bluuebunny/crossref_metadata_2025 huggingface dataset:
Planarian dorsoventral Netrins control a muscle midline signaling center and regulate blastema formation
Authors: Schad Erik G. , Petersen Christian P.
Published: September 2022

Integration of positional information across body axes is likely critical for whole-body regeneration to define the territories of missing tissue in three dimensions with fidelity. The body-wall musculature in planarians expresses patterning factors regulating the anteroposterior, dorsoventral, and mediolateral axes, but how this information coordinates is not fully understood. We identify a previously described factor specifically expressed in dorsal midline muscle as a BMP/Activin decoy receptorbambi-2. Analysis of scRNAseq indicatesbambi-2+cells coexpress midline-specifying transcription factorpitxand longitudinal muscle-specifying factormyoD, and production ofbambi-2+cells requires these factors. In laterally amputated animals regenerating an entirely new midline,bambi-2+cells are initially formed at the wound site, then dynamically spread, and ultimately reset to restore bilateral symmetry. We further identify a system of dorsoventral Netrin and Netrin receptor signals expressed from body-wall muscle that control midline identity and blastema morphology. Ventral and laterally expressednetrins -1, -4,and-5signal via dorsally-enriched netrin repulsion receptorsunc5-C, unc5-E,anddcc-2, which together limit mediolateral spread ofbambi-2+dorsal midline muscle and influence the architecture of the muscle system. Our results suggest a model in which ventral determinants dictate mediolateral information important for blastema morphology.
Enhancers display constrained sequence flexibility and context-specific modulation of motif function
Authors: Reiter Franziska , de Almeida Bernardo P. , Stark Alexander
Published: September 2022

The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, while the enhancer syntax, i.e. the flexibility of important motif positions and how the sequence context modulates the activity of TF motifs, remain poorly understood. Here, we explore the rules of enhancer syntax by a two-pronged approach inDrosophila melanogasterS2 cells: we (1) replace important motifs by an exhaustive set of all possible 65,536 eight-nucleotide-long random sequences and (2) paste eight important TF motif types into 763 positions within 496 enhancers. These complementary strategies reveal that enhancers display constrained sequence flexibility and the context-specific modulation of motif function. Important motifs can be functionally replaced by hundreds of sequences constituting several distinct motif types, but only a fraction of all possible sequences and motif types restore enhancer activity. Moreover, TF motifs contribute with different intrinsic strengths that are strongly modulated by the enhancer sequence context (the flanking sequence, presence and diversity of other motif types, and distance between motifs), such that not all motif types can work in all positions. The context-specific modulation of motif function is also a hallmark of human enhancers and TF motifs, as we demonstrate experimentally. Overall, these two general principles of enhancer sequences are important to understand and predict enhancer function during development, evolution and in disease.
The rate of inversion fixation in plant genomes is highly variable
Authors: Hirabayashi Kaede , Owens Gregory L.
Published: September 2022

Abstract

Chromosomal inversions are theorized to play an important role in adaptation by preventing recombination, but testing this hypothesis requires an understanding of the rate of inversion fixation. Here we use chromosome-level whole genome assemblies for 32 genera of plants to ask how fast inversions accumulate and what factors affect this rate. We find that on average species accumulate 4 to 28 inversions per million generations, but this rate is highly variable, and we find no correlation between sequence divergence or repeat content and the number of inversions and only a small correlation with chromosome size. We also find that inversion regions are depleted for genes and enriched for TEs compared to the genomic background. This suggests that idiosyncratic forces, like natural selection and demography, are controlling how fast inversions fix.
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni
Authors: Newman Kahlan E. , Khalid Syma
Published: September 2022

The outer membrane factor CmeC of the efflux machinery CmeABC plays an important role in conferring antibiotic and bile resistance to Campylobacter jejuni. Curiously, the protein is N-glycosylated, with the glycans playing a key role in the effective function of this system. In this work we have employed atomistic equilibrium molecular dynamics simulations of CmeC in a representative model of the C. jejuni outer membrane to characterise the dynamics of the protein and its associated glycans. We show that the glycans are more conformationally labile than had previously been thought. The extracellular loops of CmeC visit the open and closed states freely suggesting the absence of a gating mechanism on this side, while the narrow periplasmic entrance remains tightly closed, regulated via coordination to solvated cations. We identify several cation binding sites on the interior surface of the protein. Additionally, we used steered molecular dynamics simulations to elucidate translocation pathways for a bile acid and a macrolide antibiotic. These, and additional equilibrium simulations suggest that the anionic bile acid utilises multivalent cations to climb the ladder of acidic residues that line the interior surface of the protein.
A metabolic sum rule dictates bacterial response to short-chain fatty acid stress
Authors: Taylor Brian R. , Patsalo Vadim , Okano Hiroyuki , Shen Yihui , Zhang Zhongge , Williamson James R. , Rabinowitz Joshua D. , Hwa Terence
Published: September 2022

