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Studies on self-binding hot-pressed fiberboards using agricultural byproducts aim to identify alternatives to scarce wood resources. Particle size and mixture significantly impact strength, although direct comparisons are difficult due to differences in study methods. We evaluated fiberboards made from the two perennial biomass crops Miscanthus and Paulownia and compared them to Picea (spruce), using five distinct particle size blends prepared from milled and sieved particles, respectively. The boards were evaluated for their modulus of elasticity, modulus of rupture, reaction to fire, water absorption, and thickness swelling. All specimens exhibited normal ignitability, as defined by Euroclass E according to EN13501-1. The results indicate that mechanical performance improves with increasing density, which correlates with higher proportions of finer particles. Notably, the finer Miscanthus blends and all Paulownia samples met the modulus of elasticity requirements of EN 622. [ABSTRACT FROM AUTHOR]

The chromosome immunoprecipitation sequencing technology（ChIP-seq）, which combines the chromatin immunoprecipitation technology（ChIP）with the second generation sequencing technology, is an important method for analyzing the epigenetic changes of the whole genome, and can quickly and effectively detect DNA and protein binding sites, transcription factor binding sites（TFBS）, histone post-translation modifications（hPTMs）, nucleosome localization and DNA methylation in the whole genome. However, for a long time, ChIP-seq needs a large number of cells to generate high-quality data sets, which limits the application of ChIP in some specific tissue and low-cell samples such as oocytes, early embryonic cells and other research fields. In recent years, based on ChIP, researchers have proposed a series of low-input ChIP-seq methods to reduce the initial sample amount and experimental cost and increase the sequencing quality, which has promoted the development of epigenomics. In this paper, we reviewed the principles of ChIP and the methodological development of ChIP-seq reducing low-input amount, compared several of the more important methods, and summarized the application of ChIP-seq with lowinput amount in epigenetic research. Finally, we prospected the application and development of low initial ChIP-seq technology, aiming to provide reference for the selection of different low-input ChIP-seq methods for low cell number samples. [ABSTRACT FROM AUTHOR]

The yield potential of switchgrass was verified by testing seven cultivars in a small-scale experiment carried out from 2018 to 2022 on Gleyic Fluvisol under Central European conditions. The treatments are as follows: pre-sowing (i/HA) soil humic preparation Humac AGRO (based on leonardite) with an ameliorative dose of 1000.0 kg ha−1 or (ii/NPK) basic nutrition with a dose of 220.0 kg ha−1 NPK; an annual dose of 70 kg ha−1 N was applied to both treatments (HA, NPK) and compared to (iii/UC) untreated control. A dry matter (DM) yield of 9.02 t ha−1 was achieved in the total average, which varied from 0.05 t ha−1 to 60.64 t ha−1. The yield was affected mainly by years (F-ratio 106.64), then by nutrition (F-ratio 79.03), followed by cultivars (F-ratio 56.87), and finally by replications (F-ratio 0.00). Switchgrass productivity increased according to the utility year; however, the driest year (2020—388 mm, 2021—372 mm, and 2022—288 mm) changed the order of the three full utility years (12.44, 19.13, and 7.73 t ha−1 DM, respectively). HA gives the highest DM yield of 13.69 t ha−1 on average with values of 9.19 and 4.19 for NPK and UC, respectively. The cultivars order was EG 1101 ˃ BO Master ˃ EG 1102 ˃ Kanlow ˃ Alamo ˃ Carthage ˃ NJ Ecotype (21.15, 12.48, 8.14, 7.70, 6.34, 4.47, and 2.89 t ha−1 DM when ranking average yield or 60.64, 45.20, 29.92, 29.15, 17.87, 9.86, and 5.93 t ha−1 DM when ranking maximal yields). [ABSTRACT FROM AUTHOR]

