bluuebunny/crossref_metadata_2025 huggingface dataset:
Transmission mode shapes host specialization of the phyllosphere microbiome
Authors: Meyer Kyle M. , Muscettola Isabella E. , Vasconcelos Ana Luisa S. , Sherman Julia K. , Metcalf C. Jessica E. , Lindow Steven E. , Koskella Britt
Published: May 2023

The collection of microorganisms inhabiting aboveground plant tissue, termed the phyllosphere microbiome, is shaped by both microbial dispersal and host filtering effects. Because plants often occur in multispecies assemblages, microbiome diversity is likely shaped by plant community composition through microbial transmission between conspecific (same species) and heterospecific (different species) host plants. Although rarely examined, the relative incidence of con-versus heterospecific transmission should impact microbiome-level specialization. Using four species of plants we experimentally tested this idea by passaging an initially diverse microbial community either between conspecific or heterospecific plants in the greenhouse. While conspecific transmission lines exhibited persistent host effects, these effects decreased in the heterospecific transmission lines, suggesting a shift towards more generalist microbiomes. Similarly, when microbiomes were transplanted onto a set of novel host plant species, host effects were weaker for these heterospecific lines than the conspecific lines. Finally, microbiomes conspecifically passaged on tomato plants were found to outcompete those passaged on either bean or pepper when co-inoculated onto tomato hosts, suggesting microbiome-level host specialization under conspecific transmission. Overall, we find that both transmission mode and host association history shape microbiome diversity, that repeated conspecific transmission results in microbiome specialization, and that repeated heterospecific transmission can drive microbiomes to develop generalist characteristics.
RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis
Authors: Kaye Emily G. , Nelson Geoffrey M. , Zomer Helena D. , Roy Debarun , Joseph Irene Infancy , Adelman Karen , Reddi Prabhakara P.
Published: May 2023

Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to mature spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double strand break formation by SPO11, and disruption of SPO11 expression in germ cells lacking NELF.
POT1 recruits and regulates CST–Polα/Primase at human telomeres
Authors: Cai Sarah W. , Takai Hiroyuki , Walz Thomas , de Lange Titia
Published: May 2023

Telomere maintenance requires extension of the G-rich telomeric repeat strand by telomerase and fill-in synthesis of the C-rich strand by Polα/Primase. Telomeric Polα/Primase is bound to Ctc1-Stn1-Ten1 (CST), a single-stranded DNA-binding complex. Like mutations in telomerase, mutations affecting CST–Polα/Primase result in pathological telomere shortening and cause a telomere biology disorder, Coats plus (CP). We determined cryogenic electron microscopy structures of human CST bound to the shelterin heterodimer POT1/TPP1 that reveal how CST is recruited to telomeres by POT1. Phosphorylation of POT1 is required for CST recruitment, and the complex is formed through conserved interactions involving several residues mutated in CP. Our structural and biochemical data suggest that phosphorylated POT1 holds CST–Polα/Primase in an inactive auto-inhibited state until telomerase has extended the telomere ends. We propose that dephosphorylation of POT1 releases CST–Polα/Primase into an active state that completes telomere replication through fill-in synthesis.
Jump-start and push-start: Mutual activation through crosstalk in coupled quorum sensing pathways
Authors: Sanders Joseph , Akl Hoda , Hagen Stephen J. , Xue BingKan
Published: May 2023

Many bacterial species are able to coordinate population-wide phenotypic responses through the exchange of diffusible chemical signals, a behavior known as quorum sensing. A quorum sensing bacterium may employ multiple types of chemical signals and detect them using inter-connected pathways that crosstalk with each other. While there are many hypotheses for the advantages of sensing multiple signals, the prevalence and functional significance of crosstalk between the sensing pathways are much less understood. Here we explore the effect of intra-cellular signal crosstalk on a simple model of a quorum sensing circuit. The model captures key aspects of typical quorum sensing pathways, including detection of multiple signals that crosstalk at the receptor and promoter levels, positive feedback, and hierarchical positioning of sensing pathways. We find that a variety of behaviors can be tuned by modifying crosstalk and feedback strengths. These include activation or inhibition of one output by the non-cognate signal, broadening of dynamic range of the outputs, and the ability of either the upstream or downstream branch to modulate the feedback circuit of the other branch. Our findings show how crosstalk between quorum sensing pathways can be viewed not solely as a detriment to the flow of information but also as a mechanism that enhances the functional range of the full regulatory system: When positive feedback systems are coupled through crosstalk, several new modes of activation or deactivation become possible.
Gibberellin and the miRNA156-targetedSlSBPssynergistically regulate tomato floral meristem activity and fruit patterning
Authors: Ferigolo Leticia F. , Vicente Mateus H. , Correa Joao P. O. , Barrera-Rojas Carlos H. , Silva Eder M. , Silva Geraldo F.F. , Carvalho Airton , Peres Lazaro E.P. , Ambrosano Guilherme B. , Margarido Gabriel R. A. , Sablowski Robert , Nogueira Fabio T.S.
Published: May 2023

