bluuebunny/crossref_metadata_2025 huggingface dataset:
GWAS and genomic selection for marker-assisted development of sucrose enriched soybean cultivars
Authors: Riaz Awais , Raza Qasim , Kumar Anuj , Dean Derek , Chiwina Kenani , Phiri Theresa Makawa , Thomas Julie , Shi Ainong
Published: April 2023

Sucrose concentration in soy-derived foods is becoming a seminal trait for the production of food-grade soybeans. However, limited scientific knowledge is reported on this increasingly important breeding objective. In this study, 473 genetically diverse soybean germplasm accessions and 8,477 high-quality single nucleotide polymorphisms (SNPs) markers were utilized to pinpoint genomic regions associated with seed sucrose contents through a genome-wide association study (GWAS). A total of 75 significant SNPs (LOD ≥6.0) were identified across GLM, FarmCPU and BLINK models, including four stable and novel SNPs (Gm03_45385087_ss715586641, Gm06_10919443_ss715592728, Gm09_45335932_ss715604570 and Gm14_10470463_ss715617454). Gene mining near 20 kb flanking genomic regions of four stable SNPs identified 23 candidate genes with the majority of them highly expressed in soybean seeds and pod shells. A sugar transporter encoding major facilitator superfamily gene (Glyma.06G132500) showing the highest expression in pod shells was also identified. Moreover, selection accuracy, efficiency and favorable alleles of 75 significantly associated SNPs were estimated for their utilization in soybean breeding programs. Furthermore, genomic predictions with three different scenarios revealed better feasibility of GWAS-derived SNPs for selection and improvement of seed sucrose concentration. These results could facilitate plant breeders in marker-assisted breeding and genomic selection of sucrose-enriched food-grade soybean cultivars for the global soy-food industry.
The pAblo·pCasso self-curing vector toolset for unconstrained cytidine and adenine base-editing in Gram-negative bacteria
Authors: Kozaeva Ekaterina , Nielsen Zacharias S. , Nieto-Domínguez Manuel , Nikel Pablo I.
Published: April 2023

A synthetic biology toolkit, exploiting clustered regularly interspaced short palindromic repeats (CRISPR) and modified CRISPR-associated protein (Cas) base-editors, was developed for genome engineering in Gram-negative bacteria. Both a cytidine base-editor (CBE) and an adenine base-editor (ABE) have been optimized for precise single-nucleotide modification of plasmid and genome targets. CBE comprises a cytidine deaminase conjugated to a Cas9 nickase fromStreptococcus pyogenes(SpnCas9), resulting in C→T (or G→A) substitutions. Conversely, ABE consists of an adenine deaminase fused toSpnCas9 for A→G (or T→C) editing. Several nucleotide substitutions were achieved using these plasmid-borne base-editing systems and a novel protospacer adjacent motif (PAM)-relaxedSpnCas9 (SpRY) variant. Base-editing was validated inPseudomonas putidaand other Gram-negative bacteria by inserting prematureSTOPcodons into target genes, thereby inactivating both fluorescent proteins and metabolic (antibiotic-resistance) functions. The functional knockouts obtained by engineeringSTOPcodonsviaCBE were reverted to the wild-type genotype using ABE. Additionally, a series of induction-responsive vectors was developed to facilitate the curing of the base-editing platform in a single cultivation step, simplifying complex strain engineering programs without relying on homologous recombination and yielding plasmid-free, modified bacterial cells.

Abstract Figure
Collaborative nowcasting of COVID-19 hospitalization incidences in Germany
Authors: Wolffram Daniel , Abbott Sam , an der Heiden Matthias , Funk Sebastian , Günther Felix , Hailer Davide , Heyder Stefan , Hotz Thomas , van de Kassteele Jan , Küchenhoff Helmut , Müller-Hansen Sören , Syliqi Diellë , Ullrich Alexander , Weigert Maximilian , Schienle Melanie , Bracher Johannes
Published: April 2023

Real-time surveillance is a crucial element in the response to infectious disease outbreaks. However, the interpretation of incidence data is often hampered by delays occurring at various stages of data gathering and reporting. As a result, recent values are biased downward, which obscures current trends. Statistical nowcasting techniques can be employed to correct these biases, allowing for accurate characterization of recent developments and thus enhancing situational awareness. In this paper, we present a preregistered real-time assessment of eight nowcasting approaches, applied by independent research teams to German 7-day hospitalization incidences. This indicator played an important role in the management of the pandemic in Germany and was linked to levels of non-pharmaceutical interventions via certain thresholds. Due to its definition, in which hospitalization counts are aggregated by the date of case report rather than admission, German hospitalization incidences are particularly affected by delays and can take several weeks or months to fully stabilize. For this study, all methods were applied from 22 November 2021 to 29 April 2022, with probabilistic nowcasts produced each day for the current and 28 preceding days. Nowcasts at the national, state, and age-group levels were collected in the form of quantiles in a public repository and displayed in a dashboard. Moreover, a mean and a median ensemble nowcast were generated. We find that overall, the compared methods were able to remove a large part of the biases introduced by delays. Most participating teams underestimated the importance of very long delays, though, resulting in nowcasts with a slight downward bias. The accompanying uncertainty intervals were also too narrow for almost all methods. Averaged over all nowcast horizons, the best performance was achieved by a model using case incidences as a covariate and taking into account longer delays than the other approaches. For the most recent days, which are often considered the most relevant in practice, a mean ensemble of the submitted nowcasts performed best. We conclude by providing some lessons learned on the definition of nowcasting targets and practical challenges.
Investigating the causal interplay between sleep traits and risk of acute myocardial infarction: a Mendelian randomization study
Authors: Arora Nikhil , Bhatta Laxmi , Skarpsno Eivind Schjelderup , Dalen Håvard , Åsvold Bjørn Olav , Brumpton Ben Michael , Richmond Rebecca Claire , Strand Linn Beate
Published: April 2023

