bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissociable plasticity of the nucleus basalis of Meynert in early and late blind individuals
Authors: Bang Ji Won , Chan Russell W. , Parra Carlos , Murphy Matthew C. , Schuman Joel S. , Nau Amy C. , Chan Kevin C.
Published: August 2021

Plasticity in the brain is differentially affected by age of blindness onset. One possible, but not yet identified mechanism is that the cholinergic signals originating from the nucleus basalis of Meynert may underlie differential extent of plasticity in early and late blind individuals. This prospect is based on the fact that the nucleus basalis of Meynert modulates cortical processes such as plasticity and sensory encoding and that the degree of cross-modal plasticity varies depending on the age of blindness onset. However, this question yet remains largely unclear. Here, we tested whether the early and late blind individuals develop dissociable plasticity in the nucleus basalis of Meynert using multi-parametric magnetic resonance imaging. We found the relatively preserved volumetric size and cerebrovascular reactivity, but significant disruption in the white matter integrity of the nucleus basalis of Meynert in both early and late blind individuals. Critically, despite its reduction in the white matter integrity, the nucleus basalis of Meynert of early blind individuals presented greater global and network functional connectivity including visual, language, and default-mode networks. Such changes in the functional connectivity were not observed in the late-blind individuals. Further, less duration of the visual experience was associated with greater global and network functional connectivity. These results indicate that the nucleus basalis of Meynert is differentially involved in the plasticity of early and late blind individuals – a similar amount of reduction in microstructural integrity in early and late blind individuals, but stronger and more widespread functional connectivity of the NBM in the early blind individuals. Our findings suggest that the nucleus basalis of Meynert may develop greater cholinergic influence on the cortex of early blind individuals. Such change may explain why early blind individuals present stronger and more widespread cross-modal plasticity during non-visual tasks compared to late blind individuals.
The PAF1 complex cell-autonomously promotes oogenesis in Caenorhabditis elegans
Authors: Kubota Yukihiro , Ota Natsumi , Takatsuka Hisashi , Unno Takuma , Onami Shuichi , Sugimoto Asako , Ito Masahiro
Published: August 2021

The RNA polymerase II-associated factor 1 complex (PAF1C) is a protein complex that consists of LEO1, RTF1, PAF1, CDC73, and CTR9, and has been shown to be involved in Pol II-mediated transcriptional and chromatin regulation. Although it has been shown to regulate a variety of biological processes, the precise role of the PAF1C during germ line development has not been clarified. In this study, we found that reduction in the function of the PAF1C components, LEO-1, RTFO-1, PAFO-1, CDC-73, and CTR-9, in Caenorhabditis elegans affects cell volume expansion of oocytes. Defects in oogenesis were also confirmed using an oocyte maturation marker, OMA-1::GFP. While four to five OMA-1::GFP-positive oocytes were observed in wild-type animals, their numbers were significantly decreased in pafo-1 mutant and leo-1(RNAi), cdc-73(RNAi), and pafo-1(RNAi) animals. Expression of a functional PAFO-1::mCherry transgene in the germline significantly rescued the oogenesis-defective phenotype of the pafo-1 mutants, suggesting that expression of the PAF1C in germ cells is required for oogenesis. Notably, overexpression of OMA-1::GFP partially rescued the oogenesis defect in the pafo-1 mutants. Based on our findings, we propose that the PAF1C promotes oogenesis in a cell-autonomous manner by positively regulating the expression of genes involved in oocyte maturation.
Horizontal transfer of a conservednpc-2like effector gene in rust fungi that suppresses cell death in plants
Authors: Jaswal Rajdeep , Dubey Himanshu , Kiran Kanti , Rawal Hukam , Kumar Gulshan , Rajarammohan Sivasubramanian , Deshmukh Rupesh , Sonah Humira , Prasad Pramod , Bhardwaj Subhash C , Gupta Naveen , Sharma Tilak Raj
Published: August 2021

