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The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of "splitting" taxa into numerous taxonomic units produces greater barcode gaps when compared to "lumping". The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species. [ABSTRACT FROM AUTHOR]

In Mexico, the State policy in favor of mining extractive -based on the idea that the exploitation of the subsoil will generate sufficient resources to achieve well-being and progress- has caused irreparable environmental damage to the mining populations, generating a paradox of abundance at the local level. This situation is analyzed here in economic, social, and environmental terms in the mining community of Valdecañas, in Fresnillo, Zacatecas; corroborating the environmental impact of mining, the scarce resources it generates for the economy, and the risk it has on the well-being and health of people. [ABSTRACT FROM AUTHOR]

Introduction: The risk of progression to tuberculosis disease is highest within the first year after M. tuberculosis infection (TBI). We hypothesize that people with newly acquired TBI have a unique cytokine/chemokine profile that could be used as a potential biomarker. Methods: We evaluated socio-demographic variables and 18 cytokines/chemokines in plasma samples from a cohort of people deprived of liberty (PDL) in two Colombian prisons: 47 people diagnosed with pulmonary TB, 24 with new TBI, and 47 non-infected individuals. We performed a multinomial regression to identify the immune parameters that differentiate the groups. Results: The concentration of immune parameters changed over time and was affected by the time of incarceration. The concentration of sCD14, IL-18 and IP-10 differed between individuals with new TBI and short and long times of incarceration. Among people with short incarceration, high concentrations of MIP-3α were associated with a higher risk of a new TBI, and higher concentrations of Eotaxin were associated with a lower risk of a new TBI. Higher concentrations of sCD14 and TNF-α were associated with a higher risk of TB disease, and higher concentrations of IL-18 and MCP-1 were associated with a lower risk of TB disease. Conclusions: There were cytokines/chemokines associated with new TBI and TB disease. However, the concentration of immune mediators varies by the time of incarceration among people with new TBI. Further studies should evaluate the changes of these and other cytokines/chemokines over time to understand the immune mechanisms across the spectrum of TB. [ABSTRACT FROM AUTHOR]

In this article, we focused on studying the current barriers to implementing innovations in order for the agricultural sector to become more sustainable. Through a systematic literature review (SLR), 73 scientific articles were obtained with a search equation in SCOPUS. Of these, 48 were analyzed because of the mention of an obstacle preventing the sector from implementing innovations towards sustainability. Information related to the publication year, abstract, authors, keywords, innovation, innovation type, relationship with Fourth Industrial Revolution (4IR), identified barrier, nature of the barrier (internal/external), agricultural subsector, country, and methodology of each article was identified, and with VantagePoint software, a technological surveillance technique was applied as a quantitative analysis of the information. The United States is the country with the most publications related to the subject. The most mentioned keywords were "Sustainable Agriculture", "Agroecology", "Climate Change", "Innovation", and "Organic Farming". Additionally, a qualitative analysis showed 43 types of innovations, 16 of them related to technology. "Organic Agriculture" is the most mentioned innovation, followed by "Genetic Engineering" and "Precision Agriculture". In addition, 51 barriers were identified, 28 external to farmers and 23 internal. "Lack of policies that promote that innovation Innovative Practices" is the most mentioned barrier, followed by "Epistemic Closure", "Unfavorable Regulation", Climate-Smart Agriculture, and "Unskilled Labor". This article is intended not only to show trends in the barriers to innovation that prevents the achievement of sustainability that the agricultural sector needs, but also to serve as an input for the development of policies that provide solutions to these impediments. It was shown that 17 out of the 28 external barriers are related to topics that could be solved by formulating policies, laws, incentives, guidelines, and regulations. [ABSTRACT FROM AUTHOR]