Short-chain fatty acids (SCFAs) such as acetate accumulate in fermentative environments, inhibiting many types of bacteria. While it is known that cells accumulate SCFAs to high concentrations internally, the cause of SCFA toxicity is not understood. By forcingEscherichia colicells to accumulate a variety of “useless metabolites”, we establish via extensive ‘omic analysis a metabolic sum rule, by which the accumulation of exogenous metabolites such as acetate forces the depletion of endogenous metabolites. The latter leads to bottlenecks in biosynthesis, manifested as a simple linear relation between useless metabolite accumulation and growth reduction. Guided by quantitative models, we show that acetate-stressed cells optimize growth by partially acidifying their own cytoplasm, which reduces acetate accumulation, restoring the endogenous metabolites as allowed by the sum rule.
In situ imaging across ecosystems to resolve the fine-scale oceanographic drivers of a globally significant planktonic grazer
Authors: Greer Adam T. , Schmid Moritz S. , Duffy Patrick I. , Robinson Kelly L. , Genung Mark A. , Luo Jessica Y. , Panaïotis Thelma , Briseño-Avena Christian , Frischer Marc E. , Sponaugle Su , Cowen Robert K.
Published: September 2022

Doliolids are common gelatinous grazers in marine ecosystems around the world and likely influence carbon cycling due to their large population sizes with high growth and excretion rates. Aggregations or blooms of these organisms occur frequently, but they are difficult to measure or predict because doliolids are fragile, under sampled with conventional plankton nets, and can aggregate on fine spatial scales (1-10 m). Moreover, ecological studies typically target a single region or site that does not encompass the range of possible habitats favoring doliolid proliferation. To address these limitations, we combined in situ imaging data from six coastal ecosystems, including the Oregon shelf, northern California, southern California Bight, northern Gulf of Mexico, Straits of Florida, and Mediterranean Sea, to resolve and compare doliolid habitat associations during warm months when environmental gradients are strong and doliolid blooms are frequently documented. Higher ocean temperature was the strongest predictor of elevated doliolid abundances across ecosystems, with additional variance explained by chlorophyll-afluorescence and dissolved oxygen. For marginal seas with a wide range of productivity regimes, the nurse stage tended to comprise a higher proportion of the doliolids when total abundance was low. However, this pattern did not hold in ecosystems with persistent coastal upwelling. The doliolids tended to be most aggregated in oligotrophic systems (Mediterranean and southern California), suggesting that microhabitats within the water column favor proliferation on fine spatial scales. Similar comparative approaches can resolve the realized niche of fast-reproducing marine animals, thus improving predictions for population-level responses to changing oceanographic conditions.
Structural basis of nirmatrelvir and ensitrelvir resistance profiles against SARS-CoV-2 Main Protease naturally occurring polymorphisms
Authors: Noske Gabriela Dias , de Souza Silva Ellen , de Godoy Mariana Ortiz , Dolci Isabela , Fernandes Rafaela Sachetto , Guido Rafael Victório Carvalho , Sjö Peter , Oliva Glaucius , Godoy Andre Schutzer
Published: September 2022

SARS-CoV-2 is the causative agent of COVID-19. Mpro is the main viral protease, with a critical role in replication and, therefore, an attractive target for antiviral drug discovery. The clinically approved drug nirmatrelvir from Pfizer, and the clinical candidate ensitrelvir from Shionogi Pharmaceuticals had so far showed great potential for treatment of viral infections. Despite the importance of new therapeutics, the broad use of antivirals is often associated with mutation selection and resistance generation. Herein, we characterized 14 naturally occurring polymorphisms that are already in circulation and are within the radius of action of these two antivirals. Nirmatrelvir retained most of its in vitro activity against most polymorphism tested, while mutants G143S and Q189K were associated with higher resistance. For ensitrelvir, higher resistance was observed for polymorphisms M49I, G143S and R188S, but not for Q189K, suggesting a distinct resistance profile difference between the two inhibitors. The crystal structures of selected polymorphism reveal the structural basis for resistance generation. Our data will assist the monitoring of potential resistant strains, support the design of combined therapy to avoid resistance, as well as assist the development of a next generation of Mpro inhibitors
Assessing biological network dynamics: Comparing numerical simulations with analytical decomposition of parameter space
Authors: Hari Kishore , Duncan William , Ibrahim Mohammed Adil , Jolly Mohit Kumar , Cummins Breschine , Gedeon Tomas
Published: September 2022

Mathematical modeling of the emergent dynamics of gene regulatory networks (GRN) faces a double challenge of (a) dependence of model dynamics on parameters, and (b) lack of reliable experimentally determined parameters. In this paper we compare two complementary approaches for describing GRN dynamics across unknown parameters: (1) parameter sampling and resulting ensemble statistics used by RACIPE (RAndom CIrcuit PErturbation), and (2) use of rigorous analysis of combinatorial approximation of the ODE models by DSGRN (Dynamic Signatures Generated by Regulatory Networks). We find a very good agreement between RACIPE simulation and DSGRN predictions for four different 2- and 3-node networks typically observed in cellular decision making. This observation is remarkable since the DSGRN approach assumes that the Hill coefficients of the models are very high while RACIPE assumes the values in the range 1-6. Thus DSGRN parameter domains, explicitly defined by inequalities between systems parameters, are highly predictive of ODE model dynamics within a biologically reasonable range of parameters.
Phenotypic Assessment of Clinical Escherichia coli Isolates Predicts Uropathogenic Potential
Authors: Shea A.E. , Frick-Cheng A.E. , Smith S.N. , Mobley H.L.T.
Published: September 2022