ML/MD-2 is a conserved lipid/sterol-binding protein family having a role in sterol transfer and innate immunity in lower and higher eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 25 fungal and five oomycetes plant pathogen, having a different nutrition mode. All the fungal species were found to have varied numbers of family members, a distinctively substantial expansion of the ML gene family was observed inRhizophagus irregularis(RI) with 33 genes. Our analysis also showed that NPC2 like proteins, a subfamily of ML domain superfamily, were not only restricted to animals and insect species but also present in plant fungal pathogens, including members ofClavicipitaceae,Pucciniacease,andTremellaceaefamily. The phylogenetic analysis showed that these NPC2 like fungal proteins are more closely related to animals/insects than other fungal species. The molecular docking studies of these proteins with cholesterol and other derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. Further, the full length CDS of one of thenpc2like genes fromPuccinia triticina(Pt5643) was PCR amplified and further characterized using various studies such as qRT-PCR, expression in onion epidermal cells,Nicotiana benthamianafor subcellular localization studies, yeast functional complementation, and expression studies. The mRNA abundance ofPt5643was observed to be increased along with the infection progression and exhibits the highest expression at 5thday post-infection (dpi), suggesting its important role in theP. triticinainfection cycle in wheat. The fluorescent confocal microscopy of transiently expressed YFP taggedPt5643in onion epidermal cells andN. benthamianashows its location in cytoplasm and nucleus, indicating its involvement in the manipulation of host genes. The functional complementation ofPt5643innpc2mutant yeast showed its functional similarity to the eukaryotic npc2 gene. Further, the overexpression ofPt5643also suppressed the BAX and H2O2 induced program cell death inN. benthamianaand yeast, respectively thus proving to be a novel horizontally transferred effector in rust fungal pathogens. Altogether the present study reports the novel function of fungal NPC2 like proteins playing a crucial role in host defense manipulation possibly through lipid binding/transport similar to animals.
The genome of stress tolerant crop wild relativePaspalum vaginatumleads to increased biomass productivity in the cropZea mays
Authors: Sun Guangchao , Wase Nishikant , Shu Shengqiang , Jenkins Jerry , Zhou Bangjun , Chen Cindy , Sandor Laura , Plott Chris , Yoshinga Yuko , Daum Christopher , Qi Peng , Barry Kerrie , Lipzen Anna , Berry Luke , Gottilla Thomas , Foltz Ashley , Yu Huihui , O’Malley Ronan , Zhang Chi , Devos Katrien M. , Sigmon Brandi , Yu Bin , Obata Toshihiro , Schmutz Jeremy , Schnable James C.
Published: August 2021

A number of crop wild relatives can tolerate extreme stressed to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. PaspalumPaspalum vaginatumis a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession ofP. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologous conserved in 6 related grass species placed paspalum as an outgroup of the maize-sorghum clade demonstrating paspalum as their closest sequenced wild relative. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibited significant increases in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, resulting in autophagy dependent increases in biomass accumulation.
Distinct fastigial output channels and their impact on temporal lobe seizures
Authors: Streng Martha L. , Tetzlaff Madison , Krook-Magnuson Esther
Published: August 2021

Despite being canonically considered a motor control structure, the cerebellum is increasingly recognized for important roles in processes beyond this traditional framework, including seizure suppression. Excitatory fastigial neurons project to a large number of downstream targets, and it is unclear if this broad targeting underlies seizure suppression, or if a specific output may be sufficient. To address this question, we used the intrahippocampal kainic acid mouse model of temporal lobe epilepsy, male and female animals, and a dual-virus approach to selectively label and manipulate fastigial outputs. We examined fastigial neurons projecting to the superior colliculus, medullary reticular formation, and central lateral nucleus of the thalamus, and found that these comprise largely non-overlapping populations of neurons which send collaterals to unique sets of additional thalamic and brainstem regions, creating distinct, somewhat overlapping, “output channels”. We found that neither optogenetic stimulation of superior colliculus nor reticular formation output channels attenuated hippocampal seizures. In contrast, on-demand stimulation of fastigial neurons targeting the central lateral nucleus robustly inhibited seizures. Our results indicate that fastigial control of hippocampal seizures does not require simultaneous modulation of many fastigial output channels. Rather, selective modulation of the fastigial output channel to the central lateral thalamus, specifically, is sufficient for seizure control. This may provide a means for more selective therapeutic interventions, which provide seizure control while minimizing unwanted side effects. More broadly, our data highlight the concept of specific cerebellar output channels, whereby discrete cerebellar nucleus neurons project to specific aggregates of downstream targets, with distinct functional outcomes.

Significance statement

The cerebellum has an emerging relationship with non-motor systems and may represent a powerful target for therapeutic intervention in temporal lobe epilepsy. We find that fastigial neurons project to numerous brain regions via largely segregated output channels, and that excitation of fastigial neurons projecting to the central lateral nucleus of the thalamus, but not the superior colliculus or reticular formation, is sufficient to attenuate hippocampal seizures. These findings illustrate an important conceptual framework: fastigial neurons project to aggregates of downstream targets via distinct output channels, which cannot be predicted simply by somatic location within the nucleus, and these channels have distinct functional outcomes. This nuanced appreciation of fastigial outputs may provide a path for therapeutic interventions with minimized side effects.
Structure-Function in Helical Cardiac Musculature Using Additive Textile Manufacturing
Authors: Chang Huibin , Liu Qihan , Zimmerman John F. , Lee Keel Yong , Jin Qianru , Peters Michael M. , Rosnach Michael , Choi Suji , Kim Sean L. , Ardoña Herdeline Ann M. , MacQueen Luke A. , Chantre Christophe O. , Motta Sarah E. , Cordoves Elizabeth M. , Parker Kevin Kit
Published: August 2021

For more than fifty years, it has been hypothesized that the helical alignment of the heart gives rise to its mechanical function. Testing this hypothesis in an engineered environment is difficult, as the fine spatial features and complex three-dimensional (3D) structures of the cardiac musculature are challenging to reproduce using current biofabrication techniques. Addressing this, here we report a new form of additive textile manufacturing, Focused Rotary Jet Spinning (FRJS). FRJS allows for the rapid manufacturing of micro/nanofibers with controlled alignments. Using this method, we manufacture 3D models of the left ventricle, showing that helically aligned scaffolds display increased strain uniformity, axial shortening, cardiac output, and ejection fractions as compared to circumferential models. We then demonstrate how FRJS can enable the assembly of a full-sized model of the human heart’s musculature. This work experimentally confirms that ventricular alignment plays a critical role in ensuring healthy cardiac performance.
The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments
Authors: Nishimura Yosuke , Yoshizawa Susumu
Published: August 2021

