Guard Cell-Inspired Ion Channels: Harnessing the Photomechanical Effect via Supramolecular Assembly of Cross-Linked Azobenzene/Polymers.

Stimuli-responsive ion nanochannels have attracted considerable attention in various fields because of their remote controllability of ionic transportation. For photoresponsive ion nanochannels, however, achieving precise regulation of ion conductivity is still challenging, primarily due to the difficulty of programmable structural changes in confined environments. Moreover, the relationship between noncontact photo-stimulation in nanoscale and light-induced ion conductivity has not been well understood. In this work, a versatile design for fabricating guard cell-inspired photoswitchable ion channels is presented by infiltrating azobenzene-cross-linked polymer (AAZO-PDAC) into nanoporous anodic aluminum oxide (AAO) membranes. The azobenzene-cross-linked polymer is formed by azobenzene chromophore (AAZO)-cross-linked poly(diallyldimethylammonium chloride) (PDAC) with electrostatic interactions. Under UV irradiation, the trans-AAZO isomerizes to the cis-AAZO, causing the volume compression of the polymer network, whereas, in darkness, the cis-AAZO reverts to the trans-AAZO, leading to the recovery of the structure. Consequently, the resultant nanopore sizes can be manipulated by the photomechanical effect of the AAZO-PDAC polymers. By adding ionic liquids, the ion conductivity of the light-driven ion nanochannels can be controlled with good repeatability and fast responses (within seconds) in multiple cycles. The ion channels have promising potential in the applications of biomimetic materials, sensors, and biomedical sciences.

Zaxinone Synthase overexpression modulates rice physiology and metabolism, enhancing nutrient uptake, growth and productivity.

The rice Zaxinone Synthase (ZAS) gene encodes a carotenoid cleavage dioxygenase (CCD) that forms the apocarotenoid growth regulator zaxinone in vitro. Here, we generated and characterized constitutive ZAS-overexpressing rice lines, to better understand ZAS role in determining zaxinone content and regulating growth and architecture. ZAS overexpression enhanced endogenous zaxinone level, promoted root growth and increased the number of productive tillers, leading to about 30% higher grain yield per plant. Hormone analysis revealed a decrease in strigolactone (SL) content, which we confirmed by rescuing the high-tillering phenotype through application of a SL analogue. Metabolomics analysis revealed that ZAS overexpressing plants accumulate higher amounts of monosaccharide sugars, in line with transcriptome analysis. Moreover, transgenic plants showed higher carbon (C) assimilation rate and elevated root phosphate, nitrate and sulphate level, enhancing the tolerance towards low phosphate (Pi). Our study confirms ZAS as an important determinant of rice growth and architecture and shows that ZAS regulates hormone homoeostasis and a combination of physiological processes to promote growth and grain yield, which makes this gene an excellent candidate for sustainable crop improvement.

On the biosynthesis and evolution of apocarotenoid plant growth regulators.

Carotenoids are an important source of metabolites with regulatory function, which include the plant hormones abscisic acid (ABA) and strigolactones (SLs), and several recently identified growth regulators and signaling molecules. These carotenoid-derivatives originate from oxidative breakdown of double bonds in the carotenoid polyene, a common metabolic process that gives rise to diverse carbonyl cleavage-products known as apocarotenoids. Apocarotenoids exert biologically important functions in all taxa. In plants, they are a major regulator of plant growth, development and response to biotic and abiotic environmental stimuli, and mediate plant's communication with surrounding organisms. In this article, we provide a general overview on the biology of plant apocarotenoids, focusing on ABA, SLs, and recently identified apocarotenoid growth regulators. Following an introduction on carotenoids, we describe plant apocarotenoid biosynthesis, signal transduction, and evolution and summarize their biological functions. Moreover, we discuss the evolution of these intriguing metabolites, which has not been adequately addressed in the literature.

WRKY63 transcriptional activation of COOLAIR and COLDAIR regulates vernalization-induced flowering.

Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS C (FLC) acts as a key flowering regulator by repressing the expression of the floral integrator FLOWERING LOCUS T (FT). Prolonged exposure to cold (vernalization) induces flowering by reducing FLC expression. The long noncoding RNAs (lncRNAs) COOLAIR and COLDAIR, which are transcribed from the 3' end and the first intron of FLC, respectively, are important for FLC repression under vernalization. However, the molecular mechanism of how COOLAIR and COLDAIR are transcriptionally activated remains elusive. In this study, we found that the group-III WRKY transcription factor WRKY63 can directly activate FLC. wrky63 mutant plants display an early flowering phenotype and are insensitive to vernalization. Interestingly, we found that WRKY63 can activate the expression of COOLAIR and COLDAIR by binding to their promoters.WRKY63 therefore acts as a dual regulator that activates FLC directly under non-vernalization conditions but represses FLC indirectly during vernalization through inducing COOLAIR and COLDAIR. Furthermore, genome-wide occupancy profile analyses indicated that the binding of WRKY63 to vernalization-induced genes increases after vernalization. In addition, WRKY63 binding is associated with decreased levels of the repressive marker Histone H3 Lysine 27 trimethylation (H3K27me3). Collectively, our results indicate that WRKY63 is an important flowering regulator involved in vernalization-induced transcriptional regulation.

Compact single-panel LCD projector with high uniformity.

In this study, we introduce a single-panel LCD projector that employs a direct-lit LED array as its illumination system. Each LED in the array is coupled to a Fresnel lens to ensure light collimation. To create a uniform light distribution on the LCD panel, the LED array is arranged in a hexagonal pattern. To eliminate the hotspot effects caused by individual LED units, the optical distance between each unit and the LCD panel is extended to allow sufficient light mixing. Köhler illumination is adopted to generate adequate and homogeneous illumination on the screen. With these design enhancements, we managed to shrink the system by 29% of the traditional designs and increase uniformity to 90.1%.

Differential characteristics among asymptomatic and symptomatic meibomian gland dysfunction and those with dry eye.

PURPOSE: To identify the characteristics of asymptomatic meibomian gland dysfunction (MGD), symptomatic MGD, and MGD coexisting with dry eye disease (DED). METHODS: This cross sectional study enrolled a total of 153 eyes of 87 MGD patients. Participants filled in ocular surface disease index (OSDI) questionnaires. Age, gender, Schirmer's test, meibomian gland (MG) related parameters, lipid layer thickness (LLT) and blinking were compared among patients with asymptomatic MGD, symptomatic MGD, and MGD with DED. Multivariate regression was used to analyze the significant factor of DED in MGD. Spearman's rank correlation analysis was used to evaluate the association between the significant factors and MG function. RESULTS: There was no difference in age, Schirmer's test, lid changes, MG secretion, and MG morphology among three groups. The OSDI of asymptomatic MGD, symptomatic MGD and MGD coexisting with DED were 8.5 ± 2.9, 28.5 ± 12.8 and 27.9 ± 10.5, respectively. Patients with MGD coexisting with DED exhibited more frequent eye blinking than that of patients with asymptomatic MGD (8.1 ± 4.1 vs. 6.1 ± 3.5 blinks/20 sec, P = 0.022), and reduced LLT than that of patients with asymptomatic MGD (68.6 ± 17.2 vs. 77.6 ± 14.5 nm, P = 0.010) and symptomatic MGD (78.0 ± 17.1 nm, P = 0.015). Multivariate analysis identified LLT (per nm, OR = 0.96, 95% CI = 0.93-0.99, P = 0.002) as a significant factor associated with DED development in MGD. The number of expressible MG was positively correlated with LLT (Spearman's correlation coefficient = 0.299, P = 0.016) but negatively correlated with the number of blinking (Spearman's correlation coefficient = -0.298, P = 0.016) in MGD patients with DED, and these findings were not identified in those without DED. CONCLUSIONS: Asymptomatic MGD, symptomatic MGD, and MGD coexisting with DED share similar characteristics, including meibum secretion and morphology, but MGD patients coexisting with DED exhibited significantly reduced LLT.

