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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.

Abstract High‐throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh‐frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single‐pot solid‐phase‐enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96‐well format. AutoSP3 performs unbiased protein purification and digestion, and delivers peptides that can be directly analyzed by LCMS, thereby significantly reducing hands‐on time, reducing variability in protein quantification, and improving longitudinal reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low‐input samples, reproducibly quantifying 500–1,000 proteins from 100 to 1,000 cells. Furthermore, we applied this approach to a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples and recapitulated their separation into known histological growth patterns. Finally, we integrated autoSP3 with AFA ultrasonication for the automated end‐to‐end sample preparation and LCMS analysis of 96 intact tissue samples. Collectively, this constitutes a generic, scalable, and cost‐effective workflow with minimal manual intervention, enabling reproducible tissue proteomics in a broad range of clinical and non‐clinical applications.

Summary: Deciphering epigenetic regulation of gene expression requires measuring the epigenome and transcriptome jointly. Single-cell multi-omics technologies have been developed for concurrent profiling of chromatin accessibility and gene expression. However, multi-omics profiling of low-input bulk samples remains challenging. Therefore, we developed low-input ATAC&mRNA-seq, a simple and robust method for studying the role of chromatin structure in gene regulation in a single experiment with thousands of cells, to maximize insights from limited input material by obtaining ATAC-seq and mRNA-seq data simultaneously from the same cells with data quality comparable to that of conventional mono-omics assays. Integrative data analysis revealed similar strong association between promoter accessibility and gene expression when using the data of low-input ATAC&mRNA-seq as when using single-assay data, underscoring the accuracy and reliability of our dual-omics assay to generate both datum types simultaneously with just thousands of cells. We envision our method to be widely applied in many biological disciplines with limited materials. Motivation: Many cutting-edge studies require both transcriptome and epigenome analyses of very small amounts of input material. However, multi-omics profiling of low-input bulk samples remains challenging with existing mono-omics techniques. Here, we present a simple and fast dual-omics method (low-input ATAC&mRNA-seq) for simultaneous profiling of chromatin accessibility and gene expression from the same cells in limited cell numbers (5,000–20,000 cells) by using commercial off-the-shelf reagents and basic molecular biology equipment, with the resultant ATAC-seq and mRNA-seq data of acceptable quality comparable to that of the counterpart data generated with standard conventional mono-omics assays.

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.)

Low-input (LI) dairy farming, relying heavily on grazing, is increasing in popularity for perceived sustainability, welfare, and milk nutritional quality benefits. However, there is little research into the breed suitability for these systems. The popular Holstein–Friesians are not well-suited to LI production as, to achieve their potential high yields, they require high levels of concentrate intakes and veterinary inputs. Holstein–Friesians were traditionally bred for high milk yields, which often correlate negatively with functional traits, such as fertility and health. This drives the need for alternative breed choices, and UK dairy farmers use several crossbreeding practices. Additionally, classic measures of production efficiency (kilogram feed per liter of milk) are not the sole priority in LI systems, which also aim for improved health, fertility, forage conversion, and milk quality. This study aimed to explore the effect of breeding strategy on LI and organic production in dairy systems, collecting data from 17 farms throughout England and Wales: 7 organic and 10 low-input conventional systems with both purebred and crossbred cows from different breeds. Records from 1,070 cows were collected, including background data, health, fertility, breeding, and parity. Additionally, milk was analyzed on four occasions (autumn 2011 and winter, spring, and summer 2012). Principal components analysis was used to visualize the effect of management, Farm ID, and stage of lactation on LI production. The analysis clustered cows by Farm ID, showing that individual management practice on each farm had the greatest impact on various production traits. Cows were allocated a composite score based on their yield, health records, and milk fatty acid profile, and a linear mixed-effects model indicated (p < 0.01) that crossbred New Zealand Friesian cows scored highest, whereas Dairy Shorthorn cows scored the lowest. This paper highlights weaknesses in current breeding programs for LI and organic farms in the UK, in terms of the alignment of breeds with husbandry practices. Additional research is needed to explore any gene by environment interactions to meet the true potential of individual cows and certain breeds under LI and organic management.

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.