Many developmental processes associated with fruit development take place at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GA) interact to control flowering time, but their interplay in subsequent stages of reproductive development is poorly understood. Here, we show that GA and miR156 function in tomato FM and fruit patterning. High GA responses or overexpression of miR156 (156OE), which leads to low levels of miR156-targetedSQUAMOSA PROMOTER BINDING PROTEIN– LIKE(SPL/SBP), resulted in enlarged FMs, defects in FM determinacy and fruits with increased locule number. Conversely, low GA responses reduced fruit indeterminacy and locule number, and overexpression of a miR156-resistantSlSBP15allele (rSBP15) reduced cell number and size in the FM, as well as locule number. GA responses were partially required for the fruit defects observed in 156OE andrSBP15plants. Transcriptome analysis and genetic interactions revealed shared and divergent functions of miR156-targetedSlSBPs, PROCERA/DELLAand the classicalWUSCHEL/CLAVATApathway, which has been previously associated with meristem size and determinacy. Our findings reveal that the miR156/SlSBP/GA regulatory module is deployed differently depending on developmental stage and create novel opportunities to genetically fine-tune aspects of fruit development that have been important for tomato domestication.
Herbarium specimens as tools for exploring the evolution of biosynthetic pathways to fatty acid-derived natural products in plants
Authors: Fitzgibbons Emma , Lastovich Jacob , Scott Samuel , Grusz Amanda L. , Busta Lucas
Published: May 2023

Plants synthesize natural products via lineage-specific offshoots of their core metabolic pathways, including fatty acid synthesis. Recent studies have shed light on new fatty acid-derived natural products and their biosynthetic pathways in disparate plant species. Inspired by this progress, we set out to expand the tools available for exploring the evolution of biosynthetic pathways to fatty-acid derived products. We sampled representative species from all major clades of euphyllophytes, including ferns, gymnosperms, and angiosperms (monocots and eudicots), and we show that quantitative profiles of fatty-acid derived surface waxes from preserved plant specimens are consistent with those obtained from freshly collected tissue. We then sampled herbarium specimens representing >50 monocot species to assess the phylogenetic distribution and infer the evolutionary origins of two fatty acid-derived natural products found in that clade: beta-diketones and alkyl resorcinols. These chemical data, combined with analyses of 26 monocot genomes, suggest whole genome duplication as a likely mechanism by which both diketone and alkylresorcinol synthesis evolved from an ancestral alkylresorcinol synthase-like polyketide synthase. This work reinforces the widespread utility of herbarium specimens for studying leaf surface waxes (and possibly other chemical classes) and reveals the evolutionary origins of fatty acid-derived natural products within monocots.

Significance Statement

Plant chemicals are key components in our food and medicine, and advances in genomic technologies are accelerating plant chemical research. However, access to tissue from specific plant species can still be rate-limiting, especially for species that are difficult to cultivate, endangered, or inaccessible. Here, we demonstrate that herbarium specimens provide a semiquantitative proxy for the cuticular wax profiles of their fresh counterparts, thus reducing the need to collect fresh tissue for studies of wax chemicals and suggesting the same may also be true of other plant chemical classes. We also demonstrate the utility of combining herbarium-based plant chemical profiling with genomic analyses to understand the evolution of plant natural products.
Evolving spike-proteinN-glycosylation in SARS-CoV-2 variants
Authors: Baboo Sabyasachi , Diedrich Jolene K. , Torres Jonathan L. , Copps Jeffrey , Singh Bhavya , Garrett Patrick T. , Ward Andrew B. , Paulson James C. , Yates John R.
Published: May 2023

Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavilyN-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installedN-glycans. Using highly-sensitive DeGlyPHER approach, we compared theN-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found thatN-glycan processing is conserved at most sites. However, in multiple variants, processing ofN-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
Endo-Lysosome-Targeted Nanoparticle Delivery of Antiviral Therapy for Coronavirus Infections
Authors: Petcherski Anton , Tingley Brett M , Martin Andrew , Adams Sarah , Brownstein Alexandra J , Steinberg Ross A , Shabane Byourak , Ngo Jennifer , Osto Corey , Garcia Gustavo , Veliova Michaela , Arumugaswami Vaithilingaraja , Colby Aaron H , Shirihai Orian S , Grinstaff Mark W
Published: May 2023