The "Green Revolution" (GR) technology-induced agricultural intensification has transformed India from food scarcity to a food surplus country. However, this has also resulted into several adverse repercussions. Increased application of chemical fertilizers and pesticides with stagnating/declining crop productivity has dovetailed with uncertain market conditions and climate change effects which has resulted in un-remunerative agriculture. Consequently, farmers have fallen into the debt trap due to the rising cost of crop production apart from health hazards due to serious exposure to harmful chemical pesticides. Natural Farming (NF), an agro-ecological approach to farming is believed to be an effective way to counter some of these challenges. The present paper presents field-level farmers' experiences of NF adoption in three states of India—Andhra Pradesh, Karnataka, and Maharashtra. The study was conducted during February–March 2019 by surveying 295 NF adopted and 170 non-NF adopted farmers. It was found that NF practice has been followed by some farmers for more than 10 years but others have adopted during the recent past. There is variation in the practice followed by the NF farmers. There are farmers who are using Farm Yard Manure (FYM). A solid form of jeevamritha (liquid concoction of microbial inoculants) called as ghanajeevamritha was also found to be used by farmers in Andhra Pradesh. It was observed that non-NF yields are superior to NF yield without FYM. In most crops, however, NF with FYM had a greater yield than NF without FYM and non-NF farms. There has been a decrease in the variable cost and a marginal increase in the market price of NF produce. The study suggests that natural farming may be seen as one of the alternative practices which has potential to rejuvenate the agro-ecosystem, besides cost saving for the individual farmers. [ABSTRACT FROM AUTHOR]

To enable diverse functions and precise regulation, an RNA sequence often folds into complex yet distinct structures in different cellular states. Probing RNA in its native environment is essential to uncovering RNA structures of biological contexts. However, current methods generally require large amounts of input RNA and are challenging for physiologically relevant use. Here, we report smartSHAPE, a new RNA structure probing method that requires very low amounts of RNA input due to the largely reduced artefact of probing signals and increased efficiency of library construction. Using smartSHAPE, we showcased the profiling of the RNA structure landscape of mouse intestinal macrophages upon inflammation, and provided evidence that RNA conformational changes regulate immune responses. These results demonstrate that smartSHAPE can greatly expand the scope of RNA structure-based investigations in practical biological systems, and also provide a research paradigm for the study of post-transcriptional regulation.

The stability of performance may be proved to be the last frontier for adopting certain genotypes in various cultivation systems and environments. The main objective of the present study was to analyze the forage yield stability performance of seven pea (Pisum sativum L.) genotypes based on various stability indices. The genotype behavior was studied based on the yield of peas under both conventional and low-input cultivation systems. Five cultivars of peas (broadly distributed) and two lines were used in a strip-plot design. Significant positive correlations were detected between forage yield and some other traits. This way, forage yield stability may be indirectly improved by improving certain traits showing qualitative inheritance. Comparisons revealed that genotypes exhibited stable performance, even in low-input farming systems. AMMI analysis, GGE biplot, and analysis of variance (ANOVA) combination showed statistically significant differences between genotypes and environments and the farming system. Our analysis depicted specific cultivars of peas for different areas and farming systems to attain highly stable performance. Vermio was confirmed to be a stable genotype for forage yield performance in low-input farming in Trikala and Kalambaka areas, while Pisso was indicated as the best in Florina and Giannitsa areas in low-input farming. The two pea lines exhibited stable performance in Giannitsa and Florina areas, especially in low-input conditions. The stable behavior of some genotypes in these conditions may be useful for farmers that raise livestock in mountainous areas. The genetic parameters show that the selection for fresh forage yield and dry matter yield in breeding programs is expected to be effective. [ABSTRACT FROM AUTHOR]

Background: DNA methylation alterations have emerged as hallmarks of cancer and have been proposed as screening, prognostic, and predictive biomarkers. Traditional approaches for methylation analysis have relied on bisulfite conversion of DNA, which can damage DNA and is not suitable for targeted gene analysis in low-input samples. Here, we have adapted methyl-CpG-binding domain protein 2 (MBD2)-based DNA enrichment for use on a semi-automated exclusion-based sample preparation (ESP) platform for robust and scalable enrichment of methylated DNA from low-input samples, called SEEMLIS. Results: We show that combining methylation-sensitive enzyme digestion with ESP-based MBD2 enrichment allows for single gene analysis with high sensitivity for GSTP1 in highly impure, heterogenous samples. We also show that ESP-based MBD2 enrichment coupled with targeted pre-amplification allows for analysis of multiple genes with sensitivities approaching the single cell level in pure samples for GSTP1 and RASSF1 and sensitivity down to 14 cells for these genes in highly impure samples. Finally, we demonstrate the potential clinical utility of SEEMLIS by successful detection of methylated gene signatures in circulating tumor cells (CTCs) from patients with prostate cancer with varying CTC number and sample purity. Conclusions: SEEMLIS is a robust assay for targeted DNA methylation analysis in low-input samples, with flexibility at multiple steps. We demonstrate the feasibility of this assay to analyze DNA methylation in prostate cancer cells using CTCs from patients with prostate cancer as a real-world example of a low-input analyte of clinical importance. In summary, this novel assay provides a platform for determining methylation signatures in rare cell populations with broad implications for research as well as clinical applications. [ABSTRACT FROM AUTHOR]

