bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial “galactosemia” is caused by cytoplasmic interference of an essential cell wall biosynthesis glycosyltransferase
Authors: Habib Cameron , Mueller Anna , Liu Ming , Zhu Jun , Schneider Tanja , Garner Ethan , Sun Yingjie , Chai Yunrong
Published: January 2021

Bacterial galactosemia or “galactose death,” triggered by incomplete galactose metabolism, was first discovered inEscherichia coliandSalmonellasix decades ago, and later in many other microorganisms, yet the mechanism for the toxicity and subsequent cell death remains unclear. InBacillus subtilis,galactosemia is manifested by a buildup of uridine-diphosphate-galactose (UDP-Gal) and a strong toxicity phenotype characterized by cell shape abnormality and rapid cell lysis. Here we present evidence that inB. subtilis,the toxicity is due to inhibition of cell wall biosynthesis through interference of the essential glycosyltransferase MurG that carries out lipid II synthesis from lipid I and uridine-diphosphate-N-acetyl-glucosamine (UDP-GlcNAc). Single-molecule imaging reveals real-time inhibition of cell wall biosynthesis and MurG activities in cells exhibiting toxicity. We further show thatin vitro, MurG is able to utilize UDP-Gal as a substrate generating a “toxic” lipid II, causing a potential poisoning effect on peptidoglycan crosslinking. Evidence also suggests a similar mechanism inVibrio choleraeandStaphylococcus aureus. Lastly, a strong synergistic lethality was seen inS. aureuswild-type cells treated with both galactose and sub-lethal doses of cell-wall antibiotics. Our study provides mechanistic explanation of the toxicity associated with bacterial galactosemia and its potential application in antibacterial solutions.

Significance

Galactosemia is a potentially fatal genetic disorder due to incomplete galactose metabolism, found in both eukaryotic and prokaryotic organisms. The molecular mechanisms of galactosemia-associated toxicity remain unclear in all cases. Here we present evidence that in the bacteriumBacillus subtilis, the toxicity is due to interference of an essential glycosyltransferase, MurG, which concerts lipid I to lipid II during peptidoglycan biosynthesis, by a nucleotide sugar derived from galactose metabolism. This interference leads to a halt of cell wall biosynthesis and structural defects causing rapid cell lysis. Our evidence also suggests a similar mechanism in other bacteria such asStaphylococcus aureusandVibrio cholerae.Our study may help solve the long-time puzzle of bacterial galactosemia first uncovered six decades ago.
Modeling post-logging height growth of black spruce forests by combining airborne LiDAR and historical forestry maps in eastern Canadian boreal forest
Authors: Bour Batistin , Danneyrolles Victor , Boucher Yan , Fournier Richard A. , Guindon Luc
Published: January 2021

Increase in forest disturbance due to land use as well as climate change has led to an expansion of young forests worldwide, which affects global carbon dynamics and forest management. In this study, we present a novel method that combines a single airborne LiDAR acquisition and historical harvesting maps to model height growth of post-logged black spruce-dominated forests in a 1700 km2eastern Canadian boreal landscape. We developed a random forest model where forest height is a function of stand age, combined with environmental variables. Our results highlight the strong predictive power of this model: least-square regression between predicted and observed height of our validation dataset was very close to the 1:1 relation and strongly supported by validation metrics (R2= 0.75; relative RMSE = 19%). Moreover, our findings indicated an ecological gradient responsible for differences in height growth at the landscape scale, with better growth rates on mesic slopes compared to badly drained soils on flat lands. With the increased availability of LiDAR data, this method is promising since it can be applied to forests across the globe that are affected by stand-replacing disturbances.
Direct imaging of anthrax intoxication in animals reveals shared and individual functions of CMG-2 and TEM-8 in cellular toxin entry
Authors: Merritt Carly , Chun Elizabeth M. , Fattah Rasem J. , Moayeri Mahtab , Paliga Dennis , Neumann Sebastian , Heumann Rolf , Leppla Stephen H. , Bugge Thomas H.
Published: January 2021

The virulence ofBacillus anthracisis linked to the secretion of anthrax lethal toxin and anthrax edema toxin. These binary toxins consist of a common cell-binding moiety, protective antigen (PA), and the enzymatic moieties, lethal factor (LF) and edema factor (EF). PA binds either of two specific cell surface receptors, capillary morphogenesis protein-2 (CMG-2) or tumor endothelial marker-8 (TEM-8), which triggers the binding, endocytosis, and cytoplasmic translocation of LF and EF. The cellular distribution of functional TEM-8 and CMG-2 receptors during anthrax toxin intoxication in animals is not fully elucidated. Herein, we describe a novel assay to image anthrax toxin intoxication in live animals, and we use the assay to visualize TEM-8- and CMG-2-dependent intoxication. Specifically, we generated a chimeric protein consisting of the N-terminal domain of LF fused to a nuclear localization signal-tagged Cre recombinase (LFn-NLS-Cre). When PA and LFn-NLS-Cre were co-administered to transgenic mice that ubiquitously express a red fluorescent protein in the absence of Cre activity and a green fluorescent protein in the presence of Cre activity, anthrax toxin intoxication could be visualized at single-cell resolution by confocal microscopy. By using this assay, we show that CMG-2 is critical for intoxication in the liver and heart, whereas TEM-8 is required for full intoxication in the kidney and spleen. Other tissues examined were largely unaffected by single deficiences in either receptor, suggesting extensive overlap in TEM-8 and CMG-2 expression. The novel assay will be useful for basic and clinical/translational studies ofBacillus anthracisinfection and for identifying on- and off-targets for reengineered toxin variants in the clinical development of cancer treatments.

