Miracle-dz/UniFAR-FTUs huggingface dataset:
In-House Packed Porous Graphitic Carbon Columns for Liquid Chromatography-Mass Spectrometry Analysis of N-Glycans

Protein glycosylation is a common post-translational modification that modulates biological processes such as the immune response and protein trafficking. Altered glycosylation profiles are associated with cancer and inflammatory diseases, as well as impacting the efficacy of therapeutic monoclonal antibodies. Consisting of oligosaccharides attached to asparagine residues, enzymatically released N-linked glycans are analytically challenging due to the diversity of isomeric structures that exist. A commonly used technique for quantitative N-glycan analysis is liquid chromatography-mass spectrometry (LC-MS), which performs glycan separation and characterization. Although many reversed and normal stationary phases have been utilized for the separation of N-glycans, porous graphitic carbon (PGC) chromatography has become desirable because of its higher resolving capability, but is difficult to implement in a robust and reproducible manner. Herein, we demonstrate the analytical properties of a 15 cm fused silica capillary (75 µm i.d., 360 µm o.d.) packed in-house with Hypercarb PGC (3 µm) coupled to an Agilent 6550 Q-TOF mass spectrometer for N-glycan analysis in positive ion mode. In repeatability and intermediate precision measurements conducted on released N-glycans from a glycoprotein standard mixture, the majority of N-glycans reported low coefficients of variation with respect to retention times (≤4.2%) and peak areas (≤14.4%). N-glycans released from complex samples were also examined by PGC LC-MS. A total of 120 N-glycan structural and compositional isomers were obtained from formalin-fixed paraffin-embedded ovarian cancer tissue sections. Finally, a comparison between early- and late-stage formalin-fixed paraffin-embedded ovarian cancer tissues revealed qualitative changes in the α2,3- and α2,6-sialic acid linkage of a fucosylated bi-antennary complex N-glycan. Although the α2,3-linkage was predominant in late-stage ovarian cancer, the alternate α2,6-linkage was more prevalent in early-stage ovarian cancer. This study establishes the utility of in-house packed PGC columns for the robust and reproducible LC-MS analysis of N-glycans.
Biofumigation With Pellets of Defatted Seed Meal of Brassica carinata: Factors Affecting Performance Against Phytophthora nicotianae in Pepper Crops

Phytophthora nicotianae is the pathogen that causes root and crown rot disease in open field paprika pepper crops of Extremadura (central-western Spain). A field experiment was established during spring, a period compatible with the pepper crop cycle in this region, to evaluate the effects of biofumigation with pellets of Brassica carinata defatted seed meal, at the rate recommended by the manufacturer (3 tons ha−1), on the survival and infectivity of P. nicotianae chlamydospores inoculum. Furthermore, three biofumigant rates (3, 6, and 20 tons ha−1) were assayed in laboratory experiments with natural soil inoculated with chlamydospores. In the field trial, the incorporation of pellets at 3 tons ha−1 did not produce remarkable changes in soil enzyme activity or soil properties. In both the field and laboratory tests, survival and infectivity in the biofumigated treatment at 3 tons ha−1 did not differ from those in the untreated control. On the contrary, the same rate added to autoclaved soil completely suppressed the inoculum, suggesting that the soil microbiota degrades B. carinata pellets before being effective against P. nicotianae. Increasing the recommended rate to 6 tons ha−1 decreased inoculum survival in the laboratory test and 20 tons ha−1 completely inhibited the inoculum, although the economic value of such a high rate application is a factor to be assessed. In phytotoxicity tests on radish and white mustard seeds with several concentrations (100, 50, 25, 10, 5, and 0%) of B. carinata pellets solution, no phytotoxic effect was observed with the two lowest concentrations, and no symptoms of phytotoxicity were found in the bioassays of pepper plants.
A habitat class to land cover translation model for mapping Area of Habitat of terrestrial vertebrates

