clean noise spectra of tunneling junctions and the superconducting energy gap of BSCCO. The successful manufacturing of such a facility opens a new window for the next generation equipment designed for experimental materials research.

Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency

BACKGROUND

Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency.

RESULTS

We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted.

CONCLUSIONS

Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.

A low-temperature scanning probe microscopy system with molecular beam epitaxy and optical access

A low-temperature ultra-high vacuum scanning probe microscopy (SPM) system with molecular beam epitaxy (MBE) capability and optical access was conceived, built, and tested in our lab. The design of the whole system is discussed here, with special emphasis on some critical parts. The SPM scanner head takes a modified Pan-type design with improved rigidity and compatible configuration to optical access and can accommodate both scanning tunneling microscope (STM) tips and tuning-fork based qPlus sensors. In the system, the scanner head is enclosed by a double-layer cold room under a bath type cryostat. Two piezo-actuated focus-lens stages are mounted on both sides of the cold room to couple light in and out. The optical design ensures the system's forward compatibility to the development of photo-assisted STM techniques. To test the system's performance, we conducted STM and spectroscopy studies. The herringbone reconstruction and atomic structure of an Au(111) surface were clearly resolved. The dI/dV spectra of an Au(111) surface were obtained at 5 K. In addition, a periodic 2D tellurium (Te) structure was grown on the Au(111) surface using MBE and the atomic structure is clearly resolved by using STM.

Reduced intrinsic DNA curvature leads to increased mutation rate

BACKGROUND

Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers our ability to identify positive selection in evolution and to identify driver mutations in tumorigenesis.

RESULTS

Here, we use a combination of synthetic genes and sequences of thousands of isolated yeast colonies to show that intrinsic DNA curvature is a major cis determinant of mutation rate. Mutation rate negatively correlates with DNA curvature within genes, and a 10% decrease in curvature results in a 70% increase in mutation rate. Consistently, both yeast and humans accumulate mutations in regions with small curvature. We further show that this effect is due to differences in the intrinsic mutation rate, likely due to differences in mutagen sensitivity and not due to differences in the local activity of DNA repair.

CONCLUSIONS

Our study establishes a framework for understanding the cis properties of DNA sequence in modulating the local mutation rate and identifies a novel causal source of non-uniform mutation rates across the genome.

HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation

DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing (BS-seq) data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http://qianlab.genetics.ac.cn/HeteroMeth.

Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory

Vernalization, the requirement of plants for long-term exposure to low environmental temperature for flowering, is an epigenetic phenomenon. Histone modification regulation has been revealed in vernalization, but is limited to key genes. Now, we know that VRN1 is epigenetically critical for monocots. Genome-wide analysis is still unavailable, however. We performed chromatin immunoprecipitation-sequencing for H3K4me3/H3K27me3 in Brachypodium distachyon to obtain a global view of histone modifications in vernalization on a genome-wide scale and for different pathways/genes. Our data showed that H3K4me3 and H3K27me3 play distinct roles in vernalization. Unlike H3K4me3, H3K27me3 exhibited regional regulation, showed main regulation targets in vernalization and contributed to epigenetic memory. For genes in four flowering regulation pathways, only FT2 (functional ortholog of VRN3 in B. distachyon) and VRN1 showed coordinated changes in H3K4me3/H3K27me3. The epigenetic response at VRN3 was weaker under short-day than under long-day conditions. VRN3 was revealed as an epigenetic regulation point integrating vernalization and day length signals. We globally identified genes maintaining vernalization-induced epigenetic changes. Most of these genes showed dose-dependent vernalization responses, revealing a quantitative 'recording system' for vernalization. Our studies shed light on the epigenetic role of VRN3 and H3K4me3/H3K27me3 in vernalization and reveal genes underlying epigenetic memory, laying the foundation for further study.