Background

Assays for imaging of anthrax toxin intoxication in animals are not available.

Results

Anthrax toxin-Cre fusions combined with fluorescent Cre reporter mice enabled imaging of anthrax toxin intoxication in animals.

Conclusion

Shared and distinct functions of toxin receptors in cellular entry were uncovered. Significance. A simple and versatile assay for anthrax toxin intoxication is described.
Human genetic analyses of organelles highlight the nucleus in age-related trait heritability
Authors: Gupta Rahul , Karczewski Konrad J. , Howrigan Daniel , Neale Benjamin M. , Mootha Vamsi K.
Published: January 2021

Most age-related human diseases are accompanied by a decline in cellular organelle integrity, including impaired lysosomal proteostasis and defective mitochondrial oxidative phosphorylation. An open question, however, is the degree to which inherited variation in or near genes encoding each organelle contributes to age-related disease pathogenesis. Here, we evaluate if genetic loci encoding organelle proteomes confer greater-than-expected age-related disease risk. As mitochondrial dysfunction is a “hallmark” of aging, we begin by assessing nuclear and mitochondrial DNA loci near genes encoding the mitochondrial proteome and surprisingly observe a lack of enrichment across 24 age-related traits. Within nine other organelles, we find no enrichment with one exception: the nucleus, where enrichment emanates from nuclear transcription factors. In agreement, we find that genes encoding several organelles tend to be “haplosufficient,” while we observe strong purifying selection against heterozygous protein-truncating variants impacting the nucleus. Our work identifies common variation near transcription factors as having outsize influence on age-related trait risk, motivating future efforts to determine if and how this inherited variation then contributes to observed age-related organelle deterioration.
Burkholderiafrom fungus gardens of fungus-growing ants produce antifungals that inhibit the specialized parasiteEscovopsis
Authors: Francoeur Charlotte B. , May Daniel S. , Thairu Margaret W. , Hoang Don Q. , Panthofer Olivia , Bugni Tim S. , Pupo Mônica T. , Clardy Jon , Pinto-Tomás Adrián A. , Currie Cameron R.
Published: January 2021

Within animal associated microbiomes, the functional roles of specific microbial taxa are often uncharacterized. Here, we use the fungus-growing ant system, a model for microbial symbiosis, to determine the potential defensive roles of key bacterial taxa present in the ants’ fungus gardens. Fungus gardens serve as an external digestive system for the ants, with mutualistic fungi in the genusLeucoagaricusspp. converting plant substrate into energy for the ants. The fungus garden is host to specialized parasitic fungi in the genusEscovopsis. Here, we examine the potential role ofBurkholderiaspp. that occur within ant fungus gardens in inhibitingEscovopsis.We isolated members of the bacterial generaBurkholderiaspp. andParaburkholderiaspp. from 50% of the 52 colonies sampled, indicating that the familyBurkholderiaceaeare common fungus garden inhabitants of a diverse range of fungus-growing ant genera. Using antimicrobial inhibition bioassays, we found that 28 out of 32 isolates inhibited at least oneEscovopsisstrain with a zone of inhibition greater than 1 cm. Genomic assessment ofBurkholderiaceaeisolates indicated that isolates with strong inhibition all belonged to the genusBurkholderiaand contained biosynthetic gene clusters that encoded the production of two antifungals: burkholdine1213 and pyrrolnitrin. Organic extracts of cultured isolates confirmed these compounds as responsible for antifungal activity that inhibitEscovopsisbut, at low concentrations, notLeucoagaricusspp. Overall, these new findings, combined with previous evidence, suggest that members of the fungus garden microbiome play an important role in maintaining the health and function of the fungus-farming ant colony.