Marine microorganisms are immensely diverse and play fundamental roles in global geochemical cycling. Recent metagenome-assembled genome studies, with special attention to large-scale projects such as Tara Oceans, have expanded the genomic repertoire of marine microorganisms. However, published marine metagenome data has not been fully explored yet. Here, we collected 2,057 marine metagenomes (>29 Tera bps of sequences) covering various marine environments and developed a new genome reconstruction pipeline. We reconstructed 52,325 qualified genomes composed of 8,466 prokaryotic species-level clusters spanning 59 phyla, including genomes from deep-sea deeper than 1,000 m (n=3,337), low-oxygen zones of <90 μmol O2 per kg water (n=7,884), and polar regions (n=7,752). Novelty evaluation using a genome taxonomy database shows that 6,256 species (73.9%) are novel and include genomes of high taxonomic novelty such as new class candidates. These genomes collectively expanded the known phylogenetic diversity of marine prokaryotes by 34.2% and the species representatives cover 26.5 - 42.0% of prokaryote-enriched metagenomes. This genome resource, thoroughly leveraging accumulated metagenomic data, illuminates uncharacterized marine microbial ‘dark matter’ lineages.
Does pollen limitation limit plant ranges? Evidence and implications
Authors: Dawson-Glass Emma , Hargreaves Anna L.
Published: August 2021

Range limits often involve declines in sexual reproduction, reducing fitness, dispersal, and adaptive potential at range edges. For plants, sexual reproduction is frequently limited by inadequate pollination. While case studies show that pollen limitation can limit plant distributions, the extent to which pollination commonly declines toward plant range edges is unknown. Here, we leverage global databases of pollen-supplementation experiments and plant occurrence data to test whether pollen limitation increases toward plant range edges, using a phylogenetically controlled meta-analysis. While there was significant pollen limitation across studies, we found little evidence that pollen limitation increases toward plant range edges. Pollen limitation was not stronger toward the tropics, nor at species’ equatorward vs poleward range limits. Meta-analysis results are consistent with results from targeted experiments, in which pollen limitation increased significantly toward only 14% of 14 plant range edges, suggesting that pollination contributes to range limits less often than do other interactions. Together, these results suggest pollination is one of the rich variety of potential ecological factors that can contribute to range limits, rather than a generally important constraint on plant distributions.
Antarctic biodiversity predictions through substrate qualities and environmental DNA
Authors: Czechowski Paul , de Lange Michel , Knapp Micheal , Terauds Aleks , Stevens Mark I.
Published: August 2021

Antarctic conservation science is important to enhance Antarctic policy and to understand alterations of terrestrial Antarctic biodiversity. Antarctic conservation will have limited long term effect in the absence of large-scale biodiversity data, but if such data were available, it is likely to improve environmental protection regimes. To enable Antarctic biodiversity prediction across continental spatial scales through proxy variables, in the absence of baseline surveys, we link Antarctic substrate-derived environmental DNA (eDNA) sequence data from the remote Antarctic Prince Charles Mountains to a selected range of concomitantly collected measurements of substrate properties. We achieve this using a statistical method commonly used in machine learning. We find neutral substrate pH, low conductivity, and some substrate minerals to be important predictors of presence for basidiomycetes, chlorophytes, ciliophorans, nematodes, or tardigrades. Our bootstrapped regression reveals how variations of the identified substrate parameters influence probabilities of detecting eukaryote phyla across vast and remote areas of Antarctica. We believe that our work may improve future taxon distribution modelling and aid targeting logistically challenging biodiversity surveys.
A comparison of the IgM and IgT repertoires reveals the structure of B cell communities in rainbow trout is a consequence of mechanistic and evolutionary forces
Authors: Costa Gregory R. , Poirier Annie , Bromage Erin S.
Published: August 2021

In rainbow trout (Oncorhynchus mykiss), three classes of antibodies have been identified: IgM, IgD, and IgT, which differ in their abundance and effector functions. Though the process of VDJ recombination that creates these antibodies is often described as a stochastic process, recent findings in mammals suggest that there are biases in antibody construction. Because class switching is absent in teleosts, studying the IgM and IgT communities of rainbow trout provides the opportunity to see how evolution has differentially shaped the IgM and IgT repertoires. Even though it has not yet been demonstrated that biases exist in variable region construction for trout immunoglobulins, it seems reasonable that both natural and artificial selection have driven preferential gene-segment usage and pairing biases in rainbow trout. In this study, we sequenced the heavy chain variable regions of membrane IgM and IgT from multiple fish and predicted that given the more generalist role of the abundant IgM there would be less pressure to bias V gene segment usage and DJ pairings; rather, natural selection would have favored diversity and the ability to respond to a plethora of pathogens. Conversely, as IgT is substantially less abundant in the serum than IgM and specialized in its function, there would be selective pressure to make the most out of a little, thus favoring biased V segment usage and preferential DJ pairings. In support of our hypotheses, for IgT, over 70% of DJ pairs were biased and over 60% of antibodies were constructed with just two V gene segments. These biases were not prevalent in the IgM repertoire, where only 4% of DJ pairs were biased and no single V gene segment was utilized in more than 10% of antibodies. We found that these biases have profound influences in the richness and evenness of the repertoires, with the IgM repertoire investing more equitably in nearly double the number of VDJ combinations compared with IgT.
A Robust, Low-Cost Instrument for Real-time Colorimetric Isothermal Nucleic Acid Amplification
Authors: Myers F. , Moffatt B. , Khaja R. , Chatterjee T. , Marwaha G. , McGee M. , Mitra D.
Published: August 2021

