Miracle-dz/UniFAR-FTUs huggingface dataset:
Nivalenol-producing Fusarium cerealis associated with fusarium head blight in winter wheat in Manitoba, Canada.

Fusarium head blight (FHB) in small grain cereals is primarily caused by the members of the Fusarium graminearum species complex. These produce mycotoxins in infected grains, primarily deoxynivalenol (DON); acetylated derivatives of DON, 3-acetyl-DON (3-ADON) and 15-acetyl-DON (15-ADON); and nivalenol (NIV). This study reports the isolation of Fusarium cerealis in infected winter wheat heads for the first time in Canada. A phylogenetic analysis based on the TRI101 gene and F. graminearum species-specific primers revealed two species of Fusarium: F. graminearum sensu stricto (127 isolates) and F. cerealis (five isolates). Chemotype determination based on the TRI3 gene revealed that 65% of the isolates were 3-ADON, 31% were 15-ADON and 4% were NIV producers. All the F. cerealis isolates were of NIV chemotype. Fusarium cerealis isolates can often be misidentified as F. graminearum as the morphological characteristics are similar. Although the cultural and macroconidial characteristics of F. graminearum and F. cerealis isolates were similar, the aggressiveness of these isolates on susceptible wheat cultivar Roblin and moderately resistant cultivar Carberry differed significantly. The F. graminearum 3-ADON isolates were most aggressive, followed by F. graminearum 15-ADON and F. cerealis NIV isolates. The findings from this study confirm the continuous shift of chemotypes from 15-ADON to 3-ADON in North America. In Canada, the presence of NIV is limited to barley samples and the discovery of NIV-producing F. cerealis species in Canadian wheat fields may pose a serious concern to the Canadian wheat industry in the future.
Yuchengia, a new polypore genus segregated from Perenniporia (Polyporales) based on morphological and molecular evidence

Yuchengia gen. nov. is proposed to accommodate Perenniporia narymica. It represents a monophyletic lineage within the core polyporoid clade based on sequences of the rDNA ITS and nLSU regions, and it is distinct from Perenniporia s.s. Yuchengia shares some characters with Perenniporia, both having thick-walled and cyanophilous basidiospores, but differs by having acyanophilous and amyloid skeletal hyphae dissolving in KOH, and non-dextrinoid basidiospores.
Quorum Sensing within the Gut Ecosystem

The successful modulation of phenotype is essential for the colonisation and proliferation of bacteria within the complex ecosystem of the gastrointestinal tract. To accomplish this, bacteria obtain and respond to information from the environment. One important parameter is the other bacteria present. The ability to correctly sense self, and also others, must therefore be advantageous for the control of mass action processes by the bacterial population. Within the gut ecosystem that may include processes involved in colonisation including those determining biofilm formation, pathogenicity, dispersal and DNA transfer. The ability to sense other bacteria may have important consequences for competitive and nutritional strategies controlling for example, entry into stationary phase, dispersal and the production of antimicrobial compounds. The ability to interfere with the signalling of bacteria will determine the fitness of the given organism to survive in the gut and may also have therapeutic potential. Keywords: quorum sensing, colonisation, pathogenicity, gene transfer, dissemination.
Description of two new species of diplogastrid nematodes (Rhabditida: Diplogastridae) from Iran