IMPORTANCE

Many organisms partner with microbes to defend themselves against parasites and pathogens. Fungus-growing ants must protectLeucoagaricusspp., the fungal mutualist that provides sustenance for the ants, from a specialized fungal parasite,Escovopsisspp. The ants take multiple approaches, including weeding their fungus gardens to removeEscovopsisspores, as well as harboringPseudonocardiathat produce antifungals that inhibitEscovopsis.In addition, a genus of bacteria commonly found in fungus gardens,Burkholderiaspp., is known to produce secondary metabolites that inhibitEscovopsisspp. In this study, we isolatedBurkholderiaspp. from fungus-growing ants, assessed the isolates’ ability to inhibitEscovopsisspp., and identified two compounds responsible for inhibition. Our findings suggest thatBurkholderiaspp. are often found in fungus gardens, adding another possible mechanism within the fungus-growing ant system to suppress the growth of the specialized parasiteEscovopsis.
Fine-scale Population Structure of North AmericanArabidopsis thalianaReveals Multiple Sources of Introduction from Across Eurasia
Authors: Shirsekar Gautam , Devos Jane , Latorre Sergio M. , Blaha Andreas , Dias Maique Queiroz , González Hernando Alba , Lundberg Derek S. , Burbano Hernán A. , Fenster Charles B. , Weigel Detlef
Published: January 2021

Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can contribute to observed patterns of genetic diversity and our understanding of the adaptive spread of alleles. While human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of non-native species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present here the most comprehensive view of population structure of North AmericanArabidopsis thalianaby studying a set of 500 (whole-genome sequenced) and over 2800 (RAD-seq genotyped) individuals in the context of global diversity represented by Afro-Eurasian genomes. We use haplotype-sharing, phylogenetic modeling and rare-allele sharing based methods to identify putative sources of introductions of extant N. AmericanA. thalianafrom the native range of Afro-Eurasia. We find evidence of admixture among the introduced lineages that has resulted in the increased haplotype diversity and reduced mutational load. Further, we also present signals of selection in the immune-system related genes that impart qualitative disease resistance to pathogens of bacterial and oomycete origins. Thus, multiple introductions to a non-native range can quickly increase adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. The results presented here lay the foundation for further investigations into the functional significance of admixture.
The Arabidopsis pattern recognition receptor EFR enhances fire blight resistance in apple
Authors: Piazza Stefano , Campa Manuela , Pompili Valerio , Costa Lorenza Dalla , Salvagnin Umberta , Nekrasov Vladimir , Zipfel Cyril , Malnoy Mickael
Published: January 2021

Fire blight disease, caused by the bacteriumErwinia amylovora(E. amylovora), is responsible for substantial losses in cultivated apple worldwide. An important mechanism of plant immunity is based on the recognition of conserved microbial molecules, named pathogen- or microbe-associated molecular patterns (PAMPs or MAMPs), through pattern recognition receptors (PRRs), leading to pattern-triggered immunity (PTI). The interspecies transfer of PRRs represents a promising strategy to engineer broad spectrum and durable disease resistance in crops. EFR, theArabidopsis thalianaPRR for the PAMP elf18 derived from the elongation factor thermal unstable (EF-Tu) proved to be effective in improving bacterial resistance when expressed into Solanaceae and other plant species,. In this study, we tested whether EFR can affect the interaction of apple withE. amylovoraby its ectopic expression in the susceptible apple rootstock M.26. StableEFRexpression led to the activation of PAMP-triggered immune response in apple leaves upon treatment with supernatant ofE. amylovora, as measured by production of reactive oxygen species and the induction of known defense genes. The amount of tissue necrosis associated withE. amylovorainfection was significantly reduced in theEFRtransgenic rootstock compared to the wild-type. Our results show that the expression ofEFRin apple rootstock may be a valuable biotechnology strategy to improve the resistance of apple to fire blight.
Deciphering the differential physiological and molecular requirements for conidial anastomosis tube fusion and germ tube formation inColletotrichum gloeosporioides
Authors: Mehta Nikita , Patil Ravindra , Baghela Abhishek
Published: January 2021

The conidia of a hemibiotrophic fungusColletotrichum gloeosporioidescan conventionally form germ tube (GT) and develop in to a fungal colony, while under certain conditions, they tend to get connected with each other through conidial anastomosis tube (CAT) so as to share the nutrients. CAT fusion is believed to be responsible for generation of genetic variations in few asexual fungi, which appears problematic for effective fungal disease management. The physiological and molecular mechanism underlying the GT versus CAT formation remained unexplored. In the present study, we have deciphered the decision switch responsible for GT formation versus CAT fusion inC. gloeosporioides. GT formation occurred at high frequency in the presence of nutrients, while CAT fusion was found to be higher in absence of nutrients. Younger conidia were found to form GT efficiently, whilst older conidia preferentially formed CAT. Whole transcriptome analysis of GT and CAT fusion revealed differential molecular requirements for these two processes. We identified 11050 and 9786 differentially expressed genes (DEGs) in GT and CAT, respectively. A total 1567 effector candidates were identified, of them 103 and 101 were uniquely secreted during GT and CAT formation respectively. Genes coding for cell wall degrading enzymes, germination, hyphal growth, host-fungus interaction and virulence were up-regulated during GT formation. Whilst, genes involved in stress response, cell wall remodelling, membrane transport, cytoskeleton, cell cycle, and cell rescue were highly up-regulated during CAT fusion. To conclude, the GT and CAT fusion were found to be mutually exclusive processes, requiring differential physiological conditions and sets of DEGs inC. gloeosporioides. This will help to understand the basic CAT biology in the genusColletotrichum.
Quantifying and cataloguing unknown sequences within human microbiomes
Authors: Modha Sejal , Robertson David L. , Hughes Joseph , Orton Richard J.
Published: January 2021

