MicroRNAs play regulatory roles in genomic balance.

Classic genetics studies found that genomic imbalance caused by changing the dosage of part of the genome (aneuploidy) has more detrimental effects than altering the dosage of the whole genome (ploidy). Previous analysis revealed global modulation of gene expression triggered by aneuploidy across various species, including maize (Zea mays), Arabidopsis, yeast, mammals, etc. Plant microRNAs (miRNAs) are a class of 20- to 24-nt endogenous small noncoding RNAs that carry out post-transcriptional gene expression regulation. That miRNAs and their putative targets are preferentially retained as duplicates after whole-genome duplication, as are many transcription factors and signaling components, indicates miRNAs are likely to be dosage-sensitive and potentially involved in genomic balance networks. This review addresses the following questions regarding the role of miRNAs in genomic imbalance. (1) How do aneuploidy and polyploidy impact the expression of miRNAs? (2) Do miRNAs play a regulatory role in modulating the expression of their targets under genomic imbalance?

A Universal Biomacromolecule-Enabled Assembly Strategy for Constructing Multifunctional Aerogels with 90% Inorganic Mass Loading from Inert Nano-Building Blocks.

Inert inorganic nano-building blocks, such as carbon nanotubes (CNTs) and boron nitride (BN) nanosheets, possess excellent physicochemical properties. However, it remains challenging to build aerogels with these inert nanomaterials unless they are chemically modified or compounded with petrochemical polymers, which affects their intrinsic properties and is usually not environmentally friendly. Here, a universal biomacromolecule-enabled assembly strategy is proposed to construct aerogels with 90 wt% ultrahigh inorganic loading. The super-high inorganic content is beneficial for exploiting the inherent properties of inert nanomaterials in multifunctional applications. Taking chitosan-CNTs aerogel as a proof-of-concept demonstration, it delivers sensitive pressure response as a pressure sensor, an ultrahigh sunlight absorption (94.5%) raising temperature under light (from 25 to 71 °C within 1 min) for clean-up of crude oil spills, and superior electromagnetic interference shielding performance of up to 68.9 dB. This strategy paves the way for the multifunctional application of inert nanomaterials by constructing aerogels with ultrahigh inorganic loading.

SCARECROW maintains the stem cell niche in Arabidopsis roots by ensuring telomere integrity.

Stem cells are the ultimate source of cells for various tissues and organs and thus are essential for postembryonic plant growth and development. SCARECROW (SCR) is a plant-specific transcription regulator well known for its role in stem cell renewal in plant roots, but the mechanism by which SCR exerts this function remains unclear. To address this question, we carried out a genetic screen for mutants that no longer express SCR in the stem cell niche of Arabidopsis (Arabidopsis thaliana) roots and characterized 1 of these mutants. Molecular genetics methods allowed us to pinpoint the causal mutation in this mutant in TELOMERIC PATHWAYS IN ASSOCIATION WITH STN 1 (TEN1), encoding a factor that protects telomere ends. Interestingly, TEN1 expression was dramatically reduced in the scr mutant. Telomerase and STN1 and CONSERVED TELOMERE MAINTENANCE COMPONENT 1 (CTC1), components of the same protein complex as TEN1, were also dramatically downregulated in scr. Loss of STN1, CTC1, and telomerase caused defects in root stem cells. These results together suggest that SCR maintains root stem cells by promoting expression of genes that ensure genome integrity. Supporting this conclusion, we demonstrated that the scr mutant accumulates more DNA damage than wild-type Arabidopsis and that this problem is aggravated after exposure to zeocin, a DNA damage reagent. Finally, we identified 2 previously uncharacterized motifs in TEN1 and provide evidence that a conserved amino acid residue in 1 of the motifs is indispensable for TEN1 function. SCR thus provides a connection between genome integrity and stem cell maintenance in Arabidopsis roots.

Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize.