For women in the United States, urinary tract infections (UTI) are the most frequent diagnosis in emergency departments, comprising 21.3% of total visits. Uropathogenic Escherichia coli (UPEC) causes ∼80% of uncomplicated UTI. To combat this public health issue, it is vital to characterize UPEC strains as well as differentiate them from commensal strains to reduce the overuse of antibiotics. Surprisingly, no genetic signature has been identified which clearly separates UPEC from other E. coli. Therefore, we examined whether phenotypic data could be predictive of uropathogenic potential. We screened 13 clinical strains of UPEC, isolated from cases of uncomplicated UTI in young otherwise healthy women, in a series of microbiological phenotypic assays using UPEC prototype strain CFT073 and non-pathogenic E. coli strain MG1655 K12 as controls. Phenotypes included adherence, iron acquisition, biofilm formation, human serum resistance, motility, and stress resistance. These data were able to predict the severity of bacterial burden in both the urine and bladders using a well-established experimental mouse model of UTI. Multiple linear regression using three different phenotypic assays, growth in minimal medium, siderophore production, and type 1 fimbrial expression, was predictive of bladder colonization (adjusted r2=0.6411). Growth in ex vivo human urine, hemagglutination of red blood cells, and motility modeled urine colonization (adjusted r2=0.4821). These results showcase the utility of phenotypic characterization to predict the severity of infection these strains may cause. We predict that these methods will also be applicable to other complex, genetically redundant, pathogens.

Importance

Urinary tract infections are the second leading infectious disease worldwide, occurring in over half of the female population during their lifetime. Most infections are caused by uropathogenic Escherichia coli (UPEC). These strains can commensally colonize the gut, but upon introduction to the urinary tract, can infect the host and cause disease. Clinically, it would be beneficial to screen patient E. coli strains to understand their pathogenic potential, which may lead to the administration of prophylactic antibiotic treatment for those with increased risk. Others have proposed the use of PCR-based genetic screening methods to detect UPEC and differentiate them from other E. coli pathotypes; however, this method has not yielded a consistent uropathogenic signature. Here, we have used phenotypic characteristics such as growth rate, siderophore production, and expression of fimbriae to successfully predict uropathogenic potential.
Oculomotor and neural correlates of semantic and morphological priming in natural sentence reading
Authors: Marjanovič Katarina , Vidal Yamil , Crepaldi Davide
Published: September 2022

Abstract

Our current understanding of visual word identification is difficult to extend to text reading–both experiments and theories focus primarily, if not exclusively, on out–of–context individual words. Here, we try to fill this gap by studying cross–word semantic and morphological priming within sentences in natural reading, in a novel coregistration paradigm with simultaneous recording of eye movements and electroencephalography. We report results from both eye tracking measures, and, more importantly, from Fixation-Related potentials, time-locked to the fixation onset on the target word. In both, semantic facilitation clearly emerged, while we observed no effect of morphological priming. These results may indicate that morphological agreement is at least partially computed outside of the lexical-semantic system which gives rise to semantic priming. These results provide new insight into the neural correlates of semantic and morphological priming in natural reading, revealing lexical dynamics as they likely emerge in our everyday reading experience.
Preschool-located influenza vaccination and influenza-like illness surveillance: an Italian pilot experience
Authors: Amendola Antonella , Barcellini Lucia , Borghi Elisa , Bianchi Silvia , Garancini Nicolò , Nava Chiara , Mari Alessandra , Sala Anna , Fappani Clara , Gori Maria , Ottaviano Emerenziana , Colzani Daniela , Biganzoli Elia Mario , Tanzi Elisabetta , Zuccotti Gianvincenzo
Published: September 2022

Improving influenza vaccination coverage in young children is crucial in reducing the spreading of influenza viruses, thus indirectly protecting the general population. Mass campaign needs to engage all the communities within the target population, overcoming socio-economic and cultural barriers. School-located interventions in some countries were successful in increasing vaccine acceptability and overall immunisation rates.

Influenza-like illnesses (ILI) share several symptoms with the ongoing COVID-19 pandemic, posing an important challenge for both diagnostics and public health burden. Self-sampling using non-invasive saliva collection could represent a suitable tool for respiratory infection surveillance.

This pilot study was carried out in a very densely populated Italian area, Milan, characterised by a high percentage of non-Italian citizens, often hard-to-reach by preventive programmes. We started a vaccine campaign with live-attenuated influenza vaccine (LAIV), recently recommended in Italy for children aged 2-6, coupled with a saliva-based ILI surveillance system in preschools.