SeedQuant: a deep learning-based tool for assessing stimulant and inhibitor activity on root parasitic seeds.

Witchweeds (Striga spp.) and broomrapes (Orobanchaceae and Phelipanche spp.) are root parasitic plants that infest many crops in warm and temperate zones, causing enormous yield losses and endangering global food security. Seeds of these obligate parasites require rhizospheric, host-released stimulants to germinate, which opens up possibilities for controlling them by applying specific germination inhibitors or synthetic stimulants that induce lethal germination in the host's absence. To determine their effect on germination, root exudates or synthetic stimulants/inhibitors are usually applied to parasitic seeds in in vitro bioassays, followed by assessment of germination ratios. Although these protocols are very sensitive, the germination recording process is laborious, representing a challenge for researchers and impeding high-throughput screens. Here, we developed an automatic seed census tool to count and discriminate germinated seeds (GS) from non-GS. We combined deep learning, a powerful data-driven framework that can accelerate the procedure and increase its accuracy, for object detection with computer vision latest development based on the Faster Region-based Convolutional Neural Network algorithm. Our method showed an accuracy of 94% in counting seeds of Striga hermonthica and reduced the required time from approximately 5 min to 5 s per image. Our proposed software, SeedQuant, will be of great help for seed germination bioassays and enable high-throughput screening for germination stimulants/inhibitors. SeedQuant is an open-source software that can be further trained to count different types of seeds for research purposes.

A Confidential QR Code Approach with Higher Information Privacy.

In present times, barcode decoders on mobile phones can extract the data content of QR codes. However, this convenience raises concerns about security issues when using QR codes to transmit confidential information, such as e-tickets, coupons, and other private data. Moreover, current secret hiding techniques are unsuitable for QR code applications since QR codes are module-oriented, which is different from the pixel-oriented hiding manner. In this article, we propose an algorithm to conceal confidential information by changing the modules of the QR Code. This new scheme designs the triple module groups based on the concept of the error correction capability. Additionally, this manner can conceal two secret bits by changing only one module, and the amount of hidden confidential information can be twice the original amount. As a result, the ordinary data content (such as URL) can be extracted correctly from the generated QR code by any barcode decoders, which does not affect the readability of scanning. Furthermore, only authorized users with the secret key can further extract the concealed confidential information. This designed scheme can provide secure and reliable applications for the QR system.

Weaning outcome of solid cancer patients requiring mechanical ventilation in the intensive care unit.

BACKGROUND: Whether the weaning outcome of solid cancer patients receiving mechanical ventilation (MV) in the intensive care unit (ICU) is comparable to that in non-cancer patients is unknown. The aim of this study was to compare the weaning outcomes between non-cancer patients and patients with different types of cancer. METHODS: We studied patients requiring MV during ICU stay for medical reasons between 2012 and 2014. Cancer patients were grouped into those with lung cancer (LC), head and neck cancer (HNC), hepatocellular carcinoma (HCC), and other cancers (OC). The primary endpoint was successful weaning at day 90 after the initiation of MV, and the main secondary endpoints were 28-day and 90-day mortality after ICU admission. RESULTS: Five hundred and eighteen patients with solid cancers and 1362 non-cancer patients were recruited. The rate of successful weaning at day 90 was 57.9% in cancer patients, which was lower than 68.9% in non-cancer patients (p < 0.001). Compared to non-cancer patients, LC was associated with a lower probability of weaning at day 90 (hazard ratio 0.565, 95% CI 0.446 to 0.715), while HNC, HCC, and OC had similar probabilities. The 28-day and 90-day mortality rates were higher in cancer patients than in non-cancer patients (45.2% vs. 29.4%, and 65.6% vs. 37.7%, respectively, both p < 0.001). CONCLUSION: Among mechanically ventilated patients in the ICU, those with LC were associated with a lower probability of weaning at day 90 compared to non-cancer patients.

Pancreatic neuro-insular network in young mice revealed by 3D panoramic histology.