SARS-CoV-2 can infect cells through endocytic uptake, a process which is targeted by inhibition of lysosomal proteases. However, clinically this approach to treat viral infections has afforded mixed results, with some studies detailing an oral regimen of hydroxychloroquine accompanied by significant off-target toxicities. We rationalized that an organelle-targeted approach will avoid toxicity while increasing the concentration of the drug at the target. Here we describe a lysosome-targeted, mefloquine-loaded poly(glycerol monostearate-co-ε-caprolactone) nanoparticle (MFQ-NP) for pulmonary delivery via inhalation. Mefloquine is a more effective inhibitor of viral endocytosis than hydroxychloroquine in cellular models of COVID-19. MFQ-NPs are less toxic than molecular mefloquine, 100-150 nm in diameter, and possess a negative surface charge which facilitates uptake via endocytosis allowing inhibition of lysosomal proteases. MFQ-NPs inhibit coronavirus infection in mouse MHV-A59 and human OC43 coronavirus model systems and inhibit SARS-CoV-2-WA1 and its Omicron variant in a human lung epithelium model. This study demonstrates that organelle-targeted delivery is an effective means to inhibit viral infection.
Ivermectin resistance in dung beetles exposed for multiple generations
Authors: González-Tokman Daniel , Arellano-Torres Antonio , Baena-Díaz Fernanda , Bustos-Segura Carlos , Martínez M. Imelda
Published: May 2023

Ivermectin is an antiparasitic drug commonly used in cattle, that is excreted in dung, causing lethal and sub-lethal effects on coprophagous non-target fauna. Given that cattle parasites generate resistance to ivermectin, farmers have increased the used doses, with a consequent threat to wild fauna. The dung beetle speciesEuoniticellus intermediusprovides ecosystem services by burying dung in cattle pastures, however it is highly threatened by ivermectin. Here we experimentally tested whetherE. intermediusgenerates resistance against ivermectin after being exposed for several generations to a sublethal dose. We generated two laboratory lines where beetles were exposed to either ivermectin-treated or ivermectin-free dung for 18 generations. We compared reproductive success (total brood balls, emerged beetles, proportion emerged and days to emergence) of beetles from both lines across generations. Additionally, for each line, we carried-out toxicity experiments with increasing ivermectin concentrations to determine if sensitivity to ivermectin was reduced after some generations of exposure (i. e. if beetles acquired ivermectin resistance by means of transgenerational effects). Our results show that dung beetles do not generate resistance to ivermectin after 18 generations of continuous exposure and quantitative genetic analyses show low genetic variation in response to ivermectin across generations. Together, these results indicate low potential for adaptation to the contaminant in the short term. Although we cannot exclude that adaptation could occur in the long term, our results and comparative evidence in other insects indicate that dung beetles, and probably other species, are at risk of extinction in ivermectin-contaminated pastures unless they are pre-adapted to tolerate high ivermectin concentrations.
Lévy movements and a slowly decaying memory allow efficient collective learning in groups of interacting foragers
Authors: Falcón-Cortés Andrea , Boyer Denis , Aldana Maximino , Ramos-Fernández Gabriel
Published: May 2023

Many animal species benefit from spatial learning to adapt their foraging movements to the distribution of resources. Learning involves the collection, storage and retrieval of information, and depends on both the random search strategies employed and the memory capacities of the individual. For animals living in social groups, spatial learning can be further enhanced by information transfer among group members. However, how individual behavior affects the emergence of collective states of learning is still poorly understood. Here, with the help of a spatially explicit agent-based model where individuals transfer information to their peers, we analyze the effects on the use of resources of varying memory capacities in combination with different exploration strategies, such as ordinary random walks and Lévy flights. We find that individual Lévy displacements associated with a slow memory decay lead to a very rapid collective response, a high group cohesion and to an optimal exploitation of the best resource patches in static but complex environments, even when the interaction rate among individuals is low.

Author Summary

How groups of social animals collectively learn to find and exploit resources in complex environments is not well-understood. By means of a computational model where individuals are initially spread out across a landscape, we study the effects of individual exploratory behaviors and memory capacities on the emergence of spatial learning. Collective learning emerges spontaneously only if group members transfer information between each other at a sufficiently high rate, so that individual experiences can be used by others. In static but heterogeneous environments with many resource sites of varying attractiveness, we find that random displacements over many spatial scales combined with a slow memory decay lead to a rapid collective response and highly cohesive groups. Collective learning is noticeable through an optimal exploitation of the best resource sites, which far exceeds what individuals would achieve on their own. Our study sheds light on important mechanisms responsible for collective learning in ecology, with potential applications in other areas of science.
Linking bacterial tetrabromopyrrole biosynthesis to coral metamorphosis
Authors: Alker Amanda T. , Farrell Morgan V. , Demko Alyssa M. , Purdy Trevor N. , Adak Sanjoy , Moore Bradley S. , Sneed Jennifer M. , Paul Valerie J. , Shikuma Nicholas J.
Published: May 2023