We enrolled 432 children from 5 schools in the Milan suburbs, 31.2% of which received the LAIV. Thanks to the undertaken multicultural approach, 59% of the vaccinated children were non-Italian citizens.

Despite the COVID-19 preventive measures, i.e., school closure upon positive cases, highly affected the programmed surveillance, all the saliva samples from ILI cases, self-collected by parents at home, resulted adequate for viral molecular testing.

With correction measures, this pilot experience could be broadened to a large population, simultaneously allowing for a widespread ILI surveillance and flu immunisation.
Real-World COVID-19 Vaccine Protection Rates against Infection in the Delta and Omicron Eras
Authors: Zhu Yuru , Gu Jia , Qiu Yumou , Chen Song Xi
Published: September 2022

The real-world protection rates of vaccination (VPRs) against the SARS-Cov-2 infection are critical in formulating future vaccination strategies against the virus. Based on a varying co-efficient stochastic epidemic model, we obtain seven countries’ real-world VPRs using daily epidemiological and vaccination data, and find that the VPRs improved with more vaccine doses. The average VPR of the full vaccination was 82% (SE: 4%) and 61% (SE: 3%) in the pre-Delta and Delta-dominated periods, respectively. The Omicron variant reduced the average VPR of the full vaccination to 39% (SE: 2%). However, the booster dose restored the VPR to 63% (SE: 1%) which was significantly above the 50% threshold in the Omicron-dominated period. Scenario analyses show that the existing vaccination strategies have significantly delayed and reduced the timing and the magnitude of the infection peaks, respectively, and doubling the existing booster coverage would lead to 29% fewer confirmed cases and 17% fewer deaths in the seven countries compared to the outcomes at the existing booster taking rates. These call for higher full vaccine and booster coverage for all countries.
Evaluating prospective study registration and result reporting of trials conducted in Canada from 2009-2019
Authors: Alayche Mohsen , Cobey Kelly D. , Ng Jeremy Y. , Ardern Clare L. , Khan Karim M. , Chan An-Wen , Chow Ryan , Masalkhi Mouayad , Ayala Ana Patricia , Ebrahimzadeh Sanam , Ghossein Jason , Alayche Ibrahim , Willis Jessie V. , Moher David
Published: September 2022

Background

Adherence to study registration and reporting best practices are vital to foster evidence-based medicine. Poor adherence to these standards in clinical trials conducted in Canada would be detrimental to patients, researchers, and the public alike.

Methods

All registered clinical trials on ClinicalTrials.gov conducted in Canada as of 2009 and completed by 2019 were identified. A cross-sectional analysis of those trials assessed prospective registration, subsequent result reporting in the registry, and subsequent publication of study findings. The lead sponsor, phase of study, clinical trial site location, total patient enrollment, number of arms, type of masking, type of allocation, year of completion, and patient demographics were examined as potential effect modifiers to these best practices.

Results

A total of 6,720 trials met the inclusion criteria. From 2009-2019, 59% (n=3,967) of them were registered prospectively and 39% (n=2,642) reported their results in the registry. Of the trials registered between 2009-2014, 55% (n=1,482) were subsequently published in an academic journal. Of the 3,763 trials conducted exclusively in Canada, 3% (n=123) met all 3 criteria of: prospective registration, reporting in the registry, and publishing findings. In contrast, of the remaining 2,957 trials with both Canadian and international sites, 41% (n=1,238) had an overall compliance to these three criteria. Overall, the odds of having adherence to all three practices concurrently in Canadian trials decreases by 95% when compared to international trials (OR = 0.05; 95CI: 0.04 – 0.06).

Conclusion

Canadian clinical trials substantially lacked adherence to study registration and reporting best practices. Knowledge of this widespread non-compliance should motivate stakeholders in the Canadian clinical trials ecosystem to address and continue to monitor this problem. The data presented provides a baseline against which to compare any improvement in the registration and reporting of clinical trials in Canada.
Porcn is essential for growth and invagination of the mammalian optic cup
Authors: Fuhrmann Sabine , Ramirez Sara , Abouda Mirna Mina , Campbell Clorissa D.
Published: September 2022