Background

Few studies have investigated the joint effects of sleep traits on the risk of acute myocardial infarction (AMI). No previous study has used factorial Mendelian randomization (MR) which may reduce confounding, reverse causation and measurement error. Thus, it is prudent to study joint effects using robust methods to propose sleep-targeted interventions which lower the risk of AMI.

Methods

The causal interplay between combinations of two sleep traits (including insomnia symptoms, sleep duration or chronotype) on the risk of AMI was investigated using factorial MR. Genetic risk scores for each sleep trait were dichotomized at their median in UK Biobank (UKBB) and the second survey of the Trøndelag Health Study (HUNT2). A combination of two sleep traits constituting 4 groups were analysed to estimate the risk of AMI in each group using a 2×2 factorial MR design.

Results

In UKBB, participants with high genetic risk for both insomnia symptoms and short sleep had the highest risk of AMI (hazard ratio (HR) 1.10; 95% confidence interval (CI) 1.03, 1.18), although there was no evidence of interaction (relative excess risk due to interaction (RERI) 0.03; 95% CI −0.07, 0.12). These estimates were less precise in HUNT2 (HR 1.02; 95% CI 0.93, 1.13), possibly due to weak instruments. Participants with high genetic risk for both a morning chronotype and insomnia symptoms (HR 1.09; 95% CI 1.03, 1.17); and a morning chronotype and short sleep (HR 1.11; 95% CI 1.04, 1.19) had the highest risk of AMI in UKBB, although there was no evidence of interaction (RERI 0.03; 95% CI −0.06, 0.12; and RERI 0.05; 95% CI −0.05, 0.14, respectively). Chronotype was not available in HUNT2.

Conclusions

This study reveals no interaction effects between sleep traits on the risk of AMI, but all combinations of sleep traits increased the risk of AMI except those with long sleep. This indicates that the main effects of sleep traits on AMI are likely to be independent of each other.
ChatGPT Decision Support System: Utility in Creating Public Policy for Concussion/Repetitive Brain Trauma Associated With Neurodegenerative Diseases
Authors: Comrie Don
Published: April 2023

This article evaluates the ChatGPT decision support system’s utility for creating policies related to concussion and repetitive brain trauma associated with neurodegenerative disease risk. It is generally stable and fast. prompt/response pairs (n=259) were examined returning: six prompt response pairs that regenerated (2.31%); one Incorrect Answer; (.38%) one fragment (.38%). Its accuracy, validity, opacity, informational latency and vulnerability to manipulation limits its utility. ChatGPT’s data can be both out-of-date and incomplete which limits its utility use to subject matter experts analyzing expert statements. ChatGPT’s performance is affected by prompts involving stakeholder bias and litigation management, such as race. Nonetheless, ChatGPT demonstrated its ability to respond in both American and British/Australian English with ease. Overall, this study suggests that ChatGPT has limitations that need to be addressed before it can be widely used in decision-making related to concussion and repetitive brain trauma policies.
Patient consent for medical student pelvic exams under anesthesia: an exploratory retrospective chart review
Authors: Jushchyshyn Jessica A. , Mulugeta-Gordon Lakeisha , Curley Cara , Polite Florencia Greer , Merz Jon F.
Published: April 2023

Background

Legal requirements and clinical practices of securing patient consent for medical student pelvic examinations under anesthesia (EUA) vary widely, while ethical arguments and patients’ preferences for being asked for consent are well known.

Objective

This study was performed to examine patients’ choices to permit or refuse medical student pelvic EUAs during planned gynecologic procedures.

Study Design

An exploratory retrospective chart review of electronic consent forms at a single academic medical center, using contingency table and logistic regression to explore relationships between patient and provider characteristics and consent.

Results

Electronic consent forms were downloaded for a census of 4000 patients undergoing gynecologic surgery from September 2020 through calendar year 2022 and linked to anonymized medical record information, including patient age, race, religion, and insurance carrier, along with physician name. Physicians were coded by gender, departmental affiliation, and status (attending, resident, or fellow). Of the 4000 patients, 142 (3.6%) patients were removed from analysis because of uncertainty about the EUA consent. Of the remainder, 308 (8.0%) were asked for EUA consent more than once. Overall, of 3858 patients, 3308 (85.7%) consented every time asked and 550 (14.2%) refused or limited EUA consent at least once. Nine patients limited their consent to female students, and 2 patients refused medical student participation at all. Of the 308 asked more than once, 46 were not consistent. Exploratory multiple logistic regression Consent for pelvic exams under anesthesia analysis showed that patients identifying as Black or African American (OR=0.482, p<0.001) or Asian (OR=0.303, p<0.001), or of Moslem/Muslim/Islamic faith (OR=0.598, p=0.008) were substantially less likely to grant EUA consent than other patients. Moreover, male physicians were somewhat more likely to secure consent from patients than their female colleagues (OR=1.427, p=0.016).

