bluuebunny/crossref_metadata_2025 huggingface dataset:
An unbiased test reveals no enrichment of sexually antagonistic polymorphisms on the human X chromosome
Authors: Ruzicka Filip , Connallon Tim
Published: January 2022

Mutations with beneficial effects in one sex can have deleterious effects in the other. Such ‘sexually antagonistic’ (SA) variants contribute to variation in life-history traits and overall fitness, yet their genomic distribution is poorly resolved. Theory predicts that SA variants could be enriched on the X chromosome or autosomes, yet current empirical tests face two formidable challenges: (i) identifying SA selection in genomic data is difficult; and (ii) metrics of SA variation show persistent biases towards the X, even when SA variants are randomly distributed across the genome. Here, we present an unbiased test of the theory that SA variants are enriched on the X. We first develop models for reproductive
F
ST
—a metric for quantifying sex-differential (including SA) effects of genetic variants on lifetime reproductive success—that control for X-linked biases. Comparing data from approximately 250 000 UK Biobank individuals to our models, we find
F
ST
elevations consistent with both X-linked and autosomal SA polymorphisms affecting reproductive success in humans. However, the extent of
F
ST
elevations does not differ from a model in which SA polymorphisms are randomly distributed across the genome. We argue that the polygenic nature of SA variation, along with sex asymmetries in SA effects, might render X-linked enrichment of SA polymorphisms unlikely.
Hybridization boosts dispersal of two contrasted ecotypes in a grass species
Authors: Curran Emma V. , Scott Matilda S. , Olofsson Jill K. , Nyirenda Florence , Sotelo Graciela , Bianconi Matheus E. , Manzi Sophie , Besnard Guillaume , Pereira Lara , Christin Pascal-Antoine
Published: January 2022

Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grassAlloteropsis angusta. In addition to an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting Miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can enter the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes ofA. angustacan thus use each other as a gateway to new locations across a large part of Africa, showing that hybridization can facilitate the geographical dispersal of distinct ecotypes of the same grass species.
Rotation of skylight polarization during learning walks is necessary to trigger neuronal plasticity inCataglyphisants
Authors: Grob Robin , Holland Cunz Oliver , Grübel Kornelia , Pfeiffer Keram , Rössler Wolfgang , Fleischmann Pauline N.
Published: January 2022

Many animals use celestial cues for impressive navigational performances in challenging habitats. Since the position of the sun and associated skylight cues change throughout the day and season, it is crucial to correct for these changes.Cataglyphisdesert ants possess a time-compensated skylight compass allowing them to navigate back to their nest using the shortest way possible. The ants have to learn the sun's daily course (solar ephemeris) during initial learning walks (LW) before foraging. This learning phase is associated with substantial structural changes in visual neuronal circuits of the ant's brain. Here, we test whether the rotation of skylight polarization during LWs is the necessary cue to induce learning-dependent rewiring in synaptic circuits in high-order integration centres of the ant brain. Our results show that structural neuronal changes in the central complex and mushroom bodies are triggered only when LWs were performed under a rotating skylight polarization pattern. By contrast, when naive ants did not perform LWs, but were exposed to skylight cues, plasticity was restricted to light spectrum-dependent changes in synaptic complexes of the lateral complex. The results identify sky-compass cues triggering learning-dependent versus -independent neuronal plasticity during the behavioural transition from interior workers to outdoor foragers.
Genetic coupling of life-history and aerobic performance in Atlantic salmon
Authors: Prokkola Jenni M. , Åsheim Eirik R. , Morozov Sergey , Bangura Paul , Erkinaro Jaakko , Ruokolainen Annukka , Primmer Craig R. , Aykanat Tutku
Published: January 2022

A better understanding of the genetic and phenotypic architecture underlying life-history variation is a longstanding aim in biology. Theories suggest energy metabolism determines life-history variation by modulating resource acquisition and allocation trade-offs, but the genetic underpinnings of the relationship and its dependence on ecological conditions have rarely been demonstrated. The strong genetic determination of age-at-maturity by two unlinked genomic regions (vgll3andsix6) makes Atlantic salmon (Salmo salar) an ideal model to address these questions. Using more than 250 juveniles in common garden conditions, we quantified the covariation between metabolic phenotypes—standard and maximum metabolic rates (SMR and MMR), and aerobic scope (AS)—and the life-history genomic regions, and tested if food availability modulates the relationships. We found that the early maturation genotype invgll3was associated with higher MMR and consequently AS. Additionally, MMR exhibited physiological epistasis; it was decreased when late maturation genotypes co-occurred in both genomic regions. Contrary to our expectation, the life-history genotypes had no effects on SMR. Furthermore, food availability had no effect on the genetic covariation, suggesting a lack of genotype-by-environment interactions. Our results provide insights on the key organismal processes that link energy use at the juvenile stage to age-at-maturity, indicating potential mechanisms by which metabolism and life-history can coevolve.
Migration restores hybrid incompatibility driven by mitochondrial–nuclear sexual conflict
Authors: Munasinghe Manisha , Haller Benjamin C. , Clark Andrew G.
Published: January 2022

