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Background Hidden Markov models (HMM) are a powerful tool for analyzing biological sequences in a wide variety of applications, from profiling functional protein families to identifying functional domains. The standard method used for HMM training is either by maximum likelihood using counting when sequences are labelled or by expectation maximization, such as the Baum–Welch algorithm, when sequences are unlabelled. However, increasingly there are situations where sequences are just partially labelled. In this paper, we designed a new training method based on the Baum–Welch algorithm to train HMMs for situations in which only partial labeling is available for certain biological problems. Results Compared with a similar method previously reported that is designed for the purpose of active learning in text mining, our method achieves significant improvements in model training, as demonstrated by higher accuracy when the trained models are tested for decoding with both synthetic data and real data. Conclusions A novel training method is developed to improve the training of hidden Markov models by utilizing partial labelled data. The method will impact on detecting de novo motifs and signals in biological sequence data. In particular, the method will be deployed in active learning mode to the ongoing research in detecting plasmodesmata targeting signals and assess the performance with validations from wet-lab experiments.

Plants need to cope with biotic and abiotic stress through well-coordinated cell-to-cell communication to survive as sedentary organisms. Environmental challenges such as wounding, low temperature, oxidative states and pathogen infection are known to affect the symplasmic molecular exchange between plant cells determined by plasmodesmal permeability. However, the signalling pathways and mechanisms by which different environmental stressors affect plasmodesmal permeability are not well understood. Here we show that regulating callose accumulation at plasmodesmal channels is a common strategy to alter plasmodesmal permeability under both pathogen infection and mechanical wounding stress. We have identified Arabidopsis callose synthase 1 ( CalS1 ) and CalS8 as key genes involved in this process, and have integrated these new players into both known and novel signalling pathways that control responses to biotic and abiotic stress. Our studies provide experimental data that indicate the presence of specialized pathways tuned to respond to particular stressors, and new insights into how plants regulate plasmodesmata in response to environmental assaults. In response to biotic or abiotic stress, plants can regulate cell–cell communication by modulating plasmodesmal permeability. Here the authors show that callose synthases CalS1/8 are involved in this process.

Lateral roots originate from initial cells deep within the main root and must emerge through several overlying layers. Lateral root emergence requires the outgrowth of the new primordium (LRP) to coincide with the timely separation of overlying root cells, a developmental program coordinated by the hormone auxin. Here, we report that in Arabidopsis thaliana roots, auxin controls the spatiotemporal expression of the plasmodesmal regulator PDLP5 in cells overlying LRP, creating a negative feedback loop. PDLP5, which functions to restrict the cell-to-cell movement of signals via plasmodesmata, is induced by auxin in cells overlying LRP in a progressive manner. PDLP5 localizes to plasmodesmata in these cells and negatively impacts organ emergence as well as overall root branching. We present a model, incorporating the spatiotemporal expression of PDLP5 in LRP-overlying cells into known auxin-regulated LRP-overlying cell separation pathways, and speculate how PDLP5 may function to negatively regulate the lateral root emergence process. Auxin promotes lateral root emergence from pericycle cells in the root vasculature. Here the authors show that induction of the plasmodesmal regulator PDLP5 during lateral root emergence restricts the spatial scope of auxin signaling to the cells overlying the primordia.

Summary Molecular farming technology using transiently transformed Nicotiana plants offers an economical approach to the pharmaceutical industry to produce an array of protein targets including vaccine antigens and therapeutics. It can serve as a desirable alternative approach for those proteins that are challenging or too costly to produce in large quantities using other heterologous protein expression systems. However, since cost metrics are such a critical factor in selecting a production host, any system‐wide modifications that can increase recombinant protein yields are key to further improving the platform and making it applicable for a wider range of target molecules. Here, we report on the development of a new approach to improve target accumulation in an established plant‐based expression system that utilizes viral‐based vectors to mediate transient expression in Nicotiana benthamiana. We show that by engineering the host plant to support viral vectors to spread more effectively between host cells through plasmodesmata, protein target accumulation can be increased by up to approximately 60%. A transgenic N. benthamiana line (Sm5) engineered to facilitate cell‐to‐cell movement enhances the local and systemic spread of a fluorescently tagged TMV vector.

Key Points Plasmodesmata are plant-unique intercellular communication channels that acquired the capacity to dilate significantly to allow the trafficking of proteins and RNA within a symplasmic domain. This property is thought to contribute to the supracellular nature of plants. A subset of proteins that regulate the signalling processes beyond the cells in which they are synthesized can traffic through plasmodesmata to function as non-cell-autonomous proteins (NCAPs). One mode of trafficking through plasmodesmata might be controlled by a gate open/gate closed (GO/GC) pathway that leads to the formation of symplasmic domains in which certain unbound molecules (up to ∼40 kDa) can diffuse between neighbouring cells. A second, selective, mode of trafficking through plasmodesmata might involve a specific interaction between each NCAP and the plasmodesmal machinery. Intercellular trafficking of transcription factors that regulate developmental patterning and/or cell-fate determination underscores the important role carried out by the NCAP pathway. RNA can function both as a local and a long-distance information macromolecule by trafficking between cells through plasmodesmata and between organs through the vascular conduit that is provided by phloem. Specific mRNA molecules that can move through phloem might enter various meristematic tissues to redirect developmental events. Phloem translocation has important roles in transmitting RNA-interference signals and systemic signals in response to wounds and pathogen attacks, and in coordinating plant nitrogen metabolism and symbiosis. The formation of a new symplasmic domain between the phloem and a nodule initial illustrates the operation of the integrated signalling system that is provided by plasmodesmata and phloem. The evolution of intercellular communication had an important role in the increasing complexity of both multicellular and supracellular organisms. Plasmodesmata, the intercellular organelles of the plant kingdom, establish an effective pathway for local and long-distance signalling. In higher plants, this pathway involves the trafficking of proteins and various forms of RNA that function non-cell-autonomously to affect developmental programmes.

