bluuebunny/crossref_metadata_2025_split huggingface dataset:
Durable resistance or efficient disease control? Adult Plant Resistance (APR) at the heart of the dilemma
Authors: Rimbaud Loup , Papaïx Julien , Rey Jean-François , Moury Benoît , Barrett Luke , Thrall Peter 
Published: September 2022

AbstractAdult plant resistance (APR) is an incomplete and delayed protection of plants against pathogens. At first glance, such resistance should be less efficient than classical major-effect resistance genes, which confer complete resistance from seedling stage, to reduce epidemics. However, by allowing some ‘leaky’ levels of disease, APR genes are predicted to be more durable than major genes because they exert a weaker selection pressure on pathogens towards adaptation to resistance. However, the impact of partial efficiency and delayed mode of action of APR on the evolutionary and epidemiological outcomes of resistance deployment has never been tested.Using the demogenetic, spatially explicit, temporal, stochastic modellandsepi, this study is a first attempt to investigate how resistance efficiency, age at the time of resistance activation and target pathogenicity trait jointly impact resistance durability and disease control at the landscape scale. Our numerical experiments explore the deployment of APR in a simulated agricultural landscape, alone or together with a major resistance gene. As a case study, the mathematical model has been parameterised for rust fungi (genusPuccinia) of cereal crops, for which extensive data are available.Our simulations confirm that weak efficiency and delayed activation of APR genes reduce the selection pressure applied on pathogens and their propensity to overcome resistance, but do not confer effective protection. On the other hand, stronger APR genes (which increase selection pressure on the pathogen) may be quickly overcome but have the potential to provide some disease protection in the short-term. This is attributed to strong competition between different pathogen genotypes and the presence of fitness costs of adaptation, especially when APR genes are deployed together with a major resistance gene via crop mixtures or rotations.
Altered population activity and local tuning heterogeneity in auditory cortex ofCacna2d3-deficient mice
Authors: Wadle Simon L. , Schmitt Tatjana T.X. , Engel Jutta , Kurt Simone , Hirtz Jan J. 
Published: September 2022

AbstractThe α2δ3 auxiliary subunit of voltage-activated calcium channels is required for normal synaptic transmission and precise temporal processing of sounds in the auditory brainstem. In mice its loss additionally leads to an inability to distinguish amplitude-modulated tones. Furthermore, loss of function of α2δ3 has been associated with autism spectrum disorder in humans. To investigate possible alterations of network activity in the higher-order auditory system in α2δ3 knockout mice, we analyzed neuronal activity patterns and topography of frequency tuning within networks of the auditory cortex (AC) using two-photon Ca2+imaging. Compared to wild-type mice we found distinct subfield-specific alterations in the primary auditory cortex, expressed in overall lower correlations between the network activity patterns in response to different sounds as well as lower reliability of these patterns upon repetitions of the same sound. Higher AC subfields did not display these alterations but showed a higher amount of well-tuned neurons along with lower local heterogeneity of the neurons’ frequency tuning. Our results provide new insight into AC network activity alterations in an autism spectrum disorder-associated mouse model.
Integrating sex-bias into studies of archaic admixture on chromosome X
Authors: Chevy Elizabeth T. , Huerta-Sánchez Emilia , Ramachandran Sohini 
Published: September 2022