In the mitochondrial genome, sexual asymmetry in transmission allows the accumulation of male-harming mutations since selection acts only on the effect of the mutation in females. Called the ‘Mother's Curse’, this phenomenon induces a selective pressure for nuclear variants that compensate for this reduction in male fitness. Previous work has demonstrated the existence of these interactions and their potential to act as Dobzhansky–Muller incompatibilities, contributing to reproductive isolation between populations. However, it is not clear how readily they would give rise to and sustain hybrid incompatibilities. Here, we use computer simulations in SLiM 3 to investigate the consequences of sexually antagonistic mitochondrial–nuclear interactions in a subdivided population. We consider distinct migration schemes and vary the chromosomal location, and consequently the transmission pattern, of nuclear restorers. Disrupting these co-evolved interactions results in less-fit males, skewing the sex ratio toward females. Restoration of male fitness depends on both the chromosomal location of nuclear restorer loci and the migration scheme. Our results show that these interactions may act as Dobzhansky–Muller incompatibilities, but their strength is not enough to drive population isolation. Overall, this model shows the varied ways in which populations can respond to migration's disruption of co-evolved mitochondrial–nuclear interactions.
A life-history trade-off gene with antagonistic pleiotropic effects on reproduction and survival in limiting environments
Authors: Saggere Rani M. S. , Lee Christopher W. J. , Chan Irina C. W. , Durnford Dion G. , Nedelcu Aurora M.
Published: January 2022

Although life-history trade-offs are central to life-history evolution, their mechanistic basis is often unclear. Traditionally, trade-offs are understood in terms of competition for limited resources among traits within an organism, which could be mediated by signal transduction pathways at the level of cellular metabolism. Nevertheless, trade-offs are also thought to be produced as a consequence of the performance of one activity generating negative consequences for other traits, or the result of genes or pathways that simultaneously regulate two life-history traits in opposite directions (antagonistic pleiotropy), independent of resource allocation. Yet examples of genes with antagonistic effects on life-history traits are limited. This study provides direct evidence for a gene—
RLS1
, that is involved in increasing survival in nutrient-limiting environments at a cost to immediate reproduction in the single-celled photosynthetic alga,
Chlamydomonas reinhardtii
. Specifically, we show that RLS1 mutants are unable to properly suppress their reproduction in phosphate-deprived conditions. Although these mutants have an immediate reproductive advantage relative to the parental strain, their long-term survival is negatively affected. Our data suggest that
RLS1
is a
bona fide
life-history trade-off gene that suppresses immediate reproduction and ensures survival by downregulating photosynthesis in limiting environments, as part of the general acclimation response to nutrient deprivation in photosynthetic organisms.
SCARF: Auto-Segmentation Clinical Acceptability & Reproducibility Framework for Benchmarking Essential Radiation Therapy Targets in Head and Neck Cancer
Authors: Marsilla Joseph , Won Kim Jun , Tkachuck Denis , Hosni Ali , Kim Sejin , Jacinto Kristine , Siraj Joshua , Cho John , Hahn Ezra , Welch Mattea , Kazmierski Michal , Rey-McIntyre Katrina , Huang Shao Hui , Patel Tirth , Tadic Tony , Liu Fei-Fei , Bratman Scott , Hope Andrew , Haibe-Kains Benjamin
Published: January 2022

Background and Purpose: Auto-segmentation of organs at risk (OAR) in cancer patients is essential for enhancing radiotherapy planning efficacy and reducing inter-observer variability. Deep learning auto-segmentation models have shown promise, but their lack of transparency and reproducibility hinders their generalizability and clinical acceptability, limiting their use in clinical settings. Materials and Methods: This study introduces SCARF (auto-Segmentation Clinical Acceptability & Reproducibility Framework), a comprehensive six-stage reproducible framework designed to benchmark open-source convolutional neural networks for auto-segmentation of 19 essential OARs in head and neck cancer (HNC). Results: SCARF offers an easily implementable framework for designing and reproducibly benchmarking auto-segmentation tools, along with thorough expert assessment capabilities. Expert assessment labelled 16/19 AI-generated OAR categories as acceptable with minor revisions. Boundary distance metrics, such as 95th Percentile Hausdorff Distance (95HD), were found to be 2x more correlated to Mean Acceptability Rating (MAR) than volumetric overlap metrics (DICE). Conclusions: The introduction of SCARF, our auto-Segmentation Clinical Acceptability & Reproducibility Framework, represents a significant step forward in systematically assessing the performance of AI models for auto-segmentation in radiation therapy planning. By providing a comprehensive and reproducible framework, SCARF facilitates benchmarking and expert assessment of AI-driven auto-segmentation tools, addressing the need for transparency and reproducibility in this domain. The robust foundation laid by SCARF enables the progression towards the creation of usable AI tools in the field of radiation therapy. Through its emphasis on clinical acceptability and expert assessment, SCARF fosters the integration of AI models into clinical environments, paving the way for more randomised clinical trials to evaluate their real-world impact.
Algorithmic Fairness in Computational Medicine
Authors: Xu Jie , Xiao Yunyu , Wang Wendy Hui , Ning Yue , Shenkman Elizabeth A , Bian Jiang , Wang Fei
Published: January 2022