Conclusions

The finding that some patients are more likely than others to refuse a pelvic EUA magnifies the dignitary harm from a nonconsensual invasion of intimate bodily integrity and perpetuates the historic wrongs visited upon vulnerable people of color and religious minorities. Patient’s rights to control over their own bodies can only be respected if their physicians take seriously the ethical obligation to inform their patients and ask them for permission.
A chromatin-associated regulator of RNA Polymerase III assembly at tRNA genes revealed by locus-specific proteomics
Authors: Breugel Maria Elize van , Kruijsbergen Ila van , Mittal Chitvan , Lieftink Cor , Brouwer Ineke , Brand Teun van den , Kluin Roelof J.C. , Menezes Renée , Welsem Tibor van , Cortona Andrea Del , Malik Muddassir , Beijersbergen Roderick , Lenstra Tineke L. , Verstrepen Kevin , Pugh B. Franklin , Leeuwen Fred van
Published: April 2023

Transcription of tRNA genes by RNA Polymerase III (RNAPIII) is tightly regulated by signaling cascades in response to nutrient availability. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulatory factors have not been described. For that reason, we decoded the proteome of a single native tRNA gene locus in yeast. We observed dynamic reprogramming of the core RNAPIII transcription machinery upon nutrient perturbation. In addition, we identified Fpt1, a protein of unknown function. Fpt1 uniquely occupied tRNA genes but its occupancy varied and correlated with the efficiency of RNAPIII eviction upon nutrient perturbation. Decoding the proteome of a tRNA gene in the absence of Fpt1 revealed that Fpt1 promotes eviction of RNAPIII. Cells without Fpt1 also showed impaired shutdown of ribosome biogenesis genes upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and for tuning an integrated physiological response to changing metabolic demands.

Abstract Figure
High-efficiency base editing for Stargardt disease in mice, non-human primates, and human retina tissue
Authors: Muller Alissa , Sullivan Jack , Schwarzer Wibke , Wang Mantian , Park-Windhol Cindy , Klingler Beryll , Matsell Jane , Hostettler Simon , Galliker Patricia , Duman Mert , Hou Yanyan , Balmer Pierre , Virág Tamás , Barrera Luis Alberto , Xu Quan , Magda Dániel Péter , Kilin Ferenc , Khadka Arogya , Quinodoz Mathieu , Hasler Pascal W. , Moreau Pierre-Henri , Fellmann Lyne , Azoulay Thierry , Cattaneo Marco , Picelli Simone , Grison Alice , Cowan Cameron S. , Janeschitz-Kriegl Lucas , Kusnyerik Ákos , Renner Magdalena , Nagy Zoltán Zsolt , Szabó Arnold , Rivolta Carlo , Scholl Hendrik P.N. , Bryson David , Ciaramella Giuseppe , Roska Botond , György Bence
Published: April 2023

Stargardt disease is a currently untreatable, inherited neurodegenerative disease that leads to macular degeneration and blindness due to loss-of-function mutations in theABCA4gene. We have designed a dual adeno-associated viral vector split-intein adenine base-editing strategy to correct the most common mutation inABCA4(c.5882G>A, p.G1961E). We optimizedABCA4base editing in human models, including retinal organoids, iPSC-derived retinal pigment epithelial (RPE) cells, as well as adult human retinal- and RPE/choroid explants in vitro. The resulting gene therapy vectors achieved high levels of gene correction in mutation-carrying mice and in non-human primates, with an average editing of 37% of photoreceptors and 73% of RPE cells in vivo. The high editing rates in primates make way for precise and efficient gene editing in other neurodegenerative ocular diseases.
Focal adhesions are controlled by microtubules through local contractility regulation
Authors: Aureille J. , Barnett S.F.H. , Arnal I. , Lafanechère L. , Low B.C. , Kanchanawong P. , Mogilner A. , Bershadsky A.D.
Published: April 2023

Microtubules regulate cell polarity and migration by local activation of focal adhesion turnover, but the mechanism of this process is insufficiently understood. Molecular complexes containing KANK family proteins connect microtubules with the major component of focal adhesions, talin. Local optogenetic activation of KANK1-mediated links which promoted microtubule targeting to individual focal adhesion resulting in its centripetal sliding and rapid disassembly. The sliding is preceded by a local increase of traction force due to accumulation of myosin-II and actin in the proximity of the focal adhesion. Knockdown of Rho activator GEF-H1 prevented development of traction force and abolished sliding and disassembly of focal adhesion upon KANK activation. Other players participating in microtubule-driven KANK-dependent focal adhesion disassembly include kinases ROCK and PAK, as well as microtubules/focal adhesions associated proteins Kinesin-1, APC and αTAT. Finally, we propose a physical model of a microtubule-driven focal adhesion disruption involving local GEF-H1/RhoA/ROCK dependent activation of contractility which is consistent with experimental data.
Heterologous Expression and Characterization ofToxA1Haplotype from India and its Interaction withTsn1for Spot Blotch Susceptibility in Spring Wheat
Authors: Chaubey Ranjan Kumar , Thakur Dharamsheela , Navathe Sudhir , Sharma Sandeep , Mishra Vinod Kumar , Singh Pawan Kumar , Chand Ramesh
Published: April 2023

Background

ToxA, a necrotrophic effector protein, is present in the genome of fungal species likeParastagnospora nodorum,Pyrenophora tritici-repentisandBipolaris sorokiniana. Tsn1is the sensitivity gene in the host whose presence indicates more susceptibility toToxAcarrying pathogen, andToxA-Tsn1interaction follows an inverse gene-for-gene relationship.