Area of Habitat (AOH) is defined as the ‘habitat available to a species, that is, habitat within its range’ and is produced by subtracting areas of unsuitable land cover and elevation from the range. Habitat associations are documented using the IUCN Habitats Classification Scheme, and unvalidated expert opinion has been used so far to match habitat to land-cover classes generating a source of uncertainty in AOH maps. We develop a data-driven method to translate IUCN habitat classes to land-cover based on point locality data for 6,986 species of terrestrial mammals, birds, amphibians and reptiles. We extracted the land-cover class at each point locality and matched it to the IUCN habitat class(es) assigned to each species occurring there. Then we modelled each land cover class as a function of IUCN habitat using logistic regression models. The resulting odds ratios were used to assess the strength of the association of each habitat land-cover class. We then compared the performance of our data-driven model with those from a published expert knowledge translation table. The results show that some habitats (e.g. forest and desert) could be more confidently assigned to land-cover classes than others (e.g. wetlands and artificial). We calculated the association between habitat classes and land-cover classes as a continuous variable, but to map AOH, which is in the form of a binary presence/absence, it is necessary to apply a threshold of association. This can be chosen by the user according to the required balance between omission and commission errors. We demonstrate that a data-driven translation model and expert knowledge perform equally well, but the model provides greater standardization, objectivity and repeatability. Furthermore, this approach allows greater flexibility in the use of the results and allows uncertainty to be quantified. Our model can be developed regionally or for different taxonomic groups.
Regulation of brain aging by neutral sphingomyelinase 2

We have shown that deficiency of neutral sphingomyelinase 2 (nSMase2), an enzyme generating the sphingolipid ceramide, improves memory in adult mice. Here, we performed sphingolipid and RNA-seq analyses on the cortex from 10 month-old nSMase2-deficient (fro/fro) and heterozygous (+/fro) mice. fro/fro cortex showed reduced levels of ceramide, particularly in astrocytes. Differentially abundant transcripts included several functionally related groups, with decreases in mitochondrial oxidative phosphorylation and astrocyte activation transcripts, while axon guidance and synaptic transmission transcripts were increased, indicating a role of nSMase2 in oxidative stress, astrocyte activation, and cognition. Experimentally induced oxidative stress decreased the level of glutathione (GSH), an endogenous inhibitor of nSMase2, and increased immunolabeling for ceramide in primary +/fro astrocytes, but not in fro/fro astrocytes. β-galactosidase activity was lower in 5-weeks old fro/fro astrocytes, indicating delayed senescence due to nSMase2 deficiency. In fro/fro cortex, levels of the senescence markers C3b and p27, and the proinflammatory cytokines interleukin 1β, interleukin 6, and tumor necrosis factor α were reduced, concurrent with 2-fold decreased phosphorylation of their downstream target, protein kinase Stat3. RNA and protein levels of the ionotropic glutamate receptor subunit 2b (Grin2b or NR2B) were increased by 2-fold, an effect known to enhance cognition. This was consistent with 3.5-fold reduced levels of exosomes carrying miR-223-3p, a micro-RNA downregulating Grin2b. In summary, our data show that nSMase2 deficiency prevents oxidative stress-induced elevation of ceramide and secretion of exosomes by astrocytes that suppress neuronal function, indicating a role of nSMase2 in the regulation of neuroinflammation and cognition during brain aging. Significance statement Oxidative stress is associated with brain aging and cognitive decline. The underlying mechanism how oxidative stress impairs brain function is still not clear. We provide evidence that oxidative stress increases ceramide in astrocytes, which is prevented by deficiency of nSMase2, an enzyme that is activated by oxidative stress and generates ceramide from sphingomyelin. Mass spectrometric and transciptomic (RNA-seq) analyses show that in middle aged (10-month old) mouse cortex, nSMase2 deficiency reduces ceramide and increases expression of genes important for synaptic transmission and cognition. Therefore, our data show that oxidative stress-induced activation of nSMase2 and generation of ceramide is significant for cognitive decline during aging.
Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors

MADS-box transcription factors (TFs) are present in nearly all major eukaryotic groups. They are divided into Type I and Type II that differ in domain structure, functional roles, and rates of evolution. In flowering plants, major evolutionary innovations like flowers, ovules and fruits have been closely connected to Type II MADS-box TFs. The role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Here, we show that the formation of angiosperm-specific Type I MADS-box clades of Mγ and Mγ-interacting Mα genes (Mα*) can be tracked back to the ancestor of all angiosperms. Angiosperm-specific Mγ and Mα* genes were preferentially expressed in the endosperm, consistent with their proposed function as heterodimers in the angiosperm-specific embryo-nourishing endosperm tissue. We propose that duplication and diversification of Type I MADS-genes underpins the evolution of the endosperm, a developmental innovation closely connected to the origin and success of angiosperms.
Intrinsic and tumor-induced JAK/STAT signaling regulate developmental timing by the Drosophila prothoracic gland

Development involves tightly paced, reproducible sequences of events, yet it must adjust to conditions external to it, such as resource availability and organismal damage. A major mediator of damage-induced immune responses in vertebrates and insects is JAK/STAT signaling. At the same time, JAK/STAT activation by the Drosophila Upd cytokines is pleiotropically involved in normal development of multiple organs. Whether inflammatory and developmental roles of JAK/STAT intersect is unknown. Here, we show that JAK/STAT is active during development of the prothoracic gland (PG), the organ that controls metamorphosis onset through ecdysone production. Reducing JAK/STAT signaling decreased PG size and slightly advanced metamorphosis. Conversely, JAK/STAT hyperactivation, achieved through overexpression of pathway components or SUMOylation loss, caused PG hypertrophy and metamorphosis delay. Interestingly, tissue damage and tumors, known to secrete Upd cytokines, also activated JAK/STAT in the PG and delayed metamorphosis. Finally, we show that expression of transcription factor Apontic, a JAK/STAT target in the PG, recapitulates PG hypertrophy and metamorphosis delay. JAK/STAT damage signaling, therefore, regulates metamorphosis onset at least in part by coopting its developmental role in the PG. Summary statement Damage signaling from tumors mediated by JAK/STAT-activating Upd cytokines delays the Drosophila larva-pupa transition through cooption of a JAK/STAT developmental role in the prothoracic gland.
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival

Genetic alterations in cancer cells trigger oncogenic transformation, a process largely mediated by the dysregulation of kinase and transcription factor (TF) activities. While the mutational profiles of thousands of tumours has been extensively characterized, the measurements of protein activities has been technically limited until recently. We compiled public data of matched genomics and (phospho)proteomics measurements for 1,110 tumours and 77 cell lines that we used to estimate activity changes in 218 kinases and 292 TFs. Kinase activities are, on average, not strongly determined by protein abundance but rather by their phosphorylation state while the reverse is more common for TFs. Co-regulation of kinase and TF activities reflects previously known regulatory relationships and allows us to dissect genetic drivers of signalling changes in cancer. Loss-of-function mutation is not often associated with dysregulation of downstream targets, suggesting frequent compensatory mechanisms. Finally, we identified the activities most differentially regulated in cancer subtypes and showed how these can be linked to differences in patient survival. Our results provide broad insights into dysregulation of protein activities in cancer and their contribution to disease severity.
An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms

The breadth of animal hosts that are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and may serve as reservoirs for continued viral transmission are not known entirely. In August 2020, an outbreak of SARS-CoV-2 occurred in multiple mink farms in Utah and was associated with high mink mortality and rapid viral transmission between animals. The outbreak’s epidemiology, pathology, molecular characterization, and tissue distribution of virus within infected mink is provided. Infection of mink was likely by reverse zoonosis. Once established, infection spread rapidly between independently housed animals and farms, and caused severe respiratory disease and death. Clinical signs were most notably sudden death, anorexia, and increased respiratory effort. Gross pathology examination revealed severe pulmonary congestion and edema. Microscopically there was pulmonary edema with moderate vasculitis, perivasculitis, and fibrinous interstitial pneumonia. Reverse transcriptase polymerase chain reaction (RT-PCR) of tissues collected at necropsy demonstrated the presence of SARS-CoV-2 viral RNA in multiple organs including nasal turbinates, lung, tracheobronchial lymph node, epithelial surfaces, and others. Whole genome sequencing from multiple mink was consistent with published SARS-CoV-2 genomes with few polymorphisms. The Utah mink SARS-CoV-2 strain fell into Clade GH, which is unique among mink and other animal strains sequenced to date and did not share other spike RBD mutations Y453F and F486L found in mink. Localization of viral RNA by in situ hybridization revealed a more localized infection, particularly of the upper respiratory tract. Mink in the outbreak reported herein had high levels of virus in the upper respiratory tract associated with mink-to-mink transmission in a confined housing environment and were particularly susceptible to disease and death due to SARS-CoV-2 infection. Author Summary The recent emergence and worldwide spread of the novel coronavirus has resulted in worldwide disease and economic hardship. The virus, known as SARS-CoV-2 is believed to have originated in bats and has spread worldwide through human-to-human virus transmission. It remains unclear which animal species, other than humans, may also be susceptible to viral infection and could naturally transmit the virus to susceptible hosts. In this study, we describe an outbreak of disease and death due to SARS-CoV-2 infection in farmed mink in Utah, United States. The investigation reveals that mink can spread the virus rapidly between animals and that the disease in mink is due to the viral infection and damage to tissues of the upper and lower respiratory system. The determination that mink are susceptible to SARS-CoV-2 indicates the need for strict biosecurity measures on mink farms to remediate mink-to-mink and human-to-mink transmission for the protection of mink, as well as prevent potential transmission from mink to humans.
TrackSOM: mapping immune response dynamics through sequential clustering of time- and disease-course single-cell cytometry data

Mapping the dynamics of immune cell populations over time or disease-course is key to understanding immunopathogenesis and devising putative interventions. We present TrackSOM, an algorithm which delineates cellular populations and tracks their development over a time- or disease-course of cytometry datasets. We demonstrate TrackSOM-enabled elucidation of the immune response to West Nile Virus infection in mice, uncovering heterogeneous sub-populations of immune cells and relating their functional evolution to disease severity. TrackSOM is easy to use, encompasses few parameters, is quick to execute, and enables an integrative and dynamic overview of the immune system kinetics that underlie disease progression and/or resolution.
Allele-Specific Gene Editing Rescues Pathology in a Human Model of Charcot-Marie-Tooth Disease Type 2E

Many neuromuscular disorders are caused by dominant missense mutations that lead to dominant-negative or gain-of-function pathology. This category of disease is challenging to address via drug treatment or gene augmentation therapy because these strategies may not eliminate the effects of the mutant protein or RNA. Thus, effective treatments are severely lacking for these dominant diseases, which often cause severe disability or death. The targeted inactivation of dominant disease alleles by gene editing is a promising approach with the potential to completely remove the cause of pathology with a single treatment. Here, we demonstrate that allele-specific CRISPR gene editing in a human model of axonal Charcot-Marie-Tooth (CMT) disease rescues pathology caused by a dominant missense mutation in the neurofilament light chain gene (NEFL, CMT type 2E). We utilized a rapid and efficient method for generating spinal motor neurons from human induced pluripotent stem cells (iPSCs) derived from a patient with CMT2E. Diseased motor neurons recapitulated known pathologic phenotypes at early time points of differentiation, including aberrant accumulation of neurofilament light chain protein in neuronal cell bodies. We selectively inactivated the disease NEFL allele in patient iPSCs using Cas9 enzymes to introduce a frameshift at the pathogenic N98S mutation. Motor neurons carrying this allele-specific frameshift demonstrated an amelioration of the disease phenotype comparable to that seen in an isogenic control with precise correction of the mutation. Our results validate allele-specific gene editing as a therapeutic approach for CMT2E and as a promising strategy to silence dominant mutations in any gene for which heterozygous loss-of-function is well tolerated. This highlights the potential for gene editing as a therapy for currently untreatable dominant neurologic diseases.
Hepatocyte androgen receptor in females mediates androgen-induced hepatocellular glucose mishandling and systemic insulin resistance