Codon-Resolution Analysis Reveals a Direct and Context-Dependent Impact of Individual Synonymous Mutations on mRNA Level

Codon usage bias (CUB) refers to the observation that synonymous codons are not used equally frequently in a genome. CUB is stronger in more highly expressed genes, a phenomenon commonly explained by stronger natural selection on translational accuracy and/or efficiency among these genes. Nevertheless, this phenomenon could also occur if CUB regulates gene expression at the mRNA level, a hypothesis that has not been tested until recently. Here, we attempt to quantify the impact of synonymous mutations on mRNA level in yeast using 3,556 synonymous variants of a heterologous gene encoding green fluorescent protein (GFP) and 523 synonymous variants of an endogenous gene TDH3. We found that mRNA level was positively correlated with CUB among these synonymous variants, demonstrating a direct role of CUB in regulating transcript concentration, likely via regulating mRNA degradation rate, as our additional experiments suggested. More importantly, we quantified the effects of individual synonymous mutations on mRNA level and found them dependent on 1) CUB and 2) mRNA secondary structure, both in proximal sequence contexts. Our study reveals the pleiotropic effects of synonymous codon usage and provides an additional explanation for the well-known correlation between CUB and gene expression level.

Direct Four-Probe Measurement of Grain-Boundary Resistivity and Mobility in Millimeter-Sized Graphene

Grain boundaries (GBs) in polycrystalline graphene scatter charge carriers, which reduces carrier mobility and limits graphene applications in high-speed electronics. Here we report the extraction of the resistivity of GBs and the effect of GBs on carrier mobility by direct four-probe measurements on millimeter-sized graphene bicrystals grown by chemical vapor deposition (CVD). To extract the GB resistivity and carrier mobility from direct four-probe intragrain and intergrain measurements, an electronically equivalent extended 2D GB region is defined based on Ohm's law. Measurements on seven representative GBs find that the maximum resistivities are in the range of several kΩ·μm to more than 100 kΩ·μm. Furthermore, the mobility in these defective regions is reduced to 0.4-5.9‰ of the mobility of single-crystal, pristine graphene. Similarly, the effect of wrinkles on carrier transport can also be derived. The present approach provides a reliable way to directly probe charge-carrier scattering at GBs and can be further applied to evaluate the GB effect of other two-dimensional polycrystalline materials, such as transition-metal dichalcogenides (TMDCs).

Trans-splicing enhances translational efficiency in C. elegans

Translational efficiency is subject to extensive regulation. However, the factors influencing such regulation are poorly understood. In Caenorhabditis elegans, 62% of genes are trans-spliced to a specific spliced leader (SL1), which replaces part of the native 5' untranslated region (5' UTR). Given the pivotal role the 5' UTR plays in the regulation of translational efficiency, we hypothesized that SL1 trans-splicing functions to regulate translational efficiency. With genome-wide analysis on Ribo-seq data, polysome profiling experiments, and CRISPR-Cas9-based genetic manipulation of trans-splicing sites, we found four lines of evidence in support of this hypothesis. First, SL1 trans-spliced genes have higher translational efficiencies than non-trans-spliced genes. Second, SL1 trans-spliced genes have higher translational efficiencies than non-trans-spliced orthologous genes in other nematode species. Third, an SL1 trans-spliced isoform has higher translational efficiency than the non-trans-spliced isoform of the same gene. Fourth, deletion of trans-splicing sites of endogenous genes leads to reduced translational efficiency. Importantly, we demonstrated that SL1 trans-splicing plays a key role in enhancing translational efficiencies of essential genes. We further discovered that SL1 trans-splicing likely enhances translational efficiency by shortening the native 5' UTRs, hence reducing the presence of upstream start codons (uAUG) and weakening mRNA secondary structures. Taken together, our study elucidates the global function of trans-splicing in enhancing translational efficiency in nematodes, paving the way for further understanding the genomic mechanisms of translational regulation.