Machine learning models are increasingly adopted for facilitating clinical decision-making. However, recent research has shown that machine learning techniques may result in potential biases when making decisions for people in different subgroups, which can lead to detrimental effects on the health and well-being of vulnerable groups such as ethnic minorities. This problem, termed algorithmic bias, has been extensive studied in theoretical machine learning recently. However, how it will impact medicine and how to effectively mitigate it still remains unclear. This paper presents a comprehensive review of algorithmic fairness in the context of computational medicine, which aims at improving medicine with computational approaches. Specifically, we overview the different types of algorithmic bias, fairness quantification metrics, and bias mitigation methods, and summarize popular software libraries and tools for bias evaluation and mitigation, with the goal of providing reference and insights to researchers and practitioners in computational medicine.
The mycotoxin Beauvericin exhibits immunostimulatory effects on dendritic cells via activating the TLR4 signaling pathway
Authors: Yang Xiaoli , Ali Shafaqat , Zhao Manman , Richter Lisa , Schäfer Vanessa , Schliehe-Diecks Julian , Frank Marian , Qi Jing , Larsen Pia-Katharina , Skerra Jennifer , Islam Heba , Wachtmeister Thorsten , Alter Christina , Huang Anfei , Bhatia Sanil , Köhrer Karl , Kirschning Carsten , Weighardt Heike , Kalinke Ulrich , Kalscheuer Rainer , Uhrberg Markus , Scheu Stefanie
Published: January 2022

Beauvericin (BEA), a mycotoxin of the enniatin family produced by various toxigenic fungi, has been attributed multiple biological activities such as anti-cancer, anti-inflammatory, and anti-microbial functions. However, effects of BEA on dendritic cells remain unknown so far. Here, we identified effects of BEA on murine granulocyte–macrophage colony-stimulating factor (GM-CSF)-cultured bone marrow derived dendritic cells (BMDCs) and the underlying molecular mechanisms. BEA potently activates BMDCs as signified by elevated IL-12 and CD86 expression. Multiplex immunoassays performed on myeloid differentiation primary response 88 (MyD88) and toll/interleukin-1 receptor (TIR) domain containing adaptor inducing interferon beta (TRIF) single or double deficient BMDCs indicate that BEA induces inflammatory cytokine and chemokine production in a MyD88/TRIF dependent manner. Furthermore, we found that BEA was not able to induce IL-12 or IFNβ production in Toll-like receptor 4 (Tlr4)-deficient BMDCs, whereas induction of these cytokines was not compromised in Tlr3/7/9 deficient BMDCs. This suggests that TLR4 might be the functional target of BEA on BMDCs. Consistently, in luciferase reporter assays BEA stimulation significantly promotes NF-κB activation in mTLR4/CD14/MD2 overexpressing but not control HEK-293 cells. RNA-sequencing analyses further confirmed that BEA induces transcriptional changes associated with the TLR4 signaling pathway. Together, these results identify TLR4 as a cellular BEA sensor and define BEA as a potent activator of BMDCs, implying that this compound can be exploited as a promising candidate structure for vaccine adjuvants or cancer immunotherapies.
Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail
Authors: Addetia Amin , Park Young-Jun , Starr Tyler , Greaney Allison J. , Sprouse Kaitlin R , Bowen John E. , Tiles Sasha W. , Van Voorhis Wesley C. , Bloom Jesse D. , Corti Davide , Walls Alexandra C. , Veesler David
Published: January 2022

The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-CoV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the cilgavimab (AZD1061) mAb. Here, we show that this residue substitution remodels the ACE2-binding site allosterically, thereby dampening receptor recognition severely and altering the epitopes recognized by these three mAbs. Although vaccine-elicited neutralizing antibody titers are decreased similarly against the E406 mutant and the Delta or Epsilon variants, broadly neutralizing sarbecovirus mAbs, including a clinical mAb, inhibit the E406W spike mutant.
Towards the identification and optimization of the "dose-response" relationship of transcranial direct current stimulation
Authors: Salvador Ricardo , Biagi Maria Chiara , Perez Pelegri Manuel , Zhou Junhong , Travison Thomas , Alvaro Pascual-Leone Alvaro , Manor Brad , Ruffini Giulio
Published: January 2022