espanolSe describen e ilustran dos nuevas especies de nematodos diplogastridos a partir de rasgos morfologicos, morfometricos, MEE y moleculares. Mononchoides iranicus sp. n. se caracteriza por su longitud corporal, el numero de crestas longitudinales (42 en la hembra y 34 en el macho), la forma y el tamano del estoma, la posicion anterior de la vulva, la forma del gubemaculo y la disposicion de las papilas genitales en el macho. Es muy similar a M. adjunctus, M. americanus, M. andrassyi, M. aphodii, M. bicornis, M. filicaudatus, M. longicaudatus, M. megaonchus M. parastriatus, M. splendidus, M. subamericanus y M. trichuris. Koerneria ruehmi sp. n. se distingue por la posicion de la vulva, la forma de embudo que presenta el gubemaculo, la disposicion de las papilas ventrales en el macho y la presencia de una pequena solapa en la bursa. Es filogeneticamente muy proxima al 'aislado japones de K. luziae', y ambas formas constituyen un pequeno clado basal proximo al resto de la familia. Se discuten las diferencias morfologicas y la relaciones filogeneticas de las dos nuevas especies con otros taxones diplogastridos. EnglishTwo new species of diplogastrid nematodes are described and illustrated based upon morphological, morphometric, SEM and molecular characters. Mononchoides iranicus sp. n. is characterized by its body length, number of longitudinal ridges (42 in female and 34 in male), shape and size of the stoma, anteriorly located vulva, shape of gubemaculum and arrangement of genital papillae in males. It is similar to M. adjunctus, M. americanus, M. andrassyi, M. aphodii, M. bicornis, M. filicaudatus, M. longicaudatus, M. megaonchus, M. parastriatus, M. splendidus, M. subamericanus and M. trichuris. Koerneria ruehmi sp. n. is distinguishable by its vulva position, funnel-shaped gubemaculum, arrangement of male ventral papillae and presence of small bursal flap. The new species is phylogenetically close to the 'Japanese isolate of K. luziae', and these two species form a small basal clade relative to the rest of the family. The morphological differences and the phylogenetic relations of both new species with other diplogastrid taxa are discussed.
Application of network analysis and cluster analysis for better prevention and control of swine diseases in Argentina

Rationale/background Though much smaller than the bovine industry, the porcine sector in Argentina involves a large number of farms and represents a significant economic sector. In recent years Argentina has implemented a national registry of swine movements amongst other measures, in an effort to control and eventually eradicate endemic Aujesky’s disease. Such information can prove valuable in assessing the risk of transmission between farms for endemic diseases but also for other diseases at risk of emergence. Methods Shipment data from 2011 to 2016 were analyzed in an effort to define strategic locations and times at which control and surveillance efforts should be focused to provide cost-effective interventions. Social network analysis (SNA) was used to characterize the network as a whole and at the individual farm and market level to help identify important nodes. Spatio-temporal trends of pig movements were also analyzed. Finally, in an attempt to classify farms and markets in different groups based on their SNA metrics, we used factor analysis for mixed data (FAMD) and hierarchical clustering. Results The network involved approximate 136,000 shipments for a total of 6 million pigs. Over 350 markets and 17,800 production units participated in shipments with another 83,500 not participating. Temporal data of shipments and network metrics showed peaks in shipments in September and October. Most shipments where within provinces, with Buenos Aires, Cordoba and Santa Fe concentrating 61% of shipments. Network analysis showed that markets are involved in relatively few shipments but hold strategic positions with much higher betweenness compared to farms. Hierarchical clustering yielded four groups based on SNA metrics and node characteristics which can be broadly described as: 1. small and backyard farms; 2. industrial farms; 3. markets; and 4. a single outlying market with extreme centrality values. Conclusion Characterizing the network structure and spatio-temporal characteristics of Argentine swine shipments provides valuable information that can guide targeted and more cost-effective surveillance and control programs. We located key nodes where efforts should be prioritized. Pig network characteristics and patterns can be used to create dynamic disease transmission models, which can both be used in assessing the impact of emerging diseases and guiding efforts to eradicate endemic ones.
Autophagy Functions to Prevent Methylglyoxal-Induced Apoptosis in HK-2 Cells

Methylglyoxal (MGO), a reactive carbonyl species, causes cellular damage and is closely related to kidney disease, particularly diabetic nephropathy. Although MGO has been reported to induce autophagy and apoptosis, the relationships between the two pathways are unclear. Here, we evaluated whether autophagy may be the underlying mechanism inhibiting MGO-induced apoptosis. MGO treatment induced concentration- and time-dependent apoptosis in HK-2 cells. Moreover, MGO upregulated the autophagy markers p62 and LC3-II. Apoptosis caused by MGO was increased in ATG5-knockdown cells compared to that in wild-type cells. In contrast, autophagy activation by 5-aminoimidazole-4-carboxamide ribonucleotide resulted in reduced apoptosis, suggesting that autophagy played a role in protecting against MGO-induced cell death. To examine the mechanisms through which autophagy occurred following MGO stimulation, we investigated changes in AKT/mammalian target of rapamycin (mTOR) signaling. Autophagy induction by MGO treatment was not related to AKT/mTOR signaling; however, it did involve autophagy-related gene expression promoted by AMP-activated protein kinase-mediated transcription factors, such as forkhead box 1. Overall, our findings indicate that MGO-induced cellular damage can be mitigated by autophagy, suggesting that autophagy may be a potential therapeutic target for diseases such as diabetic nephropathy.
Mitochondrial Control Region DNA Variation in Turbot Populations from the Bulgarian and Romanian Black Sea Coasts