The phenotypic consequences of the addition or subtraction of part of a chromosome is more severe than changing the dosage of the whole genome. By crossing diploid trisomies to a haploid inducer, we identified 17 distal segmental haploid disomies that cover ∼80% of the maize genome. Disomic haploids provide a level of genomic imbalance that is not ordinarily achievable in multicellular eukaryotes, allowing the impact to be stronger and more easily studied. Transcriptome size estimates revealed that a few disomies inversely modulate most of the transcriptome. Based on RNA sequencing, the expression levels of genes located on the varied chromosome arms (cis) in disomies ranged from being proportional to chromosomal dosage (dosage effect) to showing dosage compensation with no expression change with dosage. For genes not located on the varied chromosome arm (trans), an obvious trans-acting effect can be observed, with the majority showing a decreased modulation (inverse effect). The extent of dosage compensation of varied cis genes correlates with the extent of trans inverse effects across the 17 genomic regions studied. The results also have implications for the role of stoichiometry in gene expression, the control of quantitative traits, and the evolution of dosage-sensitive genes.

Genomic imbalance determines positive and negative modulation of gene expression in diploid maize.

Genomic imbalance caused by changing the dosage of individual chromosomes (aneuploidy) has a more detrimental effect than varying the dosage of complete sets of chromosomes (ploidy). We examined the impact of both increased and decreased dosage of 15 distal and 1 interstitial chromosomal regions via RNA-seq of maize (Zea mays) mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated toward the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which the expression of many genes under genome imbalance are modulated toward the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.

Programmable Electrical Signals Induce Anisotropic Assembly of Multilayer Chitosan Hydrogels.

Multilayer hydrogels are widely used in biomedical-related fields due to their complex and variable spatial structures. Various strategies have been developed for preparing multilayer hydrogels, among which electrically induced self-assembly provides a simple and effective method for multilayer hydrogel fabrication. By application of an oscillatory electrical signal sequence, multilayer hydrogels with distinct boundaries can be formed according to the provided programmable signals. In this work, we establish an electrical field in microfluidics combined with polarized light microscopy for in situ visualization of anisotropic construction of multilayer chitosan hydrogel. The noninvasive, real-time birefringence images allow us to monitor the orientation within the hydrogel in response to electrical signals. An increased birefringence was observed from the solution-gel side to the electrode surface side, and a brief electrical signal interruption did not affect the anisotropic assembly process. This understanding of the oscillatory electrical signal-induced hydrogel anisotropy assembly allows us to fabricate chitosan hydrogels with a complex and spatially varying structure.

Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution.

B chromosomes are enigmatic elements in thousands of plant and animal genomes that persist in populations despite being nonessential. They circumvent the laws of Mendelian inheritance but the molecular mechanisms underlying this behavior remain unknown. Here we present the sequence, annotation, and analysis of the maize B chromosome providing insight into its drive mechanism. The sequence assembly reveals detailed locations of the elements involved with the cis and trans functions of its drive mechanism, consisting of nondisjunction at the second pollen mitosis and preferential fertilization of the egg by the B-containing sperm. We identified 758 protein-coding genes in 125.9 Mb of B chromosome sequence, of which at least 88 are expressed. Our results demonstrate that transposable elements in the B chromosome are shared with the standard A chromosome set but multiple lines of evidence fail to detect a syntenic genic region in the A chromosomes, suggesting a distant origin. The current gene content is a result of continuous transfer from the A chromosomal complement over an extended evolutionary time with subsequent degradation but with selection for maintenance of this nonvital chromosome.

Impacts of urbanization on ecosystem carbon cycle: a case study of land use change in Tianjin metropolitan area.

For the sustainable development of the city, in a study of Tianjin's rapid urbanization, we explore the complex interplay between land use change and the ecosystem carbon cycle from 2000 to 2020. Spatial analysis and profit-loss matrix calculations reveal contrasting ecological impacts: expansion of woodlands and grasslands enhances Net Primary Productivity (NPP) and reduces carbon emissions, while urban construction shows the opposite effect. Over 20 years, Tianjin's urban transformation led to a 16.91 GgC decline in NPP amidst a construction boom. However, post-2015 ecological policy shifts resulted in a significant net carbon uptake of 0.85 Gt, demonstrating the potential of policy interventions in mitigating environmental impacts of urbanization. This study underscores the importance of sustainable urban planning and ecological conservation strategies in highly urbanized settings.

Effect of aneuploidy of a non-essential chromosome on gene expression in maize.

