bluuebunny/crossref_metadata_2025 huggingface dataset:
Farnesol abrogates biofilm- and efflux pump- associated genes in drug resistant Candida auris strains
Authors: Srivastava Vartika , Ahmad Aijaz
Published: December 2021

Background:

Candida auris, a decade old Candida species, has been identified globally as a significant nosocomial multidrug resistant (MDR) pathogen responsible for causing invasive outbreaks. Biofilms and over expression of efflux pumps such as Major Facilitator Superfamily and ATP Binding Cassette are known to cause multidrug resistance in Candida species, including C. auris. Therefore, targeting these factors may prove an effective approach to combat MDR in C. auris.

Methods:

In this study, 25 clinical isolates of C. auris from different hospitals of South Africa were used. Antifungal susceptibility profile of all the isolates against commonly used drugs was determined following CLSI recommended guidelines. Rhodamine-6-G extracellular efflux and intracellular accumulation assays were used to study active drug efflux mechanism. We further studied the role of farnesol in modulating development of biofilms and drug efflux in C. auris. Down-regulation of biofilm- and efflux pump- associated genes by farnesol was also investigated. CLSM analysis for examining C. auris biofilm architecture among treated and untreated isolates.

Results:

Most of the isolates (twenty-two) were found resistant to FLZ whereas five were resistant to AmB. All the isolates were found capable of biofilm formation and ornamented with active drug efflux mechanism. The MIC for planktonic cells ranged from 62.5-125 mM and for sessile cells was 125 mM (0 h and 4 h biofilm) and 500 mM (12 h and 24 h biofilm), CLSM studies also confirmed these findings. Farnesol also blocked efflux pumps and down-regulated biofilm- and efflux pump- associated genes.

Conclusion:

Modulation of biofilm- and efflux pump- associated genes by farnesol represent a promising approach in combating C. auris infection.
Quorum sensing plays a key role in controlling beta-glucan exposure in response to environmental pH
Authors: Cottier Fabien , Sherrington Sarah , Cockerill Sarah , del Olmo Toledo Valentina , Kissane Stephen , Tournu Helene , Orsini Luisa , Palmer Glen , Christian Perez J. , Hall Rebecca
Published: December 2021

Candida albicans is a commensal yeast of the human gut, which is tolerated by the immune system, but has the potential to become an opportunistic pathogen. One way in which C. albicans achieves this duality is through concealing, or exposing cell wall pathogen-associated molecular patterns (PAMPs) in response to host derived environment cues (pH, hypoxia, lactate). This cell wall remodelling allows C. albicans to evade or hyperactivate the host’s innate immune responses leading to disease. Previously, we identified that adaptation of C. albicans to acidic environments, conditions encountered during colonisation of the female reproductive tract, induce significant cell wall remodelling resulting in the exposure of two key fungal PAMPs (glucan and chitin). Here we report that this pH-dependent cell wall remodelling is time dependent with the initial change in pH driving cell wall unmasking, which is then remasked at later time points. Remasking ofglucan was mediated via the cell density dependent fungal quorum sensing molecule farnesol, while chitin remasking was mediated via a small, heat-stable, non-proteinaceous secreted molecule(s). Transcript profiling identified a core set of 42 genes significantly regulated by pH over time, and identified the transcription factor Efg1 as a regulator of chitin exposure through regulation of CHT2. This dynamic cell wall remodelling influenced innate immune recognition of C. albicans, suggesting that during infection C. albicans can manipulate the host innate immune responses.
Candida albicans phosphate transport, facilitating nucleotide sugar biosynthesis, contributes to cell wall stability.
Authors: Acosta-Zaldivar Maikel , Qi Wanjun , Liu Ning-Ning , Diray-Arce Joann , Walker Louise A. , Kottom Theodore J. , Kelly Rachel , Yuan Min , Asara John M. , Lasky-Su Jessica Ann , Levy Ofer , Limper Andrew H. , Gow Neil A. R. , Köhler Julia Ruth
Published: December 2021

The Candida albicans high-affinity phosphate transporter Pho84 is required for normal Target of Rapamycin signaling, oxidative stress resistance and virulence of this fungal pathogen. It also contributes to C. albicans’ tolerance of two antifungal drug classes, polyenes and echinocandins. Echinocandins inhibit biosynthesis of a major cell wall component, beta-1,3-glucan. Cells lacking Pho84 were hypersensitive to other forms of cell wall stress beyond echinocandin exposure, while their cell wall integrity signaling response was weak. Metabolomics experiments showed that levels of phosphoric intermediates, including nucleotides like ATP and nucleotide sugars, were low in pho84 mutant compared to wild type cells recovering from phosphate starvation. Non-phosphoric precursors like nucleobases and nucleosides were elevated. Outer cell wall phosphomannan biosynthesis requires a nucleotide sugar,GDP-mannose. The nucleotide sugar UDP-glucose is the substrate of enzymes that synthesize two major structural cell wall polysaccharides, beta-1,3- and beta-1,6-glucan. Another nucleotide sugar, UDP-N-acetylglucosamine, is the substrate of chitin synthases which produce a stabilizing component of the intercellular septum and of lateral cell walls. Lack of Pho84 activity, and phosphate starvation, potentiated pharmacological or genetic perturbation of these enzymes. Our model is that low substrate concentrations of beta-D-glucan- and chitin synthases diminish enzymatic reaction rates and potentiate pharmacologic inhibitors to decrease the yield of their cell wall-stabilizing products. Phosphate import is not conserved between fungal and human cells, and humans do not synthesize beta-D-glucans or chitin. Hence inhibiting these processes simultaneously could yield potent antifungal effects with low toxicity to humans.
Tolerance to fluconazole in Candida albicans is regulated by temperature and aneuploidy
Authors: YANG FENG , JIANG YUANYING , BERMAN JUDITH
Published: December 2021