The COVID-19 pandemic has highlighted the need for broader access to molecular diagnostics. Colorimetric isothermal nucleic acid amplification assays enable simplified instrumentation over more conventional PCR diagnostic assays and, as such, represent a promising approach for addressing this need. In particular, colorimetric LAMP (loop-mediated isothermal amplification) has received a great deal of interest recently. However, there do not currently exist robust instruments for performing these kinds of assays in high throughput with real-time readout of amplification signals. To address this need, we developed LARI, the LAMP Assay Reader Instrument. We have deployed over 50 LARIs for routine use in R&D and production environments, with over 12,000 assays run to date. In this paper, we present the design and construction of LARI along with thermal, optical, and assay performance characteristics. LARI can be produced for under $1500 and has broad applications in R&D, point-of-care diagnostics, and global health.
Does plant diversity determine the diversity of the rhizosphere microbial community?
Authors: Zverev Aleksei , Kichko Arina , Shapkin Vasiliy , Pinaev Aleksandr , Provorov Nikolay , Andronov Evgeny
Published: August 2021

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Close connection and mutual influence in this communication allow to talk about the self-adjusting “plant-rhizosphere community” system, which should be be studied in connection. Diversity estimation is one of the ways of describing both bacterial and plant communities. Based on the literature, there are two assumptions of how the diversity of plant communities related to the diversity of bacterial communities: 1) an increase in the species richness of plants leads to an increase in the number of available micro-niches, and increasing of microbial diversity, 2) an increase in the species richness of plants is accompanied by the predominant development of bacteria from highly productive specific taxa and decreasing in the diversity of microorganisms. Experimental studies show controversial results.

We analyzed field sites (rye crop field and two fallow sites), using DNA isolation of both the plant root mass (followed by sequencing of the ITS1 region) and rhizosphere microorganisms (followed by sequencing of the 16s rDNA V4 region). This allowed us to 1) accurately determine the abundance and taxonomic position of plant communities; 2) extract information about both plant and microbial communities from the same sample.

There was no correlation between alpha-diversity indices of plants and rhizosphere communities. Alpha-diversity connection should be explored in similar plant communities, such as synusia. We hypothesize, that the significant differences in plant abundances lead to significant changes in exudation profiles, and the loss of diversity connection. The beta-diversity between rhizosphere communities and plant communities is highly correlated, in particular in terms of the abundance of taxa. This can be explained by a potential correlation (as reported in the literature) or by the presence of statistical artifacts.
The Troyer syndrome protein spartin mediates selective autophagy of lipid droplets
Authors: Chung Jeeyun , Park Joongkyu , Lai Zon Weng , Lambert Talley J. , Richards Ruth C. , Farese Robert V. , Walther Tobias C.
Published: August 2021

Lipid droplets (LDs) are crucial organelles for energy storage and lipid homeostasis. Autophagy of LDs is an important pathway for their catabolism, but the molecular mechanisms mediating targeting of LDs for degradation by selective autophagy (lipophagy) are unknown. Here we identify spartin as a receptor localizing to LDs and interacting with core autophagy machinery, and we show that spartin is required to deliver LDs to lysosomes for triglyceride (TG) mobilization. Mutations in SPART (encoding spartin) lead to Troyer syndrome, a form of hereditary spastic paraplegia. We find that interfering with spartin function leads to LD and TG accumulation in motor cortex neurons of mice. Our findings thus identify spartin as a lipophagy receptor and suggest that impaired LD turnover may contribute to Troyer syndrome development.
A bacterial genome and culture collection of gut microbial in weanling piglet
Authors: Dong Bo , Lin Xiaoqian , Jing Xiaohuan , Hu Tuanyuan , Zhou Jianwei , Chen Jianwei , Xiao Liang , Wang Bo , Chen Zhuang , Liu Jing , Hu Yiyin , Liu Guilin , Liu Shanshan , Liu Junnian , Wei Wenkang , Zou Yuanqiang
Published: August 2021