The purpose of this study was to develop a prediction model for stroke-associated pneumonia (SAP) based on risk factors for SAP and to suggest nursing interventions to prevent SAP. In addition, a nomogram was developed to enhance its utility in nursing practice. The retrospective cohort study included 551 patients hospitalized for acute ischemic stroke at a university hospital in South Korea. Data were collected through a structured questionnaire and a review of the electronic medical record (EMR). In the development of a predictive model for SAP, multivariate logistic regression analysis showed that independent risk factors for SAP were age ≥ 65 years, National Institute of Health Stroke Scale (NIHSS) score ≥ 7, nasogastric tube feeding, and C-reactive protein (CRP) ≥ 5.0 mg/dL. The logit model was used to construct the SAP prediction nomogram, and the area under the curve (AUC) of the nomogram was 0.94. Furthermore, the slope of the calibration plot was close to the 45-degree line, indicating that the developed nomogram may be useful for predicting SAP. It is necessary to monitor the age, NIHSS score, nasogastric tube feeding status, and CRP level of stroke patients and identify high-risk groups using the developed nomogram to provide active nursing interventions to prevent SAP.

The collection also includes articles that review progress with respect to cytoskeletal connections to basic plasmodesmal function or to interspecific plasmodesmata formed between hosts and their parasitic plants, or share perspectives on how plasmodesmal research may be relevant to addressing critical issues in producing resilient crops in the face of imminent challenges associated with climate change. Krause group addresses the functional specialization of secondary plasmodesmata (Fischer et al.), examining what is known about interspecific plasmodesmata formed between parasitic plants and their plant hosts and provides cogent arguments for the value of parasitic plant-host systems in investigating various aspects of plasmodesmal formation and structure, and the establishment of symplastic domains. Conflict of Interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem. Although the primary unloading event from the sieve elements to the phloem pole pericycle has been characterized to some extent, little is known about post-sieve element unloading. Here, we report a novel gene, PHLOEM UNLOADING MODULATOR ( PLM ), in the absence of which plasmodesmata-mediated symplastic transport through the phloem pole pericycle–endodermis interface is specifically enhanced. Increased unloading is attributable to a defect in the formation of the endoplasmic reticulum–plasma membrane tethers during plasmodesmal morphogenesis, resulting in the majority of pores lacking a visible cytoplasmic sleeve. PLM encodes a putative enzyme required for the biosynthesis of sphingolipids with very-long-chain fatty acid. Taken together, our results indicate that post-sieve element unloading involves sphingolipid metabolism, which affects plasmodesmal ultrastructure. They also raise the question of how and why plasmodesmata with no cytoplasmic sleeve facilitate molecular trafficking. Plasmodesmata channel substance transportation between neighbouring cells, including the sieve tube elements and the phloem companion cells. Now, the plasmodesmal ultrastructure is shown to be regulated by a newly identified phloem unloading modulator that participates in sphingolipid biosynthesis in Arabidopsis .

Comparative analyses of SARS-CoV-2-specific immune responses elicited by diverse prime-boost regimens are required to establish efficient regimens for the control of COVID-19. In this prospective observational cohort study, spike-specific immunoglobulin G (IgG) and neutralizing antibodies (nAbs) alongside spike-specific T-cell responses in age-matched groups of homologous BNT162b2/BNT162b2 or AZD1222/AZD1222 vaccination, heterologous AZD1222/BNT162b2 vaccination, and prior wild-type SARS-CoV-2 infection/vaccination were evaluated. Peak immune responses were achieved after the second vaccine dose in the naïve vaccinated groups and after the first dose in the prior infection/vaccination group. Peak titers of anti-spike IgG and nAb were significantly higher in the AZD1222/BNT162b2 vaccination and prior infection/vaccination groups than in the BNT162b2/BNT162b2 or AZD1222/AZD1222 groups. However, the frequency of interferon-γ-producing CD4+ T cells was highest in the BNT162b2/BNT162b2 vaccination group. Similar results were observed in the analysis of polyfunctional T cells. When nAb and CD4+T-cell responses against the Delta variant were analyzed, the prior infection/vaccination group exhibited higher responses than the groups of other homologous or heterologous vaccination regimens. nAbs are efficiently elicited by heterologous AZD1222/BNT162b2 vaccination, as well as prior infection/vaccination, whereas spike-specific CD4+T-cell responses are efficiently elicited by homologous BNT162b2 vaccination. Variant-recognizing immunity is more efficiently generated by prior infection/vaccination than the other homologous or heterologous vaccination regimens.

This review attempts to integrate dynamic and spatiotemporal regulation of plasmodesmata with various cellular signalling processes involved in developmental, physiological, and environmental responses. To survive as sedentary organisms built of immobile cells, plants require an effective intercellular communication system, both locally between neighbouring cells within each tissue and systemically across distantly located organs. Such a system enables cells to coordinate their intracellular activities and produce concerted responses to internal and external stimuli. Plasmodesmata, membrane-lined intercellular channels, are essential for direct cell-to-cell communication involving exchange of diffusible factors, including signalling and information molecules. Recent advances corroborate that plasmodesmata are not passive but rather highly dynamic channels, in that their density in the cell walls and gating activities are tightly linked to developmental and physiological processes. Moreover, it is becoming clear that specific hormonal signalling pathways play crucial roles in relaying primary cellular signals to plasmodesmata. In this review, we examine a number of studies in which plasmodesmal structure, occurrence, and/or permeability responses are found to be altered upon given cellular or environmental signals, and discuss common themes illustrating how plasmodesmal regulation is integrated into specific cellular signalling pathways.