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Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P<0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6%; indigenous plants 3.1–16.9%; crop residues 15.8–20.6%; agro-industrial by-products 12.8–18.7%), and within category, e.g., Trifolium acaule (3.1%), Acacia nilotica L. (7.1%), Ziziph

The world is facing severe consequences of chemical fertilizers and synthetic pesticides. As a safer and eco-friendly option for crop nutrition and pest control, endophytic fungi (EFs) are now hotpots in sustainable crop production research. This comprehensive review elucidated the potentials of EF in sustainable crop production amid various biotic and abiotic stress conditions as well as their extraordinary role in phyto- and bioremediation. A critical investigation on how climatic factors such as temperature, rainfall, nutrient level, pH and storage condition affect the survival and performance of EFs are also presented. On-going research majorly focused on the application of endophytic fungi as crop growth promoters, biocontrol agents, and stress mediators. However, a lack of in-depth understanding of the underlying mechanism is predominant. Nevertheless, challenges of successful isolation and identification of EFs hinder their commercialization. Modern genomic technologies and nanotechnology-based applications of EFs can help in overcome the barriers. This review will provide direction for future research where EFs will lead next-generation sustainable strategies to cope with climate change.

Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.

The greatest challenge for the agriculture sector in the twenty-first century is to increase agricultural production to feed the burgeoning global population while maintaining soil health and the integrity of the agroecosystem. Currently, the application of biochar is widely implemented as an effective means for boosting sustainable agriculture while having a negligible influence on ecosystems and the environment. In comparison to traditional biochar, nano-biochar (nano-BC) boasts enhanced specific surface area, adsorption capacity, and mobility properties within soil, allowing it to promote soil properties, crop growth, and environmental remediation. Additionally, carbon sequestration and reduction of methane and nitrous oxide emissions from agriculture can be achieved with nano-BC applications, contributing to climate change mitigation. Nonetheless, due to cost-effectiveness, sustainability, and environmental friendliness, waste-derived nano-BC may emerge as the most viable alternative to conventional waste management strategies, contributing to the circular bioeconomy and the broader goal of achieving the Sustainable Development Goals (SDGs). However, it's important to note that research on nano-BC is still in its nascent stages. Potential risks, including toxicity in aquatic and terrestrial environments, necessitate extensive field investigations. This review delineates the potential of waste-derived nano-BC for sustainable agriculture and environmental applications, outlining current advancements, challenges, and possibilities in the realms from a sustainability and circular bioeconomy standpoint.

Heavy Metal Toxicity and Tolerance in Plants provides a comprehensive overview of the physiological, biochemical, and molecular basis of heavy metal tolerance and functional omics that allow for a deeper understanding of using heavy metal tolerance for deliberate manipulation of plants. Through the authors’ unique approach, the text enables researchers to develop strategies to enhance metal toxicity and deficiency tolerance as well as crop productivity under stressful conditions, in order to better utilize natural resources to ensure future food security. The text presents the basic knowledge of plant heavy metal/metalloid tolerance using modern approaches, including omics, nanotechnology, and genetic manipulation, and covers molecular breeding, genetic engineering, and approaches for high yield and quality under metal toxicity or deficiency stress conditions. With a collection of 26 chapters contributed by the leading experts in the fields surrounding heavy metal and metalloids toxicity and tolerance in crop plants, Heavy Metal Toxicity and Tolerance in Plants includes further information on: Advanced techniques in omics research in relation to heavy metals/metalloids toxicity and toleranceHeavy metals/metalloids in food crops and their implications for human healthMolecular mechanisms of heavy metals/metalloids toxicity and tolerance in plantsMolecular breeding approaches for reducing heavy metals load in the edible plant partsHormonal regulation of heavy metals toxicity and toleranceApplications of nanotechnology for improving heavy metals stress toleranceGenetic engineering for heavy metals/metalloids stress tolerance in plantsWith comprehensive coverage of the subject, Heavy Metal Toxicity and Tolerance in Plants is an essential reference for researchers working on developing plants tolerant to metals/metalloids stress and effective strategies for reducing the risk of health hazards.

High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to success

Dislocation theory is the fundamental tool for explaining plasticity in the material. The elastic field of a material is always influenced by the presence of dislocations and other defects independent of the loading configurations. Scientists and researchers have minimal success in solving plasticity problems analytically. And for this reason, the capturing of dislocation dynamics is highly dependent on numerical modeling, which is always a challenge for its inherent multi-scale nature. Current research investigates and develops self-consistent numerical models for different plasticity problems based on the distributed-dislocation technique and the collocation-point method. Numerical methods are developed for different boundary conditions in the presence of crystal dislocations and discontinuities in the material. Boundary conditions due to the discontinuity in the material are satisfied by placing image or fictitious dislocations or dislocations of unknown Burgers vectors at predefined places. On the free surfaces, some designated points are selected (termed as “collocation points”) to enforce the boundary conditions there only. Numerical models are developed to satisfy the boundary conditions at those collocation points, assuming that satisfying the boundary conditions at those collocation points is sufficient to capture the field solution of the problem. Burgers vectors of those fictitious dislocations are solved for using a system of linear equations that ensures the tractions on the collocation points are zero. It is evident from the assumption that the numerical solution improves as the number of collocation points on the free surfaces increases. The developed numerical scheme is implemented in one of the existing Dislocation Dynamics (DD) codes by Zbib et al. to show the free surface effect in a constant strain-rate simulation. The applications extend to free surfaces with complex geometry and can thus capture the interaction of multiple voids of any geome