Upgrade of a commercial four-probe scanning tunneling microscopy system

Upgrade of a commercial ultra-high vacuum four-probe scanning tunneling microscopy system for atomic resolution capability and thermal stability is reported. To improve the mechanical and thermal performance of the system, we introduced extra vibration isolation, magnetic damping, and double thermal shielding, and we redesigned the scanning structure and thermal links. The success of the upgrade is characterized by its atomically resolved imaging, steady cooling down cycles with high efficiency, and standard transport measurement capability. Our design may provide a feasible way for the upgrade of similar commercial systems.

Na7CrCuW11O39.16H2O induces apoptosis in human ovarian cancer SKOV3 cells through the p38 signaling pathway

Ovarian carcinoma is a common malignant disease worldwide with a poor therapeutic response. The present study investigated the effects of Na₇CrCuW₁₁O₃₉.16H₂O (CrCuW₁₁) on ovarian cancer cell growth and investigated the mechanisms underlying its actions. The effects of CrCuW₁₁ on cell viability and apoptosis were measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, acridine orange/ethidium bromide staining and electron microscopy in human ovarian cancer SKOV3 cells. The expression of bcl-2-like protein 4 (Bax), B-cell lymphoma 2 (Bcl-2), cytochrome c, phosphorylated (p)-p38 and p38 was determined by western blot analysis. Caspase-3 activity was measured by caspase-3 activity kit. CrCuW₁₁ concentrations of 1.87×10^-3 mol. l^-1 at 12 h reduced viability induced apoptosis in SKOV3 cells in a concentration-and time-dependent manner. Forced expression of CrCuW₁₁ upregulated the expression of certain proteins (Bax, cytochrome c, and p-p38), and downregulated Bcl-2 protein expression. Furthermore, CrCuW₁₁ also enhanced caspase-3 activity. The p38 inhibitor SB203580 was able to inhibit the activity of CrCuW₁₁. Caspase-3 and p38 signaling pathways were associated with CrCuW₁₁-regulated multiple targets involved in SKOV3 cell proliferation. Therefore, the results of the present study indicated that CrCuW₁₁ may be used as a novel clinical drug for the treatment of ovarian cancer.

Promoted photoelectrocatalytic hydrogen evolution of a type II structure via an Al2O3 recombination barrier layer deposited using atomic layer deposition

The introduction of an Al₂O₃ recombination barrier layer at the interface between TiO₂ and CdSe can effectively improve the PEC hydrogen evolution performance.

Expression and function of the ID1 gene during transforming growth factor-β1-induced differentiation of human embryonic stem cells to endothelial cells

ID1 can mediate transforming growth factor-β (TGF-β)/activin receptor-like kinase-1 (ALK1)-induced (and Smad-dependent) migration in endothelial cells (ECs). However, the role that ID1 plays during differentiation of human embryonic stem cells (hESCs) into ECs induced by TGF-β1 remains unclear. In this study, a hESC differentiation model that recapitulates the developmental steps of vasculogenesis during the early stages of embryonic development was used to explore this question. We found that TGF-β1 increases endothelial cell differentiation and inhibits endothelial tube formation. Furthermore, at an early stage of differentiation, TGF-β1 may induce in vitro differentiation of hESCs into ECs by inhibiting expression of ID1, while at a later stage of differentiation, TGF-β1 may stimulate the proliferation and migration of ECs via the ALK1/Smad1/5/ID1 pathway. Downregulation of ID1 by gene silencing can lead to acceleration of TGF-β1-induced hESC differentiation into ECs and inhibition of proliferation and migration of ECs. This study may reveal some mechanisms of in vivo vasculogenesis in the early stages of embryonic development.