Transcranial direct current stimulation (tDCS) is being investigated as a therapeutic tool in several neuropsychiatric disorders, but its mechanisms of action remain incompletely understood and its effectiveness is highly variable from subject to subject. Some of this inter-subject variance is thought to stem from individual differences in head anatomy, which result in different electric field distributions across individuals for the same stimulation settings. In a recent block-randomized, sham-controlled pilot study, 18 older adults with mild-to-moderate motor and cognitive impairments underwent a 2-week, 10-session intervention of 2 mA bipolar tDCS with the anode over the left dorsolateral prefrontal cortex (DLPFC) and cathode over the right supraorbital region (anodal F3 vs. FP2 using sponge electrodes in the 10-20 EEG system). tDCS, compared to sham stimulation, improved average cognitive-motor performance over a two-week follow-up. For a subset of 12 participants from this cohort who underwent structural brain MRIs at baseline, we derived tDCS-induced electric field properties using MRI-derived realistic, individualized finite element modeling. We hypothesized that the electric field component orthogonal (E_n) to the cortex over the left DLPFC would correlate with observed cognitive-motor improvements. Across the 12 subjects the average tDCS-induced electric field over the target area was highly variable with a standard deviation of the surface average E_n over the left DLPFC of 21% of the mean. For those subjects who were randomized to tDCS intervention (n=6), those who exhibited greater improvement in cognitive-motor performance were exposed to greater normal component of the tDCS electric field averaged over the left DLPFC (r_(95 %) ∈[-0.99,-0.59]). In contrast, averaged over the right DLPFC, E_n was a poor predictor of outcome (r_(95 %) ∈[-0.08,0.97]), as was the amplitude of the current injected (a widely adopted dosing parameter). In light of these results, we conducted a retrospective modeling experiment using personalized montage optimization algorithms to achieve a desired E_namplitude over the left DLPFC. The optimized montages induced an average E_n on the left DLPFC comparable to the bipolar montages, but with half the variability (standard deviation was 11% compared to 21% with bipolar montages). In addition, these results suggest that optimized multichannel montages afford more focal targeting, with lower "spill-over" of electric field onto other cortical areas. These proof-of-concept results, though based upon a small sample size, indicate that assessment of the E-field distribution is critical when evaluating the effects of tDCS intervention. They also reinforce the importance of controlled cortical electric field dosing in tDCS and the potential advantages of optimized multichannel stimulation.
SARS-CoV-2 antibody profile of naturally infected and vaccinated individuals detected using qualitative, semi-quantitative and multiplex immunoassays
Authors: Meyers Jamie , Windau Anne , Schmotzer Christine , Saade Elie , Noguez Jaime , Stempak Lisa , Zhang Xiaochun
Published: January 2022

Antibody profiling of vaccinated versus naturally infected individuals is important in evaluating immunity and aiding diagnosis and booster strategies. This study measured antibodies against different antigen targets in healthcare workers (HCW) who have been fully vaccinated with mRNA vaccines, recovered from natural infection, or patients during active infection. All vaccinated individuals were positive for anti-RBD, anti-S1, and anti-S2 antibodies. The median index and interquartile range (IQR) by the Atellica IgG assay were 179 and 140-291 respectively. Among the different antigen targets within the Bioplex assay, the levels of anti-RBD were highest (median >3200 U/mL; IQR >3200 to >3200 U/mL), followed by anti-S1 (median 2132 U/mL; IQR 1649->3200 U/mL) and anti-S2 (median=42 U/mL; IQR=24-76 U/mL). The non-vaccinated recovered cohort showed 90% seropositivity (median index >10; IQR 3.6->10) by Atellica total antibody, 73% by Atellica IgG (median index 3.3; IQR 0.9-9.4), 84% by Bioplex anti-RBD (median 62; IQR 12-269 U/mL), 77% by Bioplex anti-S1 (median 45; IQR 10-83 U/mL), 37% by Bioplex anti-S2 (median 7; IQR 1-12 U/mL), and 79% by Bioplex anti-nucleocapsid (median 69; IQR 20-185U/mL) respectively. The active infection cohort exhibited a similar pattern as the recovered cohort. About 88% and 78% of the recovered and active infection cohort produced both anti-spike and anti-N antibodies with Anti-S1/anti-N ratios ranging from 0.07-16.26. In summary, fully vaccinated individuals demonstrated an average of 50-fold higher antibody levels than naturally infected unvaccinated individuals with immune reactivity strongly towards RBD/S1 and a weak response to S2. The results support vaccination regardless of previous COVID-infection status.
Designing isolation guidelines for COVID-19 patients utilizing rapid antigen tests: a simulation study using viral dynamics models
Authors: Jeong Yong Dam , Ejima Keisuke , Kim Kwang Su , Joohyeon Woo , Iwanami Shoya , Fujita Yasuhisa , Jung Il Hyo , Shibuya Kenji , Iwami Shingo , Bento Ana I. , Ajelli Marco
Published: January 2022

Appropriate isolation guidelines for COVID-19 patients are warranted. Currently, isolating for fixed time is adapted in most countries. However, given the variability in viral dynamics between patients, some patients may no longer be infectious by the end of isolation (thus they are redundantly isolated), whereas others may still be infectious. Utilizing viral test results to determine ending isolation would minimize both the risk of ending isolation of infectious patients and the burden due to redundant isolation of noninfectious patients. In our previous study, we proposed a computational framework using SARS-CoV-2 viral dynamics models to compute the risk and the burden of different isolation guidelines with PCR tests. In this study, we extend the computational framework to design isolation guidelines for COVID-19 patients utilizing rapid antigen tests. Time interval of tests and number of consecutive negative tests to minimize the risk and the burden of isolation were explored. Furthermore, the approach was extended for asymptomatic cases. We found the guideline should be designed considering various factors: the infectiousness threshold values, the detection limit of antigen tests, symptom presence, and an acceptable level of releasing infectious patients. Especially, when detection limit is higher than the infectiousness threshold values, more consecutive negative results are needed to ascertain loss of infectiousness. To control the risk of releasing of infectious individuals under certain levels, rapid antigen tests should be designed to have lower detection limits than infectiousness threshold values to minimize the length of prolonged isolation, and the length of prolonged isolation increases when the detection limit is higher than the infectiousness threshold values, even though the guidelines are optimized for given conditions.
Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): a point-of-care PCR test for rapid detection of SARS-CoV-2 infection
Authors: Achenbach Chad J , Caputo Matthew , Hawkins Claudia , Balmert Lauren C , Qi Chao , Odorisio Joseph , Dembele Etienne , Jackson Alema , Abbas Hiba , Frediani Jennifer K , Levy Joshua M , Rebolledo Paulina A. , Kempker Russell R. , Esper Annette M. , Lam Wilbur A. , Martin Greg S. , Murphy Robert L
Published: January 2022

Background

Rapid and accurate testing for SARS-CoV-2 is an essential tool in the medical and public health response to the COVID-19 pandemic. An ideal test for COVID-19 would combine the sensitivity of laboratory-based PCR combined with the speed and ease of use of point-of-care (POC) or home-based rapid antigen testing.