Genomic analysis of hundreds of individuals is increasingly becoming standard in evolutionary and ecological research. Individual‐based sequencing generates large amounts of valuable data from experimental and field studies, while using preserved samples is an invaluable resource for studying biodiversity in remote areas or across time. Yet, small‐bodied individuals or specimens from collections are often of limited use for genomic analyses due to a lack of suitable extraction and library preparation protocols for preserved or small amounts of tissues. Currently, high‐throughput sequencing in zooplankton is mostly restricted to clonal species, that can be maintained in live cultures to obtain sufficient amounts of tissue, or relies on a whole‐genome amplification step that comes with several biases and high costs. Here, we present a workflow for high‐throughput sequencing of single small individuals omitting the need for prior whole‐genome amplification or live cultures. We establish and demonstrate this method using 27 species of the genus Daphnia, aquatic keystone organisms, and validate it with small‐bodied ostracods. Our workflow is applicable to both live and preserved samples at low costs per sample. We first show that a silica‐column based DNA extraction method resulted in the highest DNA yields for nonpreserved samples while a precipitation‐based technique gave the highest yield for ethanol‐preserved samples and provided the longest DNA fragments. We then successfully performed short‐read whole genome sequencing from single Daphnia specimens and ostracods. Moreover, we assembled a draft reference genome from a single Daphnia individual (>50× coverage) highlighting the value of the workflow for non‐model organisms. [ABSTRACT FROM AUTHOR]

An on-farm experiment was conducted in order to evaluate effects of graded supplementation with chestnut tannin extract to cows in situations of excessive dietary protein supply on a low-input organic dairy farm. Respectively 10 Swiss Fleckvieh cows received twice per day 1 kg of experimental pellets containing either 0, 50 or 100 g/kg of chestnut extract (targeted at approximately 0, 5 and 10 g extract/kg of total dietary dry matter). Experimental feeding lasted for 21 days. Measurements and collection of milk, faeces and urine spot samples were performed in weeks 0 (baseline), 1 and 3. All cows were kept in one herd on pasture; fresh grass and grass hay were provided in the barn during night. Milk yield was recorded and cows wore sensor halters for recording chewing activity. In urine, total nitrogen and purine derivatives were measured; faeces were analyzed for protein, fibre and particle fractions; in milk, solid concentrations were determined. The data was analyzed with a general linear model. Cows did not show differences in general eating and rumination behaviour, but needed time to accept the tannin-containing pellets. Milk yield and composition were not affected by treatment, except for lactose content. No relevant differences between treatments were found for urinary and faecal parameters. In conclusion, although technically easy to supplement, pellets containing chestnut tannin extract were not readily accepted by the cows and effects on protein digestion and metabolism were not found. Successful on-farm application of chestnut extract in order to improve nitrogen efficiency therefore seems questionable. [ABSTRACT FROM AUTHOR]

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.)

Common vetch (Vicia sativa L.) is a widespread legume crop in the Mediterranean mega-environment, due to its versatile uses and its compatibility with organic and low-input farming systems. However, its adaptation to various such environments should be studied and varieties suitable for forage yield must be selected. This study aimed to explore forage yield stability of common vetch varieties based on the stability index, with a specific target to explore common vetch variety behavior in various environments. Six Greek varieties of common vetch were used over four environments for two years. The cultivation was conducted using a strip plot with the varieties randomized within each plot in both conventional and low-input cultivation systems. (Alexandros) and (Tempi) varieties showed stability for days to 50% of flowering (index >4000), while (Pigasos) and (Zefyros) for fresh forage yield (>200) across environments. Combined estimations, also showed stability of (Pigasos) and (Zefyros) for fresh forage yield. Comparisons between the conventional and low-input farming systems generally showed minor differences but revealed varieties that exhibit stable performance even in the low-input farming systems, where stability is generally a little higher. The AMMI and GGE biplot analysis depicted the stability performance of the varieties regarding the traits under experimentation. As far as the fresh forage and dry matter yield, (Zefyros) was the most stable and productive variety over all others. Correlations between traits displayed the positive relation of fresh forage yield with days for 50% flowering and dry forage yield. Positive correlations may be proved useful for indirect breeding through traits with high stability leading to the selection of traits that show low stability.