The microbiota hosted in the pig gastrointestinal tract are important for productivity of livestock. However, the individual species and functional repertoires that make up the pig gut microbiome remain largely undefined. Here we comprehensively investigated the genomes and functions of the piglet gut microbiome using culture-based and metagenomics approaches. A collection included 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) that were clustered to 428 species across 10 phyla was established. Among these clustered species, 333 genomes represent potential new species. Less matches between cultured genomes and MAGs revealed a substantial bias for the acquisition of reference genomes by the two strategies. Glycoside hydrolases was the dominant category of carbohydrate-active enzymes. 445 secondary metabolite biosynthetic genes were predicted from 292 genomes with bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri uncover the biosynthesis of reuterin was strain-specific and the production was experimentally determined. These genomic resources will enable a comprehensive characterization of the microbiome composition and function of pig gut.
Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD
Authors: Larsen Joachim S. , Miller Michael , Oakley Aaron J. , Dixon Nicholas E. , Lewis Peter J.
Published: August 2021

Efficient control of transcription is essential in all organisms. In bacteria, where DNA replication and transcription occur simultaneously, the replication machinery is at risk of colliding with highly abundant transcription complexes. This can be exacerbated by the fact that transcription complexes pause frequently. When pauses are long-lasting, the stalled complexes must be removed to prevent collisions with either another transcription complex or the replication machinery. HelD is a protein that represents a new class of ATP-dependent motor protein distantly related to helicases. It was first identified in the model Gram-positive bacterium Bacillus subtilis and is involved in removing and recycling stalled transcription complexes. To date, two classes of HelD have been identified: one in the low G+C and the other in the high G+C Gram-positive bacteria. In this work we have undertaken the first comprehensive investigation of the phylogenetic diversity of HelD proteins. We show that genes in certain bacterial classes have been inherited by horizontal gene transfer, many organisms contain multiple expressed isoforms of HelD, some of which are associated with antibiotic resistance, and that there is a third class of HelD protein found in Gram-negative bacteria. Therefore, HelD proteins represent an important new class of transcription factor associated with genome maintenance and antibiotic resistance that are conserved across the Eubacterial kingdom.
Estimating genetic correlation jointly using individual-level and summary-level GWAS data
Authors: Zhang Yiliang , Cheng Youshu , Ye Yixuan , Jiang Wei , Lu Qiongshi , Zhao Hongyu
Published: August 2021

With the increasing accessibility of individual-level data from genome wide association studies, it is now common for researchers to have individual-level data of some traits in one specific population. For some traits, we can only access public released summary-level data due to privacy and safety concerns. The current methods to estimate genetic correlation can only be applied when the input data type of the two traits of interest is either both individual-level or both summary-level. When researchers have access to individual-level data for one trait and summary-level data for the other, they have to transform the individual-level data to summary-level data first and then apply summary data-based methods to estimate the genetic correlation. This procedure is computationally and statistically inefficient and introduces information loss. We introduce GENJI (Genetic correlation EstimatioN Jointly using Individual-level and summary data), a method that can estimate within-population or transethnic genetic correlation based on individual-level data for one trait and summary-level data for another trait. Through extensive simulations and analyses of real data on within-population and transethnic genetic correlation estimation, we show that GENJI produces more reliable and efficient estimation than summary data-based methods. Besides, when individual-level data are available for both traits, GENJI can achieve comparable performance than individual-level data-based methods. Downstream applications of genetic correlation can benefit from more accurate estimates. In particular, we show that more accurate genetic correlation estimation facilitates the predictability of cross-population polygenic risk scores.
Designing and interpreting 4D tumour spheroid experiments
Authors: Murphy Ryan J. , Browning Alexander P. , Gunasingh Gency , Haass Nikolas K. , Simpson Matthew J.
Published: August 2021

Tumour spheroid experiments are routinely used to study cancer progression and treatment. Various and inconsistent experimental designs are used, leading to challenges in interpretation and reproducibility. Using multiple experimental designs, live-dead cell staining, and real-time cell cycle imaging, we measure necrotic and proliferation-inhibited regions in over 1000 4D tumour spheroids (3D space plus cell cycle status). By intentionally varying the initial spheroid size and temporal sampling frequencies across multiple cell lines, we collect an abundance of measurements of internal spheroid structure. These data are difficult to compare and interpret. However, using an objective mathematical modelling framework and statistical identifiability analysis we quantitatively compare experimental designs and identify design choices that produce reliable biological insight. Measurements of internal spheroid structure provide the most insight, whereas varying initial spheroid size and temporal measurement frequency is less important. Our general framework applies to spheroids grown in different conditions and with different cell types.
Development of an in vitro model for animal species susceptibility to SARS-CoV-2 replication based on expression of ACE2 and TMPRSS2 in avian cells
Authors: Kapczynski Darrell R. , Sweeney Ryan , Suarez David L. , Spackman Erica , Pantin-Jackwood Mary
Published: August 2021