Methods

To evaluate the performance of the Diagnostic Analyzer for Selective Hybridization (DASH) SARS-CoV-2 POC PCR (sample insertion to result time of 16 minutes), we conducted a cross-sectional study of adults with and without symptoms of COVID-19 at four clinical sites. We collected two bilateral anterior nasal swabs from each participant and information on COVID-19 symptoms, vaccination, and exposure. One swab was tested with the DASH SARS-CoV-2 POC PCR and the second in a central laboratory using Cepheid Xpert Xpress SARS-CoV-2 PCR. We assessed test concordance and calculated sensitivity, specificity, negative and positive predictive values using Xpert as the “gold standard.”

Results

We enrolled 315 and analyzed 313 participants with median age 42 years; 65% were female, 62% symptomatic, 75% had received ≥2 doses of mRNA COVID-19 vaccine, and 16% currently COVID-19 positive. There were concordant results for 307 tests indicating an overall agreement for DASH of 0.98 [95% CI 0.96, 0.99] compared to Xpert. DASH performed at 0.96 [95% CI 0.86, 1.00] sensitivity and 0.98 [95% CI 0.96, 1.00] specificity, with a positive predictive value of 0.85 [95% CI 0.73, 0.96] and negative predictive value of 0.996 [95% CI 0.99, 1.00]. The six discordant tests between DASH and Xpert all had high Ct values (>30) on the respective positive assay. DASH and Xpert Ct values were highly correlated (R=0.89 [95% CI 0.81, 0.94]).

Conclusions

DASH POC SARS-CoV-2 PCR was accurate, easy to use, and provided fast results in real-life clinical settings with an overall performance similar to an EUA-approved laboratory-based PCR. Its compact design and ease of use are optimal for a variety of healthcare, and potentially community settings, including areas with lack of access to central laboratory-based PCR testing.

DASH is an accurate, easy to use, and fast point-of-care test with applications for diagnosis and screening of SARS-CoV-2 infection.
Substantial immune response in Omicron infected breakthrough and unvaccinated individuals against SARS-CoV-2 variants of concerns
Authors: Yadav Pragya D. , Sapkal Gajanan N. , Sahay Rima R. , Potdar Varsha A. , Deshpande Gururaj R. , Patil Deepak Y. , Nyayanit Dimpal A. , Shete Anita M. , Shastri Jayanthi , Awate Pradeep , Malhotra Bharti , Abraham Priya
Published: January 2022

The recent emergence of highly mutated SARS-CoV-2 Omicron variant has debilitating effect on public health system of the affected countries worldwide. Currently India is facing third wave of COVID-19 pandemic and going through a severe crisis. Within short span of time, the variant has shown high transmissibility and capability of evading the immune response generated against natural infection and vaccination. The immune escape potential of Omicron is a serious concern and further needs to be explored. In the present study, we have assessed the IgG and neutralizing antibody (NAb) response in breakthrough individuals vaccinated with two doses ChAdOx1 nCoV-19 vaccine (n=25), breakthrough individuals vaccinated with two doses of BNT162b2 mRNA vaccine (n=8) and unvaccinated individuals (n=6). All these individuals were infected with Omicron variant. The IgG antibody activity in the sera of the ChAdOx1 nCoV-19 and BNT162b2 mRNA breakthrough individuals was comparable with S1-RBD, while it was lesser in BNT162b2 mRNA breakthrough individuals with N protein and inactivated whole antigen IgG ELISA. BNT162b2 mRNA breakthrough individuals showed moderate reduction in NAb GMTs compared to ChAdOx1 nCoV-19 against Alpha, Beta and Delta. However, 3-fold higher reduction was observed with omicron variant in BNT162b2 mRNA than ChAdOx1 nCoV-19. Apparently, Alpha variant was modestly resistant to the sera of unvaccinated individuals than Beta, Delta and Omicron. Our study demonstrated substantial immune response in the individuals infected with Omicron. The neutralizing antibodies could effectively neutralize the Omicron and other VOCs including the most prevalent Delta variant.
An efficient CRISPR-Cas9 enrichment sequencing strategy for characterizing complex and highly duplicated genomic regions. A case study in the Prunus salicina LG3-MYB10 genes cluster
Authors: Fiol Arnau , Jurado-Ruiz Federico , López-Girona Elena , Aranzana Maria José
Published: January 2022