Advances in genome sequencing technologies and lower costs have enabled the exploration of a multitude of known and novel environments and microbiomes. This has led to an exponential growth in the raw sequence data that is deposited in online repositories. Metagenomic and metatranscriptomic data sets are typically analysed with regards to a specific biological question. However, it is widely acknowledged that these data sets are comprised of a proportion of sequences that bear no similarity to any currently known biological sequence, and this so-called ‘dark matter’ is often excluded from downstream analyses. In this study, a systematic framework was developed to assemble, identify, and measure the proportion of unknown sequences present in distinct human microbiomes. This framework was applied to forty distinct studies, comprising 963 samples, and covering ten different human microbiomes including fecal, oral, lung, skin and circulatory system microbiomes. The framework was used to determine the proportion of taxonomically unknown sequences present within samples, and to compare such sequences both within and across assembled metagenomes. We found that whilst the human microbiome is one of the most extensively studied, on average 2% of assembled sequences have not yet been taxonomically defined. However, this proportion varied extensively among different microbiomes and was as high as 25% for skin and oral microbiomes that have more interactions with the environment. The publicly available data sets used have not previously been systematically mined to quantify and compare such dark matter. Typically, these unknown sequences are found in several microbiomes and potentially belong to unidentified novel microbes that we interact with on a daily basis. A cross-study comparison led to the identification of similar unknown sequences in different samples and/or microbiomes. A rate of taxonomic characterisation of 1.64% of unknown sequences being characterised per month was calculated from these taxonomically unknown sequences discovered in this study. Additionally, the approach led to the discovery of several potentially novel viral genomes that bear no similarity to sequences in the public databases. Both our computational framework and the novel unknown sequences produced are publicly available for future cross-referencing.
Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh
Authors: Rani Pallavali Roja , Imran Mohamed , Lakshmi J. Vijaya , Jolly Bani , Afsar S. , Jain Abhinav , Divakar Mohit Kumar , Suresh Panyam , Sharma Disha , Rajesh Nambi , Bhoyar Rahul C. , Ankaiah Dasari , Kumari Sanaga Shanthi , Ranjan Gyan , Lavanya Valluri Anitha , Rophina Mercy , Umadevi S. , Sehgal Paras , Devi Avula Renuka , Surekha A. , Sekhar Pulala Chandra , Hymavathy Rajamadugu , Vanaja P.R. , Scaria Vinod , Sivasubbu Sridhar
Published: January 2021

Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
Nucleotide limitation results in impaired photosynthesis, reduced growth and seed yield together with massively altered gene expression
Authors: Bellin Leo , Melzer Michael , Hilo Alexander , Amaya Diana Laura Garza , Keller Isabel , Meurer Jörg , Möhlmann Torsten
Published: January 2021

Nucleotide limitation and imbalance is a well described phenomenon in animal research but understudied in the plant field. A peculiarity of pyrimidine de novo synthesis in plants is the complex subcellular organization. Here, we studied two organellar localized enzymes in the pathway, with chloroplast aspartate transcarbamoylase (ATC), and mitochondrial dihydroorotate dehydrogenase (DHODH).ATCknockdowns were most severely affected, exhibiting low levels of pyrimidine nucleotides, a low energy state, reduced photosynthetic capacity and accumulation of reactive oxygen species (ROS). Furthermore, altered leaf morphology and chloroplast ultrastructure were observed inATCmutants. Although less affected,DHODHknockdown mutants showed impaired seed germination and altered mitochondrial ultrastructure. Transcriptome analysis of anATC-amiRNA line revealed massive alterations in gene expression with central metabolic pathways being downregulated and stress response and RNA related pathways being upregulated. In addition, genes involved in central carbon metabolism, intracellular transport and respiration were mainly downregulated in ATC mutants, being putatively responsible for the observed impaired growth.

ONE-SENTENCE SUMMARY

Impaired pyrimidine nucleotide synthesis results in nucleotide limitation and imbalance, resulting in impaired photosynthesis, reduced growth, reproduction, and seed yield together with massively altered gene expression
The developmental stage of the medulloblastoma cell-of-origin restricts Hedgehog pathway usage and drug sensitivity
Authors: Smit Marlinde J. , Armandari Inna , Bockaj Irena , Martini Tosca E.I. , Zomerman Walderik W. , Siragna Zillah , Meeuwsen Tiny G.J. , Scherpen Frank J.G. , Schoots Mirthe H. , Ritsema Martha , den Dunnen Wilfred F.A. , Hoving Eelco W. , Paridaen Judith T.M.L. , de Haan Gerald , Guryev Victor , Bruggeman Sophia W.M.
Published: January 2021

Sonic Hedgehog (SHH) medulloblastoma originates from the cerebellar granule neuron progenitor (CGNP) lineage that depends on Hedgehog signaling for its perinatal expansion. While SHH tumors exhibit overall deregulation of this pathway, they also show patient age-specific aberrations.