Candida albicans is a prevalent human fungal pathogen. Azoles are the most widely used antifungal drugs. Drug tolerance in bacteria is well defined and thoroughly studied, but in fungi, the definition of drug tolerance and the mechanism that drive it are not well understood. Here, we found that a large proportion of clinical isolates were intrinsically tolerant to fluconazole, and/or could be induced by high temperature (37°C) to become tolerant (conditionally tolerant). When treated with inhibitory doses of fluconazole, non-tolerant strains became tolerant by forming aneuploids involving different chromosomes, with chromosome R duplication as the most recurrent mechanism. Tolerance determines the ability to grow in the presence of fluconazole and other azoles, in a manner independent of the MIC. Both temperature conditional tolerance and the associated aneuploidy were sensitive to FK506, an inhibitor of calcineurin. Intrinsic and conditional tolerance were also abolished by deletions of genes encoding the calcineurin (CMP1 and CNB1). However, the dependence of tolerance on calcineurin could be bypassed by a different aneuploid chromosome. Thus, fluconazole tolerance in C. albicans is regulated by temperature and by aneuploidy and is dependent upon aneuploidy, but this dependence can be bypassed by an additional aneuploidy.
Precise editing using CRISPR-Cas9 to explore the contribution of clinically-derived mutations to antifungal resistance in the pathogenic yeast Candida parapsilosis
Authors: Hartuis Sophie , Robert Estelle , Lombardi Lisa , Butler Geraldine , Le Pape Patrice , Morio Florent
Published: December 2021

Introduction

Candida parapsilosis is both a commensal/saprophytic yeast of the human skin and an opportunistic pathogen which can be responsible for life-threatening infections. The increasing reports of clonal outbreaks involving azole-resistant C. parapsilosis in the clinical setting is worrisome and urges for a better understanding of antifungal resistance in this species. Previous studies have identified mutations in key genes which can explain acquired fluconazole resistance. Reverse genetics approaches are now warranted to confirm their involvement and to determine whether they can affect other clinically-licensed antifungals. Here, we used a CRISPR-Cas9 technique to study the relative contributions of clinically-derived mutations to antifungal resistance and provide answers to these questions.

Materials and Methods

Six clinically-derived mutations were selected (ERG11Y132F, ERG11K143R,ERG11R398I, TAC1G650E, MRR1G583R, ERG3G111R) to be engineered in two C. parapsilosis fluconazole-susceptible backgrounds (ATCC22019, STZ5) using a previously described CRISPR-Cas9 method. In vitro susceptibility of the transformants to fluconazole, voriconazole, posaconazole, isavuconazole and micafungin was determined by Etest®.

Results/Discussion

The impact on fluconazole susceptibility was highly variable depending on the residue/gene involved, but roughly similar between the two genetic backgrounds. All but two(ERG11R398I, ERG3G111R) conferred fluconazole resistance, though the highest MIC increase was observed for MRR1G583R (≥650 fold). As expected in a diploid species, we noted an impact of allelic dosage. Some kind of cross-resistance to the other azoles was noted from some mutations, although the impact was lower for posaconazole and isavuconazole, except for MRR1G583R which led to multi-azole resistance. Finally, ERG3G111R increased tolerance to both azoles and echinocandins.
The effect of acquired triazole resistance on abiotic stress tolerance and virulence in Candida auris micro evolved strains
Authors: Bohner Flora , Papp Csaba , Varga Mónika , Szekeres András , Tóth Renáta , Gacser Attila
Published: December 2021

Recently, C. auris become one of the most prominent members of the genus Candida. Since its occurrence, several C. auris outbreaks have been reported worldwide. These outbreaks were associated with isolates displaying decreased susceptibility towards fluconazole, the first-line agent for prophylaxis. Fluconazole is the most frequently used antifungal drug to treat bloodstream Candida infections.

The physiological effects of acquired antifungal resistance was investigated in this species using fluconazole, posaconazole and voriconazole resistant mutant strains generated by the in vitro microevolution method. Alterations in antifungal susceptibility and cross resistance were determined by the microdilution method, utilizing azoles (fluconazole, voriconazole, posaconazole), echinocandins (caspofungin, micafungin, anidulafungin) and a polyene (amphotericin B). Changes in the abiotic stress tolerance was examined by spotting assay, using osmotic stressors, cell wall perturbants and a membrane detergent. To evaluate the impact of the acquired resistance on sterol biosynthesis, ergosterol composition of all generated mutant strains were examined. A potential relationship between virulence and acquired antifungal resistance was also studied both in vitro and in vivo. Phagocytosis of the generated strains by J774.2 mouse macrophage-like cells was measured and analyzed by flow cytometry. In the murine infection model fungal burden of the triazole evolved strains was determined in spleen, kidney, liver and brain and compared to the fungal burden associated with the initial azole susceptible strain. Significant differences in virulence of the initial and the generated strains was observed suggesting a potential connection between the virulence and antifungal susceptibility of the emerging fungal pathogen, C. auris.
Liposomes functionalized with fungi-targeting peptide demonstrate increased interaction with Candida albicans
Authors: LaMastro Ronnie , Vera-Gonzalez Noel , Campbell Kayla , Shukla Anita
Published: December 2021