The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost–benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.

OBJECTIVES: This study aimed to compare the risk of surgical site infection with open vs laparoscopic cholecystectomy. METHODOLOGY: This randomized control trial was done at the Department of Surgery, Hayatabad Medical Complex, Peshawar, for 12 months from 11/5/2018 to 11/5/2019. 116 patients were recruited for this study, 58 for each group randomly allocated to a group by lottery method and concealed Allocation. Patients in Group A underwent laparoscopic cholecystectomy, while patients in group B underwent open cholecystectomy. According to ward protocol, post-operative analgesia & antibiotics were given to patients in both groups. Expert consultant general surgeons did all the evaluation & procedures; all the patients were followed up to 30 days after the procedure & any surgical site infections, if found, were noted. RESULTS: The mean age was 36 years ± 12.19 SD and 38 years ± 11.88 SD in laparoscopic and open cholecystectomy, respectively. In laparoscopic cholecystectomy, 28% of patients were male, and 72% of patients were female, while in open cholecystectomy, 29% of patients were male, and 71% of patients were female. 07% of laparoscopic and 26% of open cholecystectomy patients had surgical site infections. CONCLUSION: Our study concludes that the frequency of surgical site infection was found less in laparoscopic cholecystectomy than in open cholecystectomy.

Beech trees (Fagus sylvatica) are prominent keystone species of great economic and environmental value for central Europe, hosting a diverse mycobiome. The composition of endophyte communities may depend on tree health, plant organ or tissue, and growth habitat. To evaluate mycobiome communalities at local scales, buds, and twigs were sampled from two young healthy mountain beech stands in Bavaria, Germany, four kilometers apart. With Illumina high-throughput sequencing, we found 113 fungal taxa from 0.7 million high-quality reads that mainly consisted of Ascomycota (52%) and Basidiomycota (26%) taxa. Significant correlations between richness and diversity indices were observed (p < 0.05), and mycobiomes did not differ between habitats in the current study. Species richness and diversity were higher in twigs compared to spring buds, and the assemblages in twigs shared most similarities. Interaction network analyses revealed that twig-bound fungi shared similar numbers of (interaction) links with others, dominated by negative co-occurrences, suggesting that competitive exclusion may be the predominant ecological interaction in the highly connected twig mycobiome. Combining community and network analyses strengthened the evidence that plant organs may filter endophytic communities directly through colonization access and indirectly by facilitating competitive interactions between the fungi.

Mycoviruses, just as the fungal endophytes they infect, are ubiquitous biological entities on Earth. Mycoviruses constitute a diverse group of viruses, and metagenomic approaches have-through recent discoveries of been mycoviruses-only recently began to provide evidence of this astonishing diversity. The current review presents (1) various mycoviruses which infect fungal endophytes and forest pathogens, (2) their presumed origins and interactions with fungi, plants and the environment, (3) high-throughput sequencing techniques that can be used to explore the horizontal gene transfer of mycoviruses, and (4) how the hypo- and hypervirulence induced by mycoviral infection is relevant to the biological control of pathogenic fungi.

A novel bisegmented double-stranded RNA virus was identified in the mycoparasitic and opportunistic fungus Hypomyces chrysospermus. The RNA1 genome segment comprises 1866 bp and encodes an RNA-dependent RNA polymerase (RdRp). The RNA2 segment comprises 1822 bp and encodes a capsid protein. Phylogenetic analysis of the RdRp protein indicated that this virus is a new member of genus Alphapartitivirus in the family Partitiviridae. We have designated this mycovirus as “Hypomyces chrysospermus partitivirus 1” (HcPV1). HcPV1 is highly transmissible with aleurioconidia and is present in large amounts within growing mycelium in comparison to the GAPDH reference gene.