Objective: To determine the gene expression profile in individuals with new latent tuberculosis infection (LTBI), and to compare them with people with active tuberculosis (TB) and those exposed to TB but not infected. Design: A prospective cohort study. Recruitment and follow-up were conducted between September 2016 to December 2018. Gene expression and data processing and analysis from April 2019 to April 2021. Setting: Two male Colombian prisons. Participants: 15 new tuberculin skin test (TST) converters (negative TST at baseline that became positive during follow-up), 11 people that continued with a negative TST after two years of follow-up, and 10 people with pulmonary ATB. Main outcome measures: Gene expression profile using RNA sequencing from PBMC samples. The differential expression was assessed using the DESeq2 package in Bioconductor. Genes with |logFC| >1.0 and an adjusted p-value < 0.1 were differentially expressed. We analyzed the differences in the enrichment of KEGG pathways in each group using InterMiner. Results: The gene expression was affected by the time of incarceration. We identified group-specific differentially expressed genes between the groups: 289 genes in people with a new LTBI and short incarceration (less than three months of incarceration), 117 in those with LTBI and long incarceration (one or more years of incarceration), 26 in ATB, and 276 in the exposed but non-infected individuals. Four pathways encompassed the largest number of down and up-regulated genes among individuals with LTBI and short incarceration: cytokine signaling, signal transduction, neutrophil degranulation, and innate immune system. In individuals with LTBI and long incarceration, the only enriched pathway within up-regulated genes was Emi1 phosphorylation. Conclusions: Recent infection with MTB is associated with an identifiable RNA pattern related to innate immune system pathways that can be used to prioritize LTBI treatment for those at greatest risk for developing active TB. [ABSTRACT FROM AUTHOR]

While nature behaves like an irreversible network with respect to entropy and time, certain systems in nature exist that are, to some extent, reversible. The property of reversibility imparts unique benefits to systems that possess them, making them suitable for designing self‐healing, stimuli‐responsive, and smart materials that can be used in widely divergent fields. Reversible networks are currently being exploited for applications in tissue engineering, drug delivery, and soft robotics. They are also being utilized as low‐calorie fat mimetics with melt‐in‐your‐mouth textures, as well as being explored as potential scaffolds for three‐dimensional (3D) printable food, among other applications. This review aims to gather representative examples of heat‐ and shear‐reversible networks in the food science literature from the last 30 or so years, in other words, reversible food gels made either from linear biopolymers or from colloidal, particulate dispersions, including those that have been modified specifically to induce reversibility. An overview of the network mechanisms involved that impart reversibility, including a discussion of the strength and range of forces involved, will be highlighted. A model that explains why certain networks are thermoreversible while others are shear‐reversible, and why others are both, will also be proposed. A fundamental understanding of these mechanisms will prove invaluable when designing reversible networks in the future, making possible the precise control of their properties, thus fostering innovative applications within the food industry and beyond. [ABSTRACT FROM AUTHOR]

Accurate identification of edible ectomycorrhizal (ECM) mushrooms and their host trees in nature is key to commercial production for consumption. For the first time we describe the ectomycorrhizal association of the three most common species of edible matsutake mushrooms with their native host trees in Yunnan Province in China. We collected ECM samples from three different localities in subtropical forests known to be highly productive areas of Tricholoma. Additionally, we collected basidiomata of Tricholoma from the field and markets in Yunnan. ECM samples were analyzed using morphological and molecular methods. We conducted phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and analyzed the intergenic spacer of cpDNA psbA-trnH to identify basidiomata and plant hosts, respectively. Three species of Tricholoma were identified: T. bakamatsutake, T. fulvocastaneum, and T. matsutake. Four ECM associations in the study area were detected: Tricholoma bakamatsutake + Castanopsis tibetana, T. fulvocastaneum + C. tibetana, T. fulvocastaneum + Pinus yunnanensis, and T. matsutake + P. yunnanensis. Detailed descriptions and illustrations of the ECM associations are presented. [ABSTRACT FROM AUTHOR]

In the last 10 years, Salmonella Heidelberg has been extensively isolated from poultry in several countries. In this context, molecular characterization is essential to understand whether the strains have entered the farms from a single or several sources. Thus, the aim of this study was to determine the genetic relationship and antimicrobial susceptibility of S. Heidelberg strains isolated between 2011 and 2012 from broiler farms belonging to three integrated poultry companies located in Argentina. The genetic relatedness of the S. Heidelberg isolates was determined by pulsed‐field gel electrophoresis (PFGE), and resistance to 21 antimicrobials was determined by the disc diffusion method. The isolates were assigned to four PFGE patterns. Most of the strains showed 100% similarity and belonged to the same integrated poultry company. This PFGE pattern was also prevalent in S. Heidelberg strains isolated from humans in several provinces of Argentina, which suggests an epidemiological association between human and poultry strains. All the isolates were classified as multidrug‐resistant (MDR), and no clear relationship was observed between PFGE and resistance patterns. S. Heidelberg strains may circulate among farms from the same integrated company due to common sources of contamination. To guarantee the safety of the poultry product for the consumers, holistic approaches including surveillance of Salmonella throughout the production chain together with control measures are crucial. [ABSTRACT FROM AUTHOR]