AbstractEvidence of interbreeding between archaic hominins and humans comes from methods that infer the locations of segments of archaic haplotypes, or ‘archaic coverage’ using the genomes of people living today. As more estimates of archaic coverage have emerged, it has become clear that most of this coverage is found on the autosomes— very little is retained on chromosome X. Here, we summarize published estimates of archaic coverage on autosomes and chromosome X from extant human samples. We find on average 7.9 times more archaic coverage on autosomes than chromosome X, and identify broad continental patterns in this ratio: greatest in American samples, and least in South Asian samples. We also perform extensive simulation studies to investigate how the amount of archaic coverage, lengths of coverage, and rates of purging of archaic coverage are affected by sex-bias caused by an unequal sex ratio within the archaic introgressors. Our results generally confirm that, with increasing male sex-bias, less archaic coverage is retained on chromosome X. Ours is the first study to explicitly model such sex-bias and its potential role in creating the dearth of archaic coverage on chromosome X.Author summaryTens of thousands of years ago, humans interbred with our close hominin relatives (e.g. Neanderthals), which we know from finding segments of archaic hominin DNA in our genomes. Up to 4% of a human genome may be archaic DNA, but most of that archaic part is on the autosomes (the non-sex chromosomes). Chromosome X usually contains 3 to 10 times less archaic DNA than the autosomes. Also unlike the autosomes, it is always passed down by mothers, but only sometimes by fathers. There are several hypotheses for why chromosome X has less archaic DNA than the autosomes; one that has not been fully explored is whether the archaic hominins that interbred with our ancestors were mostly male or mostly female, known as ‘sex-bias’. In this paper, we use simulations to investigate whether sex-bias could produce less archaic DNA on chromosome X. Using simulation studies, we find that when the archaics are mostly male, modern humans end up with less archaic DNA on chromosome X than their autosomes, compared to when there is a female-bias or no sex-bias. Therefore, male sex-bias could be contributing to the difference in the amount of archaic DNA on chromosome X versus the autosomes. Of course, there are still plenty of other factors to be explored about how demography and selection have shaped our DNA. Studying patterns like this helps us learn more about early hominin natural history, and contextualizes archaic interbreeding events among other sex-biased events in human history.
Differences in anti-viral immune responses in individuals of Indian and European origin: relevance for the COVID-19 pandemic
Authors: Geckin Büsranur , Zoodsma Martijn , Kilic Gizem , Debisarun Priya A. , Rakshit Srabanti , Adiga Vasista , Ahmed Asma , Parthiban Chaitra , Kumar Nirutha Chetan , D’Souza George , Baltissen Marijke P , Martens Joost H A , Andres Jorge Dominguez , Li Yang , Vyakarnam Annapurna , Netea Mihai G 
Published: September 2022

AbstractDuring the COVID-19 pandemic, large differences in susceptibility and mortality due to SARS-CoV-2 infection have been reported between populations in Europe and South Asia. While both host and environmental factors (including BCG vaccination) have been proposed to explain this, the potential biological substrate of these differences is unknown. We purified peripheral blood mononuclear cells from individuals living in India and the Netherlands at baseline and 10-12 weeks after BCG vaccination. We compared chromatin accessibility between the two populations at baseline, as well as gene transcription profiles and cytokine production capacities upon viral stimulation with influenza and SARS-CoV-2. The chromatin accessibility of genes important for adaptive immunity was higher in Indians compared to Europeans, while the latter had more accessible chromatin regions in genes of the innate immune system. At the transcriptional level, we observed that Indian volunteers displayed a more tolerant immune response to viral stimulation, in contrast to a more exaggerated response in Europeans. BCG vaccination strengthened the tolerance program in Indians, but not in Europeans. These differences may partly explain the different impact of COVID-19 on the two populations.
Evolutionary states and trajectories characterized by distinct pathways stratify ovarian high-grade serous carcinoma patients
Authors: Lahtinen Alexandra , Lavikka Kari , Li Yilin , Virtanen Anni , Jamalzadeh Sanaz , Huhtinen Kaisa , Carpén Olli , Hietanen Sakari , Häkkinen Antti , Hynninen Johanna , Oikkonen Jaana , Hautaniemi Sampsa 
Published: September 2022

ABSTRACTOvarian high-grade serous carcinoma (HGSC) is typically diagnosed at an advanced stage, with multiple genetically heterogeneous clones existing in the tumors long before therapeutic intervention. Herein we characterized HGSC evolutionary states using whole-genome sequencing data from 214 samples of 55 HGSC patients in the prospective, longitudinal, multiregion DECIDER study. Comparison of the tissues revealed that site-of-origin samples have 70% more unique clones than the metastatic tumors or ascites. By integrating clonal composition and topology of HGSC tumors we discovered three evolutionary states that represent a continuum from genomically highly variable to stable tumors with significant association to treatment response. The states and their evolutionary trajectories were characterized by unique, targetable pathways, which were validated with RNA-seq data. Our study reveals that genomic heterogeneity is unaffected by the current standard-of-care and pinpoints effective treatment targets for each group. All genomics data are available via an interactive visualization platform for rapid exploration.
Hepatic fibrosis induced zinc-deficient dermatosis in American alligators (Alligator mississippiensis)
Authors: Piras Ilaria M. , Bezuidenhout Annemarie , Díaz-Delgado Josué , Slawski Deirdre , Kelly Pamela A. 
Published: September 2022