O-GlcNAc-mediated interaction between VER2 and TaGRP2 elicits TaVRN1 mRNA accumulation during vernalization in winter wheat

Vernalization, sensing of prolonged cold, is important for seasonal flowering in eudicots and monocots. While vernalization silences a repressor (FLC, MADS-box transcription factor) in eudicots, it induces an activator (TaVRN1, an AP1 clade MADS-box transcription factor) in monocots. The mechanism for TaVRN1 induction during vernalization is not well understood. Here we reveal a novel mechanism for controlling TaVRN1 mRNA accumulation in response to prolonged cold sensing in wheat. The carbohydrate-binding protein VER2, a jacalin lectin, promotes TaVRN1 upregulation by physically interacting with the RNA-binding protein TaGRP2. TaGRP2 binds to TaVRN1 pre-mRNA and inhibits TaVRN1 mRNA accumulation. The physical interaction between VER2 and TaGRP2 is controlled by TaGRP2 O-GlcNAc modification, which gradually increases during vernalization. The interaction between VER2 and O-GlcNAc-TaGRP2 reduces TaGRP2 protein accumulation in the nucleus and/or promotes TaGRP2 dissociation from TaVRN1, leading to TaVRN1 mRNA accumulation. Our data reveal a new mechanism for sensing prolonged cold in temperate cereals.

Construction of 2D atomic crystals on transition metal surfaces: graphene, silicene, and hafnene

The synthesis and structures of graphene on Ru(0001) and Pt(111), silicene on Ag(111) and Ir(111) and the honeycomb hafnium lattice on Ir(111) are reviewed. Epitaxy on a transition metal (TM) substrate is a pro-mising method to produce a variety of two dimensional (2D) atomic crystals which potentially can be used in next generation electronic devices. This method is particularly valuable in the case of producing 2D materials that do not exist in 3D forms, for instance, silicene. Based on the intensive investigations of epitaxial graphene on TM in recent years, it is known that the quality of graphene is affected by many factors, including the interaction between the 2D material overlayer and the substrate, the lattice mismatch, the nucleation density at the early stage of growth. It is found that these factors also apply to many other epitaxial 2D crystals on TM. The knowledge from the reviewed systems will shine light on the design and synthesis of new 2D crystals with novel properties.

Transcriptome-wide analysis of vernalization reveals conserved and species-specific mechanisms in Brachypodium

Several temperate cereals need vernalization to promote flowering. Little, however, is known about the vernalization-memory-related genes, and almost no comparative analysis has been performed. Here, RNA-Seq was used for transcriptome analysis in non-vernalized, vernalized and post-vernalized Brachypodium distachyon (L.) Beauv. seedlings. In total, the expression of 1,665 genes showed significant changes (fold change ≥4) in response to vernalization. Among them, 674 putative vernalization-memory-related genes with a constant response to vernalization were significantly enriched in transcriptional regulation and monooxygenase-mediated biological processes. Comparative analysis of vernalization-memory-related genes with barley demonstrated that the oxidative-stress response was the most conserved pathway between these two plant species. Moreover, Brachypodium preferred to regulate transcription and protein phosphorylation processes, while vernalization-memory-related genes, whose products are cytoplasmic membrane-bound-vesicle-located proteins, were preferred to be regulated in barley. Correlation analysis of the vernalization-related genes with barley revealed that the vernalization mechanism was conserved between these two plant species. In summary, vernalization, including its memory mechanism, is conserved between Brachypodium and barley, although several species-specific features also exist. The data reported here will provide primary resources for subsequent functional research in vernalization.