An important factor dictating coral fitness is the quality of bacteria associated with corals and coral reefs. One way that bacteria benefit corals is by stimulating the larval to juvenile life cycle transition of settlement and metamorphosis. Tetrabromopyrrole (TBP) is a small molecule produced by bacteria that stimulates metamorphosis in a range of coral species. A standing debate remains, however, about whether TBP biosynthesis from livePseudoalteromonasbacteria is the primary stimulant of coral metamorphosis. In this study, we create aPseudoalteromonassp. PS5 mutant lacking the TBP brominase gene,bmp2. Using this mutant, we confirm that thebmp2gene is critical for TBP biosynthesis inPseudoalteromonassp. PS5. Mutation of this gene ablates the bacterium’s ability in live cultures to stimulate the metamorphosis of the stony coralPorites astreoides. We further demonstrate that expression of TBP biosynthesis genes is strongest in stationary and biofilm modes of growth, wherePseudoalteromonassp. PS5 might exist within surface-attached biofilms on the sea floor. Finally, we create a modular transposon plasmid for genomic integration and fluorescent labeling ofPseudoalteromonassp. PS5 cells. Our results functionally link a TBP biosynthesis gene from live bacteria to a morphogenic effect in corals. The genetic techniques established here provide new tools to explore coral-bacteria interactions and could help to inform future decisions about utilizing marine bacteria or their products for restoring degraded coral reefs.
Succinylation of a KEAP1 sensor lysine promotes NRF2 activation
Authors: Ibrahim Lara , Stanton Caroline , Nutsch Kayla , Nguyen Thu , Li-Ma Chloris , Ko Yeonjin , Lander Gabriel C. , Wiseman R. Luke , Bollong Michael J.
Published: May 2023

Crosstalk between metabolism and stress-responsive signaling is essential to maintaining cellular homeostasis. One way this crosstalk is achieved is through the covalent modification of proteins by endogenous, reactive metabolites that regulate the activity of key stress-responsive transcription factors such as NRF2. Several metabolites including methylglyoxal, glyceraldehyde 3-phosphate, fumarate, and itaconate covalently modify sensor cysteines of the NRF2 regulatory protein KEAP1, resulting in stabilization of NRF2 and activation of its cytoprotective transcriptional program. Here, we employed a shRNA-based screen targeting the enzymes of central carbon metabolism to identify additional regulatory nodes bridging metabolic pathways to NRF2 activation. We found that succinic anhydride, increased by genetic depletion of the TCA cycle enzyme succinyl-CoA synthetase or by direct administration, results in N-succinylation of lysine 131 of KEAP1 to activate NRF2 transcriptional signaling. This study identifies KEAP1 as capable of sensing reactive metabolites not only by several cysteine residues but also by a conserved lysine residue, indicating its potential to sense an expanded repertoire of reactive metabolic messengers.
Dark nanodiscs as a model membrane for evaluating membrane protein thermostability by differential scanning fluorimetry
Authors: Selvasingh Jazlyn A. , McDonald Eli Fritz , Mckinney Jacob R. , Meiler Jens , Ledwitch Kaitlyn V.
Published: May 2023

Measuring protein thermostability provides valuable information on the biophysical rules that govern structure-energy relationships of proteins. However, such measurements remain a challenge for membrane proteins. Here, we introduce a new experimental system to evaluate membrane protein thermostability. This system leverages a recently-developed non-fluorescent membrane scaffold protein (MSP) to reconstitute proteins into nanodiscs and is coupled with a nano-format of differential scanning fluorimetry (nanoDSF). This approach offers a label-free and direct measurement of the intrinsic tryptophan fluorescence of the membrane protein as it unfolds in solution without signal interference from the “dark” nanodisc. In this work, we demonstrate the application of this method using the disulfide bond formation protein B (DsbB) as a test membrane protein. NanoDSF measurements of DsbB reconstituted in dark nanodiscs show a complex biphasic thermal unfolding pattern in the presence of lipids with a minor unfolding transition followed by a major transition. The inflection points of the thermal denaturation curve reveal two distinct unfolding midpoint melting temperatures (Tm) of 70.5 °C and 77.5 °C, consistent with a three-state unfolding model. Further, we show that the catalytically conserved disulfide bond between residues C41 and C130 drives the intermediate state of the unfolding pathway for DsbB in a nanodisc. We introduce this method as a new tool that can be used to understand how compositionally, and biophysically complex lipid environments drive membrane protein stability.
Medication-Invariant Resting Aperiodic and Periodic Neural Activity in Parkinson’s Disease
Authors: McKeown Daniel J , Jones Manon , Pihl Camilla , Finley Anna , Kelley Nicholas , Baumann Oliver , Schinazi Victor R. , Moustafa Ahmed A. , Cavanagh James F. , Angus Douglas J
Published: May 2023