A two-year field experiment was conducted in Niger to explore the effects of integrated use of millet glume-derived compost (MGD-Compost) and NP fertilizer on soil microbial biomass carbon (Cmic), nitrogen (Nmic) and millet yields. Three compost rates (3000 kg ha−1, 1500 kg ha−1 and 0 kg ha−1) and three NP fertilizer rates (100%, 50% and 0% of recommended NP fertilizer) were arranged in a factorial experiment organized in a randomized complete block design with three replications. Combined application of compost and NP fertilizer induced a synergistic effect on Cmic and Nmic. Compost application increased millet grain yield from 59% to 91% compared to control. Combined application of compost and NP fertilizer increased millet grain yields from 57% to 70% in 2013 and from 36% to 82% in 2014 compared to sole application of mineral fertilizer. Agronomic efficiency (AE) of nitrogen values increased by 3.7 and 2.3 times than those of sole NP fertilizer application in 2013 and 2014, respectively. Phosphorus AE was 1.6 times higher than that of the sole application of NP fertilizer. These findings indicate that integrated application of MGD-Compost and NP fertilizer enhances soil microbial biomass content and increases millet grain yield in a low-input cropping system. [ABSTRACT FROM AUTHOR]

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.)

This study investigated the effect of, and interactions between, US Brown Swiss (BS) genetics and season on milk yield, basic composition and fatty acid profiles, from cows on low-input farms in Switzerland. Milk samples (n = 1,976) were collected from 1,220 crossbreed cows with differing proportions of BS, Braunvieh and Original Braunvieh genetics on 40 farms during winter-housing and summer-grazing. Cows with more BS genetics produced more milk in winter but not in summer, possibly because of underfeeding potentially high-yielding cows on low-input pasture-based diets. Cows with more Original Braunvieh genetics produced milk with more (i) nutritionally desirable eicosapentaenoic and docosapentaenoic acids, throughout the year, and (ii) vaccenic and α-linolenic acids, total omega-3 fatty acid concentrations and a higher omega-3/omega-6 ratio only during summer-grazing. This suggests that overall milk quality could be improved by re-focussing breeding strategies on cows’ ability to respond to local dietary environments and seasonal dietary changes. [ABSTRACT FROM AUTHOR]

To promote the utilization of West and Central African (WCA) genetic resources of pearl millet [Pennisetum glaucum (L.) R. Br.], this study aimed at agro-morphological characterization of selected accessions from the pearl millet reference collection, established by the Generation Challenge Program and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). A total of 81 accessions were included, comprising 78 landraces originating from 13, predominantly WCA countries and three improved cultivars. All 81 accessions were evaluated together with 18 checks for resistance to the parasitic weed Striga hermonthica (Del.) Benth. in an artificially infested field at one location in Niger. Determined by available seed quantity, 74 accessions were characterized together with seven checks in the rainy season 2009 in field trials under low-input and fertilized conditions in Nigeria, Niger and Mali, respectively. Wide ranges were observed for various traits. Several accessions were identified as sources for specific traits of interest, i.e. long panicles, high-grain density, earliness, Striga resistance and stable yielding across environments. The observed yield inferiority of all Genebank accessions compared with checks may indicate lost adaptation or inbreeding depression due to an insufficient effective population size during multiplication. A principal component analysis revealed an immense diversity but also strong admixture among the tested accessions, i.e. there were no clearly distinct groups. The seed of all genotypes is available from ICRISAT. The online availability of the characterization data is expected to facilitate efficient use of these pearl millet accessions by breeding programmes in WCA and worldwide. [ABSTRACT FROM AUTHOR]

Obtaining high quality RNA from complex biological tissues, such as the brain, is needed for establishing high-fidelity cell-type specific transcriptomes. Although combining genetic labeling techniques with laser capture microdissection (LCM) is generally sufficient, concerns over RNA degradation and limited yields call into question results of many sequencing studies. Here we set out to address both of these issues by: (1) developing a fluorescence-assisted LCM protocol that yields high quality RNA from fresh-frozen tissues; and (2) determining a suitable RNA-Seq library generation method for limited amounts of RNA (1–5 ng total RNA). The latter focused on comparing commercially available kits able to produce libraries of sufficient concentration and complexity while limiting PCR amplification biases. We find that high quality RNA (RNA integrity number, RIN, >9) of sufficient concentration can be isolated from laser-captured material from thinly-sectioned tissues when digestion time and temperature are minimized. Furthermore, we found that library generation approaches that retain ribosomal RNA (rRNA) through cDNA library generation required fewer cycles of PCR, minimizing bias in the resulting libraries. Lastly, end stage depletion of rRNA prior to sequencing enriches for target RNAs, thereby increasing read depth and level of gene detection while decreasing sequencing costs. Here we describe our protocol for generating robust RNA-Seq libraries from laser-captured tissue and demonstrate that with this method, we obtain samples with RNA quality superior to the current standard in the LCM field, and show that low-input RNA-Seq kits that minimize PCR bias produce high fidelity sequencing metrics with less variability compared to current practices.