Methods and Results

The present study involved cloning and expressing theToxA1haplotype fromB. sorokiniana. It was found that the amplicon exhibited an expected product size of 471 bp. Sequence analysis of theToxA1nucleotide sequence revealed the highest identity, 99.79%, withP. tritici-repentis. The protein expression analysis showed peak expression at 16.5kDa. Phylogenetic analysis of theToxA1sequence from all theBipolarisisolates formed an independent clade along withP. tritici-repentisand diverged fromP. nodorum.ToxA-Tsn1interaction was studied in 18 wheat genotypes (11Tsn1and 7tsn1) at both seedling and adult stages, validating the inverse gene-for-gene relationship, as the toxin activity was highest in the K68 genotype (Tsn1) and lowest in WAMI280 (tsn1).

Conclusion

The study indicates that the haplotypeToxA1is prevailing in the Indian population ofB. sorokiniana. It would be desirable for wheat breeders to select genotypes withtsn1locus for making wheat resistant to spot blotch.
Loss-of-function mutation in Omicron variants reduces spike protein expression and attenuates SARS-CoV-2 infection
Authors: Vu Michelle N. , Alvarado R. Elias , Morris Dorothea R. , Lokugamage Kumari G. , Zhou Yiyang , Morgan Angelica L. , Estes Leah K. , McLeland Alyssa M. , Schindewolf Craig , Plante Jessica A. , Ahearn Yani P. , Meyers William M. , Murray Jordan T. , Crocquet-Valdes Patricia A. , Weaver Scott C. , Walker David H. , Russell William K. , Routh Andrew L. , Plante Kenneth S. , Menachery Vineet
Published: April 2023

SARS-CoV-2 Omicron variants emerged in 2022 with >30 novel amino acid mutations in the spike protein alone. While most studies focus on receptor binding domain changes, mutations in the C-terminus of S1 (CTS1), adjacent to the furin cleavage site, have largely been ignored. In this study, we examined three Omicron mutations in CTS1: H655Y, N679K, and P681H. Generating a SARS-CoV-2 triple mutant (YKH), we found that the mutant increased spike processing, consistent with prior reports for H655Y and P681H individually. Next, we generated a single N679K mutant, finding reduced viral replicationin vitroand less diseasein vivo.Mechanistically, the N679K mutant had reduced spike protein in purified virions compared to wild-type; spike protein decreases were further exacerbated in infected cell lysates. Importantly, exogenous spike expression also revealed that N679K reduced overall spike protein yield independent of infection. Although a loss-of-function mutation, transmission competition demonstrated that N679K had a replication advantage in the upper airway over wild-type SARS-CoV-2 in hamsters, potentially impacting transmissibility. Together, the data show that N679K reduces overall spike protein levels during Omicron infection, which has important implications for infection, immunity, and transmission.
Benchmarking Uncertainty Quantification for Protein Engineering
Authors: Greenman Kevin P. , Amini Ava P. , Yang Kevin K.
Published: April 2023

Machine learning sequence-function models for proteins could enable significant ad vances in protein engineering, especially when paired with state-of-the-art methods to select new sequences for property optimization and/or model improvement. Such methods (Bayesian optimization and active learning) require calibrated estimations of model uncertainty. While studies have benchmarked a variety of deep learning uncertainty quantification (UQ) methods on standard and molecular machine-learning datasets, it is not clear if these results extend to protein datasets. In this work, we implemented a panel of deep learning UQ methods on regression tasks from the Fitness Landscape Inference for Proteins (FLIP) benchmark. We compared results across different degrees of distributional shift using metrics that assess each UQ method’s accuracy, calibration, coverage, width, and rank correlation. Additionally, we compared these metrics using one-hot encoding and pretrained language model representations, and we tested the UQ methods in a retrospective active learning setting. These benchmarks enable us to provide recommendations for more effective design of biological sequences using machine learning.
Nucleosome reorganisation in breast cancer tissues
Authors: Jacob Divya R. , Guiblet Wilfried M. , Mamayusupova Hulkar , Shtumpf Mariya , Ciuta Isabella , Ruje Luminita , Gretton Svetlana , Bikova Milena , Correa Clark , Dellow Emily , Agrawal Shivam P. , Shafiei Navid , Drobysevskaja Anastasija , Armstrong Chris M. , Lam Jonathan D. G. , Vainshtein Yevhen , Clarkson Christopher T. , Thorn Graeme J. , Sohn Kai , Pradeepa Madapura M. , Chandrasekharan Sankaran , Brooke Greg N. , Klenova Elena , Zhurkin Victor B. , Teif Vladimir B.
Published: April 2023

Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. Here we have generated high resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. This analysis has detected single-nucleosome repositioning at key regulatory regions in a patient-specific manner and common cancer-specific patterns across patients. The nucleosomes gained in tumour versus normal tissue were particularly informative of cancer pathways, with ∼20-fold enrichment at CpG islands, a large fraction of which marked promoters of genes encoding DNA-binding proteins. In addition, tumour tissues were characterised by a 5-10 bp decrease in the average distance between nucleosomes (nucleosome repeat length, NRL), which is qualitatively similar to the differences between pluripotent and differentiated cells. These effects were correlated with gene activity, DNA sequence repeats abundance, differential DNA methylation and binding of linker histone variants H1.4 and H1X. Our findings provide a new mechanistic understanding of nucleosome repositioning in tumour tissues that can be valuable for patient stratification and monitoring using liquid biopsies.
Metabolism of host lysophosphatidylcholine inPlasmodium falciparum-infected erythrocytes
Authors: Liu Jiapeng , Dapper Christie , Klemba Michael
Published: April 2023

The human malaria parasitePlasmodium falciparumrequires exogenous fatty acids to support its growth during the pathogenic, asexual erythrocytic stage. Host serum lysophosphatidylcholine (LPC) is a significant fatty acid source, yet the metabolic processes responsible for the liberation of free fatty acids from exogenous LPC are unknown. Using a novel assay for LPC hydrolysis inP. falciparum-infected erythrocytes, we have identified small-molecule inhibitors of keyin situlysophospholipase activities. Competitive activity-based profiling and generation of a panel of single-to-quadruple knockout parasite lines revealed that two enzymes of the serine hydrolase superfamily, termed exported lipase (XL) 2 and exported lipase homolog (XLH) 4, are the dominant lysophospholipase activities in parasite-infected erythrocytes. The parasite ensures efficient exogenous LPC hydrolysis by directing these two enzymes to distinct locations: XL2 is exported to the erythrocyte, while XLH4 is retained within the parasite. While XL2 and XLH4 were individually dispensable with little effect on LPC hydrolysisin situ, loss of both enzymes resulted in a strong reduction in fatty acid scavenging from LPC, hyperproduction of phosphatidylcholine, and an enhanced sensitivity to LPC toxicity. Notably, growth of XL/XLH- deficient parasites was severely impaired when cultured in media containing LPC as the sole exogenous fatty acid source. Furthermore, when XL2 and XLH4 activities were ablated by genetic or pharmacologic means, parasites were unable to proliferate in human serum, a physiologically-relevant fatty acid source, revealing the essentiality of LPC hydrolysis in the host environment and its potential as a target for anti-malarial therapy.
CD45 limits Natural Killer cell development from common lymphoid progenitors
Authors: Guzman Lizeth G Meza , Hyland Craig D , Bidgood Grace M , Leong Evelyn , Shen Zihan , Goh Wilford , Kratina Tobias , Rautela Jai , Vince James E , Nicholson Sandra E , Huntington Nicholas D
Published: April 2023

The clinical development of Natural Killer (NK) cell-mediated immunotherapy marks a milestone in the development of new cancer therapies and has gained traction due to the intrinsic ability of the NK cell to target and kill tumour cells. To fully harness the tumour killing ability of NK cells, we need to improve NK cell persistence and overcome suppression of NK cell activation in the tumour microenvironment. The trans-membrane, protein tyrosine phosphatase CD45, regulates NK cell homeostasis, with genetic loss of CD45 in mice resulting in increased numbers of mature NK cells [1–3]. This suggests that CD45-deficient NK cells might display enhanced persistence following adoptive transfer. However, here we demonstrated that adoptive transfer of CD45-deficiency did not enhance NK cell persistence in mice, and instead, the homeostatic disturbance of NK cells in CD45-deficient mice stemmed from a developmental defect in the common lymphoid progenitor population. The enhanced maturation within the CD45-deficient NK cell compartment was intrinsic to the NK cell lineage, and independent of the developmental defect. CD45 is not a conventional immune checkpoint candidate, as systemic loss is detrimental to T and B cell development [4–6], compromising the adaptive immune system. Nonetheless, this study suggests that inhibition of CD45 in progenitor or stem cell populations may improve the yield ofin vitrogenerated NK cells for adoptive therapy.
The enemy of my enemy is my friend: a plausible defense mechanism against antagonism in bacterial communities
Authors: Sánchez-Gómez Laura , Santillán Moisés
Published: April 2023

In a recent work we studied an artificial bacterial community where resistant bacteria assisted sensitive bacteria in surviving in the presence of antagonistic bacteria. Typically, this behavior is attributed to lateral gene exchange. However, we identified evidence of a distinct mechanism, which operates on the principle of “the enemy of my enemy is my friend”. Here, we explore the viability of this mechanism by means of a reaction-diffusion mathematical model. Our findings suggest that this mechanism is feasible under specific circumstances, particularly when bacteria undergo significant metabolic changes at high population densities.

Author summary

The importance of studying the formation of bacterial communities cannot be overstated. Initially, it was believed that the environment alone determined the assembly of these communities, but recent research has demonstrated that interactions among members of the community also have a crucial impact. For instance, it has been observed in some cases that, even when susceptible bacteria are confronted with antagonism, they can survive with the aid of resistant bacteria. Lateral gene exchange is typically considered the underlying mechanism responsible for this phenomenon. However, we identified in a recent work an alternative mechanism that does not involve gene exchange but operates on the principle of “the enemy of my enemy is my friend”. Using a mathematical model, we examine the plausibility of this mechanism in a small artificial bacterial community. Our results indicate that this mechanism alone cannot account for all the experimental observations, but including the assumption that bacteria undergo significant metabolic changes at high concentrations may suffice.
Trypanosoma cruziVDU deubiquitinase mediates surface protein trafficking and infectivity
Authors: Souza-Melo Normanda , Brito Silva Nathalia , Malvezzi Amaranta Muniz , dos Santos Gregory Pedroso , Alcântara Laura Maria , de Lima Alcantara Carolina , da Cunha e Silva Narcisa Leal , Zoltner Martin , Field Mark C. , Schenkman Sergio
Published: April 2023