Parkinson’s Disease (PD) has been associated with greater total power in canonical frequency bands (i.e., alpha, beta) of the resting electroencephalogram (EEG). However, PD has also been associated with a reduction in the proportion of total power across all frequency bands. This discrepancy may be explained by aperiodic activity (exponent and offset) present across all frequency bands. Here, we examined differences in the eyes-open and eyes-closed resting EEG of PD participants (N= 26) on and off medication, and age-matched controls (CTL;N= 26). We extracted power from canonical frequency bands using traditional methods (total alpha and beta power) and extracted separate parameters for periodic (parameterized alpha and beta power) and aperiodic activity (exponent and offset). Cluster-based permutation tests over spatial and frequency dimensions indicated that total alpha and beta power, and aperiodic exponent and offset were greater in PD participants, independent of medication status. After removing the exponent and offset, greater alpha power in PD (vs. CTL) was only present in eyes-open recordings and no reliable differences in beta power were observed. Differences between PD and CTLs in the resting EEG are likely driven by aperiodic activity, suggestive of greater relative inhibitory neural activity and greater neuronal spiking. Our findings suggest that resting EEG activity in PD is characterized by medication-invariant differences in aperiodic activity which is independent of the increase in alpha power with EO. This highlights the importance of considering aperiodic activity contributions to the neural correlates of brain disorders.
First trimester maternal serum microRNA expression profile differentiates between uncomplicated pregnancies, and pregnancies which develop pre-eclampsia
Authors: Hedley Paula L. , Larsen Severin Olesen , Wøjdemann Karen R. , Shalmi Anne-Cathrine , Placing Sophie , Rode Line , Gjerris Anne Catrine , Sundberg Karin , Tabor Ann , Christiansen Michael
Published: May 2023

Numerous circulating microRNAs (miRNAs) have been detected in maternal blood. Initial studies in third trimester demonstrated differential miRNA expression profiles between uncomplicated pregnancies and pregnancies complicated by pre-eclampsia (PE). Recently, studies in first trimester have shown similar differential profiles, however, these studies were often under-powered. We conducted a nested case-control study, in which serum samples, taken between 10-14 weeks gestation, were obtained from 413 singleton pregnant women, 126 of which later developed PE. Total RNAs were purified and a selection of 46 miRNAs plus two miRNA controls were quantitated by real time quantitative PCR. Seven of the miRNAs, hsa-miR-181b-5p, -323a-3p, -518b, -363-3p, -20a-5p, -29a-3p, and -142-3p, could differentiate between uncomplicated pregnancies and pregnancies which develop PE, but only a single miRNA, hsa-miR-363-3p, could differentiate between mild and severe PE. A combination of all seven differentiating miRNAs was the best at discriminating between PE and uncomplicated pregnancies (AUC= 0.879). In conclusion, first trimester maternal serum miRNA expression profile could differentiate between uncomplicated pregnancies and pregnancies complicated by PE. These circulating miRNA markers have the potential to improve risk assessment of PE in the first trimester, weeks before the onset of symptoms.
The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs
Authors: Frediani Jennifer K. , Parsons Richard , McLendon Kaleb B. , Westbrook Adrianna L. , Lam Wilbur , Martin Greg , Pollock Nira R.
Published: May 2023

Background

Early in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads.

Methods

We assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants ≥16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated.

Results

Of 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.

In 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms.

Conclusions

In a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.

Key Points

In a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.
Two-Step Light Gradient Boosted Model to identify human West Nile Virus infection risk factor in Chicago
Authors: Wan Guangya (Wayne) , Allen Joshua , Ge Weihao , Rawlani Shubham , Uelmen John , Mainzer Liudmila Sergeevna , Smith Rebecca Lee
Published: May 2023

West Nile virus (WNV), a flavivirus transmitted by mosquito bites, causes primarily mild symptoms but can also be fatal. Therefore, predicting and controlling the spread of West Nile virus is essential for public health in endemic areas. We hypothesized that socioeconomic factors may influence human risk from WNV. We analyzed a list of weather, land use, mosquito surveillance, and socioeconomic variables for predicting WNV cases in 1-km hexagonal grids across the Chicago metropolitan area. We used a two-stage lightGBM approach to perform the analysis and found that hexagons with incomes above and below the median are influenced by the same top characteristics. We found that weather factors and mosquito infection rates were the strongest common factors. Land use and socioeconomic variables had relatively small contributions in predicting WNV cases. The Light GBM handles unbalanced data sets well and provides meaningful predictions of the risk of epidemic disease outbreaks.
Evidence for a Male Bias in Atlantic Blue Crab Pot-Based Sampling
Authors: Brunson Jeff F. , Sitta Kimberly A. , Kendrick Michael R. , Kingsley-Smith Peter R.
Published: May 2023