AIMS/HYPOTHESIS: It has been proposed that the neuro-insular network enables rapid, synchronised insulin secretion. However, to date, acquiring the pancreatic tissue map to study the neural network remains a challenging task as there is a lack of feasible approaches for large-scale tissue analysis at the organ level. Here, we have developed 3-dimensional (3D) panoramic histology to characterise the pancreatic neuro-insular network in young mice. METHODS: Pancreases harvested from young wild-type B6 mice (3 and 8 weeks old) and db/db mice (3 weeks old; db/db vs db/+) were used to develop 3D panoramic histology. Transparent pancreases were prepared by optical clearing to enable deep-tissue, tile-scanning microscopy for qualitative and quantitative analyses of islets and the pancreatic tissue network in space. RESULTS: 3D panoramic histology reveals the pancreatic neurovascular network and the coupling of ganglionic and islet populations via the network. This integration is identified in both 3- and 8-week-old mice, featuring the peri-arteriolar neuro-insular network and islet-ganglionic aggregation. In weaning hyperphagic db/db mice, the 3D image data identifies the associated increases in weight, adipose tissue attached to the pancreas, density of large islets (major axis > 150 µm) and pancreatic sympathetic innervation compared with db/+ mice. CONCLUSIONS/INTERPRETATION: Our work provides insight into the neuro-insular integration at the organ level and demonstrates a new approach for investigating previously unknown details of the pancreatic tissue network in health and disease.

PanIN-associated pericyte, glial, and islet remodeling in mice revealed by 3D pancreatic duct lesion histology.

Pericytes and glial cells are accessory cells of neurovascular networks, which have been reported to participate in scar formation after tissue injury. However, it remains unclear whether similar reactive cellular responses occur in pancreatic intraepithelial neoplasia (PanIN). In this study we developed three-dimensional (3D) duct lesion histology to investigate PanIN and the associated pericyte, glial, and islet remodeling. Transparent mouse pancreata with a Kras(G12D) mutation were used to develop 3D duct lesion histology. Deep-tissue, tile-scanning microscopy was performed to generate panoramic views of the diseased pancreas for global examination of early stage and advanced duct lesion formation. Fluorescence signals of ductal and neurovascular networks were simultaneously detected to reveal associated remodeling. Significantly, in Kras(G12D)-mutant mice, when the low-grade PanINs emerge, duct lesions appear as epithelial buds with perilesional pericyte and glial activation. When PanINs occur in large scale (induced by cerulein injections to the mutant mice), the 3D image data identifies 1) aggregation of PanINs in clusters in space; 2) overexpression of the pericyte marker NG2 in the PanIN microenvironment; and 3) epithelial in-growth to islets, forming the PanIN-islet complexes. Particularly, the PanIN-islet complexes associate with proliferating epithelial and stromal cells and receive substantial neurovascular supplies, making them landmarks in the atrophic lobe. Overall, perilesional pericyte and glial activation and formation of the PanIN-islet complex underline cellular heterogeneity in the duct lesion microenvironment. The results also illustrate the advantage of using 3D histology to reveal previously unknown details of neurovascular and endocrine links to the disease.

[A Delphi Method Survey of the Core Competences of Post-Acute-Care Nurses in Caring for Acute Stroke Patients].

BACKGROUND: Post-acute care (PAC) service is becoming increasingly important in Taiwan as a core focus of government policies that are designed to ensure continuity of care. PURPOSE: In order to improve PAC nursing education and quality of care, the present study applies a modified Delphi method to identify the core competences of nurses who provide PAC services to acute stroke patients. METHODS: We surveyed 18 experts in post-acute care and long-term care anonymously using a 29-question questionnaire in order to identify the essential professional skills that are required to perform PAC effectively. The results of this survey indicate that the core competences of PAC may be divided into two categories: Case Management and Care Management. Case Management includes Direct Care, Communication, Health Care Education, Nursing Consulting, and Family Assessment & Health Care. Care Management includes Interdisciplinary Teamwork, Patient Care Management, and Resource Integration. The importance and practicality of each item was evaluated using a 7-point Likert scale. RESULTS: The experts required 2 rounds to reach a consensus about the importance and 3 rounds to determine the practicality of PAC core competences. This process highlighted the differing points of view that are held by professionals in the realms of nursing, medicine, and national health policy. CONCLUSIONS / IMPLICATIONS FOR PRACTICE: The PAC in-job training program in its current form inadequately cul-tivates core competence in Care Management. The results of the present study may be used to inform the development of PAC nurse orientation training programs and continuing education courses.