To investigate if the developmental stage of the CGNP can account for these age-specific lesions, we analyzed developing murine CGNP transcriptomes and observed highly dynamic gene expression as function of age. Cross-species comparison with human SHH medulloblastoma showed partial maintenance of these expression patterns, and highlighted low primary cilium expression as hallmark of infant medulloblastoma and early embryonic CGNPs. This coincided with reduced responsiveness to upstream Shh pathway component Smoothened, while sensitivity to downstream components Sufu and Gli was retained.

Together, these findings can explain the preference forSUFUmutations in infant medulloblastoma and suggest that drugs targeting the downstream SHH pathway will be most appropriate for infant patients.
Facilitation and biodiversity jointly drive mutualistic networks
Authors: Losapio Gianalberto , Norton Hasday Elizabeth , Espadaler Xavier , Germann Christoph , Ortiz‐Sánchez Francisco Javier , Pont Adrian , Sommaggio Daniele , Schöb Christian
Published: January 2021

Facilitation by nurse plants increases understorey diversity and supports ecological communities. In turn, biodiversity shapes ecological networks and enhances ecosystem functioning. However, whether and how facilitation and increased biodiversity jointly influence community structure and ecosystem functioning remains unclear.

We performed a field experiment disentangling the relative contribution of nurse plants and increasing understorey plant diversity in driving pollination interactions. Both the presence of nurse shrubs and increased understorey plant diversity increased pollinator diversity and visitation rates. While nurse and understorey diversity effects on pollinator visitation rates did not interact, the effects of increasing understorey plant diversity on pollinator diversity were stronger in the absence than in the presence of shrubs, meaning that nurse shrubs attenuated the effects of high understorey diversity and buffered the effects of low understorey diversity.

We also found positive complementarity effects among understorey species as well as complementarity between nurse plants and understorey species at high diversity. Results also indicate negative selection effects, suggesting that species with generally few pollinators benefit the most in the polyculture while a species (possibly the nurse plant) with generally lots of pollinators does not. The corresponding changes in pollination networks with the experimental treatments were due to both changes in the frequency of visits and turnover in pollinator community composition.

Synthesis. Plant–plant facilitative systems, where a nurse plant increases understorey plant diversity, are common in stressful environments. Here, we show that these facilitative systems positively influence mutualistic interactions with pollinators via both direct nurse effects and indirect positive effects of increasing plant diversity. Conserving and supporting nurse plant systems is crucial not only for maintaining plant diversity but also for supporting ecosystem functions and services.
Re‐Embodying History's ‘Lady’: Women's History, Materiality and Public Space in Early‐Twentieth‐Century Vienna
Authors: Motyl Katya
Published: January 2021

In ‘The Disembodied Lady’, neurologist Oliver Sacks recounts the case of Christina, a woman who suddenly lost her corporeal sense of self. This article uses this case as a metaphor for the state of women's history at the turn of the millennium. With the turn to discourse, even the so‐called ‘lady’ within the academy had become disembodied. As Christina mouthed to Sacks, however, to be disembodied is awful. The purpose of this article is to follow the more recent trend in scholarship that has sought to re‐embody the ‘lady’ of history. The article begins by tracing the development of women's history and how its subject, the ‘lady’, came to disappear. It then draws on the ‘material’ turn in feminist theory to consider the implications of this vanishing act by looking, first, to lived experience, and second, to materiality/discursive production. I argue that Women are not only a matter of language, but a matter of matter, and further, that matter itself must be re‐evaluated as agential and entangled with discourse. Finally, an example from my research on street walking in early‐twentieth‐century Vienna illustrates how to bring this new women's history to life.
Lactic acid fermentation in the development of a seaweed sauerkraut‐style product: Microbiological, physicochemical, and sensory evaluation
Authors: Skonberg D.I. , Fader S. , Perkins L.B. , Perry J.J.
Published: January 2021

Consumption of nutrient‐rich seaweeds and fermented nondairy foods represent fast growing trends among health‐minded consumers. Assessment of lacto‐fermented seaweed was performed to address these trends, and to offer shelf‐life extension and product diversification for fresh kelps. The objectives were to evaluate the effects of kelp species and inclusion level on fermentation kinetics, physicochemical quality, safety, shelf‐life, and consumer acceptability of a seaweed sauerkraut‐style product. Six formulations with different inclusion levels (25, 50, and 75%) of shredded kelp (sugar kelp, SK or winged kelp, WK) were mixed with cabbage, 2% salt, and inoculated with Lactobacillus plantarum (approximately 106 CFU/g) and Leuconostoc mesenteroides (approximately 101 CFU/g). Products were processed in triplicate, fermented until a target pH of ≤4.6 was achieved, and sampled periodically for 60 days. Kelp species and inclusion level significantly affected most variables tested. The most rapid fermentation (3 days), as evidenced by pH decrease, lactic acid bacteria counts, and lactic acid levels, was noted in WK formulations. Some SK formulations took up to 14 days to achieve the target pH, and coliforms persisted to a greater extent in the SK formulations. Higher levels of kelp decreased the fermentation rate and concentration of fermentable sugars in the brine, but increased the total phenolic content and antioxidant activity of the sauerkrauts. Despite differences in instrumental color (L*a*b*) and texture (shear force) among formulations, overall liking as rated by a consumer panel was not significantly affected by species or inclusion level. Results support the use of lacto‐fermentation in the production of refrigeration‐stable seaweed sauerkraut‐style product.