Ubiquitylation is a post-translational modification promoting protein degradation. Within the endomembrane system ubiquitylation marks proteins for lysosomal processing. Deubiquitinases (DUBs) cleave ubiquitin from modified proteins and, in the case of surface proteins, prevent lysosomal targeting and thus play a major role in controlling turnover. InTrypanosoma cruzi,the etiological agent of Chagas disease, acquisition of nutrients in parasites proliferating within the blood meal of insect vectors occurs via the cytostome, a unique structure connected to a long tubular cytopharynx. Contents are delivered to late endosomes and accumulate in reservosomes, equivalent to lysosomes. When starved,T. cruzidifferentiates into mammalian infective trypomastigotes, which are cell cycle arrested. Here we asked what roles ubiquitylation plays in this unique endocytic process by interrogation of theT. cruziortholog of VDU (von Hippel-Lindau-interacting deubiquitylating enzyme)/USP33 (ubiquitin-specific protease). We found that TcVDU expression level inversely correlated with transferrin endocytosis, and that overexpression led to a longer retention of the endocytic cargo near the cytostome. TcVDU itself was found enriched in the anterior region of the parasite, in proximity to endocytic cargo. Most importantly, TcVDU overexpression reduced parasite invasion capacity and led to increased release oftrans-sialidase. These alterations in the abundance of multiple surface proteins in TcVDU mutants indicate a key role of TcVDU in modulating theT. cruzisurface by affecting the endosomal traffic and consequently the host-parasite interface.

Author summary

Trypanosoma cruziis the cause of Chagas disease that affects large populations of Central and South America. Disease is spreading to other continents due to poor control of blood transfusion from donors with chronic and undiagnosed infection, migration and drug treatment with limited performance and undesired side effects. Proliferating forms ofT. cruziacquire nutrients through the cytostome, a cell surface opening connected to a long tubular cytopharynx. Internalized material is endocytosed in the cytopharynx. This is distinct from other members of the Trypanosomatids, which endocytose material exclusively through the flagellar pocket. By using CRISPR gene editing and overexpression we demonstrated that a conserved deubiquitinase (VDU) is a key control element for traffic from the cytopharynx to endosomal compartments inT. cruzi. Changed levels of VDU modify endosomal traffic and largely impact the parasite surface, causing changes in infectivity.
Metabolic specialization drives reduced pathogenicity inPseudomonas aeruginosaCF clinical isolates
Authors: Pedersen Bjarke H. , Simões Filipa B. , Pogrebnyakov Ivan , Welch Martin , Johansen Helle Krogh , Molin Søren , La Rosa Ruggero
Published: April 2023

Metabolism provides the foundation for all cellular functions. During persistent infections, in adapted pathogenic bacteria metabolism functions radically differently compared with more naïve strains. Whether this is simply a necessary accommodation to the persistence phenotype or if metabolism plays a direct role in achieving persistence in the host is still unclear. Here, we characterize a convergent shift in metabolic function(s) linked with the persistence phenotype duringPseudomonas aeruginosacolonization in the airways of people with cystic fibrosis. We show that clinically-relevant mutations in the key metabolic enzyme, pyruvate dehydrogenase, lead to a host-specialized metabolism together with a lower virulence and immune response recruitment. These changes in infection phenotype are mediated by impaired type III secretion system activity and by secretion of the antioxidant metabolite, pyruvate, respectively. Our results show how metabolic adaptations directly impinge on persistence and pathogenicity in this organism.
Matrigel inhibits elongation and drives endoderm differentiation in aggregates of mouse embryonic stem cells
Authors: Amel Atoosa , Goolam Mubeen
Published: April 2023

Modelling peri-implantation mammalian development using the self-organising properties of stem cells is a rapidly growing field that has advanced our understanding of cell fate decisions occurring in the early embryo. Matrigel, a basement membrane matrix, is a critical substrate used in various protocols for its efficacy in promoting stem cell growth and self-organization. However, its role in driving stem cell lineage commitment, and whether this effect is driven by biochemical or physical cues is not being clearly defined. Here, we grow embryoid bodies in suspension, Matrigel, and agarose, an inert polysaccharide, to attempt to decouple the physical and biochemical roles of Matrigel and better understand how it drives stem cell differentiation. We show that stem cell aggregates in Matrigel are hindered in their ability to elongate compared to those grown in agarose or in suspension indicating that prohibitive role in self-organisation. Aggregates in Matrigel are also driven to differentiate into endoderm with ectoderm differentiation inhibited. Furthermore, these effects are not due to the physical presence of Matrigel as the same effects are not witnessed in aggregates grown in agarose. Our results thus indicate that Matrigel has a significant and complex effect on the differentiation and morphology of embryoid bodies.
AHL10 phosphorylation determines RRP6L1 chromatin association and growth suppression during water stress
Authors: Wong Min May , Huang Xin-Jie , Bau Yu-Chiuan , Verslues Paul E.
Published: April 2023