Microphthalmia, anophthalmia, and coloboma (MAC) are congenital ocular malformations causing 25% of childhood blindness. The X-linked disorder Focal Dermal Hypoplasia is frequently associated with MAC and results from mutations in Porcn, a membrane bound O-acyl transferase required for palmitoylation of Wnts to activate multiple Wnt-dependent pathways. Wnt/β-catenin signaling is suppressed in the anterior neural plate for initiation of eye formation and is subsequently required during differentiation of the retinal pigment epithelium (RPE). Non-canonical Wnts are critical for early eye formation in frog and zebrafish, however, it is unclear whether this also applies to mammals. We performed ubiquitous conditional inactivation of Porcn in mouse around the eye field stage. In PorcnCKO, optic vesicles (OV) arrest in growth and fail to form an optic cup. Ventral proliferation is significantly decreased in the mutant OV, with a concomitant increase in apoptotic cell death. While pan-ocular transcription factors such as PAX6, SIX3, LHX2, PAX2 are present, indicative of maintenance of OV identity, regional expression of VSX2, MITF, OTX2 and NR2F2 is downregulated. Failure of RPE differentiation in PorcnCKO is consistent with downregulation of the Wnt/β-catenin effector LEF1, starting around 2.5 days after inactivation. This suggests that Porcn inactivation affects signaling later than a potential requirement for Wnts to promote eye field formation. Altogether, our data shows a novel requirement for Porcn in regulating growth and morphogenesis of the OV, likely by controlling proliferation and survival. In FDH patients with ocular manifestations, growth deficiency during early ocular morphogenesis may be the underlying cause for microphthalmia.
Nogo-A regulates the fate of human dental pulp stem cells towards osteogenic, adipogenic, and neurogenic differentiation
Authors: Lai Chai Foong , Shen Juliet , Balic Anamaria , Pagella Pierfrancesco , Schwab Martin E. , Mitsiadis Thimios A.
Published: September 2022

Human teeth are highly innervated organs that contain a variety of mesenchymal stem cell populations that could be used for cell-based regenerative therapies. Specific molecules are often used in these treatments to favorably modulate stem cells function and fate. Nogo-A, a key regulator of neuronal growth and differentiation, is already used in clinical tissue regeneration trials. While the functions of Nogo-A in neuronal tissues are extensively explored, its role in teeth still remains unknown. In this work, we first immunohistochemically analyzed the distribution of Nogo-A protein in the dental pulp of human teeth. Nogo-A is localized in a variety of cellular and structural components of the dental pulp, including odontoblasts, fibroblasts, neurons and vessels. We also cross-examined Nogo expression in the various pulp cell clusters in a single cell RNA sequencing dataset of human dental pulp, which showed high levels of expression in all cell clusters, including that of stem cells. We then assessed the role of Nogo-A on the fate of human dental pulp stem cells and their differentiation capacity in vitro. Using immunostaining, Alizarin Red S and Oil Red O staining we showed that Nogo-A delayed the differentiation of cultured dental pulp stem cells towards the osteogenic, adipogenic and neurogenic lineages, while addition of the blocking anti-Nogo-A antibody had opposite effects. These results were further confirmed by qRT-PCR, which demonstrated overexpression of genes involved in osteogenic (RUNX2, ALP, SP7/OSX), adipogenic (PPAR-γ2, LPL) and neurogenic (DCX, TUBB3, NEFL) differentiation in presence of the anti-Nogo-A antibody. Conversely, the osteogenic and adipogenic genes were downregulated by Nogo-A. Taken together, our results show that the functions of Nogo-A are not restricted to neuronal cells, but are extended to other cell populations, including dental pulp stem cells. We show that Nogo-A regulates their fates towards osteogenic, adipogenic and neurogenic differentiation, thus indicating its potential use in the clinics.
Prevalence and genetic characterisation of Giardia duodenalis in river water and riverbed sediment using next-generation sequencing
Authors: Mphephu Muofhe Grace , Momba Maggy Ndombo Benteke
Published: September 2022

Giardia duodenalis has been reported in different sources such as water, human stools, animal stools, vegetable farms and markets and soil of public places. However, different assemblages of G.duodenalis harboured in riverbed sediments have not yet been investigated. Thus, in this study, we quantified and genetically characterised G.duodenalis harboured in the water column and the riverbed sediment of the Apies River to cross this frontier of the unknown in freshwater sediment. Enumeration of G.duodenalis cysts was performed by epifluorescence microscopy observation and quantitative polymerase chain reaction (qPCR). Genetic characterisation was achieved by next-generation sequencing (NGS) using the β-giardin gene and bioinformatics analysis of the NGS data. Results obtained through epifluorescence microscopy revealed a prevalence rate of 87% (140/160) of G.duodenalis cysts in river water, which was higher than that observed in riverbed sediments (78%, 125/160). However, the qPCR assay showed that gene copies of G.duodenalis, which ranged between3.27 log10 and 7.26 log10 copies/L in re-suspended riverbed sediments, and between 0.49 log10 and 3.95 log10 copies/L in river water Genetic characterisation revealed six and seven assemblages in river water (A, B, C, D, E and F) and riverbed sediment (A, B, C, D, E, F and G), respectively. Both matrices carried similar sub-assemblages belonging to assemblages A (AI, AII and AIII) and B (BI, BII, BIII, BIV and BV), whereas riverbed sediment carried an additional sub-assemblage BX belonging to the assemblage B. The present genetic characterisation results suggest that Apies River water and its bed sediment harbour considerable quantities of G.duodenalis cysts that may cause infections in humans and animals if ingested. Consequently, monitoring of both the water column and respective bed sediments for the presence of G.duodenalis is justified to develop strategies for the protection of public health. This study also calls for urgent identification of point sources that are responsible for the contamination of this freshwater source and its sediment.