Dynamics of brassinosteroid response modulated by negative regulator LIC in rice

Brassinosteroids (BRs) regulate rice plant architecture, including leaf bending, which affects grain yield. Although BR signaling has been investigated in Arabidopsis thaliana, the components negatively regulating this pathway are less well understood. Here, we demonstrate that Oryza sativa LEAF and TILLER ANGLE INCREASED CONTROLLER (LIC) acts as an antagonistic transcription factor of BRASSINAZOLE-RESISTANT 1 (BZR1) to attenuate the BR signaling pathway. The gain-of-function mutant lic-1 and LIC–overexpressing lines showed erect leaves, similar to BZR1–depleted lines, which indicates the opposite roles of LIC and BZR1 in regulating leaf bending. Quantitative PCR revealed LIC transcription rapidly induced by BR treatment. Image analysis and immunoblotting showed that upon BR treatment LIC proteins translocate from the cytoplasm to the nucleus in a phosphorylation-dependent fashion. Phosphorylation assay in vitro revealed LIC phosphorylated by GSK3–like kinases. For negative feedback, LIC bound to the core element CTCGC in the BZR1 promoter on gel-shift and chromatin immunoprecipitation assay and repressed its transcription on transient transformation assay. LIC directly regulated target genes such as INCREASED LEAF INCLINATION 1 (ILI1) to oppose the action of BZR1. Repression of LIC in ILI1 transcription in protoplasts was partially rescued by BZR1. Phenotypic analysis of the crossed lines depleted in both LIC and BZR1 suggested that BZR1 functionally depends on LIC. Molecular and physiology assays revealed that LIC plays a dominant role at high BR levels, whereas BZR1 is dominant at low levels. Thus, LIC regulates rice leaf bending as an antagonistic transcription factor of BZR1. The phenotypes of lic-1 and LIC–overexpressing lines in erect leaves contribute to ideal plant architecture. Improving this phenotype may be a potential approach to molecular breeding for high yield in rice.

Brassinosteroids (BRs) are phytohormones mediating multiple biological processes, such as development and stress response. They have been used in crops to produce high yield. In rice, the ideal plant architecture for high yield includes effective tillers, as well as height and leaf angle, which is modulated by BRs. Activation of BRI1–mediated BR signaling is well understood, but much less is known about its inactivating mechanism. Here, we found a gain-of-function mutant lic-1 with the phenotype of the ideal rice plant architecture. The C3H-type transcription factor LIC antagonizes BZR1 to repress BR signaling in rice. We used BR to induce the negative regulator LIC and found that it functioned at high BR level, which may restrain plant development. LIC was phosphorylated by GSK3–like kinases. Phosphorylated LIC mainly localized in cytoplasm, whereas dephosphorylated LIC was in nucleus, which was regulated by BR treatment. LIC regulated transcription patterns of the downstream genes in an opposite direction to BZR1. BZR1 activated BR signaling, but the brake module of LIC repressed BR cascade amplification. LIC and BZR1 may balance BR signaling to control growth and development in rice.

Human fetal trophonema matrix and uterine endometrium support better human embryonic stem cell growth and neural differentiation than mouse embryonic fibroblasts

The concerns over xenogeneic pathogens and immunogenic molecules derived from mouse embryonic fibroblasts (MEFs) trigger the development of human-derived feeder layers for human embryonic stem cell (hESC) maintenance. It is essential to evaluate the capability of these human feeder layers to retain the stemness and pluripotency of hESCs. In the present study, two Chinese hESC lines, SDU-hESCm-1 and SDU-hESCm-2, were continuously cultured on human adult uterine endometrial cells (hUEC), human fetal trophonema matrix cells (hFTMC), and MEFs for at least two month (up to 10 passages). A side-by-side comparison of the abilities to support: (1) self-renewal of the hESCs, (2) expression of undifferentiated markers, and (3) neural differentiation, was made between the human and mouse feeder layers. We demonstrated that the hESCs maintained on hUEC and hFTMC exhibited significantly higher growth rates and generated higher levels of DNA content than those on MEFs. Under neural differentiation-promoting conditions, greater neural differentiation was found in the hESCs maintained on human than on mouse feeder layers. These results suggest that human feeder layers derived from hUECs and hFTMCs are more efficient in supporting a long-term growth and neural differentiation of hESCs than MEFs.

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

Background

MicroRNAs (miRNAs) are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs.

Results

High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition.

Conclusion

Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

BACKGROUND

MicroRNAs (miRNAs) are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs.

RESULTS

High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition.

CONCLUSION

Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.