The Atlantic Blue CrabCallinectes sapidusis an ecologically- and economically-important species that supports one of the highest valued commercial fisheries in coastal South Carolina, USA. Researchers at the South Carolina Department of Natural Resources conduct multiple surveys to monitor the status of the Atlantic Blue Crab using a variety of gear configurations. Demographic characterizations, however, can often be influenced by sampling gear-related biases. We compared blue crab sex ratios between passive, pot-based, sampling and active, trawl-based, sampling across three estuaries in the fall and for year-round sampling in a single estuary. For fall sampling, the percent of males in pots was 20.1% higher than values observed for trawl-based sampling, while an overall male bias of 22.7% was observed for year-round sampling; however, this bias was only significant in certain months. Our findings suggest that while different sampling gears may offer their own advantages, such as greater suitability to effectively sample specific habitats, the resulting characterizations of population demographics can differ among gear types. Recognizing gear related biases is important for ensuring that field surveys are representative of populations, particularly when sex-specific modeling approaches are used as part of stock assessments to determine population status.
Type-IV pili tune an adhesion-migration trade-off during surface colonization ofPseudomonas aeruginosa
Authors: Simsek Ahmet Nihat , Koch Matthias D. , Sanfilippo Joseph E. , Gitai Zemer , Gompper Gerhard , Sabass Benedikt
Published: May 2023

Bacterial pathogenicity relies on both firm surface adhesion and cell dissemination. How twitching bacteria resolve the fundamental contradiction between adhesion and migration is unknown. To address this question, we employ live-cell imaging of type-IV pili (T4P) and therewith construct a comprehensive mathematical model ofPseudomonas aeruginosamigration. The data show that only 10% to 50% of T4P bind to substrates and contribute to migration through random extension and retraction. Individual T4P do not display a measurable sensory response to surfaces, but their number increases on cellular surface contact. Attachment to surfaces is mediated, besides T4P, by passive adhesive forces acting on the cell body. Passive adhesions slow down cell migration and result in local random motion on short time scales, which is followed by directionally persistent, superdiffusive motion on longer time scales. Moreover, passive adhesions strongly enhance surface attachment under shear flow. ΔpilAmutants, which produce no T4P, robustly stick to surfaces under shear flow. In contrast, rapidly migrating ΔpilHcells, which produce an excessive number of T4P, are easily detached by shear. Wild-type cells sacrifice migration speed for robust surface attachment by maintaining a low number of active pili. The different cell strains pertain to disjunct regimes in a generic adhesion-migration trait space. Depending on the nature of the adhesion structures, adhesion and migration are either compatible or a trade-off is required for efficient bacterial surface colonization under different conditions.
Engineering dynamic gates in binding pocket of penicillin G acylase to selectively degrade bacterial signaling molecules
Authors: Grulich Michal , Surpeta Bartlomiej , Palyzova Andrea , Maresova Helena , Zahradnik Jiri , Brezovsky Jan
Published: May 2023

The rapid rise of antibiotic-resistant bacteria necessitates the search for alternative, unconventional solutions, such as targeting bacterial communication. Signal disruption can be achieved by enzymatic degradation of signaling compounds, reducing the expression of genes responsible for virulence, biofilm formation, and drug resistance while evading common resistance mechanisms. Therefore, enzymes with such activity have considerable potential as antimicrobial agents for medicine, industry, and other areas of life. Here, we designed molecular gates that control the binding site of penicillin G acylase to shift its preference from native substrate to signaling molecules. Using an ensemble-based design, three variants carrying triple-point mutations were proposed and experimentally characterized. Integrated inference from biochemical and computational analyses demonstrated that these three variants had markedly reduced activity towards penicillin and each preferred specific signal molecules of different pathogenic bacteria, exhibiting up to three orders of magnitude shifts in substrate specificity. Curiously, while we could consistently expand the pockets in these mutants, the reactive binding of larger substrates was limited, either by overpromoting or overstabilizing the pocket dynamics. Overall, we demonstrated the designability of this acylase for signal disruption and provided insights into the role of appropriately modulated pocket dynamics for such a function. The improved mutants, the knowledge gained, and the computational workflow developed to prioritize large datasets of promising variants may provide a suitable toolbox for future exploration and design of enzymes tailored to disrupt specific signaling pathways as viable antimicrobial agents.
Extreme genome scrambling in crypticOikopleura dioicaspecies
Authors: Plessy Charles , Mansfield Michael J. , Bliznina Aleksandra , Masunaga Aki , West Charlotte , Tan Yongkai , Liu Andrew W. , Grašič Jan , Pisula María Sara del Río , Sánchez-Serna Gaspar , Fabrega-Torrus Marc , Ferrández-Roldán Alfonso , Roncalli Vittoria , Navratilova Pavla , Thompson Eric M. , Onuma Takeshi , Nishida Hiroki , Cañestro Cristian , Luscombe Nicholas M.
Published: May 2023