Candida albicans infections can be challenging to treat, as current antifungal drugs exhibit poor water solubility and host toxicity. To overcome these issues, new methods of drug delivery are needed. Liposomes have been shown to be an effective method for administrating antifungals and can increase bioavailability and solubility while decreasing toxicity. However, existing antifungal liposomal formulations lack infection specificity. For example, AmBisome, a liposomal formulation of amphotericin B, relies on passive accumulation to infection sites. We have developed antifungal liposomes that display fungi-targeting moieties to promote interaction with Candida;we predict that these formulations can increase fungal eradication and decrease off-site toxicity. Here, the C. albicans-targeting peptide P-113Q2.10 (AQRHHGYKRQFH), a derivative of the antifungal peptide histatin 5, was incorporated into liposomes via conjugation to palmitic acid (PA). PA-P-113Q2.10 conjugates were synthesized using solid phase peptide synthesis, confirmed by liquid-chromatography-mass spectrometry. Liposomes composed of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine and cholesterol with 1% w/w PA-P-113Q2.10 were formed via thin film-hydration and extrusion, yielding ∼100 nm liposomes with a polydispersity index of ∼0.1. Flow cytometry demonstrated that interaction with C. albicans SC5314 was enhanced for P-113Q2.10 liposomes, increasing from ∼60% in cells incubated with liposomes lacking peptide to ∼79%. These liposomes preferentially interact with C. albicans compared to NIH 3T3 murine fibroblasts; on average, only ∼15% of fibroblasts incubated with liposomes (with and without peptide) showed positive liposome interaction. This liposome formulation has the potential to serve as an antifungal delivery platform that selectively targets C. albicans cells for increased efficacy in treatment of fungal infections.
Ambisome shows potent anti-Candida auris in vitro and in vivo activity
Authors: Ghannoum Mahmoud , Herrada Janet , Gamal Ahmed , Long Lisa , McCormick Thomas
Published: December 2021

Candida auris is an emerging multidrug resistant Candida species that has been reported in many parts of the world for causing severe illness in hospitalized patients especially bloodstream infections. The challenge with this type of yeast is its resistance to commonly used antifungal drugs, thus identifying antifungals that are effective against this species is critical.

In this study, we determined the in vitro activity of Ambisome against 35 clinical isolates of C. auris using minimum inhibitory concentration (MIC) assay as well as the efficacy of Ambisome compared to Amphotericin B and fluconazole using a C. auris murine disseminated model.

Antifungal activity of C. auris against Ambisome and comparators was assessed using amicrodilution method performed according to the Clinical and Laboratory Standard Institute (CLSI) M27-A4 methodology. Mice were immunocompromised and challenged with 3 x 107
C. auris blastopores in 0.1 ml of normal saline (via the tail vein). Treatment efficacy was assessed by determining reductions in mortality as well as decrease in tissue fungal burden (CFUs).

Ambisome showed lower MIC50 and MIC90 values (1 and 2 μg/mL, respectively) than the comparators tested. Significant efficacy was observed in the Ambisome 7.5 mg/kg -treated group (100% and 90% survival by day 7- and 14-days post inoculation, respectively). Additionally, Ambisome and fluconazole treated groups showed significant reduction in CFUs in the kidneys (P- values of 0.028 and 0.022, respectively) compared to the untreated group.

Our data shows that Ambisome shows significant antifungal activity against C. auris in vitro as well as in vivo.
Arthrobacter cheniae and Arthrobacter frigidicola sp. nov., isolated from a glacier
Authors: Yang Lei-Lei , Liu Hong-Can , Liu Qing , Xin Yu-Hua
Published: December 2021

Two Gram-stain-positive, aerobic, rod-shaped, pink and light pink colony-forming bacteria, designated as Hz2T and MDT2-14T, respectively, were isolated from glacier cryoconite samples. Comparisons based on 16S rRNA gene sequences showed that strains Hz2T and MDT2-14T take

Arthrobacter bussei

KR32T and

Arthrobacter zhaoguopingii

J391T as their closest neighbours, respectively. The average nucleotide identity values between the two novel strains and their closest relatives were 83.56 and 93.06 %, respectively. The two strains contain MK-9(H2) as their predominant menaquinone. The polar lipids of both strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The major fatty acids of strain Hz2T were anteiso-C15 : 0, summed feature 3 (comprising C16 : 1
 ω7c and/or C16 : 1
 ω6c) and iso-C15 : 0, while the major fatty acids of strain MDT2-14T were anteiso-C15 : 0 and anteiso-C17 : 0. Based on these data, we propose two novel species, Arthrobacter cheniae sp. nov. (Hz2T = CGMCC 1.9262T=NBRC 113086T) and Arthrobacter frigidicola sp. nov. (MDT2-14T=CGMCC 1.9882T=NBRC 113089T).
Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa
Authors: Amsalu Anteneh , Sapula Sylvia A. , Whittall Jonathan J. , Hart Bradley J. , Bell Jan M. , Turnidge John , Venter Henrietta
Published: December 2021