Genome complexity is largely linked to diversification and crop innovation. Examples of regions with duplicated genes with relevant roles in agricultural traits are found in many crops. In both duplicated and non-duplicated genes, much of the variability in agronomic traits is caused by large as well as small and middle scale structural variants (SVs), which highlights the relevance of the identification and characterization of complex variability between genomes for plant breeding. Here we improve and demonstrate the use of CRISPR-Cas9 enrichment combined with long-read sequencing technology to resolve the MYB10 region in the linkage group 3 (LG3) of Japanese plum (Prunus salicina), which has a length from 90 kb to 271 kb according to the P. salicina genomes available. We demonstrate the high complexity of this region, with homology levels between Japanese plum varieties comparable to those between Prunus species. We cleaved MYB10 genes in five plum varieties using the Cas9 enzyme guided by a pool of crRNAs. The barcoded fragments were then pooled and sequenced in a single MinION Oxford Nanopore Technologies (ONT) run, yielding 194 Mb of sequence. The enrichment was confirmed by aligning the long reads to the plum reference genomes, with a mean read on-target value of 4.5% and a depth per sample of 11.9x. From the alignment, 3,261 SNPs and 287 SVs were called and phased. A de novo assembly was constructed for each variety, which also allowed detection, at the haplotype level, of the variability in this region. CRISPR-Cas9 enrichment is a versatile and powerful tool for long-read targeted sequencing even on highly duplicated and/or polymorphic genomic regions, being especially useful when a reference genome is not available. Potential uses of this methodology as well as its limitations are further discussed.
Preclinical Characterization of Relatlimab, a Human LAG-3–Blocking Antibody, Alone or in Combination With Nivolumab
Authors: Thudium Kent , Selby Mark , Zorn Julie A. , Rak Gregory , Wang Xi-Tao , Bunch Roderick Todd , Hogan Jason M. , Strop Pavel , Korman Alan J.
Published: January 2022

Novel therapeutic approaches combining immune checkpoint inhibitors are needed to improve clinical outcomes for patients with cancer. Lymphocyte-activation gene 3 (LAG-3) is an immune checkpoint molecule that inhibits T-cell activity and antitumor immune responses, acting through an independent mechanism from that of programmed death-1 (PD-1) and cytotoxic T lymphocyte associated antigen-4 (CTLA-4). Here, we describe the development and preclinical characterization of relatlimab, a human antibody that binds to human LAG-3 with high affinity and specificity to block the interaction of LAG-3 with the ligands MHC II and fibrinogen like protein-1, and to reverse LAG-3–mediated inhibition of T-cell function in vitro. Consistent with previous reports, in mouse models, the combined blockade of LAG-3 and PD-1 with surrogate antibodies resulted in enhanced anti-tumor activity greater than the individual blockade of either receptor. In toxicity studies in cynomolgus monkeys, relatlimab was generally well tolerated when combined with nivolumab. These results are consistent with findings from the RELATIVITY-047 phase 2/3 trial showing that relatlimab combined with nivolumab is a well-tolerated regimen that demonstrated superior progression-free survival compared with nivolumab monotherapy in patients with unresectable or metastatic melanoma.

Synopsis

Preclinical studies demonstrate that relatlimab specifically blocks the interaction between LAG-3 and its ligands, and provide a biological rationale for combining relatlimab with the anti−PD-1 antibody nivolumab as an effective cancer immunotherapeutic strategy.
Interaction among bacterial cells triggers exit from lag phase
Authors: Ardré Maxime , Doulcier Guilhem , Brenner Naama , Rainey Paul B.
Published: January 2022

The relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the “inoculum effect”. Its mechanistic basis is unclear with possible explanations ranging from the independent actions of individual cells, to collective actions of populations of cells. Progress requires precise measurement of lag time distributions while at the same time, experimentally controlling inoculum size. Here we use a millifluidic droplet device in which the growth dynamics of hundreds of populations founded by different numbers of Pseudomonas fluorescens cells, ranging from a single cell, to one thousand cells, were followed in real time. Our data show that lag phase decreases with inoculum size. The average decrease, variance across droplets, and distribution shapes, follow predictions of extreme value theory, where the inoculum lag time is determined by the minimum value sampled from the single-cell distribution. Our experimental results show that exit from lag phase depends on strong interactions among cells, consistent with a “leader-cell” triggering end of lag phase for the entire population.
MX2 viral substrate breadth and inhibitory activity are regulated by protein phosphorylation
Authors: Betancor Gilberto , Bangham Madeleine , Jeon Jun Ki , Shah Kanisha , Lynham Steven , Jimenez-Guardeño Jose M , Malim Michael H
Published: January 2022

Human immunodeficiency virus type-1 (HIV-1) infection is potently inhibited by human myxovirus resistance 2 (MX2/MxB), which binds to the viral capsid and blocks the nuclear import of viral DNA. We have recently shown that phosphorylation is a key regulator of MX2 antiviral activity, with phosphorylation of serine residues at positions 14, 17 and 18 repressing MX2 function. Here, we extend the study of MX2 post-translational modifications, and identify serine and threonine phosphorylation in all domains of MX2. By substituting these residues with aspartic acid or alanine, hence mimicking the presence or absence of a phosphate group, respectively, we identified key positions that control MX2 antiviral activity. Aspartic acid substitutions of residues Ser306 or Thr334 and alanine substitutions of Thr343 yielded proteins with substantially reduced antiviral activity, whereas the presence of aspartic acid at positions Ser28, Thr151 or Thr343 resulted in enhanced activity: referred to as hypermorphic mutants. In some cases, these hypermorphic mutations, particularly when paired with other MX2 mutations (e.g., S28D/T151D or T151D/T343A) acquired the capacity to inhibit HIV-1 Capsid mutants known to be insensitive to wild type MX2, such as P90A or T210K, as well as MX2-resistant retroviruses such as equine infectious anaemia virus (EIAV) and murine leukaemia virus (MLV). This work highlights the complexity and importance of MX2 phosphorylation in the regulation of antiviral activity, and in the selection of susceptible viral substrates.