The “Green Revolution” (GR) technology-induced agricultural intensification has transformed India from food scarcity to a food surplus country. However, this has also resulted into several adverse repercussions. Increased application of chemical fertilizers and pesticides with stagnating/declining crop productivity has dovetailed with uncertain market conditions and climate change effects which has resulted in un-remunerative agriculture. Consequently, farmers have fallen into the debt trap due to the rising cost of crop production apart from health hazards due to serious exposure to harmful chemical pesticides. Natural Farming (NF), an agro-ecological approach to farming is believed to be an effective way to counter some of these challenges. The present paper presents field-level farmers’ experiences of NF adoption in three states of India—Andhra Pradesh, Karnataka, and Maharashtra. The study was conducted during February–March 2019 by surveying 295 NF adopted and 170 non-NF adopted farmers. It was found that NF practice has been followed by some farmers for more than 10 years but others have adopted during the recent past. There is variation in the practice followed by the NF farmers. There are farmers who are using Farm Yard Manure (FYM). A solid form of jeevamritha (liquid concoction of microbial inoculants) called as ghanajeevamritha was also found to be used by farmers in Andhra Pradesh. It was observed that non-NF yields are superior to NF yield without FYM. In most crops, however, NF with FYM had a greater yield than NF without FYM and non-NF farms. There has been a decrease in the variable cost and a marginal increase in the market price of NF produce. The study suggests that natural farming may be seen as one of the alternative practices which has potential to rejuvenate the agro-ecosystem, besides cost saving for the individual farmers.

Spatial tissue proteomics integrating whole-slide imaging, laser microdissection, and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE robotic system, which has the capacity to process 192 samples in 3 h. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking, and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows 'on-the-fly' sample clean-up, particularly pertinent for laser microdissection workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell, and epithelial microregions of 4000 μm 2 to a depth of ∼2000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility., Competing Interests: Conflict of interest D. H. and A. S. are employees at Cellenion. All other authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The stability of performance may be proved to be the last frontier for adopting certain genotypes in various cultivation systems and environments. The main objective of the present study was to analyze the forage yield stability performance of seven pea (Pisum sativum L.) genotypes based on various stability indices. The genotype behavior was studied based on the yield of peas under both conventional and low-input cultivation systems. Five cultivars of peas (broadly distributed) and two lines were used in a strip-plot design. Significant positive correlations were detected between forage yield and some other traits. This way, forage yield stability may be indirectly improved by improving certain traits showing qualitative inheritance. Comparisons revealed that genotypes exhibited stable performance, even in low-input farming systems. AMMI analysis, GGE biplot, and analysis of variance (ANOVA) combination showed statistically significant differences between genotypes and environments and the farming system. Our analysis depicted specific cultivars of peas for different areas and farming systems to attain highly stable performance. Vermio was confirmed to be a stable genotype for forage yield performance in low-input farming in Trikala and Kalambaka areas, while Pisso was indicated as the best in Florina and Giannitsa areas in low-input farming. The two pea lines exhibited stable performance in Giannitsa and Florina areas, especially in low-input conditions. The stable behavior of some genotypes in these conditions may be useful for farmers that raise livestock in mountainous areas. The genetic parameters show that the selection for fresh forage yield and dry matter yield in breeding programs is expected to be effective.