Two new species of yellow Cantharellus and a new record of Cantharellus tabernensis associated with tropical species of Quercus are presented, based on the taxonomic study of fresh specimens and in a phylogenetic analysis of transcription elongation factor 1-alpha (tef-1a) and the large subunit of the ribosome (nLSU) sequences. One of the new species proposed here, corresponds to a choice edible mushroom, which, in our molecular phylogeny, resulted in it being related to the group of species around C. lateritius and sister with Craterellus confluens type specimen. This latter is here formally transferred to Cantharellus and consequently a new name, Cantharellus furcatus, is proposed to replace the homonym Cantharellus confluens (Schwein.) Schwein. 1834 a later synonym of Byssomerulius corium. Detailed macroscopic and microscopic descriptions accompanied with illustrations and a taxonomic discussion are presented for each species. [ABSTRACT FROM AUTHOR]

Palm oil is the most consumed vegetable oil globally, and Colombia is the largest palm oil producer in South America and fourth worldwide. However, oil palm plantations in Colombia are affected by bud rot disease caused by the oomycete Phytophthora palmivora, leading to significant economic losses. Infection processes by plant pathogens involve the secretion of effector molecules, which alter the functioning or structure of host cells. Current long-read sequencing technologies provide the information needed to produce high-quality genome assemblies, enabling a comprehensive annotation of effectors. Here, we describe the development of genomic resources for P. palmivora, including a high-quality genome assembly based on long and short-read sequencing data, intraspecies variability for 12 isolates from different oil palm cultivation regions in Colombia, and a catalog of over 1,000 candidate effector proteins. A total of 45,416 genes were annotated from the new genome assembled in 2,322 contigs adding to 165.5 Mbp, which represents an improvement of two times more gene models, 33 times better contiguity, and 11 times less fragmentation compared with currently available genomic resources for the species. Analysis of nucleotide evolution in paralogs suggests a recent whole-genome duplication event. Genetic differences were identified among isolates showing variable virulence levels. We expect that these novel genomic resources contribute to the characterization of the species and the understanding of the interaction of P. palmivora with oil palm and could be further exploited as tools for the development of effective strategies for disease control. [ABSTRACT FROM AUTHOR]

Background: Immune parameters (IP) have been extensively studied to distinguish between latent tuberculosis (LTBI) and active tuberculosis (TB).Objective: To determine the IP associated with LTBI, compared to active TB and individuals not infected by M. tuberculosis published in literature.Methods: We conducted a systematic search using Google Scholar and PubMed databases, combining the MeSH terms latent tuberculosis, Mycobacterium tuberculosis, cytokines, and biological markers, with the free terms, biomarkers and cytokines. Spanish, English, and Portuguese articles comparing the concentration of IP associated with LTBI, either in plasma/serum or in vitro, in adults and nonimmunocompromised versus individuals with TB or without M. tuberculosis infection between 2006 July and 2018 July were included. Two blinded reviewers carried out the searches, read the abstracts, and selected the articles for analysis. Participants' information, diagnostic criteria, IP, detection methods, and biases were collected.Results: We analyzed 36 articles (of 637 abstracts) with 93 different biomarkers in different samples. We found 24 parameters that were increased only in active TB (TGF-α, CSF3, CSF2, CCL1 [I-309], IL-7, TGF-β1, CCL3 [MIP-1α], sIL-2R, TNF-β, CCL7 [MCP-3], IFN-α, fractalkine, I-TAG, CCL8 [MCP-2], CCL21 [6Ckine], PDGF, IL-22, VEGF-A, LXA4, PGE2, PGF2α, sCD163, sCD14, and 15-Epi-LXA4), five were elevated in LTBI (IL-5, IL-17F, IL-1, CCL20 [MIP-3α], and ICAM-1), and two substances were increased among uninfected individuals (IL-23 and basic FGF). We found high heterogeneity between studies including failure to account for the time/illness of the individuals studied; varied samples and protocols; different clinical classification of TB; different laboratory methods for IP detection, which in turn leads to variable units of measurement and assay sensitivities; and selection bias regarding TST and booster effect. None of the studies adjusted the analysis for the effect of ethnicity.Conclusions: It is mandatory to harmonize the study of immune parameters for LTBI diagnosis. This systematic review is registered with PROSPERO CRD42017073289. [ABSTRACT FROM AUTHOR]