Phosphorylation of AHL10, one of the AT-hook family of plant-specific DNA binding proteins, is critical for growth suppression during moderate severity drought (low water potential, ψw) stress. To understand how AHL10 phosphorylation determines drought response, we identified putative AHL10 interacting proteins and further characterized interaction with RRP6L1, a protein involved in epigenetic regulation. RRP6L1 and AHL10 mutants, as well asahl10-1rrp6l1-2, had similar phenotype of increased growth maintenance during low ψw. Chromatin precipitation demonstrated that RRP6L1 chromatin association increased during low ψwstress and was dependent upon AHL10 phosphorylation. Transcriptome analyses showed that AHL10 and RRP6L1 have concordant effects on expression of stress- and development-related genes. Together these results indicate that stress signaling can act via AHL10 phosphorylation to control the chromatin association of the key regulatory protein RRP6L1. AHL10 and RRP6L1 interaction in meristem cells is part of a mechanism to down-regulate growth during low ψwstress. Interestingly, loss of AHL13, which is homologous to AHL10 and phosphorylated at similar C-terminal site, blocked the enhanced growth maintenance ofahl10-1. Thus, AHL10 and AHL13, despite their close homology, are not redundant but rather have distinct roles, likely related to the formation of AHL hetero-complexes.

Summary Statement

Phosphorylation ofArabidopsis thalianaAHL10 is important to control growth during drought stress, a function which is distinct from the closely related AHL13. One way that phosphorylation determines AHL10 function is by altering its ability to mediate chromatin recruitment of RRP6L1.
Transformers enable accurate prediction of acute and chronic chemical toxicity in aquatic organisms
Authors: Gustavsson Mikael , Käll Styrbjörn , Svedberg Patrik , Inda-Diaz Juan S. , Molander Sverker , Coria Jessica , Backhaus Thomas , Kristiansson Erik
Published: April 2023

Environmental safety assessments, as mandated by many regulations, require that toxicity data is generated for up to three trophic levels, algae, aquatic invertebrates, and fish. Conducting these testsin vivois resource-intensive, time-consuming, and causes undue suffering. Computational methods are fast and cost-efficient alternatives, however, their adaptation in regulatory settings has been slow, both due to low accuracy and narrow applicability domains. Here we present a new method for predicting chemical toxicity based on molecular structure. The method is based on a transformer, capturing structural features associated with toxicity, followed by a deep neural network that predicts the corresponding effect concentrations. After training on data from tens of thousands of exposure experiments, the model shows high predictive performance for each of the three trophic levels. Compared to commonly used QSAR methods, the model has both a larger applicability domain and a considerably lower error. In addition, training the model on data that combines multiple types of effect concentrations further improves the performance. We conclude that transformer-based models have the potential to significantly advance computational predictions of chemical toxicity and makein silicoapproaches a more attractive alternative when compared to animal-based exposure experiments.
BREADR: An R Package for the Bayesian Estimation of Genetic Relatedness from Low-coverage Genotype Data
Authors: Rohrlach Adam B , Tuke Jonathan , Popli Divyaratan , Haak Wolfgang
Published: April 2023

Robust and reliable estimates of how individuals are biologically related to each other are a key source of information when reconstructing pedigrees. In combination with contextual data, reconstructed pedigrees can be used to infer possible kinship practices in prehistoric populations. However, standard methods to estimate biological relatedness from genome sequence data cannot be applied to low coverage sequence data, such as are common in ancient DNA (aDNA) studies. Critically, a statistically robust method for assessing and quantifying the confidence of a classification of a specific degree of relatedness for a pair of individuals, using low coverage genome data, is lacking.

In this paper we present the R-package BREADR (Biological RElatedness from Ancient DNA in R), which leverages the so-called pairwise mismatch rate, calculated on optimally-thinned genome-wide pseudo-haploid sequence data, to estimate genetic relatedness up to the second degree, assuming an underlying binomial distribution. BREADR also returns a posterior probability for each degree of relatedness, from identical twins/same individual, first-degree, second-degree or “unrelated” pairs, allowing researchers to quantify and report the uncertainty, even for particularly low-coverage data. We show that this method accurately recovers degrees of relatedness for sequence data with coverage as low as 0.04Xusing simulated data, and then compare the performance of BREADR on empirical data from Bronze Age Iberian human sequence data. The BREADR package is designed for pseudo-haploid genotype data, common in aDNA studies.
AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data
Authors: Silva Jorge M. , Qi Weihong , Pinho Armando J. , Pratas Diogo
Published: April 2023