Practical Application

Health‐conscious consumers are becoming increasingly interested in plant‐based diets and fermented foods, and the development of novel seaweed sauerkraut‐style products can help to meet these needs. This study demonstrated the successful production of a sauerkraut‐style product formulated with up to 50% farm‐raised kelp. Physical, chemical, microbiological, and consumer acceptability testing established lactic acid fermentation as a viable method for shelf life extension and value addition of fresh kelps. These results provide science‐based information on an alternative processing method for cultivated seaweeds and can assist the industry in product diversification efforts.
Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy
Authors: Shastry Vivaswat , Adams Paula E. , Lindtke Dorothea , Mandeville Elizabeth G. , Parchman Thomas L. , Gompert Zachariah , Buerkle C. Alex
Published: January 2021

Non‐random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping the genetics of traits and learning about the formative evolutionary processes that shape genetic variation among individuals and populations. Stratified genetic relatedness among individuals is commonly quantified using estimates of ancestry that are derived from a statistical model. Development of these models for polyploid and mixed‐ploidy individuals and populations has lagged behind those for diploids. Here, we extend and test a hierarchical Bayesian model, called entropy, which can use low‐depth sequence data to estimate genotype and ancestry parameters in autopolyploid and mixed‐ploidy individuals (including sex chromosomes and autosomes within individuals). Our analysis of simulated data illustrated the trade‐off between sequencing depth and genome coverage and found lower error associated with low‐depth sequencing across a larger fraction of the genome than with high‐depth sequencing across a smaller fraction of the genome. The model has high accuracy and sensitivity as verified with simulated data and through analysis of admixture among populations of diploid and tetraploid Arabidopsis arenosa.
Comparative genomics analyses indicate differential methylated amine utilization trait within members of the genus Gemmobacter
Authors: Kröber Eileen , Cunningham Mark R. , Peixoto Julianna , Spurgin Lewis , Wischer Daniela , Kruger Ricardo , Kumaresan Deepak
Published: January 2021

Methylated amines are ubiquitous in the environment and play a role in regulating the earth's climate via a set of complex biological and chemical reactions. Microbial degradation of these compounds is thought to be a major sink. Recently we isolated a facultative methylotroph, Gemmobacter sp. LW‐1, an isolate from the unique environment Movile Cave, Romania, which is capable of methylated amine utilization as a carbon source. Here, using a comparative genomics approach, we investigate how widespread methylated amine utilization is within members of the bacterial genus Gemmobacter. Seven genomes of different Gemmobacter species isolated from diverse environments, such as activated sludge, fresh water, sulphuric cave waters (Movile Cave) and the marine environment were available from the public repositories and used for the analysis. Our results indicate that methylamine utilization is a distinctive feature of selected members of the genus Gemmobacter, namely G. aquatilis, G. lutimaris, G. sp. HYN0069, G. caeni and G. sp. LW‐1 have the genetic potential while others (G. megaterium and G. nectariphilus) have not.
A randomized trial comparing prescribed light exercise to standard management for emergency department patients with acute mild traumatic brain injury
Authors: Varner Catherine E. , Thompson Cameron , de Wit Kerstin , Borgundvaag Bjug , Houston Reaves , McLeod Shelley
Published: January 2021

Background

There is a paucity of effective management strategies to prevent prolonged symptoms following mild traumatic brain injury (mTBI), and emerging evidence suggesting possible benefits of exercise. The objective of this trial was to determine whether adult patients presenting to the emergency department (ED) with a diagnosis of acute mTBI prescribed light exercise were less likely to develop persistent postconcussion symptoms (PCS).

Methods

This was a randomized controlled trial conducted in three Canadian EDs. Consecutive, adult (18–64 years) ED patients with an mTBI sustained within the preceding 48 hours were eligible for enrollment. The intervention group received discharge instructions prescribing 30 minutes of daily light exercise, and the control group was given standard mTBI instructions advising gradual return to exercise following symptom resolution. The primary outcome was the proportion of patients with PCS at 30 days, defined as the presence of three or more symptoms on the Rivermead Post‐concussion Symptoms Questionnaire (RPQ).