The SARS-CoV-2 (SC2) virus has caused a worldwide pandemic because of the virus’s ability to transmit efficiently human-to-human. A key determinant of infection is the attachment of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Because of the presumed zoonotic origin of SC2, there is no practical way to assess every species susceptibility to SC2 by direct challenge studies. In an effort to have a better predictive model of animal host susceptibility to SC2, we expressed the ACE2 and/or transmembrane serine protease 2 (TMPRSS2) genes from humans and other animal species in the avian fibroblast cell line, DF1, that is not permissive to infection. We demonstrated that expression of both human ACE2 and TMPRSS2 genes is necessary to support SC2 infection and replication in DF1 and a non-permissive sub-lineage of MDCK cells. Titers of SC2 in these cell lines were comparable to those observed in control Vero cells. To further test the model, we developed seven additional transgenic cell lines expressing the ACE2 and TMPRSS2 derived from Felis (cat), Equus (horse), Sus (pig), Capra (goat), Mesocricetus (Golden hamster), Myotis lucifugus (Little Brown bat) and Hipposideros armiger (Great Roundleaf bat) in DF1 cells. Results demonstrate permissive replication of SC2 in cat, Golden hamster, and goat species, but not pig or horse, which correlated with the results of reported challenge studies. The development of this cell culture model allows for more efficient testing of the potential susceptibility of many different animal species for SC2 and emerging variant viruses.

IMPORTANCE

SARS-CoV-2 (SC2) is believed to have originated in animal species and jumped into humans where it has produced the greatest viral pandemic of our time. Identification of animal species susceptible to SC2 infection would provide information on potential zoonotic reservoirs, and transmission potential at the human-animal interface. Our work provides a model system to test the ability of the virus to replicate in an otherwise non-permissive cell line by transgenic insertion of the ACE2 and TMPRSS2 genes from human and other animal species. The results from our in vitro model positively correlate with animal infection studies enhancing the predicative capability of the model. Importantly, we demonstrate that both proteins are required for successful virus replication. These findings establish a framework to test other animal species for susceptibility to infection that may be critical zoonotic reservoirs for transmission, as well as to test variant viruses that arise over time.
Selection against admixture and gene regulatory divergence in a long-term primate field study
Authors: Vilgalys Tauras P. , Fogel Arielle S. , Mututua Raphael S. , Kinyua Warutere J. , Siodi Long’ida , Anderson Jordan A. , Kim Sang Yoon , Voyles Tawni N. , Robinson Jacqueline A. , Wall Jeffrey D. , Archie Elizabeth A. , Alberts Susan C. , Tung Jenny
Published: August 2021

Admixture has profoundly influenced evolution across the tree of life, including in humans and other primates1,2. However, we have limited insight into the genetic and phenotypic consequences of admixture in primates, especially during its key early stages. Here, we address this gap by combining 50 years of field observations with population and functional genomic data from yellow (Papio cynocephalus) and anubis (P. anubis) baboons in Kenya, in a longitudinally studied population that has experienced both historical and recent admixture3. We use whole-genome sequencing to characterize the extent of the hybrid zone, estimate local ancestry for 442 known individuals, and predict the landscape of introgression across the genome. Despite no major fitness costs to hybrids, we identify signatures of selection against introgression that are strikingly similar to those described for archaic hominins4–6. These signatures are strongest near loci with large ancestry effects on gene expression, supporting the importance of gene regulation in primate evolution and the idea that selection targeted large regulatory effects following archaic hominin admixture7,8. Our results show that genomic data and field observations of hybrids are important and mutually informative. They therefore demonstrate the value of other primates as living models for phenomena that we cannot observe in our own lineage.
MEKK3-TGFβ crosstalk regulates inward arterial remodeling
Authors: Deng Hanqiang , Xu Yanying , Hu Xiaoyue , Zhuang Zhen W. , Chang Yuzhou , Wang Yewei , Ntokou Aglaia , Schwartz Martin A. , Su Bing , Simons Michael
Published: August 2021

Arterial remodeling is an important adaptive mechanism that maintains normal fluid shear stress in a variety of physiologic and pathologic conditions. Inward remodeling, a process that leads to reduction in arterial diameter, plays a critical role in progression of such common diseases as hypertension and atherosclerosis. Yet despite its pathogenic importance, molecular mechanisms controlling inward remodeling remain undefined. Mitogen-activated protein kinases (MAPKs) perform a number of functions ranging from control of proliferation to migration and cell fate transitions. While the MAPK ERK1/2 signaling pathway has been extensively examined in the endothelium, less is known about the role of the MEKK3/ERK5 pathway in vascular remodeling. To better define the role played by this signaling cascade, we studied the effect of endothelial-specific deletion of its key upstream MAP3K, MEKK3, in adult mice. The gene’s deletion resulted in a gradual inward remodeling of both pulmonary and systematic arteries leading to spontaneous hypertension in both vascular circuits and accelerated progression of atherosclerosis in hyperlipidemic mice. Molecular analysis revealed activation of TGFβ signaling both in vitro and in vivo. Endothelial-specific TGFβR1 knockout prevented inward arterial remodeling in MEKK3 endothelial knockout mice. These data point to the unexpected participation of endothelial MEKK3 in regulation of TGFβR1-Smad2/3 signaling and inward arterial remodeling in artery diseases.