Carbapenems are potent broad-spectrum β-lactam antibiotics reserved for the treatment of serious infections caused by multidrug-resistant bacteria such as

Pseudomonas aeruginosa

. The surge in

P. aeruginosa

resistant to carbapenems is an urgent threat, as very few treatment options remain. Resistance to carbapenems is predominantly due to the presence of carbapenemase enzymes. The assessment of 147

P

.

aeruginosa

isolates revealed that 32 isolates were carbapenem non-wild-type. These isolates were screened for carbapenem resistance genes using PCR. One isolate from wastewater contained the Adelaide imipenemase gene (bla
AIM-1) and was compared phenotypically with a highly carbapenem-resistant clinical isolate containing the bla
AIM-1 gene. A further investigation of wastewater samples from various local healthcare and non-healthcare sources as well as river water, using probe-based qPCR, revealed the presence of the bla
AIM-1 gene in all the samples analysed. The widespread occurrence of bla
AIM-1 throughout Adelaide hinted at the possibility of more generally extensive spread of this gene than originally thought. A blast search revealed the presence of the bla
AIM-1 gene in Asia, North America and Europe. To elucidate the identity of the organism(s) carrying the bla
AIM-1 gene, shotgun metagenomic sequencing was conducted on three wastewater samples from different locations. Comparison of these nucleotide sequences with a whole-genome sequence of a

P. aeruginosa

isolate revealed that, unlike the genetic environment and arrangement in

P. aeruginosa

, the bla
AIM-1 gene was not carried as part of any mobile genetic elements. A phylogenetic tree constructed with the deduced amino acid sequences of AIM-1 suggested that the potential origin of the bla
AIM-1 gene in

P. aeruginosa

might be the non-pathogenic environmental organism,

Pseudoxanthomonas mexicana

.
A reusable benchmark of brain-age prediction from M/EEG resting-state signals
Authors: Engemann Denis A. , Mellot Apolline , Höchenberger Richard , Banville Hubert , Sabbagh David , Gemein Lukas , Ball Tonio , Gramfort Alexandre
Published: December 2021

Population-level modeling can define quantitative measures of individual aging by applying machine learning to large volumes of brain images. These measures of brain age, obtained from the general population, helped characterize disease severity in neurological populations, improving estimates of diagnosis or prognosis. Magnetoencephalography (MEG) and Electroencephalography (EEG) have the potential to further generalize this approach towards prevention and public health by enabling assessments of brain health at large scales in socioeconomically diverse environments. However, more research is needed to define methods that can handle the complexity and diversity of M/EEG signals across diverse real-world contexts. To catalyse this effort, here we propose reusable benchmarks of competing machine learning approaches for brain age modeling. We benchmarked popular classical machine learning pipelines and deep learning architectures previously used for pathology decoding or brain age estimation in 4 international M/EEG cohorts from diverse countries and cultural contexts, including recordings from more than 2500 participants. Our benchmarks were built on top of the M/EEG adaptations of the BIDS standard, providing tools that can be applied with minimal modification on any M/EEG dataset provided in the BIDS format. Our results suggest that, regardless of whether classical machine learning or deep learning was used, the highest performance was reached by pipelines and architectures involving spatially aware representations of the M/EEG signals, leading to R^2 scores between 0.60-0.71. Hand-crafted features paired with random forest regression provided robust benchmarks even in situations in which other approaches failed. Taken together, this set of benchmarks, accompanied by open-source software and high-level Python scripts, can serve as a starting point and quantitative reference for future efforts at developing M/EEG-based measures of brain aging. The generality of the approach renders this benchmark reusable for other related objectives such as modeling specific cognitive variables or clinical endpoints.

Highlights

- We provide systematic reusable benchmarks for brain age from M/EEG signals

- The benchmarks were carried out on M/EEG from four countries > 2500 recordings

- We compared machine learning pipelines capable of handling the non-linear regression task of relating biomedical outcomes to M/EEG dynamics, based on classical machine learning and deep learning

- Next to data-driven methods we benchmarked template-based source localization as a practical tool for generating features less affected by electromagnetic field spread

- The benchmarks are built on top of the MNE ecosystem and the braindecode package and can be applied on any M/EEG dataset presented in the BIDS format
Opposing regulation of short-term memory by basal ganglia direct and indirect pathways that are coactive during behavior
Authors: Tang Yingjun , Yang Hongjiang , Chen Xia , Zhang Zhouzhou , Yao Xiao , Yin Xinxin , Guo Zengcai V.
Published: December 2021