Author summary
Using ‘sentinel’ plants to improve early detection of invasive plant pathogens
Authors: Lovell-Read Francesca A. , Parnell Stephen R. , Cunniffe Nik J. , Thompson Robin N.
Published: September 2022

Infectious diseases of plants present an ongoing and increasing threat to international biosecurity, with wide-ranging implications. An important challenge in plant disease management is achieving early detection of invading pathogens in new locations, which requires effective surveillance through the implementation of appropriate monitoring programs. However, when monitoring relies on visual inspection as a means of detection, surveillance is often hindered by a long incubation period (delay from infection to symptom onset) during which plants may be infectious but not displaying visible symptoms. ‘Sentinel’ plants – alternative susceptible host species that display visible symptoms of infection more rapidly – could be introduced to at-risk populations and included in monitoring programs to act as early warning beacons for infection. However, while sentinel hosts exhibit faster disease progression and so allow pathogens to be detected earlier, this often comes at a cost: faster disease progression typically promotes earlier onward transmission. Here, we construct a computational model of pathogen transmission to explore this trade-off and investigate how including sentinel plants in monitoring programmes could facilitate earlier detection of invasive plant pathogens. Using Xylella fastidiosa infection in Olea europaea (European olive) as a current high profile case study, for which Catharanthus roseus (Madagascan periwinkle) is a candidate sentinel host, we apply a Bayesian optimisation algorithm to determine the optimal number of sentinel hosts to introduce for a given sampling effort, as well as the optimal division of limited surveillance resources between crop and sentinel plants. Our results demonstrate that including sentinel plants in monitoring programmes can reduce the expected prevalence of infection upon outbreak detection substantially, increasing the feasibility of local outbreak containment.
ZEB2 regulates the development of CD11c+ atypical B cells
Authors: Gao Xin , Shen Qian , Roco Jonathan A. , Frith Katie , Munier C. Mee Ling , Nekrasov Maxim , Dalton Becan , He Jin-Shu , Jaeger Rebecca , Cook Matthew C. , Zaunders John J. , Cockburn Ian A.
Published: September 2022

CD11c+ atypical B cells (ABC) are an alternative memory B cell lineage identified both in normal immune responses as well as pathogenic responses in autoimmunity. While it is clear that ABCs have a distinct transcriptional program, the factors that direct this program have not been identified. Here, we generated a human tonsil single-cell RNA-seq dataset and identified candidate transcription factors associated with the ABC population. We selected 8 of these transcription factors for further analysis based on their conserved expression in mouse ABC bulk RNA-seq datasets. Using an optimized CRSPR-Cas9 knockdown method we found that only zinc finger E-box binding homeobox 2 (Zeb2) knock-out impaired ABC formation. To assess the role of Zeb2 in ABC formation in vivo we used Zeb2fl/fl mice crossed to a CD23Cre line. Germinal center and plasma cell responses in these mice after Plasmodium sporozoite immunization were largely unaltered but we observed a specific defect in ABC formation. We further determined that ZEB2 haploinsufficient Mowat Wilson syndrome patients also have decreased circulating ABCs in the blood, supporting a role for this transcription factor in humans as well as mice. In sum, we identified Zeb2 as a key TF governing the formation of ABCs.
Interactions between culturable bacteria are highly non-additive
Authors: Baichman-Kass Amichai , Song Tingting , Friedman Jonathan
Published: September 2022

Microorganisms are found in diverse communities whose structure and function are determined by interspecific interactions. Just as single species seldom exist in isolation, communities as a whole are also constantly challenged and affected by external species. Though much work has been done on characterizing how individual species affect each other through pairwise interactions, the joint effects of multiple species on a single (focal) species, remain under explored. As such, it is still unclear how single species effects combine to a community-level effect on a species of interest. To explore this relationship, we assayed over 14,000 communities of two, three, and four bacterial species, measuring the effect of single, pairs of, and trios of 61 affecting species on six different focal species. Our results demonstrate that joint effects of multiple species on a focal species are typically not given by the sum of the effects of individual affecting species. Rather, they are dominated by the strongest individual-species effect. Therefore, while joint effects of multiple species are often highly non-additive, they can still be derived from the effects of individual species, making it plausible to map complex interaction networks based on pairwise measurements. This finding is important for understanding the fate of species introduced into an occupied environment, and is relevant for applications in medicine and agriculture, such as probiotics and biocontrol agents, as well as for ecological questions surrounding migrating and invasive species.
Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance
Authors: Hendriks Kasper P. , Kiefer Christiane , Al-Shehbaz Ihsan A. , Bailey C. Donovan , Hooft van Huysduynen Alex , Nikolov Lachezar A. , Nauheimer Lars , Zuntini Alexandre R. , German Dmitry A. , Franzke Andreas , Koch Marcus A. , Lysak Martin A. , Toro-Núñez Óscar , Özüdoğru Barış , Invernón Vanessa R. , Walden Nora , Maurin Olivier , Hay Nikolai M. , Shushkov Philip , Mandáková Terezie , Thulin Mats , Windham Michael D. , Rešetnik Ivana , Španiel Stanislav , Ly Elfy , Pires J. Chris , Harkess Alex , Neuffer Barbara , Vogt Robert , Bräuchler Christian , Rainer Heimo , Janssens Steven B. , Schmull Michaela , Forrest Alan , Guggisberg Alessia , Zmarzty Sue , Lepschi Brendan J. , Scarlett Neville , Stauffer Fred W. , Schönberger Ines , Heenan Peter , Baker William J. , Forest Félix , Mummenhoff Klaus , Lens Frederic
Published: September 2022