Significance

Inward remodeling of arteries to reduce lumen diameter is a major factor in disease progression and morbidity in multiple vascular diseases, including hypertension and atherosclerosis. However, molecular mechanisms controlling inward arterial remodeling remain largely undefined. In this study, we identify endothelial MEKK3 as an unexpected regulator of inward remodeling via inhibition of TGFβ-Smad2/3 signaling. Genetic deletion of MEKK3 in adult endothelium results in induction of TGFβ-Smad2/3 signaling, endothelial-to-mesenchymal transition and inward remodeling in both pulmonary and arterial circuits. The latter process results in pulmonary and systemic hypertension and accelerates atherosclerosis. These results provide a new basis for understanding the inward artery remodeling that leads to reduced blood flow to affected tissues and exacerbates hypertension in vascular disease.
Conformable and robust force sensors to enable precision joint replacement surgery
Authors: Ives Liam , Pace Alizée , Bor Fabian , Jing Qingshen , Wade Tom , Cama Jehangir , Khanduja Vikas , Kar-Narayan Sohini
Published: August 2021

Balancing forces within weight-bearing joints such as the hip during joint replacement surgeries is essential for implant longevity. Minimising implant failure is vital to improve patient wellbeing and alleviate pressure on healthcare systems. With improvements in surgery, hip replacement patients are now often younger and more active than in previous generations, and their implants correspondingly need to survive higher stresses. However, force balancing currently depends entirely on surgical skill: no sensors can provide quantitative force feedback within the hip joint’s small, complex geometry. Here, we solve this unmet clinical need by presenting a thin and conformable microfluidic force sensor, which is compatible with the standard surgical process. We optimised the design using finite element modelling, then incorporated and calibrated our sensor in a model hip implant. Using a bespoke testing rig, we demonstrated high sensitivity at typical forces experienced during hip replacements. We anticipate that these sensors will aid implant positioning, increasing the lifetime of hip replacements, and represent a powerful new surgical tool for a range of orthopaedic procedures where force balancing is crucial.
Characterising the Photoplethysmography Pulse Waveform for Use in Human Neuroscience: The Hybrid Excess and Decay (HED) Model
Authors: Williamson Simon , Daniel-Watanabe Lucie , Finnemann Johanna , Powell Craig , Teed Adam , Allen Micah , Paulus Martin , Khalsa Sahib S. , Fletcher Paul C.
Published: August 2021

Photoplethysmography (PPG) offers a widely-used, convenient and non-invasive approach to monitoring basic indices of cardiovascular function such as heart rate and blood oxygenation. However, while the pulse waveform, generated by PPG comprises features that are shaped by physiological and psychological factors, it is frequently overlooked in analyses of such data. We suggest that studies could be enriched by exploiting the possibilities afforded by a systematic analysis of PPG waveforms. To do this we initially require a robust and automated means of characterising it, thereby allowing us to examine variations across individuals and between different physiological and psychological contexts. We present a psychophysiologically-relevant model, the Hybrid Excess and Decay (HED) Model, which characterises pulse wave morphology in terms of three underlying pressure waves and a decay function. We show that these parameters capture PPG data with a high degree of precision and, moreover, are sensitive to specific, physiologically-relevant changes within individuals. We present the theoretical and practical basis for the model and demonstrate its performance when applied to a pharmacological dataset of 105 participants receiving intravenous administrations of the sympathomimetic drug isoproterenol (Isoprenaline). We conclude by discussing the possible value in using the HED model to complement standard measures of PPG outputs.
Neuroblast migration along cellular substrates in the developing porcine brain
Authors: Porter Demisha D.L. , Henry Sara N. , Ahmed Sadia , Morton Paul D.
Published: August 2021

In the past decade it has become evident that neuroblasts continue to supply the human cortex with interneurons via unique migratory streams shortly following birth. Due to the size of the human brain, these newborn neurons must migrate long distances through complex cellular landscapes to reach their final locations. This process is poorly understood, largely due to technical difficulties in acquiring and studying neurotypical postmortem human samples along with diverging developmental features of well-studied mouse models. We reasoned that migratory streams of neuroblasts utilize cellular substrates, such as blood vessels, to guide their trek from the subventricular zone to distant cortical targets. Here we evaluate the association between young interneuronal migratory streams and their preferred cellular substrates in gyrencephalic piglets during the developmental equivalent of human birth, infancy, and toddlerhood.
Critical Role for Isoprenoids in Apicoplast Biogenesis by Malaria Parasites
Authors: Okada Megan , Rajaram Krithika , Swift Russell P. , Mixon Amanda , Maschek John Alan , Prigge Sean T. , Sigala Paul A.
Published: August 2021

Isopentenyl pyrophosphate (IPP) is an essential metabolic output of the apicoplast organelle inPlasmodium falciparummalaria parasites and is required for prenylation-dependent vesicular trafficking and other cellular processes. We have elucidated a critical and previously uncharacterized role for IPP in apicoplast biogenesis. Inhibiting IPP synthesis blocks apicoplast elongation and inheritance by daughter merozoites, and apicoplast biogenesis is rescued by exogenous IPP and polyprenols. Knockout of the only known isoprenoid-dependent apicoplast pathway, tRNA prenylation by MiaA, has no effect on blood-stage parasites and thus cannot explain apicoplast reliance on IPP. However, we have localized an annotated polyprenyl synthase (PPS) to the apicoplast lumen. PPS knockdown is lethal to parasites, rescued by IPP, and blocks apicoplast biogenesis, thus explaining apicoplast dependence on isoprenoid synthesis. We hypothesize that PPS synthesizes long-chain polyprenols critical for apicoplast membrane fluidity and biogenesis. This work critically expands the paradigm for isoprenoid utilization in malaria parasites and identifies a novel essential branch of apicoplast metabolism suitable for therapeutic targeting.
Methods for recording and imaging spreading depolarizations and seizure-like events in mouse hippocampal slices
Authors: Lu Yi-Ling , Scharfman Helen E.
Published: August 2021