ABSTRACT The mitochondrial control region/CR/of 76 turbot specimens collected from the south and north Bulgarian and north Romanian regions of the west Black Sea coastal area was characterized. A total of 36 haplotypes were identified. Twenty-seven of these haplotypes were new and nine haplotypes were identical to previously reported Pmax haplotypes. The constructed haplotype parsimony network showed star-like phylogeny of the identified haplotypes, supporting the suggested Black Sea fish population bottleneck during the height of the last glacial period. The analysis of the haplotype sequences data did not provide clear indications on the existence of phylogeographic differentiation among the studied turbot populations inhabiting the west coast of the Black Sea. At the same time the haplotype phylogenetic analysis provided further support to the earlier proposed existence of two distinct turbot mitochondrial lineages, ‘western Mediterranean ‘and’ eastern secluded Mediterranean basins’. The present study offers an essential background for long term monitoring of the changes of the Black Sea turbot populations.
Postrepression Activation of NF-κB Requires the Amino-Terminal Nuclear Export Signal Specific to IκBα

ABSTRACT One of the most prominent NF-κB target genes in mammalian cells is the gene encoding one of its inhibitor proteins, IκBα. The increased synthesis of IκBα leads to postinduction repression of nuclear NF-κB activity. However, it is unknown why IκBα, among multiple IκB family members, is involved in this process and what significance this feedback regulation has beyond terminating NF-κB activity. Herein, we report an important IκBα-specific function dictated by its amino-terminal nuclear export sequence (N-NES). The IκBα N-NES is necessary for the postinduction export of nuclear NF-κB, which is a critical event in reestablishing a permissive condition for NF-κB to be rapidly reactivated. We show that although IκBα and another IκB member, IκBβ, can enter the nucleus and repress NF-κB DNA-binding activity during the postinduction phase, only IκBα allows the efficient export of nuclear NF-κB. Moreover, swapping the N-terminal region of IκBβ for the corresponding IκBα sequence is sufficient for the IκB chimera protein to export NF-κB similarly to IκBα during the postinduction state. Our findings provide a mechanistic explanation of why IκBα but not other IκB members is crucial for postrepression activation of NF-κB. We propose that this IκBα-specific function is important for certain physiological and pathological conditions where NF-κB needs to be rapidly reactivated.
The CNS-specific proteoglycan, brevican, and its ADAMTS4-cleaved fragment show differential serological levels in Alzheimer’s disease, other types of dementia and non-demented controls: A cross-sectional study

Evidence indicate that the brain-specific protein, brevican, is proteolytically cleaved during neurodegeneration, hence positioning fragments of brevican as potential blood biomarkers of neurodegenerative diseases, such as dementia. We aimed to develop two assays capable of detecting the brevican N-terminal (N-Brev) and the ADAMTS4-generated fragment (Brev-A), cleaved at Ser401, in serum and to perform a preliminary assessment of their diagnostic potential in dementias. Monoclonal antibodies against N-Brev and Brev-A were used to develop two ELISAs detecting each epitope. A comparison of brevican fragments in serum from individuals with AD (n = 28), other dementia (OD) (n = 41), and non-dementia-related memory complaints (NDCs) (n = 48) was conducted. Anti-N-Brev and anti-Brev-A antibodies selectively recognized their targets and dilution and spike recoveries were within limits of ±20%. Intra- and inter-assay CVs were below limits of 10% and 15%, respectively. For the N-Brev biomarker, serum from patients with OD showed significantly lower levels than those with AD (p = 0.05) and NDCs (p < 0.01). The opposite pattern was evident for Brev-A: serum levels in patients with OD were significantly higher than for AD (p = 0.04) and NDCs (p = 0.01). For both N-Brev and Brev-A, levels did not differ between AD and NDCs. The ratio of N-Brev/Brev-A resulted in increased significant differences between OD and AD (p < 0.01) and between OD and NDCs (p < 0.0001). The ratio discriminated between NDCs and OD (AUC: 0.75, 95% CI: 0.65–0.85, p < 0.0001) and between OD and AD (AUC: 0.72, 95% CI: 0.59–0.85, p < 0.01). In conclusion, we developed the first assays detecting the N-terminal of brevican as well as an ADAMTS4-cleaved fragment of brevican in blood. Differential levels of N-Brev and Brev-A between AD and OD allow for these biomarkers to possibly distinguish between different forms of dementias.
Distribution of the 21-Gene Breast Recurrence Score in Patients with Primary Breast Cancer in Germany