The basal ganglia direct and indirect pathways are viewed to mediate opposing functions in movement. However, this classic model is challenged by recent findings that both pathways are coactive during behavior. We examined the roles of direct (dSPNs) and indirect (iSPNs) pathway spiny projection neurons in a decision-making task with a short-term memory (STM) component. Optogenetic stimulation of cortical-input-defined dSPNs and iSPNs during STM oppositely biased upcoming licking choice, without affecting licking execution. Optogenetically identified dSPNs and iSPNs showed similar response patterns, although with quantitative difference in spatiotemporal organization. To understand how coactive dSPNs and iSPNs play opposing roles, we recorded population activity in frontal cortex and the basal ganglia output nucleus SNr. Stimulation of dSPNs and iSPNs bidirectionally regulated cortical decision variable through the differential modulation of SNr ramping activity. These results reconcile different views by demonstrating that coactive dSPNs and iSPNs precisely shape cortical activity in a push-pull balance.
Age determination through DNA methylation patterns of fingernails and toenails
Authors: Fokias Kristina , Dierckx Lotte , Van de Voorde Wim , Bekaert Bram
Published: December 2021

Over the past decade, age prediction based on DNA methylation has become a vastly investigated topic; many age prediction models have been developed based on different DNAm markers and using various tissues. However, the potential of using nails to this end has not yet been explored. Their inherent resistance to decay and ease of sampling would offer an advantage in cases where post-mortem degradation poses challenges concerning sample collection and DNA-extraction. In the current study, clippings from both fingernails and toenails were collected from 108 living test subjects (age range: 0 – 96 years). The methylation status of 15 CpGs located in 4 previously established age-related markers (ASPA, EDARADD, PDE4C, ELOVL2) was investigated through pyrosequencing of bisulphite converted DNA. Significant dissimilarities in methylation levels were observed between all four limbs, hence limb-specific age prediction models were developed using ordinary least squares, weighted least squares and quantile regression analysis. When applied to their respective test sets, these models yielded a mean absolute deviation between predicted and chronological age ranging from 6.71 to 8.48 years. In addition, the assay was tested on methylation data derived from 5 nail samples collected from deceased individuals, demonstrating its feasibility for application in post-mortem cases. In conclusion, this study provides the first proof that chronological age can be assessed through DNA methylation patterns in nails.
Dynamic in situ confinement triggers ligand-free neuropeptide receptor signaling
Authors: Sánchez M. Florencia , Dietz Marina S. , Müller Ulrike , Weghuber Julian , Gatterdam Karl , Wieneke Ralph , Heilemann Mike , Lanzerstorfer Peter , Tampé Robert
Published: December 2021

Membrane receptors are central to cell-cell communication. Receptor clustering at the plasma membrane modulates physiological responses, and mesoscale receptor organization is critical for downstream signaling. Spatially restricted cluster formation of the neuropeptide Y2 hormone receptor (Y2R) was observed in vivo; however, the relevance of this confinement is not fully understood. Here, we controlled Y2R clustering in situ by a chelator nanotool. Due to the multivalent interaction, we observed a dynamic exchange in the microscale confined regions. Fast Y2R enrichment in clustered areas triggered a ligand-independent downstream signaling determined by an increase in cytosolic calcium, cell spreading, and migration. We revealed that the cell response to ligand-induced activation was amplified when cells were pre-clustered by the nanotool. Ligand-independent signaling by clustering differed from ligand-induced activation in the binding of arrestin-3 as downstream effector, which was recruited to the confined regions only in the presence of the ligand. This approach enables in situ clustering of membrane receptors and raises the possibility to explore different modalities of receptor activation.

Abstract Figure
Macrogenetics reveals multifaceted influences of environmental variation on vertebrate population genetic diversity across the Americas
Authors: Lawrence Elizabeth R. , Fraser Dylan J.
Published: December 2021

Relative to species diversity gradients, the broad scale distribution of population-specific genetic diversity (PGD) across taxa remains understudied. We used nuclear DNA data collected from 6285 vertebrate populations across the Americas to assess the role environmental variables play in structuring the spatial/latitudinal distribution of PGD, a key component of adaptive potential in the face of environmental change. Our results provide key evidence for taxa-specific responses and that temperature variability in addition to mean temperature may be a primary driver of PGD. Additionally, we found some positive influence of precipitation, productivity, and elevation on PGD; identified trends were dependent on the metric of PGD. In contrast to the classic negative relationship between species diversity and latitude, we report either a positive or taxa-dependent relationship between PGD and latitude, depending on the metric of PGD. The inconsistent latitudinal gradient in different metrics of PGD may be due to opposing processes diminishing patterns across latitudes that operate on different timescales, as well as the flattening of large-scale genetic gradients when assessing across species versus within species. Our study highlights the nuance required to assess broad patterns in genetic diversity, and the need for developing balanced conservation strategies that ensure population, species, and community persistence.
Matchtigs: minimum plain text representation of kmer sets
Authors: Schmidt Sebastian , Khan Shahbaz , Alanko Jarno , Pibiri Giulio E. , Tomescu Alexandru I.
Published: December 2021

We propose a polynomial algorithm computing aminimumplain-text representation of kmer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a minor runtime increase, we shrink the representation by up to 60% over unitigs and 27% over previous work. Additionally, the number of strings is decreased by up to 97% over unitigs and 91% over previous work. Finally, a small representation has advantages in downstream applications, as it speeds up SSHash-Lite queries by up to 4.26× over unitigs and 2.10× over previous work.