Author summary

Productive infection by human immunodeficiency virus type-1 (HIV-1) requires the import of viral replication complexes into the nuclei of infected cells. Myxovirus resistance 2 (MX2/MxB) blocks this step, halting nuclear accumulation of viral DNA and virus replication. We recently demonstrated how phosphorylation of a stretch of three serines in the amino-terminal domain of MX2 inhibits the antiviral activity. Here, we identify additional positions in MX2 whose phosphorylation status reduces or enhances antiviral function (hypomorphic and hypermorphic variants, respectively). Importantly, hypermorphic mutant proteins not only increased inhibitory activity against wild type HIV-1, but can also exhibit antiviral capabilities against HIV-1 Capsid mutant viruses that are resistant to wild type MX2. Furthermore, some of these proteins were also able to inhibit retroviruses that are insensitive to MX2. Therefore, we propose that phosphorylation comprises a major element of MX2 regulation and substrate determination.
Biogenic methane cycling is controlled by microbial cohorts
Authors: Mondav Rhiannon , Martin Gaëtan , Peura Sari , Garcia Sarahi L.
Published: January 2022

The generation and consumption of methane by aquatic microbial communities is an important contribution to the global carbon budget. We sought to broaden understanding of consortia members and interactions by combining multiple methods including analysis of natural and cultivated microbial communities. By analysing the microbial community composition and co-occurrence patterns of a lake time-series we were able to identify potential consortia involved in methane cycling. In combination with methane flux, we also analysed the community composition and co-occurrence patterns of reduced microbial model communities with inoculum from the same lake. While the network analyses confirmed many known associations, when combined with results from mixed cultures, we noted new players in methane cycling. Cultivated model communities were shown to be an effective method to explore the rarer but still important players in methane cycling and for identifying new putative members. Here we show that using multiple methods to approach the complex problem of methane cycling consortia yields not just insights into the known taxa but highlights potential new members creating new hypotheses to be tested.
L-threonine mediated DAF-16/HSF-1 activation inhibits ferroptosis and increases healthspan
Authors: Kim Juewon , Jo Yunju , Cho Donghyun , Ryu Dongryeol
Published: January 2022

The pathways that impact longevity in the wake of dietary restriction (DR) pathway remain still ill-defined. Most studies have focused on nutrient limitation and perturbations of energy metabolism to explain the beneficial effects of DR. We showed that the essential amino acid L-threonine was elevated in Caenorhabditis elegans under DR, and that L-threonine supplementation increased its healthspan. To elucidate the underlying mechanism, we conducted metabolic and transcriptomic profiling using LC-MS/MS and RNA-seq analyses in worms that were fed with RNAi to induce loss of function of key candidate mediators and evaluated healthspan. L-threonine supplementation and loss-of-threonine dehydrogenase, which govern L-threonine metabolism, increased the healthspan of C. elegans by attenuating ferroptosis in a ferritin-dependent manner. Tran-scriptomic analysis of C. elegans supplemented with L-threonine showed that FTN-1 encoding ferritin was elevated, implying FTN-1 is an essential mediator of longevity promotion through L-threonine. Organismal ferritin levels were positively correlated with chronological aging and L-thre-onine supplementation further increased ferritin levels, which protected against age-associated ferroptosis through the DAF-16 and HSF-1 pathways. Our investigation uncovered the role of a distinct and universal metabolite, L-threonine, in DR-mediated improvement in organismal healthspan, suggesting it could be an effective intervention for preventing senescence progression and age-induced ferroptosis.
Choice of 16S ribosomal RNA primers impacts urinary microbiota profiling
Authors: Heidrich Vitor , Inoue Lilian T. , Asprino Paula F. , Bettoni Fabiana , Mariotti Antonio C.H. , Bastos Diogo A. , Jardim Denis L.F. , Arap Marco A. , Camargo Anamaria A.
Published: January 2022

Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, sequencing the full-length 16S rRNA gene is impractical. Therefore, choosing which 16S rRNA hypervariable region to sequence is critical in microbiota profiling studies. All nine 16S rRNA hypervariable regions are taxonomically informative, but due to variability in profiling performance for specific clades, choosing the ideal 16S rRNA hypervariable region will depend on the bacterial composition of the habitat under study. Recently, NGS allowed the identification of microbes in the urinary tract, and urinary microbiota has become an active research area. However, there is no current study evaluating the performance of different 16S rRNA hypervariable regions for urinary microbiota profiling. We collected urine samples from male volunteers and profiled their urinary microbiota by sequencing a panel of six amplicons encompassing all nine 16S rRNA hypervariable regions. After systematically comparing their performance, we show that V1V2 hypervariable regions better assess the taxa commonly present in urine samples and V1V2 amplicon sequencing is more suitable for urinary microbiota profiling. We believe our results will be helpful to guide this crucial methodological choice in future urinary microbiota studies.
Structural Ramifications of Spike Protein D614G Mutation in SARS-CoV-2
Authors: Dokainish Hisham M. , Sugita Yuji
Published: January 2022