Androgen excess is one of the most common endocrine disorders of reproductive-aged women, affecting up to 20% of this population. Women with elevated androgens often exhibit hyperinsulinemia and insulin resistance. The mechanisms of how elevated androgens affect metabolic function are not clear. Hyperandrogenemia in a dihydrotestosterone (DHT)-treated female mouse model induces whole body insulin resistance possibly through activation of the hepatic androgen receptor (AR). We investigated the role of hepatocyte AR in hyperandrogenemia-induced metabolic dysfunction by using several approaches to delete hepatic AR via animal-, cell-, and clinical-based methodologies. We conditionally disrupted hepatocyte AR in female mice developmentally (LivARKO) or acutely by tail vein injection of an adeno-associated virus with a liver-specific promoter for Cre expression in ARfl/fl mice (adLivARKO). We observed normal metabolic function in littermate female Control (ARfl/fl) and LivARKO (ARfl/fl; Cre+/-) mice. Following chronic DHT treatment, female Control mice treated with DHT (Con-DHT) developed impaired glucose tolerance, pyruvate tolerance, and insulin tolerance, not observed in LivARKO mice treated with DHT (LivARKO-DHT). Further, during an euglycemic hyperinsulinemic clamp, the glucose infusion rate was improved in LivARKO-DHT mice compared to Con-DHT mice. Liver from LivARKO, and primary hepatocytes derived from LivARKO, and adLivARKO mice were protected from DHT-induced insulin resistance and increased gluconeogenesis. These data support a paradigm in which elevated androgens in females disrupt metabolic function via hepatic AR and insulin sensitivity was restored by deletion of hepatic AR.
TaxoNERD: deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature

Given the biodiversity crisis, we more than ever need to access information on multiple taxa (e.g. distribution, traits, diet) in the scientific literature to understand, map and predict all-inclusive biodiversity. Tools are needed to automatically extract useful information from the ever-growing corpus of ecological texts and feed this information to open data repositories. A prerequisite is the ability to recognise mentions of taxa in text, a special case of named entity recognition (NER). In recent years, deep learning-based NER systems have become ubiquitous, yielding state-of-the-art results in the general and biomedical domains. However, no such tool is available to ecologists wishing to extract information from the biodiversity literature. We propose a new tool called TaxoNERD that provides two deep neural network (DNN) models to recognise taxon mentions in ecological documents. To achieve high performance, DNN-based NER models usually need to be trained on a large corpus of manually annotated text. Creating such a gold standard corpus (GSC) is a laborious and costly process, with the result that GSCs in the ecological domain tend to be too small to learn an accurate DNN model from scratch. To address this issue, we leverage existing DNN models pretrained on large biomedical corpora using transfer learning. The performance of our models is evaluated on four GSCs and compared to the most popular taxonomic NER tools. Our experiments suggest that existing taxonomic NER tools are not suited to the extraction of ecological information from text as they performed poorly on ecologically-oriented corpora, either because they do not take account of the variability of taxon naming practices, or because they do not generalise well to the ecological domain. Conversely, a domain-specific DNN-based tool like TaxoNERD outperformed the other approaches on an ecological information extraction task. Efforts are needed in order to raise ecological information extraction to the same level of performance as its biomedical counterpart. One promising direction is to leverage the huge corpus of unlabelled ecological texts to learn a language representation model that could benefit downstream tasks. These efforts could be highly beneficial to ecologists on the long term.