Background Multigene assays are being used increasingly to aid in decision-making about chemotherapy in breast cancer. Here, we present the 21-gene recurrence score (RS) of patients tested in routine clinical practice in Germany. Patients and Methods In a retrospective analysis, 4695 patients with hormone receptor-positive and HER2-negative early breast cancer (pT1 – 3, pN0 – 1, M0) were included in whom RS testing was conducted in Germany between November 2015 and July 2018. RS groups as defined in the TAILORx trial (RS result 0 – 10; 11 – 25; 26 – 100) were used. Results Of these patients, 21% were assigned to the low RS group, 63% to the midrange RS group, and 15% to the high RS group. 1772 (81%) of 2175 node-negative patients over 50 years of age were grouped either into the low RS group or the midrange RS group. The portion of patients with a low or midrange RS was 90% among node-positive patients (1284 of 1432 patients), 79% among patients with Ki-67-high (≥ 20%) tumors (1829 of 2310 patients), 86% vs. 70% among patients with G2 and G3 tumors (3244 of 3762 patients and 368 of 522 patients), respectively, 88% among patients with a tumor size of > 5 cm (140 of 159 patients), and 82% among node-negative patients at high clinical risk (1110 of 1352). Conclusions The distribution of the 21-gene RS in German patients that were tested in routine clinical practice indicates that, according to the results of the TAILORx trial, chemotherapy may not be beneficial in most of these.
The role of ROC75 as a daytime component of the circadian oscillator in Chlamydomonas reinhardtii

The circadian clocks in chlorophyte algae have been studied in two model organisms, Chlamydomonas reinhardtii and Ostreococcus tauri. These studies revealed that the chlorophyte clocks include some genes that are homologous to those of the angiosperm circadian clock. However, the genetic network architectures of the chlorophyte clocks are largely unknown, especially in C. reinhardtii. In this study, using C. reinhardtii as a model, we characterized RHYTHM OF CHLOROPLAST (ROC) 75, a clock gene encoding a putative GARP DNA-binding transcription factor similar to the clock proteins LUX ARRHYTHMO (LUX, also called PHYTOCLOCK 1 [PCL1]) and BROTHER OF LUX ARRHYTHMO (BOA, also called NOX) of the angiosperm Arabidopsis thaliana. We observed that ROC75 is a day/subjective day-phase-expressed nuclear-localized protein that associates with some night-phased clock genes and represses their expression. This repression may be essential for the gating of reaccumulation of the other clock-related GARP protein, ROC15, after its light-dependent degradation. The restoration of ROC75 function in an arrhythmic roc75 mutant under constant darkness leads to the resumption of circadian oscillation from the subjective dawn, suggesting that the ROC75 restoration acts as a morning cue for the C. reinhardtii clock. Our study reveals a part of the genetic network of C. reinhardtii clock that could be considerably different from that of A. thaliana.
Phylogenetic Relationships of the Perianthless Piperales: Reconstructing the Evolution of Floral Development