Frequent methylation of HOXA9 gene in tumor tissues and plasma samples from human hepatocellular carcinomas.

BACKGROUND: Aberrant DNA methylation is associated with the development of hepatocellular carcinoma (HCC), suggesting that gene methylation could be a potential biomarker for detection of HCC. The aim of this study is to identify potential biomarkers in HCC. METHODS: We used the Infinium methylation array and a DNA-pooling strategy to analyze the genome-wide methylation profile in HCC. Quantitative methylation-specific PCR (Q-MSP) was used to validate homeobox A9 (HOXA9) methylation in 29 normal controls, 100 HCC samples and adjacent non-tumor tissues and in 74 plasma samples, including 40 patients with HCC. RESULTS: Ten genes (HOXA9, NEUROG1, TNFRSF10C, IRAK3, GFPT2, ZNF177, DPYSL4, ELOVL4, FSD1, and CACNA1G) showed differences in methylation between controls and HCCs. Of these, HOXA9 was significantly hypermethylated in HCCs (76.7%; 23/30) compared with controls (3.4%; 1/29). In addition, combination analysis of two- and three-gene sets for HCC detection showed greater sensitivity (90%-96.7%) and comparable specificity (93.1%-96.6%) to each individual gene (33.3%-76.7% and 55.2%-100.0%). HOXA9 methylation was further validated by Q-MSP in two independent set of clinical samples including 100 HCC and paired non-tumor tissues. Further, HOXA9 methylation could be detected in plasma from HCC patients (n=40) but not in normal plasma (n=34) (p<0.0005). Combined testing (either parameter positive) for α-fetoprotein (AFP, a plasma protein biomarker) and HOXA9 methylation showed greater sensitivity (94.6%) for detection of HCC than AFP alone (75.7%). CONCLUSIONS: These data suggest that methylation of HOXA9 could be a helpful biomarker to assist in HCC detection.

Risk factors for the development of oral precancerous lesions in a cohort of 293 oral lichen planus patients with or without chronic periodontitis in southern Taiwan.

Background/purpose: Oral lichen planus (OLP) may contribute to the risk of chronic periodontitis, and no reports have shown whether OLP patients with periodontitis have a greater risk of oral precancerous lesions, Candida infection or other clinicopathological diseases. This study aimed to assess the risk factors for the development of oral precancerous lesions in a cohort of 293 OLP patients with or without chronic periodontitis in southern Taiwan. Materials and methods: The current study recruited 293 OLP patients without preexisting periodontitis at a tertiary institution from 1995 to 2018. The patients were divided into two groups based on the presence or absence of periodontitis. The study compared various clinical and pathological characteristics between the two groups, and also estimated the odds ratio (OR) and the 10-year cumulative risk of chronic periodontitis in OLP patients using logistic regression models and Kaplan‒Meier analysis methods, respectively. Results: After adjusting for age and gender, the significant contributors to oral precancerous lesions in OLP patients (P < 0.05) were periodontal disease (OR = 2.24) and the male gender (OR = 7.52). Betel nut consumption (OR = 2.61), smoking (OR = 2.46), and candidiasis infection (OR = 3.02) also showed significant associations. Older OLP patients had a lower lesion risk, while a longer OLP duration heightened the periodontal disease likelihood. Conclusion: The present study demonstrated that coexisting periodontal disease increases the likelihood of developing precancerous lesions in patients with OLP. Periodontal management with oral hygiene care and quitting betel nut consumption and smoking can reduce the risk.

Pseudopterygia in Fuchs Superficial Marginal Keratitis: Clinical Course and Surgical Outcome.