Genes are not randomly distributed throughout chromosomes. How gene order evolves and how selective constraints act to preserve or vary gene order, both at the macrosyntenic level of whole chromosomes or microsyntenic level of gene blocks, are central questions of evolutionary biology and genomics that remain largely unsolved. Here, after sequencing several genomes of the appendicularian tunicateOikopleura dioicafrom different locations around the globe, we show an unprecedented amount of genome scrambling in animals with no obvious morphological differences, consistent with cryptic speciation. Our assemblies suggest that all members of this clade possess a common 3-chromosome karyotype, and that different species largely preserve gene content, despite the presence of thousands of rearrangements in gene order. The movements of genes are largely restricted to chromosome arms and sex-specific regions, which appear to be the primary unit of macrosynteny conservation, and examples of these within-arm movements can be seen in theHoxandFgfgene families. Our approach employing whole-genome alignments demonstrates that segments containing protein-coding elements tend to be preserved at the microsyntenic scale, consistent with strong purifying selection, with appreciably less preservation of non-coding elements. Unexpectedly, scrambling did not preserve operon structure across species, suggesting an absence of selective pressure to maintain operon structure. As well, genome scrambling does not occur uniformly across all chromosomes, as short chromosome arms possess shorter genes, smaller operons, more breakpoints, and elevated dN/dS values compared to long chromosome arms. Estimation of divergence times among the crypticO. dioicalineages yielded an estimated breakpoint accumulation rate of 6 to 25 breakpoints per megabase per million years, which is an order of magnitude higher than the rates for other ascidian tunicates orDrosophilaspecies. Therefore,O. dioicaappears to be an attractive animal system to unravel the mechanisms that underlie gene order and synteny conservation, as well as exploring the limits of genome scrambling without an apparent impact on phenotypic evolution.
B-Cell Precursor Acute Lymphoblastic Leukemia elicits an Interferon-α/β response in Bone Marrow-derived Mesenchymal Stroma
Authors: Smeets Mandy W. E. , Steeghs Elisabeth M. P. , Orsel Jan , Stalpers Femke , Vermeeren Myrthe M. P. , Veltman Christina H. J. , Nierkens Stefan , van de Ven Cesca , den Boer Monique L.
Published: May 2023

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) can hijack the normal bone marrow microenvironment to create a leukemic niche which facilitates blast cell survival and promotes drug resistance. Bone marrow-derived mesenchymal stromal cells (MSCs) mimic this protective environment inex vivoco-cultures with leukemic cells obtained from children with newly diagnosed BCP-ALL. We examined the potential mechanisms of this protection by RNA sequencing of flow-sorted MSCs after co-culture with BCP-ALL cells. Leukemic cells induced an interferon (IFN)-related gene signature in MSCs, which was partially dependent on cell-cell signaling by tunneling nanotubes. The signature was selectively induced by BCP-ALL cells, most profoundly byETV6-RUNX1positive ALL cells, as co-culture of MSCs with healthy immune cells did not provoke a similar IFN signature. Leukemic cells and MSCs both secreted IFNα and IFNβ, but no IFNγ. In line, the IFN-gene signature was sensitive to blockade of IFNα/β signaling, but less to that of IFNγ. The viability of leukemic cells and level of resistance to three chemotherapeutic agents was not affected by interference with IFN signaling using selective IFNα/β inhibitors or silencing of IFN-related genes. Taken together, our data suggest that the leukemia-induced expression of IFNα/β-related genes by MSCs does not support survival of BCP-ALL cells but may serve a different role in the pathobiology of BCP-ALL.
Unravelling the relationship between isolated bone matrix vesicles and forming mineral at the nanometer scale
Authors: Cruz Marcos A. E. , Rutten Luco , Martens Martijn , Arntz Onno , van de Loo Fons , Macías-Sánchez Elena , Akiva Anat , Ciancaglini Pietro , Ramos Ana P. , Sommerdijk Nico
Published: May 2023