The non-essential supernumerary maize (Zea mays) B chromosome (B) has recently been shown to contain active genes and to be capable of impacting gene expression of the A chromosomes. However, the effect of the B chromosome on gene expression is still unclear. In addition, it is unknown whether the accumulation of the B chromosome has a cumulative effect on gene expression. To examine these questions, the global expression of genes, microRNAs (miRNAs), and transposable elements (TEs) of leaf tissue of maize W22 plants with 0-7 copies of the B chromosome was studied. All experimental genotypes with B chromosomes displayed a trend of upregulated gene expression for a subset of A-located genes compared to the control. Over 3000 A-located genes are significantly differentially expressed in all experimental genotypes with the B chromosome relative to the control. Modulations of these genes are largely determined by the presence rather than the copy number of the B chromosome. By contrast, the expression of most B-located genes is positively correlated with B copy number, showing a proportional gene dosage effect. The B chromosome also causes increased expression of A-located miRNAs. Differentially expressed miRNAs potentially regulate their targets in a cascade of effects. Furthermore, the varied copy number of the B chromosome leads to the differential expression of A-located and B-located TEs. The findings provide novel insights into the function and properties of the B chromosome.

Electro-Biofabrication. Coupling Electrochemical and Biomolecular Methods to Create Functional Bio-Based Hydrogels.

Twenty years ago, this journal published a review entitled "Biofabrication with Chitosan" based on the observations that (i) chitosan could be electrodeposited using low voltage electrical inputs (typically less than 5 V) and (ii) the enzyme tyrosinase could be used to graft proteins (via accessible tyrosine residues) to chitosan. Here, we provide a progress report on the coupling of electronic inputs with advanced biological methods for the fabrication of biopolymer-based hydrogel films. In many cases, the initial observations of chitosan's electrodeposition have been extended and generalized: mechanisms have been established for the electrodeposition of various other biological polymers (proteins and polysaccharides), and electrodeposition has been shown to allow the precise control of the hydrogel's emergent microstructure. In addition, the use of biotechnological methods to confer function has been extended from tyrosinase conjugation to the use of protein engineering to create genetically fused assembly tags (short sequences of accessible amino acid residues) that facilitate the attachment of function-conferring proteins to electrodeposited films using alternative enzymes (e.g., transglutaminase), metal chelation, and electrochemically induced oxidative mechanisms. Over these 20 years, the contributions from numerous groups have also identified exciting opportunities. First, electrochemistry provides unique capabilities to impose chemical and electrical cues that can induce assembly while controlling the emergent microstructure. Second, it is clear that the detailed mechanisms of biopolymer self-assembly (i.e., chitosan gel formation) are far more complex than anticipated, and this provides a rich opportunity both for fundamental inquiry and for the creation of high performance and sustainable material systems. Third, the mild conditions used for electrodeposition allow cells to be co-deposited for the fabrication of living materials. Finally, the applications have been expanded from biosensing and lab-on-a-chip systems to bioelectronic and medical materials. We suggest that electro-biofabrication is poised to emerge as an enabling additive manufacturing method especially suited for life science applications and to bridge communication between our biological and technological worlds.

First-Principles Studies on the Structural and Electronic Properties of α-Na2FePO4F with Strong Antisite Disorder.

Polyanionic Na2FePO4F is one of the most important cathode materials for sodium-ion batteries. The orthorhombic ß-Na2FePO4F material has been studied extensively and intensively since it was proposed. In this article, a novel monoclinic sodium phosphate fluoride α-Na2FePO4F is concerned. Kirsanova's experiment showed that Na and Fe ions in α-Na2FePO4F are prone to antisite, leading to strong antisite disorder. Through first-principle calculations, we show that the steric effect, the magnetic exchange and superexchange interactions between transition-metal cations are shown to be the main driving forces for Na+/Fe2+ antisite disorder. We first calculated the crystal structures, electronic properties, and cohesive energies of all the 10 antisite phases of α-Na2FePO4F and ß-Na2FePO4F. Then, we compared the difference charge densities, magnetism, binding energies, and electrostatic potentials of α-Na2FePO4F and ß-Na2FePO4F materials in the antisite and pristine phases. In α-Na2FePO4F, the binding energy of the antisite phase with the lowest binding energy is almost degenerate with that of the pristine phase. Moreover, only small differences of the electrostatic potential and the charge density distribution are found between the antisite (with lowest energy) and the pristine phases of α-Na2FePO4F, which also helped elaborate the facile formation of Na+/Fe2+ antisite in the α-Na2FePO4F material. Our research contributes to the understanding of the mechanism of Na+/Fe2+ antisite and the development of high-performance polyanionic cathode materials.