Deep proteomic profiling of rare cell populations has been constrained by sample input requirements. Here, we present DROPPS (droplet-based one-pot preparation for proteomic samples), an accessible low-input platform that generates high-fidelity proteomic profiles of 100-2,500 cells. By applying DROPPS within the mammary epithelium, we elucidated the connection between mitochondrial activity and clonogenicity, identifying CD36 as a marker of progenitor capacity in the basal cell compartment. We anticipate that DROPPS will accelerate biology-driven proteomic research for a multitude of rare cell populations., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and clinical questions. DNA methylation analysis bears the particular promise to supplement or replace biochemical and imaging-based tests for the next generation of personalized medicine. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines. Here, we provide a detailed protocol based on a commercial kit for the preparation of sequencing libraries for the comprehensive whole-genome analysis of DNA methylation and/or hydroxymethylation. The protocol is based on the construction of sequencing libraries from limited amounts of input DNA by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. For analyses requiring a quantitative distinction between 5-methylcytosine and 5-hydroxymethylcytosines levels, an oxidation step is included in the same workflow to perform oxidative bisulfite sequencing (OxBs-Seq). In this case, two sequencing libraries will be generated and sequenced: a classic methylome following bisulfite conversion and analyzing modified cytosines (not distinguishing between methylated and hydroxymethylated cytosines) and a methylome analyzing only methylated cytosines, respectively. Hydroxymethylation levels are deduced from the differences between the two reactions. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocol has been successfully applied to different human and plant samples and yields robust and reproducible results., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Tn5 transposase has been widely used to simultaneously fragment and tag double-stranded DNA (dsDNA) with sequencing adaptors in library construction for next-generation sequencing. Recently, we demonstrated that Tn5 transposase also possesses tagmentation activity toward RNA/DNA hybrids, in addition to its canonical dsDNA substrates. Based on this new activity, we are able to skip multiple laborious and time-consuming steps in traditional RNA-seq methods, and rapid, low-input, cost-effective, one-tube RNA-seq library construction is thus enabled. The libraries constructed by Transposase-assisted RNA/DNA hybrids Co-tagmEntation (termed "TRACE-seq") demonstrate excellent performance in terms of gene expression measurement and differential gene expression analysis. Here, we present detailed protocols for TRACE-seq that will be broadly useful for the study of RNA biology and biomedical research. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Total RNA preparation Basic Protocol 2: TRACE-seq library construction Support Protocol: Tn5 transposome assembly., (© 2023 Wiley Periodicals LLC.)

Climate change models predict an increase in climate variability in the future, with more rainfall extremes and greater risks, causing a negative impact on crops produced by smallholders in West Africa. Conservation Agriculture (CA) systems can be effective in mitigating yield loss in environments with increased weather risk. This study aimed to evaluate CA cropping systems that can minimize both economic and climatic risks under erratic climatic conditions in West Africa. We tested upland rice-based CA systems and conventional systems with tillage (CT), in rotation with maize in some of the cases, without and with fertilization, at different sowing windows in the Bouaké region, Côte d'Ivoire, from 2015 to 2020. Sowing in June showed in a higher rice yield (1183 kg ha-1 and 1370 kg ha-1 without and with fertilization, on average over the 2017–2020 period) than in March (521 kg ha-1 and 495 kg ha-1 without and with fertilization) or in July or August (335 kg ha-1 and 498 kg ha-1 without and with fertilization). During the first four years, rice yields tended to be lower under the CA systems than under the CT systems, especially when water availability was not a major constraint. However, after this transition period, and especially when water stress occurred, as in 2020, rice yields under CA systems (1835–2021 and 2147–2254 kg ha-1 without and with fertilization) were higher than under CT systems (1350 kg ha-1 and 1435 kg ha-1 without and with fertilization). CA systems having relatively longer duration for growing cover crops tended to produce higher upland rice yield grown in the subsequent season. In both CT and CA systems, the impact of fertilization on rice yield was small over the study period, and the mean rice yield increase due to fertilization was on average 451 kg ha-1 even when rice was sown in the summer season, resulting in negative economic return. These results indicate that whereas low-input CA upland rice-based systems together with optimizing sowing window for rice could be promising options for sustaining rice yield and mitigating yield loss in environments with increased weather risk, further research is needed for reducing transition period to CA systems in order to enhance their adoption by smallholder farmers. Desirable cover crops should be less labor-demanding, generate incomes from their products, and produce large biomass under erratic climatic conditions. • Conservation agriculture (CA) was compared to conventional tillage (CT) for 6 years. • In years 1–4, CT performed better than CA in favorable climatic years. • After 4 years, CA performed better than CT, especially in dry conditions. • Fertilization was not profitable in both CT and CA systems. • Associating cassava and stylo is a profitable option for soil regeneration. [ABSTRACT FROM AUTHOR]

Chromatin immunoprecipitation (ChIP) enables the study of DNA-protein interactions. When coupled with high-throughput sequencing (ChIP-seq), this method allows the generation of genome-wide profiles of the distribution of specific proteins in a given cellular context. Typical ChIP-seq experiments require millions of cells as input material and thus are not ideal to study many in vivo cell populations. Here, we describe an ultra-low-input native ChIP-seq method, ULI-NChIP-seq, to profile histone modification patterns in as low as 150 cells., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)