Spreading depolarization (SD) is a sudden and synchronized depolarization of principal cells followed by depression of activity, which slowly propagates across brain regions like cortex or hippocampus. SD is considered to be mechanistically relevant to migraine, epilepsy, and traumatic brain injury. Interestingly, research into SD typically uses SD triggered immediately after a focal stimulus. Here we optimize an in vitro experimental model allowing us to record SD without focal stimulation. This method uses electrophysiological recordings and intrinsic optical imaging in slices. The method is also relatively easy and inexpensive. Acute hippocampal slices from mice or rats were prepared and used for extracellular and whole-cell recordings. Recordings were made in a submerged-style chamber with flow of artificial cerebrospinal fluid (aCSF) above and below the slices. Flow was fast (> 5ml/min), and temperature was 32°C. As soon as slices were placed in the chamber, aCSF containing 0 mM Mg2+ and 5 mM K+ (0 Mg2+/5 K+ aCSF) was used. Two major types of activity were observed: SD and seizure-like events (SLEs). Both occurred after many minutes of recording. Although both mouse and rat slices showed SLEs, only mouse slices developed SD and did so in the first hour of 0 Mg2+/5 K+ aCSF exposure. Intrinsic optical imaging showed that most SDs initiated in CA3 and could propagate into CA1 and dentate gyrus. In dentate gyrus, SD propagated in two separate waves: (1) into the hilus and (2) into granule cell and molecular layers simultaneously. This in vitro model can be used to better understand the mechanisms and relationship between SD and SLEs. It could also be useful in preclinical drug screening.
Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans
Authors: Perez-Borrajero Cecilia , Podvalnaya Nadezda , Holleis Kay , Lichtenberger Raffael , Karaulanov Emil , Simon Bernd , Basquin Jérôme , Hennig Janosch , Ketting René F. , Falk Sebastian
Published: August 2021

Piwi-interacting RNAs (piRNAs) constitute a class of small RNAs that bind PIWI proteins and are essential to repress transposable elements in the animal germline, thereby promoting genome stability and maintaining fertility. C. elegans piRNAs (21U RNAs) are transcribed individually from minigenes as precursors that require 5′ and 3′ processing. This process depends on the PETISCO complex, consisting of four proteins: IFE-3, TOFU-6, PID-3, and ERH-2. We used biochemical and structural biology approaches to characterize the PETISCO architecture and its interaction with RNA, together with its effector proteins TOST-1 and PID-1. These two proteins define different PETISCO functions: PID-1 governs 21U processing, whereas TOST-1 links PETISCO to an unknown process essential for early embryogenesis. Here, we show that PETISCO forms an octameric assembly with each subunit present in two copies. Determination of structures of the TOFU-6/PID-3 and PID-3/ERH-2 subcomplexes, supported by in vivo studies of subunit interaction mutants, allows us to propose a model for the formation of the TOFU-6/PID-3/ERH-2 core complex and its functionality in germ cells and early embryos. Using NMR spectroscopy, we demonstrate that TOST-1 and PID-1 bind to a common surface on ERH-2, located opposite its PID-3 binding site, explaining how PETISCO can mediate different cellular roles.
Evolution of the magnetic hyperfine field profiles in an ion-irradiated Fe60Al40 film measured by nuclear resonant reflectivity
Authors: Andreeva Marina , Smekhova Alevtina , Baulin Roman , Repchenko Yurii , Bali Rantej , Schmitz-Antoniak Carolin , Wende Heiko , Sergueev Ilya , Schlage Kai , Wille Hans-Christian
Published: August 2021

Nuclear resonant reflectivity (NRR) from an Fe60Al40 film was measured using synchrotron radiation at several grazing angles near the critical angle of total external reflection. Using laterally resolved measurements after irradiation with 20 keV Ne+ ions of gradually varying fluence of 0–3.0 × 1014 ions cm−2, the progressive creation of the ferromagnetic A2 phase with increasing ion fluence was confirmed. The observed depth selectivity of the method has been explained by application of the standing wave approach. From the time spectra of the nuclear resonant scattering in several reflection directions the depth profiles for different hyperfine fields were extracted. The results show that the highest magnetic hyperfine fields (∼18–23 T) are initially created in the central part of the film and partially at the bottom interface with the SiO2 substrate. The evolution of the ferromagnetic onset, commencing at a fixed depth within the film and propagating towards the interfaces, has been directly observed. At higher fluence (3.0 × 1014 ions cm−2) the depth distribution of the ferromagnetic fractions became more homogeneous across the film depth, in accordance with previous results.