Availability

matchtigs:https://github.com/algbio/matchtigs

SSHash-Lite:https://github.com/jermp/sshash-lite
Comparative evaluation of rapid isothermal amplification and antigen assays for screening testing of SARS-CoV-2
Authors: Salcedo Nol , Sena Brena F. , Qu Xiying , Herrera Bobby Brooke
Published: December 2021

Human transmission of SARS-CoV-2 and emergent variants of concern has continued to occur globally, despite mass vaccination campaigns. Public health strategies to reduce virus spread should therefore rely, in part, on frequent screening with rapid, inexpensive, and sensitive tests. We evaluated two digitally integrated rapid tests and assessed their performance using stored nasal swab specimens collected from individuals with or without COVID-19. An isothermal amplification assay combined with a lateral flow test had a limit of detection of 10 RNA copies per reaction, and a positive percent agreement (PPA)/negative percent agreement (NPA) during the asymptomatic and symptomatic phases of 100%/100% and 95.83/100%, respectively. Comparatively, an antigen-based lateral flow test, had a limit of detection of 30,000 copies, and a PPA/NPA during the asymptomatic and symptomatic phases of 82.86%/98.68% and 91.67/100%, respectively. Both the isothermal amplification and antigen-based lateral flow tests had optimized detection of SARS-CoV-2 during the peak period of transmission; however, the antigen-based test had reduced sensitivity in clinical samples with qPCR Ct values greater than 29.8. Low-cost, high-throughput screening enabled by isothermal amplification or antigen-based techniques have value for outbreak control.
HLA-B27 and not variation in MICA is responsible for genotype by sex interaction in risk of Ankylosing Spondylitis
Authors: Li Zhixiu , McRae Allan F. , Wang Geng , Ellis Jonathan J. , Kenna Tony J. , Whyte Jessica , Brown Matthew A. , Evans David M.
Published: December 2021

Ankylosing Spondylitis (AS) is a highly heritable inflammatory arthritis which occurs more frequently in men than women. In their recent publication examining sex differences in the genetic aetiology of common complex traits and diseases, Bernabeu et al. (2021) observe differences in heritability of AS between sexes, and a genome-wide significant genotype by sex interaction in risk of AS at the major histocompatability (MHC) locus1. The authors then present evidence suggesting that this genotype by sex interaction arises primarily as a result of differential expression of the gene MICA across the sexes in skeletal muscle tissue. Through a series of conditional association analyses in the UK Biobank, reanalysis of the GTEx gene expression resource and RNASeq experiments on peripheral blood cells from AS cases and controls, we show that the genotype by sex interaction the authors’ report is unlikely to be a result of variation in MICA, but probably reflects a known interaction between the HLA-B gene, sex and risk of AS. We demonstrate that the diagnostic accuracy of AS in the UK Biobank is low, particularly amongst women, likely explaining some of the observed differences in heritability across the sexes and the difficulty in precisely locating association signals in the cohort.
A Competing Risk Analysis of Early COVID-19 Treatments
Authors: Gonzalez-Arroyo Gilberto , Rodriguez-Moran Mario F. , Garcia-Arreola Maricela , Lopez-Lopez Karla Guadalupe , Ortiz-Castillo Tonatihu , Gomez-Garcia Salvador , Alvarez-Aguilar Cleto , Gomez-Garcia Anel , Lopez-Pineda Arturo
Published: December 2021

Introduction

The advent of the SARS-CoV-2 virus posed formidable challenges on a global scale. In the year 2020, existing treatments were not tailored specifically to combat this novel virus, and the absence of a developed vaccine added to the complexity. Clinical guidelines underwent rapid evolution during the initial months of the pandemic, leaving uncertainty about the efficacy of various drug combinations in treating the disease. This study delves into an analysis of outcomes during the early stages of the pandemic within the Mexican Institute of Social Security (IMSS), the largest healthcare system in Mexico.

Material and Methods

In this retrospective observational study, we examined the medical records of 130,216 COVID-19 patients treated in two Mexican states throughout the year 2020. We conducted a competing risk analysis, considering death and recovery as potential outcomes. This was further complemented by a Cox-regression and Kaplan-Meier analysis. To enhance predictive insights, machine learning models were constructed to forecast outcomes at 10, 20, and 30 days.

Results

Our analysis revealed a heightened prevalence of comorbidities, including obesity, diabetes, and heart disease, aligning with Mexico’s established epidemiological profile. Mortality patterns indicated occurrences approximately 15-20 days from the onset of symptoms. Notably, patients undergoing treatment with cephalosporin in conjunction with neuraminidase inhibitors (NAIs) exhibited the poorest survival rates, whereas those receiving adamantane, fluoroquinolone, or penicillin demonstrated the most favorable survival outcomes.

Conclusions

The identified associations caution against the utilization of specific treatment combinations, providing crucial insights for refining the country’s clinical guidelines and optimizing patient care strategies.
Individualized exercise in chronic non-specific low back pain: a systematic review with meta-analysis on the effects of exercise alone or in combination with psychological interventions on pain and disability
Authors: Fleckenstein Johannes , Flössel Philipp , Engel Tilman , Klewinghaus Laura , Stoll Josefine , Behrens Martin , Niederer Daniel
Published: December 2021

This systematic review with meta-analysis and meta-regression investigated the effects of individualized exercise interventions consisting with or without combined psychological intervention on pain intensity and disability in patients with chronic non-specific low-back-pain. Databases were searched up to 31 January 2022 and we selected randomized controlled trials involving adults with chronic non-specific low-back-pain being treated with individualized/personalized/stratified exercise interventions with or without psychological treatment compared to any control.