Sunflower (Helianthus annuus L.) crop is often labelled as environmental-friendly for many objective reasons: limited amounts of N fertiliser, no irrigation, and limited use of pesticides. In addition, sunflower has a potential for providing multiple ecosystem services in diverse cropping systems (e.g. pollinators feeding). However agroecological innovations have been less developed or disseminated than for cereals or oilseed rape. Based on results from the sunflower research consortium in Toulouse (Mestries and Debaeke. 2016. Journées d’échanges Tournesol, 28 et 29 juin 2016, Toulouse (France)), we illustrate some innovating and promising approaches for more agroecological practices in sunflower cropping. Our results suggested that: integrated crop management could be proposed to limit the use of pesticides and mitigate crop damages; cover crops could be used as biofumigants to control soilborne diseases in sunflower; intercropping sunflower with soybean could be a valuable option for maximizing resource-use efficiency in low-input environments; sunflower yield could be maintained at good level in very low input cropping systems. Previous examples point out how agroecological principles could be applied to sunflower crop to improve its production in low-input conditions, and enhance the ecosystem services deliverable by this oilseed crop.

The use of quantitative population epigenetics and the related importance of stress can lead to a paradigm shift, away from a high-input and high-output agriculture with a maximum utilization of the genetic potential to an ecological intensification, to a low-input and high-output agriculture which is optimization and harmonization of limiting stress factors to achieve maximum results with limited environmental or ecological resources.

Chemical input reduction in agricultural systems is strongly demanded with the aim to improve the quality and the safety of food/feed products in an environmental sustainable perspective. Durum wheat is the most important food crop widely grown across the Mediterranean basin. However, the choice of tailored-genotypes can represent a key strategy in resource limiting conditions. The present study investigated the performance of fourteen commercial durum wheat varieties, in terms of morphologic, productive and quality traits under two cropping systems, conventional (CH) and no-chemical input (NC), for two growing seasons. The NC cropping system affected plant phenology, grain yield, and its components (i.e., ears m−2 and test weight). However, the negative influence exerted by the NC depended by the growing season (significant interaction between growing season and cropping system), which in turn affected the production behavior of genotypes (significant interaction between growing season and genotype). The additive main effect and multiplicative interaction (AMMI) analysis showed that genotype (G) effect explained the 4.3% of the total variability, the environment (E) the 71.7% and the G × E interaction the 9.4%. The AMMI stability value (ASV) indicated that Meridiano, Claudio, Saragolla, and Normanno were the most stable genotypes among environments (combination of years and management systems). An integrated environmental assessment, including a soil nitrogen balance, can help to provide a more holistic approach to the sustainability of the no-chemical Mediterranean cropping systems based on cereal-legume rotation.

According to the knowledge that the composition in fatty acids of milk is related to the production system, we determined the fatty acid composition of goat milk yielded in three different Italian farms. Two low-input system farms; one organic (LI-O) and one conventional (LI-C), and one high-input system conventional farm (HI-C) were involved in the study. Significant differences were detected among the different groups considering the fatty acid pattern of milk. Fatty acids (FA) strictly related to the rearing system, such as odd and branched chain fatty acids (OBCFA), linoleic acid (LA, 18:2 n6), alpha-linolenic acid (ALA, 18:3 n3), elaidic acid (EA, 18:1 n9), total n6 and total n3 FA, were identified as the most significant factors in the characterization of samples coming from low- or high-input systems. OBCFA amounts were found to be higher (p < 0.05) in the LI-O milk (4.7%), followed by the LI-C milk (4.5%) and then by the HI-C milk (3.4%). The same trend was observed for Σn3 FAs, mainly represented by ALA (0.72%−0.81% in LI-O systems and 0.41% in HI-system), and the opposite for Σn6 FAs, principally represented by LA (2.0%−2.6% in LI-systems and 3.1% in HI-system). A significant (p < 0.01) discrimination among samples clusters coming from the different systems was allowed by the principal component analysis (PCA).