AbstractCrocodilian farming generates strong economic incentives for the conservation of several species previously endangered by intensive hunting. Ranching farms, in particular, are intimately connected to the natural crocodilian habitat and have a significant impact on wetland preservation. The financial sustainability of this industry relies on the production of first grade skins for the luxury leather market. Only flawless skins are considered of first grade by the stringent standards of the market, and even a single defect represents an economical loss. “Double scale” is one such defect that drastically reduces the appeal of crocodilian skin. Although double scale defects represent a threat to the economical sustainability of the farming industry, there is no scientific literature available on this topic. This study, carried out in a ranching farm of American alligators (Alligator mississippiensis), represents the first investigation into the pathogenesis of double scale. Our results indicate that double scale is a keratinization disorder associated with zinc deficiency. Furthermore, we found that portal hypertension due to liver fibrosis, underlies zinc deficiency in cases of double scale. Lastly, we found that chronic vitamin A toxicity can cause liver fibrosis in crocodilians. For the first time, we demonstrate a causal association between liver disease and skin quality in a crocodilian species. This study reveals the conserved role of zinc in the homeostasis of reptilian skin. Also, we show that, like mammals, reptiles may develop liver fibrosis following chronic vitamin A toxicity and through activation of hepatic stellate cells. Our results advance herpetological medicine and will translate into improved captive crocodilian welfare and husbandry.
A red fluorescent genetically encoded biosensor for extracellular L-lactate
Authors: Nasu Yusuke , Kamijo Yuki , Hashizume Rina , Sato Haruaki , Hori Yukiko , Tomita Taisuke , Drobizhev Mikhail , Campbell Robert E. 
Published: September 2022

AbstractL-Lactate, traditionally recognized as a waste product of metabolism, is now appreciated as a key intercellular energy currency in mammals. To enable investigations of intercellular shuttling of L-lactate, we have previously reported eLACCO1.1, a green fluorescent genetically encoded biosensor for extracellular L-lactate. eLACCO1.1 enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue. However, eLACCO1.1 spectrally overlaps with commonly used optical biosensors and actuators, limiting its application for multiplexed imaging or combined use with optogenetic actuators. Here, we report a red fluorescent extracellular L-lactate biosensor, designated R-eLACCO2. R-eLACCO2 is the end-product of extensive directed evolution and exhibits a large fluorescence response to L-lactate with high molecular specificity in vitro. We demonstrate that R-eLACCO2 with optimized leader and anchor sequences shows a large fluorescence change in response to extracellular L-lactate on the membrane of live mammalian cells. R-eLACCO2 should enable multicolor imaging of extracellular L-lactate in combination with other fluorescent probes and optogenetic actuators.
Influenza virus transcription and progeny production are poorly correlated in single cells
Authors: Bacsik David J. , Dadonaite Bernadeta , Butler Andrew , Greaney Allison J. , Heaton Nicholas S. , Bloom Jesse D. 
Published: September 2022

AbstractThe ultimate success of a viral infection at the cellular level is determined by the number of progeny virions produced. However, most single-cell studies of infection quantify the expression of viral transcripts and proteins, rather than the amount of progeny virions released from infected cells. Here we overcome this limitation by simultaneously measuring transcription and progeny production from single influenza-virus-infected cells by embedding nucleotide barcodes in the viral genome. We find that viral transcription and progeny production are poorly correlated in single cells. The cells that transcribe the most viral mRNA do not produce the most viral progeny, and often represent aberrant infections that fail to express the influenza NS gene. However, only some of the discrepancy between transcription and progeny production can be explained by viral gene absence or mutations: there is also a wide range of progeny production among cells infected by complete unmutated virions. Overall, our results show that viral transcription is a relatively poor predictor of an infected cell’s contribution to the progeny population.
Silencing long-descending inter-enlargement propriospinal neurons improves hindlimb stepping after contusive spinal cord injuries
Authors: Shepard Courtney T , Brown Brandon L , Van Rijswijck Morgan A , Zalla Rachel M , Burke Darlene A , Morehouse Johnny R , Riegler Amberley S , Whittemore Scott R , Magnuson David SK 
Published: September 2022