The perianthless members of the Piperales are unique among the basal lineages of angiosperms because they are mainly herbaceous plants with over 2000 species possessing highly reduced flowers. There have been several attempts to address the evolution of the flower morphology in the group, but no previous study has included a DNA‐based estimate of phylogeny. Here we present a robust reconstruction of the phylogenetic relationships of the genera in the perianthless Piperales using DNA sequence data from three genes (rbcL, atpB, and 18S) and two genomes (nuclear and chloroplast). We estimated the likelihood values of ancestral character states of mature floral structures. Developmental sequences also were analyzed using step matrices under specific models of character state change to examine the origin of meristic differences of the androecium and gynoecium. Developmental lability is the general theme in the evolution of floral merosity in the perianthless Piperales, with different developmental processes giving rise to morphologically identical mature stages. Our findings confirm this notion based on several distinct patterns: (1) nonidentical ontogenies give rise to homoplasious, six‐staminate androecia of Saururaceae and some Piperaceae most likely through terminal addition; (2) identical ontogenies produce the homoplasious two‐staminate flowers in Peperomia and Piper umbellatum through deletion; and (3) nearly identical ontogenies produce homplasious tricarpellate gynoecia of Piper and \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$Anemopsis+Houttuynia$$ \end{document} clade, and the apocarpous gynoecium of Saururus may be secondarily derived, both end products occurring through deletion. We note that changes in organ number and the degree of carpel fusion have been important during the evolutionary history of the perianthless Piperales as well as the basal angiosperms in general and should be studied more extensively. Overall we emphasize the lability of developmental pathways, especially in the flower, and endorse the methodological utility of developmental sequences for directing future investigations of floral evolution.
Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure–Activity Relationship Studies

The novel coronavirus, SARS-CoV-2, has caused a recent pandemic called COVID-19 and a severe health threat around the world. In the current situation, the virus is rapidly spreading worldwide, and the discovery of a vaccine and potential therapeutics are critically essential. The crystal structure for the main protease (Mpro) of SARS-CoV-2, 3-chymotrypsin-like cysteine protease (3CLpro), was recently made available and is considerably similar to the previously reported SARS-CoV. Due to its essentiality in viral replication, it represents a potential drug target. Herein, a computer-aided drug design (CADD) approach was implemented for the initial screening of 13 approved antiviral drugs. Molecular docking of 13 antivirals against the 3-chymotrypsin-like cysteine protease (3CLpro) enzyme was accomplished, and indinavir was described as a lead drug with a docking score of −8.824 and a XP Gscore of −9.466 kcal/mol. Indinavir possesses an important pharmacophore, hydroxyethylamine (HEA), and thus, a new library of HEA compounds (>2500) was subjected to virtual screening that led to 25 hits with a docking score more than indinavir. Exclusively, compound 16 with a docking score of −8.955 adhered to drug-like parameters, and the structure–activity relationship (SAR) analysis was demonstrated to highlight the importance of chemical scaffolds therein. Molecular dynamics (MD) simulation analysis performed at 100 ns supported the stability of 16 within the binding pocket. Largely, our results supported that this novel compound 16 binds with domains I and II, and the domain II–III linker of the 3CLpro protein, suggesting its suitability as a strong candidate for therapeutic discovery against COVID-19.
HIGH PREVALENCE OF ENAMEL HYPOPLASIA IN AN EARLY PLIOCENE GIRAFFID (SIVATHERIUM HENDEYI) FROM SOUTH AFRICA

Abstract Almost two thousand mandibular teeth of the short-necked giraffid, Sivatherium hendeyi, from Langebaanweg, South Africa, were examined for dental pathologies. Enamel hypoplasia is present in 0 to 34 percent of deciduous teeth and 40 to 75 percent of permanent teeth. No linear enamel hypoplasias were found in the deciduous teeth, while 20 to 35 percent of the permanent teeth have this defect. The linear defects at the base of the first molar are thought to relate to stress associated with weaning. The defects in the later erupting permanent teeth are, however, widely distributed over tooth crowns. Several linear defects are present on some teeth suggesting that these stress episodes were periodic. We propose that poor environmental conditions, possibly seasonal nutritional stress, are responsible for the observed enamel hypoplasia in the permanent dentition of S. hendeyi. This study provides new insight into the current understanding of the paleoenvironment at Langebaanweg, South Africa.