PURPOSE: Surgery for pseudopterygia in Fuchs superficial marginal keratitis (FSMK) bears the risk of corneal perforation, as described in a few case reports. The aim of this case series was to understand the clinical course and surgical outcomes of pseudopterygia in FSMK. METHODS: A retrospective case series included patients meeting FSMK criteria with pseudopterygia in at least 1 eye. The severity grading of pseudopterygia and peripheral infiltration events at follow-up were analyzed. Pseudopterygia involving corneal central 3 mm diameter (grade III) received surgery. Peripheral corneal infiltrate events within 1 week after surgery were recorded. RESULTS: Thirty-three eyes of 19 patients (8 men, 11 women; age 40-85 years; mean, 65 years) were included, with an average 48.1-month follow-up (range 0-188.8 months). At presentation, 7 eyes (21%) had grade III pseudopterygia. One patient showed corneal perforation 3 days after "pterygium" surgery elsewhere. The contralateral eye met the diagnosis of FSMK. During follow-up, 16 eyes (49%) exhibited peripheral corneal infiltrates, and 7 eyes (21%) showed progression of pseudopterygia to higher grades before or without any surgery. Ten eyes with grade III pseudopterygia underwent surgery. The best-corrected visual acuity in Logarithm of the Minimum Angle of Resolution improved from 0.34 ± 0.18 (range 0.05-0.52) to 0.13 ± 0.11 (range 0.05-0.4) (P = 0.0023). Six eyes (60%) developed peripheral corneal infiltrates within 1 week after surgery, which responded well to topical corticosteroids. CONCLUSIONS: Pseudopterygia in FSMK may progress to threaten visual acuity. Surgical excision can be safe and can effectively improve vision on the condition that the patients are closely followed in the early postoperative period to notice the corneal infiltrates.

Novel Manifestation of Corneal Dystrophy After Keratorefractive Surgery.

PURPOSE: This study aimed to report cases of bilateral corneal Bowman layer deposits in 4 patients with a history of keratorefractive surgery. To our knowledge, this condition has not previously been reported and should be distinguished from granular corneal dystrophy type 2 and other corneal dystrophies. METHODS: We reviewed all available medical records that were collected between January 2010 and December 2021 at a tertiary referral center and performed whole-exome sequencing to provide diagnostic information. RESULTS: Four patients exhibited similar bilateral corneal deposits that were observed more than 10 years after keratorefractive surgery. The patients' ages ranged from 36 to 53 years; 3 of the 4 patients were female. Three patients received laser in situ keratomileusis surgery, and 1 received radial keratotomy. All 4 patients denied having a family history of ocular diseases and reported an uneventful postoperative course. On examination, the best-corrected visual acuity ranged from 6/10 to 6/6 in all 4 patients. Slit-lamp examination revealed bilateral superficial corneal deposits involving the central cornea, and anterior segment optical coherence tomography revealed hyperreflective deposits located in the Bowman layer. Such unique manifestations suggested corneal dystrophy; thus, whole-exome sequencing was performed on all 4 patients. Only 1 patient exhibited a missense mutation in TGFBI . We further analyzed common de novo mutations to explore possible candidate genes associated with this presentation. CONCLUSIONS: We report a rare entity of presumed corneal dystrophy with deposits located in the Bowman layer in 4 patients who had received keratorefractive surgery. Clarifying the underlying pathophysiology and genetic predisposition of this disease may aid in diagnosing and preventing potential complications after keratorefractive surgery.

Exome sequencing and genome-wide association analyses unveils the genetic predisposition in hydroxychloroquine retinopathy.