Geometric, electronic and transport properties of bulged graphene: A theoretical study.

Out-of-plane deformation in graphene is unavoidable during both synthesis and transfer procedures due to its special flexibility, which distorts the lattice and eventually imposes crucial effects on the physical features of graphene. Nowadays, however, little is known about this phenomenon, especially for zero-dimensional bulges formed in graphene. In this work, employing first-principles-based theoretical calculations, we systematically studied the bulge effect on the geometric, electronic, and transport properties of graphene. We demonstrate that the bulge formation can introduce mechanical strains (lower than 2%) to the graphene's lattice, which leads to a significant charge redistribution throughout the structure. More interestingly, a visible energy band splitting was observed with the occurrence of zero-dimensional bulges in graphene, which can be attributed to the interlayer coupling that stems from the bulged structure. In addition, it finds that the formed bulges in graphene increase the electron states near the Fermi level, which may account for the enhanced carrier concentration. However, the lowered carrier mobility and growing phonon scattering caused by the formed bulges diminish the transport of both electrons and heat in graphene. Finally, we indicate that bulges arising in graphene increase the possibility of intrinsic defect formation. Our work will evoke attention to the out-of-plane deformation in 2D materials and provide new light to tune their physical properties in the future.

Janus Fibrous Mats Based Suspended Type Evaporator for Salt Resistant Solar Desalination and Salt Recovery.

Solar desalination has been recognized as an emerging strategy for solving the pressing global freshwater crisis. However, salt crystallization at the photothermal interface frequently causes evaporator failure. In addition, arbitrary discharge of concentrated brine produced during desalination results in potential ecological impacts as well as wastage of valuable minerals. In the present work, a suspended-type evaporator (STEs) constructed using Janus fibrous mats is reported. The fibrous structure wicks brine to the evaporation layer and the salt gets confined in the evaporation layer until crystallization for zero liquid discharge due to the suspended design. Enhanced evaporation is observed because STEs have an additional low-resistance vapor escape path directly from the evaporation layer to the atmosphere compared to traditional floating Janus evaporators. Moreover, owing to the drastically different wettability on both sides, the evaporator allows salt crystallization only on the hydrophilic bottom layer, thus eliminating salt accumulation at the hydrophobic photothermal interface. With this unique structural design, the proposed evaporator not only maintains a high evaporation rate of 1.94 kg m-2 h-1 , but also demonstrates zero liquid discharged salt resistance and ideal recovery of the mineral in brine.

GNET2: an R package for constructing gene regulatory networks from transcriptomic data.

MOTIVATION: The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. RESULTS: Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. AVAILABILITY AND IMPLEMENTATION: The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation.

Studies of the structural and functional role of chromosomes in cytogenetics have spanned more than 10 decades. In this work, we take advantage of the coherent X-rays available at the latest synchrotron sources to extract the individual masses of all 46 chromosomes of metaphase human B and T cells using hard X-ray ptychography. We have produced 'X-ray karyotypes' of both heavy metal-stained and unstained spreads to determine the gain or loss of genetic material upon low-level X-ray irradiation doses due to radiation damage. The experiments were performed at the I-13 beamline, Diamond Light Source, Didcot, UK, using the phase-sensitive X-ray ptychography method.

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks.