Salicinoid phenolic glycosides are common defence substances in salicaceous trees and specialist leaf beetles use these compounds for their own defence against predators. Salicinoids vary qualitatively and qualitatively in aspen (Populus tremula) and this variation has a genetic basis. The foliar endophyte mycobiome is plentiful and we hypothesised that it is related to plant genotype, potentially mediated by salicinoid composition, and that interactions with the leaf beetle Chrysomela tremula may alter this relationship. We studied these three-way interactions in controlled greenhouse experiments. Endophytic fungi were isolated from sterilised leaf tissues with and without beetle damage, and from beetles. We confirmed that endophyte composition was influenced by host genotype. Beetle activity added generalist morphs to the mycobiome that overrode the initial host association. Yeast-like genera (Cryptococcus and Rhodotorula) were isolated only from beetle-damaged tissues and from beetles, whereas fast-growing filamentous fungi dominated beetle-free control plants. Competition experiments between filamentous fungi of plant origin and beetle-related yeasts suggested interaction of both stimulating and inhibiting modes of action amongst the fungi. As a result, we detected examples of amensalism, commensalism, parasitism and competition between the morphs tested, but we found no evidence of mutualism, and consequently no co-evolutionary relationship could be demonstrated, between yeasts carried by beetles, host genotype and associated filamentous morphs. Endophyte studies are method-dependent and high-throughput sequencing technology best define the fungal mycobiome, culturing however continues to be a cheap way to provide fundamental ecological insights and it is also required for experimental studies.

Comparative simultaneous studies of environmental high-throughput sequencing (HTS) and cultivation of plant-associated fungi have rarely been conducted in the past years. For the present contribution, HTS and extinction culturing were applied for the same leaf samples of European beech (Fagus sylvatica) in order to trace both “real” environmental drivers as well as method-dependent signals of the observed mycobiomes. Both approaches resulted in non-overlapping community composition and pronounced differences in taxonomic classification and trophic stages. However, both methods revealed similar correlations of the fungal communities with local environmental conditions. Our results indicate undeniable advantages of HTS over cultivation in terms of revealing a good representation of the major functional guilds, rare taxa and biodiversity signals of leaf-inhabiting fungi. On the other hand our results demonstrate that the immense body of literature about cultivable endophytic fungi can and should be used for the interpretation of community signals and environmental correlations obtained from HTS studies and that cultivation studies should be continued at the highest standards, e.g. when sequencing facilities are not available or if such surveys are expanded into functional aspects with experiments on living isolates.

This paper proposes a novel entropy encoding technique for lossless data compression. Representing a message string by its lexicographic index in the permutations of its symbols results in a compressed version matching Shannon entropy of the message. Commercial data compression standards make use of Huffman or arithmetic coding at some stage of the compression process. In the proposed method, like arithmetic coding entire string is mapped to an integer but is not based on fractional numbers. Unlike both arithmetic and Huffman coding no prior entropy model of the source is required. Simple intuitive algorithm based on multinomial coefficients is developed for entropy encoding that adoptively uses low number of bits for more frequent symbols. Correctness of the algorithm is demonstrated by an example.

In recent years a large body of research has investigated the dynamics of complex networks, including percolation [1, 2], epidemics [3, 4], synchronization [5, 6], evolutionary game theory [7, 8], and traffic dynamics [9, 10, 11]. These study apply to technological networks, biological networks, and social networks. In general, it has been shown that the topology of these networks (e.g. the degree distribution [12, 13], degree correlation [14, 15], community structure [16], etc.) plays a significant role in their dynamical time evolution., Master of Science in Mechanical Engineering, Masters, University of New Mexico. Dept. of Mechanical Engineering, Sorrentino, Francesco, Shen, Yu-Lin, Kouzehgarani, Asal Naseri

Comparative investigations of plant-associated fungal communities (mycobiomes) in distinct habitats and under distinct climate regimes have been rarely conducted in the past. Nowadays, high-throughput sequencing allows routine examination of mycobiome responses to environmental changes and results at an unprecedented level of detail. In the present study, we analysed Illumina-generated fungal ITS1 sequences from European beech (Fagus sylvatica) originating from natural habitats at two different altitudes in the German Alps and from a managed tree nursery in northern Germany. In general, leaf-inhabiting mycobiome diversity and composition correlated significantly with the origin of the trees. Under natural condition the mycobiome was more diverse at lower than at higher elevation, whereas fungal diversity was lowest in the artificial habitat of the tree nursery. We further identified significant correlation of leaf chlorophylls and flavonoids with both habitat parameters and mycobiome biodiversity. The present results clearly point towards a pronounced importance of local stand conditions for the structure of beech leaf mycobiomes and for a close interrelation of phyllosphere fungi and leaf physiology.

We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000 m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.

In recent years a large body of research has investigated the dynamics of complex networks, including percolation [1, 2], epidemics [3, 4], synchronization [5, 6], evolutionary game theory [7, 8], and traffic dynamics [9, 10, 11]. These study apply to technological networks, biological networks, and social networks. In general, it has been shown that the topology of these networks (e.g. the degree distribution [12, 13], degree correlation [14, 15], community structure [16], etc.) plays a significant role in their dynamical time evolution.