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While most studies of biomolecular phase separation have focused on the condensed phase, relatively little is known about the dilute phase. Theory suggests that stable complexes form in the dilute phase of two-component phase-separating systems, impacting phase separation; however, these complexes have not been interrogated experimentally. We show that such complexes indeed exist, using an in vitro reconstitution system of a phase-separated organelle, the algal pyrenoid, consisting of purified proteins Rubisco and EPYC1. Applying fluorescence correlation spectroscopy (FCS) to measure diffusion coefficients, we found that complexes form in the dilute phase with or without condensates present. The majority of these complexes contain exactly one Rubisco molecule. Additionally, we developed a simple analytical model which recapitulates experimental findings and provides molecular insights into the dilute phase organization. Thus, our results demonstrate the existence of protein complexes in the dilute phase, which could play important roles in the stability, dynamics, and regulation of condensates. Stable hetero-complexes exist in the dilute phase of phase-separating algal pyrenoid proteins in vitro. [ABSTRACT FROM AUTHOR]

Summary: Tillering is an important parameter of plant architecture in cereal crops. In this study, we identified the PHYTOCHROME‐INTERACTING FACTOR‐LIKE (PIL) family transcription factors as new repressors of tillering in cereal crops.Using biochemical and genetic approaches, we explore the roles of TaPIL1 in regulating wheat plant architecture. We found that the PIL protein TaPIL1 controls tiller number in wheat.Overexpression of TaPIL1 reduces wheat tiller number; additionally, overexpression of TaPIL1‐SUPERMAN repression domain increases wheat tiller number. Furthermore, we show that TaPIL1 activates the transcriptional expression of wheat TEOSINTE BRANCHED1 (TaTB1); moreover, TaPIL1 physically interacts with wheat SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE (TaSPL)3/17, which are activators of TaTB1 transcription. In rice, overexpression and loss‐of‐function mutations of OsPIL11 reduce or increase tiller number by regulating the expression of OsTB1. In Arabidopsis, we demonstrate that PHYTOCHROME‐INTERACTING FACTOR 4 interacts with SPL9 to inhibit shoot branching.This study reveals that PIL family transcription factors directly interact with SPLs and play an important role in repressing tillering/branching in plants. [ABSTRACT FROM AUTHOR]

Summary: The domestication gene Q is largely responsible for the widespread cultivation of wheat because it confers multiple domestication traits. However, the underlying molecular mechanisms of how Q regulates these domestication traits remain unclear.In this study, we identify a Q‐interacting protein TaLAX1, a basic helix–loop–helix transcription factor, through yeast two‐hybrid assays. Using biochemical and genetic approaches, we explore the roles of TaLAX1 in regulating wheat domestication traits.Overexpression of TaLAX1 produces phenotypes, reminiscent of the q allele; loss‐of‐function Talax1 mutations confer compact spikes, largely similar to the Q‐overexpression wheat lines. The two transcription factors TaLAX1 and Q disturb each other's activity to antagonistically regulate the expression of the lignin biosynthesis‐related gene TaKNAT7‐4D. More interestingly, a natural variation (InDel, +/− TATA), which occurs in the promoter of TaLAX1, is associated with the promoter activity difference between the D subgenome of bread wheat and its ancestor Aegilops tauschii accession T093.This study reveals that the transcription factor TaLAX1 physically interacts with Q to antagonistically regulate wheat domestication traits and a natural variation (InDel, +/− TATA) is associated with the diversification of TaLAX1 promoter activity. [ABSTRACT FROM AUTHOR]

The blue-light receptor cryptochrome 1 (CRY1) primarily mediates blue-light inhibition of hypocotyl elongation in Arabidopsis. However, the underlying mechanisms remain largely elusive. We report here that CRY1 inhibits hypocotyl elongation by repressing brassinosteroid (BR) signaling. A genetic interaction assay reveals the negative regulatory effect of CRY1 on the function of BZR1, a core transcription factor in the BR signaling pathway. We demonstrated that CRY1 interacts with the DNA-binding domain of BZR1 to interfere with the DNA-binding ability of BZR1, and represses its transcriptional activity. Furthermore, we found that CRY1 promotes the phosphorylation of BZR1 and inhibits the nuclear accumulation of BZR1. Interestingly, we discovered that CRY1 interacts with the GSK3-like kinase BIN2 and enhances the interaction of BIN2 and BZR1 in a light-dependent manner. Our findings revealed that CRY1 negatively regulates the function of BZR1 through at least two mechanisms: interfering with the DNA-binding ability of BZR1 and promoting the phosphorylation of BZR1. Therefore, we uncover a novel CRY1-BIN2-BZR1 regulatory module that mediates crosstalk between blue light and BR signaling to coordinate plant growth in Arabidopsis. The blue-light receptor CRY1 interacts with the DNA-binding domain of BZR1 to interfere with its DNA-binding ability. Moreover, CRY1 also interacts with BIN2 to modulate the phosphorylation status and nuclear accumulation of BZR1 and thus repress BR signaling. [ABSTRACT FROM AUTHOR]