AbstractSpinal locomotor circuitry is comprised of rhythm generating centers, one for each limb, that are interconnected by local and long-distance propriospinal neurons thought to carry temporal information necessary for interlimb coordination and gait control. We showed previously that conditional silencing of the long ascending propriospinal neurons (LAPNs) that project from the lumbar to the cervical rhythmogenic centers (L1/L2 to C6), disrupts right-left alternation of both the forelimbs and hindlimbs without significantly disrupting other fundamental aspects of interlimb and speed-dependent coordination (Pocratsky et al., 2020). Subsequently, we showed that silencing the LAPNs after a moderate thoracic contusive spinal cord injury (SCI) resulted in better recovered locomotor function (Shepard et al., 2021). In this research advance, we focus on the descending equivalent to the LAPNs, the long descending propriospinal neurons (LDPNs) that have cell bodies at C6 and terminals at L2. We found that conditional silencing of the LDPNs in the intact adult rat resulted in disrupted alternation of each limb pair (forelimbs and hindlimbs) and after a thoracic contusion SCI significantly improved locomotor function. These observations lead us to speculate that the LAPNs and LDPNs have similar roles in the exchange of temporal information between the cervical and lumbar rhythm generating centers, but that the partial disruption of the pathway after SCI limits the independent function of the lumbar circuitry. Silencing the LAPNs or LDPNs effectively permits or frees-up the lumbar circuitry to function independently.
Mutations in CmVPS41 controlling resistance toCucumber Mosaic Virusdisplay specific subcellular localizations
Authors: Real Núria , Villar Irene , Serrano Irene , Guiu-Aragonés Cèlia , Martín-Hernández Ana Montserrat 
Published: September 2022

AbstractResistance toCucumber mosaic virus(CMV) in melon has been described in several exotic accessions. It is controlled by a recessive resistance gene,cmv1, which encodes a Vacuolar Protein Sorting 41 (CmVPS41).Cmv1prevents systemic infection by restricting the virus to the bundle sheath cells, preventing viral phloem entry. CmVPS41 from different resistant accessions carried two causal mutations, either a G85E change, found in Pat-81 and Freeman’s Cucumber, or L348R found inPI161375, cultivar Songwhan Charmi (SC). The analysis of the subcellular localization of CmVPS41 inN. benthamianahas revealed differential structures in resistant and susceptible accessions. Susceptible accessions showed nuclear and membrane spots and many transvacuolar strands, whereas the resistant accessions showed many intravacuolar invaginations. These specific structures colocalize with late endosomes. Artificial CmVPS41 carrying individual mutations causing resistance in the genetic background of CmVPS41 from the susceptible variety Piel de Sapo (PS), revealed that the structure most correlated with resistance was the absence of transvacuolar strands. Co-expression of CmVPS41 with the viral MPs, the determinant of virulence, did not change these localizations; however, infiltration of CmVPS41 from either SC or PS accessions in CMV-infectedN. benthamianaleaves showed a localization pattern closer to each other, with up to 30% cells showing some membrane spots in the CmVPS41SC and fewer transvacuolar strands (from a mean of 4 to 1-2) with CmVPS41PS. Our results suggest that the distribution of CmVPS41PS in late endosomes includes transvacuolar strands that facilitate CMV infection and that CmVPS41 is re-localized during viral infection.
Defining a Nonribosomal Specificity Code for Design
Authors: Stanišić Aleksa , Svensson Carl-Magnus , Ettelt Ulrich , Kries Hajo 
Published: September 2022