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plantArabidopsis thalianaand numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene ‘icehouse origin’ of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodateArabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.
Cellular senescence promotes progenitor cell expansion during axolotl limb regeneration
Authors: Yu Qinghao , Walters Hannah E. , Pasquini Giovanni , Singh Sumeet Pal , Lachnit Martina , Oliveira Catarina , León-Periñán Daniel , Petzold Andreas , Kesavan Preethi , Subiran Cristina , Garteizgogeascoa Ines , Knapp Dunja , Wagner Anne , Bernardos Andrea , Alfonso María , Nadar Gayathri , Graf Alwin M. , Troyanovskiy Konstantin E. , Dahl Andreas , Busskamp Volker , Martínez-Máñez Ramón , Yun Maximina H.
Published: September 2022

Axolotl limb regeneration is accompanied by the transient induction of cellular senescence within the blastema, the structure which nucleates regeneration. The precise role of this blastemal senescent cell (bSC) population, however, remains unknown. Here, through a combination of gain- and loss-of-function assays, we elucidate the functions and molecular features of cellular senescencein vivo. We demonstrate that cellular senescence plays a positive role during axolotl regeneration, by creating a pro-proliferative niche that supports progenitor cell expansion and blastema outgrowth. Senescent cells impact on their microenvironment via Wnt pathway modulation. Further, we uncover a link between Wnt signalling and senescence induction, and propose that bSC-derived Wnt signals facilitate the proliferation of neighbouring cells in part by preventing their induction into senescence. This work defines the roles of cellular senescence in regeneration of complex structures.
The oxygen tolerant reductive glycine pathway in eukaryotes – a native methanol, formate and CO2 assimilation pathway in the yeast Komagataella phaffii
Authors: Mitic Bernd M. , Troyer Christina , Hann Stephan , Mattanovich Diethard
Published: September 2022

The current climate change is mainly driven by excessive anthropogenic CO2 emissions. As industrial bioprocesses depend mostly on food competing organic feedstocks or fossil raw materials, we regard CO2 co-assimilation or the use of CO2-derived methanol or formate as carbon source as pathbreaking contribution to the solution of this global problem. The number of industrially relevant microorganisms that can use these two carbon sources is limited, and even less can concurrently co-assimilate CO2. Hence, we searched for alternative native methanol and native formate assimilation pathways which co-assimilate CO2 in the industrially relevant methylotrophic yeast Komagataella phaffii (Pichia pastoris). Using 13C-tracer-based metabolomics techniques and metabolic engineering approaches we discovered and confirmed a natively active pathway that can perform all three assimilations: the oxygen tolerant reductive glycine pathway. This finding paves the way towards metabolic engineering of formate and CO2 utilisation for the production of proteins, biomass or chemicals in yeast.
ONECUT2 restricts Microfold cell numbers in the small intestine; a multi-omics study
Authors: Luna Velez Maria V. , Neikes Hannah K. , Snabel Rebecca R. , Quint Yarah , Qian Chen , Martens Aniek , Veenstra Gert Jan C. , Freeman Michael R. , van Heeringen Simon J. , Vermeulen Michiel
Published: September 2022

Microfold (M) cells reside in the intestinal epithelium of Peyer’s patches. Their unique ability to take up and transport antigens from the intestinal lumen to the underlying lymphoid tissue is key in the regulation of the gut-associated immune response. Here, we applied a (single-cell) multi-omics approach to investigate the molecular mechanisms that drive M cell differentiation in mouse small intestinal organoids. We generated a comprehensive profile of chromatin accessibility changes and transcription factor dynamics duringin vitroM cell differentiation, allowing us to uncover numerous cell type-specific regulatory elements and associated transcription factors. Single-cell RNA sequencing resulted in the identification of an M cell precursor population. Our new computational tool SCEPIA determined that these precursor cells were characterized by high expression of and motif activity for the transcription factor ONECUT2. Subsequent perturbation experiments revealed that ONECUT2 acts downstream of the RANK/RANKL signalling to support Enterocyte differentiation and restrict M cell lineage specificationin vitroandin vivo, thereby regulating mucosal immunity. This study provides a useful blueprint for future investigations of cell fate switches in the intestinal epithelium.
Inferring protein fitness landscapes from laboratory evolution experiments
Authors: D’Costa Sameer , Hinds Emily C. , Freschlin Chase R. , Song Hyebin , Romero Philip A.
Published: September 2022