BACKGROUND: Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and experimental results from parallel sequencing provide available information about the affinity and accessibility of genome and are commonly used features in binding sites prediction. The attention mechanism in deep learning has shown its capability to learn long-range dependencies from sequential data, such as sentences and voices. Until now, no study has applied this approach in binding site inference from massively parallel sequencing data. The successful applications of attention mechanism in similar input contexts motivate us to build and test new methods that can accurately determine the binding sites of transcription factors. RESULTS: In this study, we propose a novel tool (named DeepGRN) for transcription factors binding site prediction based on the combination of two components: single attention module and pairwise attention module. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets. The results show that DeepGRN achieves higher unified scores in 6 of 13 targets than any of the top four methods in the DREAM challenge. We also demonstrate that the attention weights learned by the model are correlated with potential informative inputs, such as DNase-Seq coverage and motifs, which provide possible explanations for the predictive improvements in DeepGRN. CONCLUSIONS: DeepGRN can automatically and effectively predict transcription factor binding sites from DNA sequences and DNase-Seq coverage. Furthermore, the visualization techniques we developed for the attention modules help to interpret how critical patterns from different types of input features are recognized by our model.

Electrical Writing to Three-Dimensional Pattern Dynamic Polysaccharide Hydrogel for Programmable Shape Deformation.

The ability to pattern and actuate hydrogels is essential for biomimetics, soft robotics, and biosensors. Here an electrical writing technique with the capability to create both surface and across thickness patterns in dynamic chitosan-H+ /agarose hydrogel by electronically generated pH gradient is introduced. The diffusible pH cues deprotonate and re-assemble chitosan chains by hydrogen bonds, changing the electrical writing domains from original loose structure to a dense layer and resulting in different mechanical stress and swell ability that causes the hydrogel to deform. The deformable trend can be modulated by writing depth and selective writing area on the surface, and significantly enhanced by temperature increment. Finally, a dual electrical writing process to create three-dimensional patterns and demonstrate programmable shape transition by differing patterns is performed.

Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa.

Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.

Wire templated electrodeposition of vessel-like structured chitosan hydrogel by using a pulsed electrical signal.

Herein, by performing a templated electrodeposition process with an oscillating electrical signal stimulation, a vessel-like structured chitosan hydrogel (diameter about 0.4 mm) was successfully prepared in the absence of salt conditions. Experimental results demonstrated that the hydrogel growth (e.g. the thickness) is linearly correlated with the imposed charge transfer and can be well quantified by using a theoretical moving front model. Morphological observations indicated that the heterogeneous multilayer structure was spatially and temporally controlled by an externally employed electrical signal sequence while the channel structure could be determined by the shaped electrode. Moreover, the oscillating ON-OFF cycles were proved to strongly affect the film structure, leading to a more compact hydrogel coating with a lower water content, higher crystallinity, complex layer architecture and relatively strong mechanical properties that could be easily peeled off as a free-standing hollow tube. Importantly, all the experiments were conducted under mild conditions that allowed additional enhancing materials to be added in to further improve the mechanical and/or biological properties. Thus, this work advances a very promising self-assembly technology for the construction of a multi-functional hydrogel coating and artificial blood vessel regeneration.

Bone Marrow Stromal Cell Transplantation Drives Molecular Switch from Autophagy to the Ubiquitin-Proteasome System in Ischemic Stroke Mice.

BACKGROUND: Bone marrow stromal cell (BMSC) transplantation is a promising therapeutic approach for cerebral ischemia, as it elicits multiple neuroprotective effects. However, it remains unclear how BMSC transplantation modulates the ubiquitin-proteasome system (UPS) and autophagy under cerebral ischemia. METHODS: In the present study, an intermediate level of cerebral ischemia (30 minutes) was chosen to examine the effect of BMSC transplantation on the molecular switch regulating UPS and autophagy. BMSC or vehicle was stereotactically injected into the penumbra 15 minutes after sham operation or transient middle cerebral artery occlusion (tMCAO). RESULTS: Thirty minutes of tMCAO artery occlusion significantly increased TUNEL-, ubiquitin-, and p62-positive cells (which peaked at 72 hours, 2 hours, and 2 hours after reperfusion, respectively) and ratios of both BAG3/BAG1 and LC3-II/LC3-I at 24 hours after reperfusion. However, intracerebral injection of BMSCs significantly reduced infarct volume and numbers of TUNEL- and p62-positive cells, and improved BAG3/BAG1 and LC3-II/LC3-I ratios. In addition, observed increases in ubiquitin-positive cells 2 hours after reperfusion were slightly suppressed by BMSC transplantation. CONCLUSIONS: These data suggest a protective role of BMSC transplantation, which drove the molecular switch from autophagy to UPS in a murine model of ischemic stroke.