Results

A total of 367 patients were enrolled (control group, n = 184; intervention, n = 183). Median age was 32 years and 201 (57.6%) were female. There was no difference in the proportion of patients with PCS at 30 days (control, 13.4% vs intervention, 14.6%; ∆1.2%, 95% confidence interval [CI] = −6.2 to 8.5). There were no differences in median change of RPQ scores, median number of return health care provider visits, median number of missed school or work days, or unplanned return ED visits within 30 days. Participants in the control group reported fewer minutes of light exercise at 7 days (30 vs 35; ∆5, 95% CI = 2 to 15).

Conclusion

In this trial of prescribed early light exercise for acute mTBI, there were no differences in recovery or health care utilization outcomes. Results suggest that early light exercise may be encouraged as tolerated at ED discharge following mTBI, but this guidance is not sufficient to prevent PCS.
SARS‐CoV‐2 viral load in nasopharyngeal swabs in the emergency department does not predict COVID‐19 severity and mortality
Authors: Le Borgne Pierrick , Solis Morgane , Severac François , Merdji Hamid , Ruch Yvon , Alamé Intern Karine , Bayle Eric , Hansmann Yves , Bilbault Pascal , Fafi‐Kremer Samira , Meziani Ferhat ,   for the CRICS TRIGGERSEP Group (Clinical Research in Intensive Care and Sepsis Trial Group for Global Evaluation and Research in Sepsis)
Published: January 2021

Introduction

The ongoing COVID‐19 pandemic has led to devastating repercussions on health care systems worldwide. This viral infection has a broad clinical spectrum (ranging from influenza‐like disease, viral pneumonia, and hypoxemia to acute respiratory distress syndrome requiring prolonged intensive care unit stays). The prognostic impact of measuring viral load on nasopharyngeal swab specimens (by reverse transcriptase polymerase chain reaction [RT‐PCR]) is yet to be elucidated.

Methods

Between March 3 and April 5, 2020, we conducted a retrospective study on a cohort of COVID‐19 patients (mild or severe disease) who were hospitalized after presenting to the emergency department (ED) and had at least one positive nasopharyngeal swab during their hospital stay. We led our study at the University Hospitals of Strasbourg in the Greater East region of France, one of the pandemic's epicenters in Europe.

Results

We have collected samples from a cohort of 287 patients with a confirmed diagnosis of COVID‐19 who were included in our study. Nearly half of them (50.5%) presented a mild form of the disease, while the other half (49.5%) presented a severe form, requiring mechanical ventilation. Median (interquartile range) viral load on the initial upper respiratory swab at admission was 4.76 (3.29–6.06) log10 copies/reaction. When comparing survivors and nonsurvivors, this viral load measurement did not differ according to subgroups (p = 0.332). Additionally, we have found that respiratory viral load measurement was predictive of neither in‐hospital mortality (adjusted odds ratio [AOR] = 1.05, 95% confidence interval [CI] = 0.85 to 1.31, p = 0.637) nor disease severity (AOR = 0.88, 95% CI = 0.73 to 1.06, p = 0.167).

Conclusion

Respiratory viral load measurement on the first nasopharyngeal swab (by RT‐PCR) during initial ED management is neither a predictor of severity nor a predictor of mortality in SARS‐CoV‐2 infection. Host response to this viral infection along with the extent of preexisting comorbidities might be more foretelling of disease severity than the virus itself.
Intrinsic factors, release conditions and presence of conspecifics affect post‐release dispersal after translocation of Iberian ibex
Authors: Garnier A. , Besnard A. , Crampe J. P. , Estèbe J. , Aulagnier S. , Gonzalez G.
Published: January 2021

Translocation is an important tool in restoring biodiversity, particularly when species have been extirpated from an area. In the period just after release, the main objective of conservation managers is to keep as many of the translocated individuals in the release area as possible, in order to maximize the number of founders of the new population. Environmental and intrinsic factors, release conditions and social behaviour are likely to influence an individual’s propensity to move away from the release site (known as post‐release dispersal); however, few studies have explored the relative importance of these factors. The aim of this study was to evaluate how these four factors affected the post‐release dispersal of 169 Iberian ibex translocated from Spain to the French Pyrenees. We modelled the linear distance between the barycentre of each individual ibex’s monthly locations and the release site. Our results indicated that most individuals stayed close to the release site, but that inter‐individual variability was high. Post‐release dispersal was higher for males than females, with male breeders exhibiting higher exploration behaviour than juveniles. Release season played a major role, with dispersal being the lowest in spring and the highest during the rutting period. Dispersal was also found to be lower when conspecifics were present in the release area, probably due to their role as a cue for favourable habitat. These findings can be used by conservation managers to inform translocation strategies in order to enhance success: for example by releasing females and young males in spring and splitting a reintroduction project into successive release operations.
Attacks of domestic dogs on Common Long‐Nosed Armadillo Dasypusnovemcinctus and Southern Brown Howler Monkey Alouatta guariba in fragmented Atlantic Forest and implications in a region of high priority for biodiversity conservation
Authors: da Silva André Luiz Ferreira , H. Varzinczak Luiz , C. Passos Fernando
Published: January 2021