Directed laboratory evolution applies iterative rounds of mutation and selection to explore the protein fitness landscape and provides rich information regarding the underlying relationships between protein sequence, structure, and function. Laboratory evolution data consist of protein sequences sampled from evolving populations over multiple generations and this data type does not fit into established supervised and unsupervised machine learning approaches. We develop a statistical learning framework that models the evolutionary process and can infer the protein fitness landscape from multiple snapshots along an evolutionary trajectory. We apply our modeling approach to dihydrofolate reductase (DHFR) laboratory evolution data and the resulting landscape parameters capture important aspects of DHFR structure and function. We use the resulting model to understand the structure of the fitness landscape and find numerous examples of epistasis but an overall global peak that is evolutionarily accessible from most starting sequences. Finally, we use the model to perform an in silico extrapolation of the DHFR laboratory evolution trajectory and computationally design proteins from future evolutionary rounds.
Hallucination of closed repeat proteins containing central pockets
Authors: An Linna , Hicks Derrick R , Zorine Dmitri , Dauparas Justas , Wicky Basile I. M. , Milles Lukas F. , Courbet Alexis , Bera Asim K. , Nguyen Hannah , Kang Alex , Carter Lauren , Baker David
Published: September 2022

In pseudocyclic proteins such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity which can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in E. coli are consistent with the design models, and two crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small molecule binders or enzymes.
Comparison of Culture Results between Specimens from Corneal Scraping with Microhomogenization and Corneal Swab in Moderate and Severe Bacterial Corneal Ulcers
Authors: Martha Faraby , Edwar Lukman , Karuniawati Anis , Fuady Ahmad , Tuasikal Ramadhiana Maktazula
Published: September 2022

Purpose

To compare bacterial culture results from corneal infiltrate specimens taken by corneal scrapping followed by microhomogenization and direct scraping methods.

Methods

This study was a comparative cross-sectional, with 18 subjects divided into two randomized groups; Group A (first scrapings then swab), and group B (first swab then scrapings). Both scraping and swab methods are separated and then compared in data analysis.

Results

The proportion of Gram according to culture in the scraping-microhomogenization technique was 6/13 (46.2%) and the proportion of Gram according to cultures in the swab technique was 5/13 (38.5%). McNemar test p-value is 1.000 (p>0.05). The proportion of positive cultures in the scraping-microhomogenization technique was 13/18 (72.2%) and the proportion of positive culture in swab technique was 9/18 (50%). McNemar test p-value is 0.219 (p> 0.05). The Kappa suitability test value from scraping-microhomogenization technique against the corneal swab is 0.333.

Conclusion

The results of bacterial culture from specimens taken by the corneal scraping followed by microhomogenization have a higher positive culture compared to those taken by corneal swab, but not statistically significant.
Age-related differences in cancer relative survival in the US: a SEER-18 analysis
Authors: Withrow Diana R , Nicholson Brian D , Morris Eva JA , Wong Melisa L , Pilleron Sophie
Published: September 2022

Cancer survival has improved since the 1990s, but to different extents across age groups, with a disadvantage for older adults. We aimed to quantify age-related differences in relative survival (RS - one-year, and one-year conditioning on surviving one year) for 10 common cancer types by stage at diagnosis. We used data from 18 United States Surveillance Epidemiology and End Results cancer registries and included cancers diagnosed between 2012-2016 followed until December 31, 2017. We estimated absolute differences in RS between the 50-64 age group and the 75-84 age group. The smallest differences were observed for prostate and breast cancers (1.8%-points [95% confidence interval (CI):1.5-2.1] and 1.9%-points [95%CI:1.5-2.3], respectively). The largest was for ovarian cancer (27%-points, 95%CI:24-29). For other cancers, differences ranged between 7 (95%CI:5-9, esophagus) and 18%-points (95%CI: 17-19, pancreas). Except for pancreatic cancer, cancer type and stage combinations with very high (>95%) or very low (<40%) 1-year RS tended to have smaller age-related differences in survival than those with mid-range prognoses. Age-related differences in one-year survival conditioning on having survived one-year were small for most cancer and stage combinations. The broad variation in survival differences by age across cancer types and stages, especially in the first year, age-related differences in survival are likely influenced by amenability to treatment. Future work to measure the extent of age-related differences that are avoidable, and identify how to narrow the survival gap, may have most benefit by prioritizing cancers with relatively large age-related differences in survival (e.g., stomach, esophagus, liver and pancreas).

Novelty and Impact

In this analysis of United States population-based cancer registry data, age-related differences in cancer survival varied widely, ranging from less than 1% absolute difference in localized breast and prostate cancer survival to over 30% absolute difference in localized pancreatic cancer survival. Focused efforts to reduce age-related differences in cancer survival may have greatest impact by prioritizing cancer site and stage combinations with the widest differences.