The low-input viticultural training system ‘Semi-minimal pruned hedge’ (SMPH) is progressively being more widely applied in the Central European grapegrowing regions. The present study examined the influence of (i) the training system (SMPH versus the vertical shoot position (VSP) system), (ii) the timing of shoot topping in SMPH, and (iii) the effects of mechanical thinning in SMPH on the bunch rot epidemic, grape maturity, and yield. Six-year field trials on Pinot blanc in Luxembourg demonstrated that yield levels in non-thinned SMPH treatments were 74% higher, and total soluble solids (TSS) at harvest 2.2 brix lower than in VSP. Non-thinned SMPH delayed the bunch rot epidemic and the maturity progress by 18 and 11 days compared to VSP, respectively. Different shoot-topping timings in SMPH did not affect the tested parameters. Mechanical thinning regimes reduced the yield by 28% (moderate thinning) and 53% (severe thinning) compared to non-thinned SMPH and increased TSS by 0.8 and 1.3 brix, respectively. Delayed bunch rot epidemic and maturity progress give rise to the opportunity for a longer maturity period in cooler conditions, making this system of particular interest in future, warmer climatic conditions. Providing that yield levels are managed properly, SMPH might represent an interesting climate change adaptation strategy.

Obtaining high quality RNA from complex biological tissues, such as the brain, is needed for establishing high-fidelity cell-type specific transcriptomes. Although combining genetic labeling techniques with laser capture microdissection (LCM) is generally sufficient, concerns over RNA degradation and limited yields call into question results of many sequencing studies. Here we set out to address both of these issues by: (1) developing a fluorescence-assisted LCM protocol that yields high quality RNA from fresh-frozen tissues; and (2) determining a suitable RNA-Seq library generation method for limited amounts of RNA (1-5 ng total RNA). The latter focused on comparing commercially available kits able to produce libraries of sufficient concentration and complexity while limiting PCR amplification biases. We find that high quality RNA (RNA integrity number, RIN, >9) of sufficient concentration can be isolated from lasercaptured material from thinly-sectioned tissues when digestion time and temperature are minimized. Furthermore, we found that library generation approaches that retain ribosomal RNA (rRNA) through cDNA library generation required fewer cycles of PCR, minimizing bias in the resulting libraries. Lastly, end stage depletion of rRNA prior to sequencing enriches for target RNAs, thereby increasing read depth and level of gene detection while decreasing sequencing costs. Here we describe our protocol for generating robust RNA-Seq libraries from laser-captured tissue and demonstrate that with this method, we obtain samples with RNA quality superior to the current standard in the LCM field, and show that low-input RNA-Seq kits that minimize PCR bias produce high fidelity sequencing metrics with less variability compared to current practices. [ABSTRACT FROM AUTHOR]

Castilla La Mancha is a Spanish region where sheep farming system is traditionally pasture-based. Recently, this territory has undergone a recession of dairy sheep activity, which changed the type and intensity of land utilization and led to environmental and landscape degradation. The present study analyzed the diversity and viability of dairy sheep of mixed systems. Multivariate analysis was conducted on 157 dairy sheep farms, factor analysis selected 3 productivity factors (level of intensification, land use, size and family labour), and cluster analysis classified farms into three groups. Group 1, smallholders – with the smallest size (405.5 ewes and 564.7 ha), lowest area in ownership (1.5%), and agriculture activity (6.5% crops area): family farms (90.8%) highly dependent on external inputs. Group 2, large-scale farms (1058.7 ewes and 1755.1 ha) – with the lowest stocking rate (0.14 livestock unit/ha) and productivity: nonfamily farms (39.1%) with low area in ownership (4.1%) and agriculture activity (7.6%). Group 3, mixed-technified – with the highest levels of technology and least use of family labour (27.0%): large-scale farms (1387.4 ewes and 955.8 ha), combining milk production with agricultural activities (55.7% crops area), with the highest area in ownership (63.1%) and the best productivity performance. In conclusion, the dry land mixed system of Castilla La Mancha showed diversity of farms. Improving viability requires a systemic approach where the key tool is grazing, allowing the mixed system to be consolidated as a model that enhances the positive impact of livestock on the environment in the Mediterranean basin.