Discovering program specifications automatically for heap-manipulating programs is a challenging task due to the complexity of aliasing and mutability of data structures. This task is further complicated by an expressive domain that combines shape, numerical and bag information. In this paper, we propose a compositional analysis framework that would derive the summary for each method in the expressive abstract domain, independently from its callers. We propose a novel abstraction method with a bi-abduction technique in the combined domain to discover pre-/post-conditions that could not be automatically inferred before. The analysis does not only infer memory safety properties, but also finds relationships between pure and shape domains towards full functional correctness of programs. A prototype of the framework has been implemented and initial experiments have shown that our approach can discover interesting properties for non-trivial programs. [ABSTRACT FROM AUTHOR]

Abstract: Automatically verifying heap-manipulating programs is a challenging task, especially when dealing with complex data structures with strong invariants, such as sorted lists and AVL/red–black trees. The verification process can greatly benefit from human assistance through specification annotations, but this process requires intellectual effort from users and is error-prone. In this paper, we propose a new approach to program verification that allows users to provide only partial specification to methods. Our approach will then refine the given annotation into a more complete specification by discovering missing constraints. The discovered constraints may involve both numerical and multi-set properties that could be later confirmed or revised by users. We further augment our approach by requiring partial specification to be given only for primary methods. Specifications for loops and auxiliary methods can then be systematically discovered by our augmented mechanism, with the help of information propagated from the primary methods. Our work is aimed at verifying beyond shape properties, with the eventual goal of analysing full functional properties for pointer-based data structures. Initial experiments have confirmed that we can automatically refine partial specifications with non-trivial constraints, thus making it easier for users to handle specifications with richer properties. [Copyright &y& Elsevier]

Abstract: Automated verification of memory safety and functional correctness for heap-manipulating programs has been a challenging task, especially when dealing with complex data structures with strong invariants involving both shape and numerical properties. Existing verification systems usually rely on users to supply annotations to guide the verification, which can be cumbersome and error-prone by hand and can significantly restrict the usability of the verification system. In this paper, we reduce the need for some user annotations by automatically inferring loop invariants over an abstract domain with both shape and numerical information. Our loop invariant synthesis is conducted automatically by a fixed-point iteration process, equipped with newly designed abstraction mechanism, together with join and widening operators over the combined domain. We have also proven the soundness and termination of our approach. Initial experiments confirm that we can synthesise loop invariants with non-trivial constraints. [Copyright &y& Elsevier]

The homeodomain-leucine zipper (HD-ZIP) family transcription factors play important roles in plant growth and development. However, the underlying mechanisms remain largely unclear. Here we found that ATHB2, encoding a HD-ZIP transcription factor, is an early auxin responsive gene. Phenotypic analyses show that overexpression of ATHB2 impairs plant architecture, including reduced plant height and small leaves, and also reduces auxin response in leaves when grown in soil. Simultaneously, the seedlings with chemical induction of ATHB2 exhibit abnormal root gravitropism, a typical auxin-related phenotype. We further show that the auxin response pattern is altered in roots of the inducible ATHB2 seedlings. Consistently, the transcript levels of some auxin biosynthetic and transport genes are significantly decreased in these transgenic seedlings. Further, protein and promoter sequence analyses in common wheat showed that the HD-ZIP II subfamily transcription factors have highly conserved motifs and most of these encoding gene promoters contain the canonical auxin-responsive elements. Expression analyses confirm that some of these HD-ZIP II genes are indeed regulated by auxin in wheat. Together, our results suggest that the HD-ZIP II subfamily transcription factors regulate plant development possibly through the auxin pathway in plants. [ABSTRACT FROM AUTHOR]