Fifty-eight studies (n = 10084) were included.

At short-term follow-up (12 weeks), low-certainty evidence for pain intensity (SMD -0.28 [95%CI -0.42 to -0.14]) and very low-certainty evidence for disability (−0.17 [-0.31 to -0.02]) indicates effects of individualized versus active exercises, and very low-certainty evidence for pain intensity (−0.40; [-0.58 to -0.22])), but not (low-certainty evidence) for disability (−0.18; [-0.22 to 0.01]) compared to passive controls.

At long-term follow-up (1 year), moderate-certainty evidence for pain intensity (−0.14 [-0.22 to -0.07]) and disability (−0.20 [-0.30 to -0.10]) indicates effects versus passive controls.

Sensitivity analyses indicates that the effects on pain, but not on disability (always short-term and versus active treatments) were robust. Pain reduction caused by individualized exercise treatments in combination with psychological interventions (in particular behavioural-cognitive therapies) (−0.28 [-0.42 to -0.14], low certainty) is of clinical importance.

Certainty of evidence was downgraded mainly due to evidence of risk of bias, publication bias and inconsistency that could not be explained.

Individualized exercise can be recommended from a clinical point of view to treat pain and disability in chronic non-specific low-back-pain. Sub-group analysis suggests a combination of individualized exercise (especially motor-control based treatments) with behavioural therapy interventions to booster effects. Certainty of evidence was moderate for long-term follow-up.

PROSPERO registration

CRD42021247331
Social mixing patterns relevant to infectious diseases spread by close contact in urban Blantyre, Malawi
Authors: Thindwa Deus , Jambo Kondwani C , Ojal John , MacPherson Peter , Phiri Mphatso Dennis , Khundi McEwen , Chiume Lingstone , Gallagher Katherine E , Heyderman Robert S , Corbett Elizabeth L , French Neil , Flasche Stefan
Published: December 2021

Introduction

Understanding human mixing patterns relevant to infectious diseases spread through close contact is vital for modelling transmission dynamics and optimisation of disease control strategies. Mixing patterns in low-income countries like Malawi are not well understood.

Methodology

We conducted a social mixing survey in urban Blantyre, Malawi between April and July 2021 (between the 2nd and 3rd wave of COVID-19 infections). Participants living in densely-populated neighbourhoods were randomly sampled and, if they consented, reported their physical and non-physical contacts within and outside homes lasting at least 5 minutes during the previous day. Age-specific mixing rates were calculated, and a negative binomial mixed effects model was used to estimate determinants of contact behaviour.

Results

Of 1,201 individuals enrolled, 702 (58.5%) were female, the median age was 15 years (interquartile range [IQR] 5-32) and 127 (10.6%) were HIV-positive. On average, participants reported 10.3 contacts per day (range: 1-25). Mixing patterns were highly age-assortative, particularly those within the community and with skin-to-skin contact. Adults aged 20-49y reported the most contacts (median:11, IQR: 8-15) of all age groups; 38% (95%CI: 16-63) more than infants (median: 8, IQR: 5-10), who had the least contacts. Household contact frequency increased by 3% (95%CI 2-5) per additional household member. Unemployed participants had 15% (95%CI: 9-21) fewer contacts than other adults. Among long range (>30 meters away from home) contacts, secondary school children had the largest median contact distance from home (257m, IQR 78-761). HIV-positive status in adults >18 years-old was not associated with increased contact patterns (1%, 95%CI -9-12). During this period of relatively low COVID-19 incidence in Malawi, 301 (25.1%) individuals stated that they had limited their contact with others due to COVID-19 precautions; however, their reported contacts were not fewer (8%, 95%CI 1-13).

Conclusion

In urban Malawi, contact rates, are high and age-assortative, with little behavioural change due to either HIV-status or COVID-19 circulation. This highlights the limits of contact-restriction-based mitigation strategies in such settings and the need for pandemic preparedness to better understand how contact reductions can be enabled and motivated.
imageseg: an R package for deep learning-based image segmentation
Authors: Niedballa Jürgen , Axtner Jan , Döbert Timm Fabian , Tilker Andrew , Nguyen An , Wong Seth T. , Fiderer Christian , Heurich Marco , Wilting Andreas
Published: December 2021

Convolutional neural networks (CNNs) and deep learning are powerful and robust tools for ecological applications. CNNs can perform very well in various tasks, especially for visual tasks and image data. Image segmentation (the classification of all pixels in images) is one such task and can for example be used to assess forest vertical and horizontal structure. While such methods have been suggested, widespread adoption in ecological research has been slow, likely due to technical difficulties in implementation of CNNs and lack of toolboxes for ecologists.

Here, we present R package imageseg which implements a workflow for general-purpose image segmentation using CNNs and the U-Net architecture in R. The workflow covers data (pre)processing, model training, and predictions. We illustrate the utility of the package with two models for forest structural metrics: tree canopy density and understory vegetation density. We trained the models using large and diverse training data sets from a variety of forest types and biomes, consisting of 3288 canopy images (both canopy cover and hemispherical canopy closure photographs) and 1468 understory vegetation images.