The identification of the livestock production systems (LPS) existing in a given area constitutes the first step to manage farms sustainably, since it improves the knowledge of its operation and subsequently allows for establishing the appropriate managerial strategies for each LPS. It is of great interest, as LPS are key for agro-ecosystem conservation and rural population in many areas. The present study was conducted in light of the importance of the beef cattle sector for one of the oldest and most heavily protected agroforestry systems (‘dehesa’, SW Spain and Portugal). A total of 63 beef cattle farms (including organic and conventional ones) were analysed from the structural and technical-economic points of view, aiming to: (i) improve the knowledge of the dehesa beef cattle sector; (ii) define specific managerial strategies tailored to each typology (LPS) in order to increase their sustainability as well as that of the dehesa ecosystem; (iii) clarify whether there is a relationship between the typologies obtained on the basis of technical-economic indicators and a previous classification of the farms based on their condition of being organic, and their productive and market orientation. For this purpose, the analysis paid special attention to the level of intensification, productive orientation (presence of a calf-finishing period) and self-reliance (related to their dependence on subsidies). The methodology yielded the following four typologies: (i) extensive farms selling at weaning with low productivity; (ii) extensive farms with low productivity and high dependence on subsidies; (iii) calf-finishing farms with average stocking rates and high profitability; (iv) irrigated farms with low presence of livestock, and high fixed capital and economic fluxes. In general terms, management and structure of dehesa beef cattle farms positioned them in a good place regarding CAP (Common Agricultural Policy) trends (mainly in terms of environmental protection). However, the farms studied must improve several aspects. Firstly, they need to increase their degree of self-reliance (reducing their dependence on external workforce and subsidies). Secondly, their productivity and economic performance must also be increased. The latter could be achieved by adding value to the products being sold, i.e. finishing more calves, developing new products and/or participating in marketing. Generally speaking, a close relationship between farm typologies and the previously established groups of farms (Conventional, Organic 1 and Organic 2) has not been observed. This was due to the similarities between organic and conventional farms in the context of the dehesas with regard to indicators used in the present study. [ABSTRACT FROM AUTHOR]

Background: ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent highthroughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. Results: In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. Conclusions: We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents. [ABSTRACT FROM AUTHOR]

Organic and low-input production systems are increasingly of interest in medicinal plant production, such as Calendula officinalis, a medicinal plant grown for essential oils. However, in these systems the effects of nutrient availability and water stress may act singularly or in combination to affect plant growth and medicinal compound production. This study investigated the effects of organic and conventional fertility sources and drought stress effects on four calendula cultivars. Soil nitrogen (N) status, plant growth, productivity, and essential oil quality and quantity were measured. The plant growth response to increased N availability varied by cultivar, indicating that some cultivars may be better suited to low-input fertility regimes. Fertility source did not significantly affect essential oil quality or quantity. Drought stress reduced plant growth but increased the quality of essential oil, as indicated by the concentrations of specific constituents, although it did not reduce total oil yield. These results indicate that organic and low-input farming systems may significantly reduce plant growth, but may not necessarily affect essential oil yield or quality. As such, the sustainability of medicinal plant production systems may be improved by reductions in water and conventional fertilizers without significant reductions in medicinal compound production. [ABSTRACT FROM AUTHOR]

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.)

In conventional agriculture, lettuce crops receive large amounts of pesticides to meet stringent industrial specifications and market requirements. Pesticides are used on lettuce to ensure high-yielding, attractive products free from foreign bodies and damage. Pesticide reduction is a major challenge for lettuce growers in this context. The objective of this study was to assess the risk arising from a reduction in pesticide applications by using a combination of alternative techniques for the management of pests and diseases in winter lettuce crops. Two alternative crop protection strategies (called low-input and intermediate) were designed by prototyping and then compared to a conventional lettuce protection strategy in independent trials carried out in three locations over two successive winters. The efficacy of each strategy for pest and pathogen control, as well as lettuce yield and quality, were assessed and compared. Pesticides were reduced by 32% in the intermediate crop protection strategy, and by 48% in the low-input crop protection strategy. At least 15% of lettuces were affected by pest and pathogen damage, whatever the strategy. Among possible pests or diseases, aphids were the only biotic stress which differed significantly between strategies (9.25% of lettuces infested and 2.7% of commercial losses under the low-input strategy, as compared to 0.83% of lettuces infested and 0% of commercial losses under the conventional strategy). Globally, biotic damage was less important than abiotic damage (frost and tip burn), and resulted in low commercial losses under all strategies. Similar yields and lettuce quality were recorded under the three systems. Therefore the performances of intermediate and low-input crop protection strategies were consistent with market expectations, and possible improvements are discussed. This work provides a methodology and landmarks for the design and dissemination of cropping systems targeted to leafy vegetables and less dependent on chemical control of pests and pathogens. [ABSTRACT FROM AUTHOR]