Drought is one of the major abiotic stresses affecting the maize production worldwide. As a cross-pollination crop, maize is sensitive to water stress at flowering stage. Drought at this stage leads to asynchronous development of male and female flower organ and increased interval between anthesis and silking, which finally causes failure of pollination and grain yield loss. In the present study, the expansin gene ZmEXPA5 was cloned and its function in drought tolerance was characterized. An indel variant in promoter of ZmEXPA5 is significantly associated with natural variation in drought-induced anthesis-silking interval. The drought susceptible haplotypes showed lower expression level of ZmEXPA5 than tolerant haplotypes and lost the cis-regulatory activity of ZmDOF29. Increasing ZmEXPA5 expression in transgenic maize decreases anthesis-silking interval and improves grain yield under both drought and well-watered environments. In addition, the expression pattern of ZmEXPA5 was analyzed. These findings provide insights into the genetic basis of drought tolerance and a promising gene for drought improvement in maize breeding. [ABSTRACT FROM AUTHOR]

Photoreceptor phytochrome B (phyB) mediates a variety of light responses in plants. To further elucidate the molecular mechanisms of phyB‐regulated hypocotyl elongation, we performed firefly luciferase complementation imaging (LCI) screening for phyB‐interacting transcription factors (TFs). LCI assays showed that phyB possibly interacts with brassinazoleresistant 1 (BZR1), BZR2, AUXIN RESPONSE FACTOR 6 (ARF6), and several WRKY DNA‐binding TFs in a red light‐dependent manner. Furthermore, biochemical assays demonstrated that photoexcited phyB specifically interacts with non‐phosphorylated BZR1, the physiologically active form of a master TF in brassinosteroid (BR) signaling, and this interaction can be competitively interfered by phytochrome‐interacting factor 4. Furthermore, we showed that phyB can directly interact with the DNA‐binding domain of BZR1 and affect the enrichment of BZR1 on the chromatin of target genes. Moreover, our genetic evidence and RNA‐seq analysis demonstrated that phyB negatively regulates BR signaling. Together, we revealed that photoexcited phyB directly interacts with the TF BZR1 to repress BR signaling in Arabidopsis. [ABSTRACT FROM AUTHOR]

Drought stress is a central environmental factor that severely limits maize production worldwide. Root architecture plays an important role in drought tolerance and can be targeted in breeding programmes. Here, we conducted phenotyping of root architecture under different water treatments for 373 maize inbred lines, representative germplasm from both China and the United States in different breeding eras. We found that seminal root length in response to drought stress experienced convergent increase during breeding in both countries. Using a genome‐wide association study, we identified a total of 221 associated loci underlying 13 root traits under well‐watered and water‐stressed conditions. These loci harboured many reported root‐ and abiotic stress‐related genes. Furthermore, a total of 75 strong candidate genes were prioritised by integrating candidate genes associated with seminal root length and differentially expressed genes in seminal root. One of high‐confidence candidate genes, ZmCIPK3 was functionally characterised and probably plays a role in enhancing drought tolerance through regulating seminal root growth. This study provides valuable information for genetic improvement of root architecture and drought tolerance in maize. SUMMARY STATEMENT: This study reports the root architecture changes associated with drought stress in maize seedlings, loci and high‐confidence candidates underlying root traits, and overexpression of ZmCIPK3 exhibiting improved drought tolerance through regulating seminal root growth, laying the foundation for genetic improvement of drought tolerance in maize. [ABSTRACT FROM AUTHOR]

Automated verification of operating system kernels is a challenging problem, partly due to the use of shared mutable data structures. In this paper, we show how we can automatically verify memory safety and functional correctness properties of the task scheduler component of the FreeRTOS kernel using the verification system Hip/Sleek. We show how some of Hip/Sleek features such as user-defined predicates and lemmas make the specifications highly expressive and the verification process viable. To the best of our knowledge, this is the first code-level verification of memory safety and functional correctness properties of the FreeRTOS scheduler. The outcome of our experiment confirms that Hip/Sleek can indeed be used to verify code that is used in production. Moreover, since the properties that we verify are quite general, we envisage that the same approach can be adopted to verify components of other operating systems. [ABSTRACT FROM AUTHOR]