A single mutation from aspartate to glycine at position 614 has dominated all circulating variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). D614G mutation induces structural changes in the Spike (S) protein that strengthen the virus infectivity. Here, we use molecular dynamics simulations to dissect the effects of mutation and 630-loop rigidification on wild-type structure. The introduction of mutation with ordered 630-loop induces structural changes toward S-G614 Cryo-EM structure. An ordered 630-loop weakens the stabilizing interactions of the anionic D614, suggesting its disorder in wild-type. The mutation allosterically alters the receptor binding domain (RBD) forming an asymmetric and mobile Down conformation, which facilitate Up transition. The loss of D614_K854 salt-bridge upon mutation, generally stabilize S-protein protomer, including the fusion peptide proximal region that mediates membrane fusion. Understanding of the molecular basis of D614G is crucial as it dominates in all variants of concern including Delta and Omicron.
Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants
Authors: Servellita Venice , Syed Abdullah M. , Brazer Noah , Saldhi Prachi , Garcia-Knight Miguel , Sreekumar Bharath , Khalid Mir M. , Ciling Alison , Chen Pei-Yi , Kumar G. Renuka , Gliwa Amelia S. , Nguyen Jenny , Sotomayor-Gonzalez Alicia , Zhang Yueyuan , Frias Edwin , Prostko John , Hackett John , Andino Raul , Doudna Jennifer , Ott Melanie , Chiu Charles Y.
Published: January 2022

Virus-like particle (VLP) and live virus assays were used to investigate neutralizing immunity to Delta and Omicron SARS-CoV-2 variants in 239 samples from 125 fully vaccinated individuals. In uninfected, non-boosted individuals, VLP neutralization titers to Delta and Omicron were reduced 2.7-fold and 15.4-fold, respectively, compared to wild-type (WT), while boosted individuals (n=23) had 18-fold increased titers. Delta breakthrough infections (n=39) had 57-fold and 3.1-fold titers whereas Omicron breakthrough infections (n=14) had 5.8-fold and 0.32-fold titers compared to uninfected non-boosted and boosted individuals, respectively. The difference in titers (p=0.049) was related to a higher proportion of moderate to severe infections in the Delta cohort (p=0.014). Correlation of neutralizing and spike quantitative antibody titers was decreased with Delta or Omicron compared to WT. Neutralizing antibodies in Delta and Omicron breakthrough infections increase overall, but the relative magnitude of increase is greater in more clinically severe infection and against the specific infecting variant.
A circuit-based approach to repair hypersexuality in Parkinson’s disease
Authors: Mata-Marín David , Pineda-Pardo José Ángel , Michiels Mario , Pagge Cristina , Ammann Claudia , Martínez-Fernández Raúl , Molina José Antonio , Vela-Desojo Lydia , Alonso-Frech Fernando , Obeso Ignacio
Published: January 2022

One common neuropsychiatric complication in patients with Parkinson’s disease treated with dopamine replacement therapy is impulse control disorders. A proportion of patients under dopamine agonist exhibit excessive desire towards appetitive cues accompanied by lost control over behaviour in forms of pathological gambling, hypersexuality or binge eating. The balance between enhanced desire towards sexual cues and cognitive control changes has been hypothesized to be biased toward the former in individuals with hypersexuality and impulse control disorders. Yet, some studies report no behavioural differences in cognitive control differences between impulsive patients and general Parkinson’s disease, suggesting possible functional changes along the mesocorticolimbic cortico-subcortical circuitry. Here, we provide evidence for this hypothesis by comparing the neurobiological substrate of sexual disturbance over response inhibition associated to medication states in Parkinson’s disease patients with a specific subtype of impulse control disorders (i.e., hypersexuality).

We assessed the impact of sexual cues on response inhibition using a novel erotic stop signal task inside an fMRI. A total of 50 participants were included divided in 16 hypersexual and 17 non-hypersexual Parkinson’s disease patients and 17 healthy controls. Task-related activations, functional and anatomical connectivity models were performed. Additionally, a separate sample of 20 hypersexual Parkinson’s disease patients received excitatory neuromodulation (sham-controlled) over the pre-supplementary motor area (based on fMRI group-based results) aiming to improve response inhibition when exposed to sexual cues.

Compared with their non-hypersexual peers, medication perturbed response inhibition upon presentation of sexual cues in patients with hypersexuality, recruiting a network involving caudate, pre-supplementary motor area, ventral tegmental area, and anterior cingulate cortex. Dynamic causal modelling revealed distinct best models to account for cortico-subcortical interactions with reduced task-related inputs in pre-supplementary motor area and descending connectivity to caudate in hypersexual compared to non- hypersexual Parkinson’s disease patients (while medicated). This was sustained by enhanced fractional anisotropy and reduced mean diffusivity in the pre-supplementary motor area-caudate pathway. Importantly, stimulation over the pre-supplementary motor area improved response inhibition when exposed to sexual cues in hypersexual Parkinson’s disease.

We identified a specific fronto-striatal and mesolimbic circuitry underlying uncontrolled sexual behaviours in Parkinson’s disease induced by medication, with recovery options by applying neuromodulation.