AbstractNonribosomal peptide synthetases (NRPSs) assemble bioactive peptides from an enormous repertoire of building blocks. How binding pocket residues of the nonribosomal adenylation domain, the so-called specificity code, determine which building block becomes incorporated has been a landmark discovery in NRPS enzymology. While specificity codes enable the prediction of substrate specificity from protein sequence, design strategies based on rewriting the specificity code have been limited in scope. An important reason for failed NRPS design has been that multispecificity has not been considered, for a lack of suitable assay formats. Here, we employ a multiplexed hydroxamate specificity assay (HAMA) to determine substrate profiles for mutant libraries of A-domain in the termination module the SrfAC of surfactin synthetase. A generalist version of SrfAC is developed and the functional flexibility of the adenylation reaction is probed by fully randomizing 15 residues in and around the active site. We identify mutations with profound impact on substrate selectivity and thus reveal a remarkable evolvability of A-domains. Statistical analysis of the specificity divergence caused by point mutations has determined the impact of each code position on specificity, which will serve as a roadmap for NRPS engineering. The shortness of evolutionary pathways between NRPS specificities explains the rich natural substrate scope and suggests directed evolution guided by A-domain promiscuity as a promising strategy.
Safe, effective, and inexpensive clearance of mycoplasma contamination from cultures of apicomplexan parasites with Sparfloxacin
Authors: Malave-Ramos Darlene R. , Kennedy Kit , Key Melanie N. , Dou Zhicheng , Kafsack Björn F.C. 
Published: September 2022

ABSTRACTMost commercial products cannot be used for clearance of mycoplasma contamination from cultures of apicomplexan parasites due to the parasites’ dependence on the apicoplast, an essential organelle with DNA replication and translation machinery of cyanobacterial origin. The lone exception, Mycoplasma Removal Agent (MRA), is relatively expensive and some mycoplasma strains have shown resistance to clearance with MRA. Here, we report that the fluoroquinolone antibiotic Sparfloxacin is a safe, effective, and inexpensive alternative for treatment of mycoplasma contamination in cultures of apicomplexan parasites. Sparfloxacin cleared both MRA- sensitive and MRA-resistant mycoplasma species from P. falciparum cultures at 1 and 4 μg/mL, respectively. We show that cultures of three different apicomplexan parasites can be maintained at concentrations of Sparfloxacin required to clear mycoplasma without resulting in substantial deleterious effects on parasite growth. We also describe an alternative low-cost, in-house PCR assay for detecting mycoplasma. These findings will be useful to laboratories maintaining apicomplexan parasites in vitro, especially in low-resource environments, where the high cost of commercial products creates an economic barrier for detecting and eliminating mycoplasma from culture.
Gene editing in the nematode parasite Nippostrongylus brasiliensis using extracellular vesicles to deliver active Cas9/guide RNA complexes
Authors: Hagen Jana , Ghosh Subhanita , Sarkies Peter , Selkirk Murray E. 
Published: September 2022

AbstractDespite recent advances, animal-parasitic nematodes have thus far been largely refractory to genetic manipulation. We describe here a new approach providing proof of principle that CRISPR/Cas9-mediated gene editing of parasitic nematodes is achievable using vesicular stomatitis virus glycoprotein-pseudotyped extracellular vesicles (EV) for the delivery of Cas9-synthetic guide RNA (RNP) complexes. We demonstrate that EV-delivered RNPs can be used to disrupt a secreted DNase II in Nippostrogylus brasiliensis. Introduction of a repair template encoding multiple stop codons led to measurable reduction in expression of the targeted gene. Altered transcripts corresponding to the edited locus were detected by RT-PCR, demonstrating that vesicles can access cells of tissues actively expressing the gene of interest. These data provide evidence that this technique can be employed for targeted gene editing in N. brasiliensis, making this species genetically tractable for the first time and providing a new platform for genetic analysis of parasitic nematodes.Author SummaryParasitic nematodes have a complex life cycle involving passage through a host organism, which makes them very difficult to manipulate genetically. Recently, a method for deleting, changing or replacing genes (gene editing) has been developed in other organisms which has revolutionised our ability to understand fine details of how these organisms work. It has generally not been possible to adapt this method to parasitic nematodes because delivery of the components is difficult, and this has proved to be a bottleneck in understanding how parasites develop, survive and interact with their host. We show here that the components for gene editing can be introduced into a widely used laboratory model of intestinal nematode infection by encapsulation in membrane-bound vesicles which have been modified to carry a protein which facilitates fusion of the vesicles with parasite cells and delivery of the contents. This resulted in accurate editing of a specific gene by deletion and repair, such that the amount of functional protein produced from that gene was reduced. This system should be applicable to all nematode species, and will facilitate understanding of their complex biology, in addition to defining new targets for control of infection.