Matrix vesicles (MVs) are involved in the initial deposition of hydroxyapatite (HAp) during bone mineralization, but their mechanism of action is not yet fully understood.In vitrostudies propose two pathways by which MVs can trigger HAp precipitation: the first is mediated by their enhanced phosphatase activity, and the second suggested to depend on structural components present in MVs to mediate nucleation directly from soluble ions without the requirement of phosphatase activity. However, the relevance of these two pathways for bone mineralization and the relationship between MVs and forming mineral in suchin vitroexperiments remains unclear. Here, we used near-native cryoTEM nanoscale imaging in combination with bulk characterizations to disentangle the content and action of MVs duringin vitromineralization. We show that MVs isolation by conventional ultracentrifugation results in heterogeneous dispersions containing non-vesicular particles, including collagens and proteoglycans, in addition to bilayered vesicles. The separation of phosphatase-enriched MVs from non-vesicular particles and comparative mineralization experiments demonstrated that the ability of MVs to induce fast mineralization, independently of phosphatase activity, depends on the presence of non-vesicular particles. Therefore, we conclude that the primary pathway by which MVs trigger mineralization is through the action of their resident phosphatase enzymes, with the direct mineral nucleation to be a secondary event consequential of their membrane components. Lastly, we observed mineral formation restricted to the extravesicular space or in close proximity to the membrane interface, suggesting that the relationship between MVs and forming mineral is more intricate than previously understood.
The Pgbd5 DNA transposase is required for mouse cerebral cortex development through DNA double-strand breaks formation
Authors: Simi Alessandro , Ansaloni Federico , Damiani Devid , Codino Azzurra , Mangoni Damiano , Lau Pierre , Vozzi Diego , Pandolfini Luca , Sanges Remo , Gustincich Stefano
Published: May 2023

Transposons are conserved mobile genetic elements and one of the major sources of genetic variability during organisms’ evolution. PiggyBac Transposable Element Derived 5 (Pgbd5), an evolutionarily conserved vertebrate DNA transposase-coding gene, is highly expressed in the central nervous system during development and adult life, suggesting it may play a role in neuronal differentiation and maintenance.

Here, we show thatPgbd5controls the expression of pro-neuronal and proliferative genes in a cell autonomous manner, leading to a decreased generation of neurons with altered migration. This activity depends on the induction of endogenous DNA double-strand breaks (DSBs).

These results positionPgbd5as a crucial regulator of brain development through its endonuclease activity.

One-Sentence Summary

Pgbd5regulates cerebral cortex neurogenesis through DNA double-strand breaks modulation.
Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
Authors: Pettersen Jakob P. , Castillo Sandra , Jouhten Paula , Almaas Eivind
Published: May 2023

Background

Use of alternative non-Saccharomycesyeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce the final alcohol content. Given the metabolic differences between the yeast species, we wanted to account for some of the differences by usingin silicomodels.

Results

We created and studied genome-scale metabolic models of five different non-Saccharomycesspecies using an automated processes. These were:Metschnikowia pulcherrima, Lachancea thermotolerans, Hanseniaspora osmophilaandKluyveromyces lactis. Using the models, we predicted thatM. pulcherrima, when compared to the other species, conducts more respiration and thus produces less fermentation products, a finding which agrees with experimental data. Complex I of the electron transport chain was to be present inM. pulcherrima, but absent in the others. The predicted importance of Complex I was diminished when we incorporated constraints on the amount of enzymatic protein, as this shifts the metabolism towards fermentation.

Conclusions

Our results suggest that Complex I in the electron transport chain is a key differentiator betweenMetschnikowia pulcherrimaand the other yeasts considered. Yet, more annotations and experimental data have the potential to improve model quality in order to increase fidelity and confidence in these results. Further experiments should be conducted to confirm thein vivoeffect of Complex I inM. pulcherrimaand its respiratory metabolism.
Temporally organized representations of reward and risk in the human brain
Authors: Man Vincent , Cockburn Jeffrey , Flouty Oliver , Gander Phillip E. , Sawada Masahiro , Kovach Christopher K. , Kawasaki Hiroto , Oya Hiroyuki , Howard Matthew A. , O’Doherty John P.
Published: May 2023

Abstract

The value and uncertainty associated with choice alternatives constitute critical features along which decisions are made. While the neural substrates supporting reward and risk processing have been investigated, the temporal organization by which these computations are encoded remains elusive. Here we leverage the high spatiotemporal precision of intracranial electroencephalography (iEEG) to uncover how representations of decision-related computations unfold in time. We present evidence of locally distributed representations of reward and risk variables that are temporally organized across multiple regions of interest. Reward outcome representations across wide-spread regions follow a temporally cascading order along the anteroposterior axis of the brain. In contrast, expected value can be decoded from multiple regions at the same time, and error signals in both reward and risk domains reflect a mixture of sequential and parallel encoding. We highlight the role of the anterior insula in generalizing between reward prediction error (RePE) and risk prediction error (RiPE), within which the encoding of RePE in the distributed iEEG signal predicts RiPE. Together our results emphasize the utility of uncovering temporal dynamics in the human brain for understanding how computational processes critical for value-based decisions under uncertainty unfold.