Overall classification accuracy of the models was high with a Dice score of 0.91 for the canopy model and 0.89 for the understory vegetation model (assessed with 821 and 367 images, respectively), indicating robustness to variation in input images and good generalization strength across forest types and biomes.

The package and its workflow allow simple yet powerful assessments of forest structural metrics using pre-trained models. Furthermore, the package facilitates custom image segmentation with multiple classes and based on color or grayscale images, e.g. in cell biology or for medical images. Our package is free, open source, and available from CRAN. It will enable easier and faster implementation of deep learning-based image segmentation within R for ecological applications and beyond.
Interest of phenomic prediction as an alternative to genomic prediction in grapevine
Authors: Brault Charlotte , Lazerges Juliette , Doligez Agnès , Thomas Miguel , Ecarnot Martin , Roumet Pierre , Bertrand Yves , Berger Gilles , Pons Thierry , François Pierre , Le Cunff Loïc , This Patrice , Segura Vincent
Published: December 2021

Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum reflects the biochemical composition within a tissue, under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been successfully applied in several cereal species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. We found that the co-inertia between spectra and genomic data was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, there was a correlation across traits between predictive ability of genomic and phenomic prediction, with a slope around 1 and an intercept of −0.2, thus suggesting that phenomic prediction could be applied for any trait.
The 677C>T variant in methylenetetrahydrofolate reductase causes morphological and functional cerebrovascular deficits in mice
Authors: Reagan Alaina M. , Christensen Karen E. , Graham Leah C. , Bedwell Amanda A. , Eldridge Kierra , Speedy Rachael , Figueiredo Lucas L. , Persohn Scott C. , Bottiglieri Teodoro , Sasner Michael , Territo Paul R. , Rozen Rima , Howell Gareth R.
Published: December 2021

Vascular contributions to cognitive impairment and dementia (VCID) particularly Alzheimer’s disease and related dementias (ADRDs) are increasing; however, mechanisms driving cerebrovascular decline are poorly understood. Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme in the folate and methionine cycles. Variants in MTHFR, notably 677C>T, are associated with dementias, but no mouse model existed to identify mechanisms by which MTHFR677C>T increases risk. Therefore, MODEL-AD created a novel knock-in (KI) strain carrying the Mthfr677C>T allele on the C57BL/6J background (Mthfr677C>T) to characterize morphology and function perturbed by the variant. Consistent with human clinical data, Mthfr677C>T mice have reduced enzyme activity in the liver and elevated plasma homocysteine levels. MTHFR enzyme activity as well as critical metabolites in the folate and methionine cycles are reduced in the Mthfr677C>T brain. Mice showed reduced tissue perfusion in numerous brain regions by PET/CT as well as significantly reduced vascular density and increased GFAP-expressing astrocytes in frontal cortex. Electron microscopy revealed cerebrovascular damage including endothelial and pericyte apoptosis, reduced luminal size, and increased astrocyte and microglial presence in the microenvironment. Collectively, these data suggest critical perturbations to cerebrovascular function in Mthfr677C>T mice supporting its use as a model for preclinical studies of VCID.
A practical guide for generating unsupervised, spectrogram-based latent space representations of animal vocalizations
Authors: Thomas Mara , Jensen Frants H. , Averly Baptiste , Demartsev Vlad , Manser Marta B. , Sainburg Tim , Roch Marie A. , Strandburg-Peshkin Ariana
Published: December 2021

The manual detection, analysis, and classification of animal vocalizations in acoustic recordings is laborious and requires expert knowledge. Hence, there is a need for objective, generalizable methods that detect underlying patterns in these data, categorize sounds into distinct groups, and quantify similarities between them. Among all computational methods that have been proposed to accomplish this, neighborhood-based dimensionality reduction of spectrograms to produce a latent-space representation of calls stands out for its conceptual simplicity and effectiveness. Using a dataset of manually annotated meerkat (Suricata suricatta) vocalizations, we demonstrate how this method can be used to obtain meaningful latent space representations that reflect the established taxonomy of call types. We analyze strengths and weaknesses of the proposed approach, give recommendations for its usage and show application examples, such as the classification of ambiguous calls and the detection of mislabeled calls. All analyses are accompanied by example code to help researchers realize the potential of this method for the study of animal vocalizations.
Specific vulnerability of long telomeres to undergo end fusions revealed by mutational analysis of Rap1
Authors: Pan Lili , Tormey Duncan , Bobon Nadine , Baumann Peter
Published: December 2021

The conserved Rap1 protein is part of the shelterin complex that plays critical roles in chromosome end protection and telomere length homeostasis. Previous studies addressed how fission yeast Rap1 contributes to telomere length maintenance, but the mechanism by which the protein inhibits end fusions has remained elusive. Here, we use a genetic screen in combination with high throughput sequencing to identify several amino acid positions in Rap1 that have a key role in end protection. Interestingly, mutations at these sites render cells susceptible to genome instability in a conditional manner with longer telomeres being prone to undergoing end fusions, while short telomeres are sufficiently protected. The protection of long telomeres requires their nuclear envelope attachment mediated by the Rap1-Bqt4 interaction. Our data demonstrates that longer telomeres pose an additional challenge for the maintenance of genome integrity and provides an explanation for a species-specific upper limit in telomere length.