Low-complexity data analysis is the area that addresses the search and quantification of regions in sequences of elements that contain low-complexity or repetitive elements. For example, these can be tandem repeats, inverted repeats, homopolymer tails, GC biased regions, similar genes, and hairpins, among many others. Identifying these regions is crucial because of their association with regulatory and structural characteristics. Moreover, their identification provides positional and quantity information where standard assembly methodologies face significant difficulties because of substantial higher depth coverage (mountains), ambiguous read mapping, or where sequencing or reconstruction defects may occur. However, the capability to distinguish low-complexity regions (LCRs) in genomic and proteomic sequences is a challenge that depends on the model’s ability to find them automatically. Low-complexity patterns can be implicit through specific or combined sources, such as algorithmic or probabilistic, and recurring to different spatial distances, namely local, medium, or distant associations.This paper addresses the challenge of automatically modeling and distinguishing LCRs, providing a new method and tool (AlcoR) for efficient and accurate segmentation and visualization of these regions in genomic and proteomic sequences. The method enables the use of models with different memories, providing the ability to distinguish local from distant low-complexity patterns. The method is reference- and alignment-free, providing additional methodologies for testing, including a highly-flexible simulation method for generating biological sequences (DNA or protein) with different complexity levels, sequence masking, and a visualization tool for automatic computation of the LCR maps into an ideogram style. We provide illustrative demonstrations using synthetic, nearly synthetic, and natural sequences showing the high efficiency and accuracy of AlcoR. As large-scale results, we use AlcoR to unprecedentedly provide a whole-chromosome low-complexity map of a recent complete human genome and the haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar.The AlcoR method provides the ability of fast sequence characterization through data complexity analysis, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format. The source code is freely provided athttps://github.com/cobilab/alcor.
Spatiotemporal dynamics across visual cortical laminae support a predictive coding framework for interpreting mismatch responses
Authors: Gallimore Connor G. , Ricci David , Hamm Jordan P.
Published: April 2023

Abstract

Context modulates neocortical processing of sensory data. Unexpected visual stimuli elicit large responses in primary visual cortex (V1) -- a phenomenon known as deviance detection (DD) at the neural level, or “mismatch negativity” (MMN) when measured with EEG. It remains unclear how visual DD/MMN signals emerge across cortical layers, in temporal relation to the onset of deviant stimuli, and with respect to brain oscillations. Here we employed a visual “oddball” sequence – a classic paradigm for studying aberrant DD/MMN in neuropsychiatric populations – and recorded local field potentials in V1 of awake mice with 16-channel multielectrode arrays. Multiunit activity and current source density profiles showed that while basic adaptation to redundant stimuli was present early (50ms) in layer 4 responses, DD emerged later (150-230ms) in supragranular layers (L2/3). This DD signal coincided with increased delta/theta (2-7Hz) and high-gamma (70-80Hz) oscillations in L2/3 and decreased beta oscillations (26-36hz) in L1. These results clarify the neocortical dynamics elicited during an oddball paradigm at a microcircuit level. They are consistent with a predictive coding framework, which posits that predictive suppression is present in cortical feed-back circuits, which synapse in L1, while “prediction errors” engage cortical feed-forward processing streams, which emanate from L2/3.
Opportunistic evidence of the impact of bacterial infections on social integration in vampire bats
Authors: Razik Imran , Stockmaier Sebastian , Abou-Elias Michael , Carter Gerald G.
Published: April 2023

Social integration can affect an individual’s susceptibility to infectious disease. Conversely, infectious disease can reduce an individual’s social activity. Yet, it remains unclear to what extent short-term infections can inhibit social integration and the formation of new relationships. During a previous study on relationship formation, we captured 21 female common vampire bats (Desmodus rotundus) from different wild populations and housed them together in captivity. Upon introduction, we observed an unplanned outbreak of bacterial infections that caused cutaneous lesions. After treating infected bats with an antibiotic, 5 bats recovered, but 4 others suffered lasting injuries. Given that observations of how natural infections alter relationship formation are rare, we analyzed how allogrooming rates changed over time among familiar and new dyads consisting of the 9 infected and 12 asymptomatic bats. We found that (1) infected bats demonstrated reduced activity and social behavior, (2) more severely infected bats gave and received less allogrooming compared to asymptomatic bats, (3) the effect of infection was larger for new dyads relative to familiar dyads, and (4) this effect decreased as infected bats recovered and new dyads became more familiar. These opportunistic observations were consistent with the hypothesis that short-term infections can impact the formation of new relationships.
The Drosophila MIC10 orthologue has a propensity to polymerize into cristae-shaping filaments
Authors: Stephan Till , Stoldt Stefan , Barbot Mariam , Carney Travis D. , Lange Felix , Bates Mark , Dib Peter Bou , Shcherbata Halyna R. , Meinecke Michael , Riedel Dietmar , Dennerlein Sven , Rehling Peter , Jakobs Stefan
Published: April 2023

Mitochondria are essential eukaryotic double-membrane organelles. The convoluted mitochondrial inner membrane forms highly organized invaginations, termed cristae, which are crucial for energy metabolism. Cristae formation requires MICOS, a conserved hetero-oligomeric inner membrane complex. The MICOS core subunit MIC10 is a small transmembrane protein that oligomerizes through highly conserved glycine-rich motifs to control cristae formation. Sequence alignments show thatD. melanogasterexhibits three MIC10-like proteins with different tissue-specific expression patterns. Here, we show that the ubiquitously expressed Dmel_CG41128/MINOS1b/DmMIC10b is the major MIC10 orthologue in flies. Loss of DmMIC10b disturbs cristae architecture of mitochondria and reduces the life-span and fertility of flies. Moreover, using fluorescence nanoscopy and electron tomography, we demonstrate that despite its high similarity to the MIC10 proteins from yeast and humans, DmMIC10b exhibits the unique ability to polymerize into elongated filaments upon overexpression. DmMIC10b filaments form bundles which accumulate in the intermembrane space and alter the shape of mitochondrial cristae membranes. We show that the formation of the filaments relies on conserved glycine and cysteine residues and is suppressed by co-expression of other MICOS proteins. Thereby, our findings provide new insights into the regulation of MICOS in flies.