Domestic dogs can negatively impact natural systems, and understanding these dynamics is essential to mitigate their impact. We report two cases of attacks of domestic dogs on native mammals in a fragmented landscape of the Atlantic Forest, southern Brazil. Our records occurred in a region of high priority for the conservation of this biome. We observed two attacks, one on a Common Long‐Nosed Armadillo Dasypus novemcinctus and another on a Southern Brown Howler Monkey Alouatta guariba clamitans. Our records highlight additional threats to the wild and native fauna reinforcing the importance of accounting for the presence of domestic fauna when delineating conservation strategies in highly fragmented environments.
Dietary variation of an endangered mycophagous mammal in novel and remnant habitats in a peri‐urban landscape
Authors: Maclagan Sarah J. , Coates Terry , O’Malley Austin , Ritchie Euan G.
Published: January 2021

Understanding how fundamental aspects of species’ ecology, such as diet, are affected in human‐dominated landscapes is vital for informing management and conserving biodiversity – particularly where species influence important ecosystem functions. Digging, mycophagous (‘fungus‐eating’) mammals play various such roles, including the dispersal of hypogeal (‘truffle‐like’) fungi. The endangered, mycophagous southern brown bandicoot (Isoodon obesulus obesulus: Peramelidae) persists in a peri‐urban landscape south‐east of Melbourne, Australia, where it occupies both ‘novel’ habitats (linear strips of vegetation along roadsides, drains and railway lines) and ‘remnant’ habitats (larger blocks of native vegetation) within dedicated conservation areas. It remains unknown how bandicoot diet, including the diversity of hypogeal fungi, varies between these habitat types, yet this could have important conservation implications. Our study aimed to (i) compare the diet ofI. o. obesulusat novel and remnant sites; and (ii) attain knowledge of hypogeal fungal diversity in these different contexts. We collected 133 bandicoot scats over 23 months and examined both broad diet composition and diversity of fungi consumed. Bandicoot diet differed between site types; in particular, ants were more prominent in scats from remnant sites, while millipedes and seeds were more prominent in scats from novel sites. All scats contained fungal spores, with hypogeal taxa comprising at least 35 of the 78 ‘morphotypes’ found at novel sites and 28 of the 59 detected at remnant sites. Fewer samples were collected at remnant sites, but they appeared to contain a greater richness of hypogeal fungi per scat. We did not detect any differences in fungal composition between site types. However, our sampling effort was insufficient to estimate true morphotype richness at either site type. Our study highlights the adaptable generalist diet of the southern brown bandicoot, as well as the likely under‐appreciated diversity of hypogeal fungi that can occur in highly modified, novel ecosystems.
Some like it odd: Long‐term research reveals unusual behaviour in the flightless Kagu of New Caledonia
Authors: Theuerkauf Jörn , Rouys Sophie , Bloc Henri , Hunt Gavin R. , Kuehn Ralph , Gula Roman
Published: January 2021

The observation of rare behaviours can provide unexpected insights into the biology of a species. Here, we report new observations of unusual or rare behaviours by the Kagu Rhynochetos jubatus of New Caledonia, a flightless bird already known for many curious traits. We observed the broken‐wing display, adoption of a chick by a neighbouring family and flexibility in the selection of cooperative breeding partners in response to disruption in their social organisation. Although infrequent, these observations demonstrate the highly developed social flexibility that enables Kagu to counter heavy population losses caused by predation. We think that rare behaviours could often be overlooked in species because restricted research objectives might not allow their discovery.
Amount and spatial distribution of habitats influence occupancy and dispersal of frogs at multiple scales in agricultural landscape
Authors: Faggioni Gabriel P. , Souza Franco L. , Paranhos Filho AntÔnio C. , Gamarra Roberto M. , Prado Cynthia P. A.
Published: January 2021

Agriculture changes the aquatic and terrestrial habitats used by animals, affecting their responses to matrix permeability. Here, we evaluated the impacts that resulted from the replacement of native vegetation with pastures on habitat occupancy, colonisation and local extinction of two Neotropical frogs with contrasting ecological strategies, Leptodactylus bufonius and L. chaquensis. We conducted fieldwork during two reproductive seasons in 50 temporary ponds in the Brazilian Chaco. We used site occupancy models in a multi‐scale approach to identify landscape changes affecting population parameters and to determine the scale of interaction between species and the landscape. At local (10 m) and scales ≤400 m, increased pasture proportion limited the availability of bare soil required by males of L. bufonius to build mud chambers for reproduction and decreased proportion of shrublands affecting L. chaquensis occupancy. At larger spatial scales (>400 m), landscape modification limited dispersal of the smaller species L. bufonius. We found that the amount of habitat available is important in maintaining population parameters such as occupancy. However, our results highlight that the spatial distribution of habitats may also play an important role in the persistence and mobility of frogs in agricultural landscapes and that it is possible to identify a scale of effect in such anthropic landscapes. We recommend the consideration of reproductive and dispersal requirements of amphibian species, along with body size, as predictors of the spatial scale for management of populations in farmlands.