[Display omitted] • Multiwalled carbon nanotube@poly(quinone-thiourea) (MWCNT@PQTU) composite was fabricated. • A core–sheath nanostructure of MWCNT@PQTU was formed. • Ultrathin PQTU layers with 10–30 nm in thickness were tightly adhered onto MWCNT. • MWCNT@PQTU exhibited a discharge capacity of 120.6 mAh/g at 100 mA g−1. Quinone-based redox active polymers are regarded as the most suitable cathode materials for constructing high-energy aqueous zinc-ion battery (AZIB) because of adjustable structure, high capacity and excellent electrochemical reversibility. However, their Zn2+ storage performances are often limited by low electronic conductivity and sluggish ion diffusion of Zn2+. Herein, a novel inorganic–organic nanocomposite of multiwalled carbon nanotube@poly(quinone-thiourea) (MWCNT@PQTU) was successfully fabricated by the method of in-situ interfacial polymerization, wherein 1,4-quinone and thiourea were used as low cost polymer precursors and MWCNT as a conductive support. The π-π stacking interaction between poly(quinone-thiourea) (PQTU) and MWCNT drove the self-assembly of the polymer around MWCNT during the polymerization process, ensuring the formation of the core–sheath nanostructure with ultrathin PQTU layers (10–30 nm in thickness). The unique nanostructure of MWCNT@PQTUs could enhance electronic conductivity, increase active carbonyl (C O) groups for charge storage, promote the Zn2+ diffusion, buffer the volume variation and inhibit the dissolution of the PQTU polymer during the charge − discharge processes. Thanks to these effects, the MWCNT@PQTU cathode exhibited high discharge capacity (120.6 mAh g−1 at 100 mA g−1), excellent rate capability (64.1 mAh g−1 at 1 A g−1) and long cycling stability (81 % capacity retention after 2000 cycles at 500 mA g−1). This work demonstrated that the fabrication of core–sheath nanostructured CNT@polymer cathodes was an effective way to improve the charge storage performance of the quinone-based polymers for Zn-ion batteries. [ABSTRACT FROM AUTHOR]

The BRASSINAZOLE‐RESISTANT 1 (BZR1) transcription factor family plays an essential role in plant brassinosteroid (BR) signaling, but the signaling mechanism through which BZR1 and its homologs cooperate with certain coactivators to facilitate transcription of target genes remains incompletely understood. In this study, we used an efficient protein interaction screening system to identify blue‐light inhibitor of cryptochromes 1 (BIC1) as a new BZR1‐interacting protein in Arabidopsis thaliana. We show that BIC1 positively regulates BR signaling and acts as a transcriptional coactivator for BZR1‐dependent activation of BR‐responsive genes. Simultaneously, BIC1 interacts with the transcription factor PIF4 to synergistically and interdependently activate expression of downstream genes including PIF4 itself, and to promote plant growth. Chromatin immunoprecipitation assays demonstrate that BIC1 and BZR1/PIF4 interdependently associate with the promoters of common target genes. In addition, we show that the interaction between BIC1 and BZR1 is evolutionally conserved in the model monocot plant Triticum aestivum (bread wheat). Together, our results reveal mechanistic details of BR signaling mediated by a transcriptional activation module BIC1/BZR1/PIF4 and thus provide new insights into the molecular mechanisms underlying the integration of BR and light signaling in plants. Synopsis: BZR1 and PIF4 are core transcription factors in brassinosteroid (BR) and light signaling, respectively. Here, Blue‐light Inhibitor of Cryptochromes 1 (BIC1) is found as a common coactivator linking BZR1 and PIF4 to synergistically and interdependently activate transcription of common target genes and promote cell elongation. BIC1 positively regulates BR responses.BIC1 interacts with BZR1 and PIF4 to synergistically co‐activate transcription of target genes, including PIF4 itself.BIC1 and BZR1/PIF4 interdependently associate with the promoters of common target genes.The interaction between BIC1 and BZR1 is evolutionally conserved in monocot and dicot plants. [ABSTRACT FROM AUTHOR]

Abstract: We study the automated verification of pointer safety for heap-manipulating imperative programs with unknown procedure calls. Given a Hoare-style partial correctness specification in separation logic, where the program contains calls to some unknown procedure , we infer a specification for the unknown procedure from the calling contexts. We show that the problem of verifying the program against the specification can be safely reduced to the problem of proving that the procedure (once its code is available) meets the derived specification . The expected specification for the unknown procedure is automatically calculated using an abduction-based shape analysis. We have also implemented a prototype system to validate the viability of our approach. Preliminary results show that the specifications derived by our tool fully capture the behaviors of the unknown code in many cases. [Copyright &y& Elsevier]