Mulching of grasslands was suggested by many that could be a feasible solution for the low productive systems to maintain their natural productivity and floristical diversity, when succesion of woody species is a threatening factor. In this middle-term experiment, we aimed to study the effects of new alternatives in Apuseni Mountains, like mulching and mulching with mineral fertilization, on the floristic structure of the oligotrophic grasslands. The experiment has started in 2009 and we followed the effects of the treatments in the 6th year. The experiment design contains seven variants in five repetitions (randomized blocks) of mowing, mulching and mulching with different doses of fertilizers applied in different time. After six years, the treatments determined no changes in the main grassland type, but significant changes have taken place in the floristic compositions of the variants. The overall effects of the treatments are negative upon the phytodiversity in some of the variants. From this reason these has to be carefully recommended if there are conservational purposes. [ABSTRACT FROM AUTHOR]

This study investigated the effect of, and interactions between, contrasting crossbreed genetics (US Brown Swiss [BS] × Improved Braunvieh [BV] × Original Braunvieh [OB]) and feeding regimes (especially grazing intake and pasture type) on milk fatty acid (FA) profiles. Concentrations of total polyunsaturated FAs, total omega-3 FAs and trans palmitoleic, vaccenic, α-linolenic, eicosapentaenoic and docosapentaenoic acids were higher in cows with a low proportion of BS genetics. Highest concentrations of the nutritionally desirable FAs, trans palmitoleic, vaccenic and eicosapentaenoic acids were found for cows with a low proportion of BS genetics (0–24% and/or 25–49%) on high grazing intake (75–100% of dry matter intake) diets. Multivariate analysis indicated that the proportion of OB genetics is a positive driver for nutritionally desirable monounsaturated and polyunsaturated FAs while BS genetics proportion was positive driver for total and undesirable individual saturated FAs. Significant genetics × feeding regime interactions were also detected for a range of FAs. [ABSTRACT FROM AUTHOR]

Castilla La Mancha is a Spanish region where sheep farming system is traditionally pasture-based. Recently, this territory has undergone a recession of dairy sheep activity, which changed the type and intensity of land utilization and led to environmental and landscape degradation. The present study analyzed the diversity and viability of dairy sheep of mixed systems. Multivariate analysis was conducted on 157 dairy sheep farms, factor analysis selected 3 productivity factors (level of intensification, land use, size and family labour), and cluster analysis classified farms into three groups. Group 1, smallholders - with the smallest size (405.5 ewes and 564.7 ha), lowest area in ownership (1.5%), and agriculture activity (6.5% crops area): family farms (90.8%) highly dependent on external inputs. Group 2, large-scale farms (1058.7 ewes and 1755.1 ha) - with the lowest stocking rate (0.14 livestock unit/ha) and productivity: nonfamily farms (39.1%) with low area in ownership (4.1%) and agriculture activity (7.6%). Group 3, mixed-technified - with the highest levels of technology and least use of family labour (27.0%): large-scale farms (1387.4 ewes and 955.8 ha), combining milk production with agricultural activities (55.7% crops area), with the highest area in ownership (63.1%) and the best productivity performance. In conclusion, the dry land mixed system of Castilla La Mancha showed diversity of farms. Improving viability requires a systemic approach where the key tool is grazing, allowing the mixed system to be consolidated as a model that enhances the positive impact of livestock on the environment in the Mediterranean basin. [ABSTRACT FROM AUTHOR]

Abstract: The aim of this study was to assess the influence of the cropping system (organic or conventional) and the growth medium (soil or soilless) on the antioxidant content of peppers from Almuden and Quito cultivars. This cultivation study complements a previous farm study. For both cultivars, organic cultivation led to higher fruit lipophilic antioxidant content than conventional management but differences in the hydrophilic fraction were not observed. The effect of the growth medium on pepper composition depended on the studied cultivar. In Almuden, neither the hydrophilic nor the lipophilic fractions were affected by the growth medium, while in Quito most compounds showed higher values in soil-grown plants. Taking into account the results from the present and the previous farm study we conclude that the effect of organic vs. conventional cultivation on pepper quality can be attributed to the different nutritional regimes and other factors associated with the agricultural system. However, both aspects are not necessarily different in organic and conventional commercial crops. The effect of the growth medium (soil or soilless) on pepper quality depended on the cultivar: Almuden was not affected by the growth medium and Quito was seen to be less suitable for soilless cultivation. [Copyright &y& Elsevier]