OBJECTIVES: To unveil the candidate susceptibility genes in chloroquine/hydroxychloroquine (CQ/HCQ) retinopathy using whole exome sequencing (WES) and genome-wide association study (GWAS). METHODS: Patients with a diagnosis of CQ/HCQ retinopathy based on the comprehensive demographic and ocular examination were included. The peripheral blood was extracted for WES and GWAS analyses. The Chinese Han Southern database from 1000 genomes was used as control group to compare the affected percentage. Multivariate logistic regression analysis adjusted for age, HCQ dose, duration and renal disease were used to analyze the correlation between genetic variants and visual outcome. A poor vision outcome was defined as visual acuity <6/12. An abnormal anatomical outcome was defined as disruption of ellipsoid zone in the fovea. RESULTS: Twenty-nine patients with an average age of 60.9 ± 13.4 years, treatment duration of 12.1 ± 6.2 years, daily dose of 8.5 ± 4.1 mg/kg, and the cumulative dose of 1637.5 ± 772.5 g, were genotyped. Several candidate genes associated with CQ/HCQ retinopathy were found, including RP1L1, RPGR and RPE65, with a difference of affected percentage over 50% in mutation between the case and control groups. New foci in CCDC66: rs56616026 (OR = 63.43, p = 1.63 × 10-8) and rs56616023 (OR = 104.7, p = 5.02 × 10-10) were identified significantly associated with HCQ retinopathy. Multivariate analysis revealed increased genetic variants were significantly associated with poor functional (OR = 1.600, p = 0.004) and structural outcome (OR = 1.318, p = 0.043). CONCLUSIONS: Several candidate susceptibility genes including RP1L1, RPGR, RPE65 and CCDC66 were identified to be associated with CQ/HCQ retinopathy. In addition to disease susceptibility, patients with increased genetic variants are more vulnerable to poor visual outcomes.

Establishing an optimized ATAC-seq protocol for the maize.

The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin structure is found to collaborate with massive transcriptional variations across tissues and developmental stages, implying intricate regulatory mechanisms, which highlights the importance of integrating chromatin information into breeding strategies for precise gene controls. The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. In this context, we developed an easy-to-implement ATAC-seq protocol for maize with fewer nuclei and simple equipment. We demonstrate a streamlined ATAC-seq protocol with four key steps for maize in which nuclei purification can be achieved without cell sorting and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, including validation by read length periodicity, key metrics, and correlation with transcript abundance, provides a precise and efficient assessment of the maize chromatin landscape. Beyond its application to maize, our testing design holds the potential to be applied to other crops or other tissues, especially for those with limited size and amount, establishing a robust foundation for chromatin structure studies in diverse crop species.

Adsorption with biodegradation for decolorization of reactive black 5 by Funalia trogii 200800 on a fly ash-chitosan medium in a fluidized bed bioreactor-kinetic model and reactor performance.

A non-steady-state mathematical model system for the kinetics of adsorption and biodegradation of reactive black 5 (RB5) by Funalia trogii (F. trogii) ATCC 200800 biofilm on fly ash-chitosan bead in the fluidized bed process was derived. The mechanisms in the model system included adsorption by fly ash-chitosan beads, biodegradation by F. trogii cells and mass transport diffusion. Batch kinetic tests were independently performed to determine surface diffusivity of RB5, adsorption parameters for RB5 and biokinetic parameters of F. trogii ATCC 200800. A column test was conducted using a continuous-flow fluidized bed reactor with a recycling pump to approximate a completely-mixed flow reactor for model verification. The experimental results indicated that F. trogii biofilm bioregenerated the fly ash-chitosan beads after attached F. trogii has grown significantly. The removal efficiency of RB5 was about 95 % when RB5 concentration in the effluent was approximately 0.34 mg/L at a steady-state condition. The concentration of suspended F. trogii cells reached up to about 1.74 mg/L while the thickness of attached F. trogii cells was estimated to be 80 µm at a steady-state condition by model prediction. The comparisons of experimental data and model prediction show that the model system for adsorption and biodegradation of RB5 can predict the experimental results well. The approaches of experiments and mathematical modeling in this study can be applied to design a full-scale fluidized bed process to treat reactive dye in textile wastewater.

There's more to it: uncovering genomewide DNA methylation heterogeneity.

Tweetable abstract Monitoring changes in methylation heterogeneity can be powerful in detecting disease progression early. This editorial highlights the importance of profiling methylation heterogeneity and identifies existing measures and research gaps.