bluuebunny/crossref_metadata_2025 huggingface dataset:
An intermediate effect size variant in UMOD confers risk for chronic kidney disease
Authors: Olinger Eric , Schaeffer Céline , Kidd Kendrah , Cheng Yurong , Dufour Inès , Schiano Guglielmo , Mabillard Holly , Pasqualetto Elena , Elhassan Elhussein A. E. , Hofmann Patrick , Fuster Daniel G. , Kistler Andreas D. , Conlon Peter J. , Wilson Ian J. , Kmoch Stanislav ,   Genomics England Research Consortium, Eckardt Kai-Uwe , Bleyer Anthony J. , Köttgen Anna , Wiesener Michael , Sayer John A. , Rampoldi Luca , Devuyst Olivier
Published: October 2021

The kidney-specific gene UMOD encodes for uromodulin, the most abundant protein excreted in normal urine. Rare, large-effect variants in UMOD cause autosomal dominant tubulointerstitial kidney disease (ADTKD) while common, low-effect variants strongly associate with kidney function and risk of chronic kidney disease (CKD) in the general population. It is unknown whether intermediate-effect variants in UMOD contribute to CKD. Here, candidate intermediate-effect UMOD variants were identified using large population and ADTKD cohorts. Biological and phenotypical effects were investigated using cell models, in silico simulations and international databases and biobanks. Eight UMOD missense variants reported in ADTKD are present in gnomAD with MAF ranging from 10−5 to 10−3. Among them, the missense variant p.Thr62Pro is detected in ∼1/1,000 individuals of European ancestry, shows incomplete penetrance but a high genetic load in familial clusters of CKD and is associated with kidney failure in the 100,000 Genomes Project (OR 3.99; 1.84-8.98) and the UK Biobank (OR 4.12; 1.32-12.85). Compared to canonical ADTKD mutations, the p.Thr62Pro carriers displayed reduced disease severity, with slower progression of CKD, intermediate reduction of urinary UMOD levels, in line with an intermediate trafficking defect in vitro. Identification of an intermediate-effect UMOD variant completes the spectrum of UMOD-associated kidney diseases and provides novel insights into the mechanisms of ADTKD and the genetic architecture of CKD.

Significance Statement

The genetic architecture of chronic kidney disease (CKD) remains incompletely understood. Variants in the kidney-specific gene UMOD cause autosomal dominant tubulointerstitial kidney disease (ADTKD) and are associated with kidney function and risk of CKD in the general population. Here, we identified an intermediate-effect variant, p.Thr62Pro, detected in ∼1:1,000 individuals of European ancestry, that showed a high genetic load in familial clusters of CKD and was associated with an OR of ∼4 for kidney failure in the 100,000 Genomes Project and the UK Biobank. Compared to canonical ADTKD mutations, p.Thr62Pro carriers displayed reduced disease severity and an intermediate trafficking defect. These findings complete the spectrum of UMOD-associated kidney diseases and provide a paradigm for the genetic contribution to CKD.
Getting to the Emergency Department in Time: Interviews With Patients and Their Caregivers on the Challenges to Emergency Care Utilization in Rural Uganda - a Grounded Theory Approach
Authors: Pickering Ashley E. , Dreifuss Heather M. , Ndyamwijuka Charles , Nichter Mark , Dreifuss Bradley A.
Published: October 2021

Objectives

Karoli Lwanga Hospital and Global Emergency Care, a 501(c)(3) nongovernmental organization, operate an Emergency Department (ED) in Uganda’s rural Rukungiri District. Despite available emergency care (EC), preventable death and disability persist due to delayed patient presentations. Implementation of effective EC requires assessment of socioeconomic, cultural, and structural factors leading to treatment delay.

Methods

We purposefully sampled and interviewed patients and caregivers presenting to the ED more than 12 hours after onset of chief complaint in January-March 2017 to include various ages, genders, and complaints. Semistructured interviews addressing actions taken before seeking EC and delays to presentation once the need for EC was recognized were conducted. Interviews were audio recorded, translated, and transcribed, enabling the interdisciplinary and multicultural research team to conduct thematic analysis utilizing a grounded theory approach.

Results

The 50 ED patients for whom care was sought (mean age 33) had approximately even distribution of gender, as well as occupation (none, subsistence farmers and small business owner). Interviews were conducted with 37 caregivers and 13 ED patients. The majority of interviewees (mean age 38 years) were women with a primary education. The median duration of patients’ chief complaint on ED presentation was 5.5 days. On average, participants identified severe symptoms necessitating EC 1 day before presentation. Four themes of treatment delay before and after severity were recognized were identified: 1) Cultural factors and limited knowledge of emergency signs and initial actions to take ; 2) Use of local health facilities despite perception of inadequate services; 3) Lack of resources to cover the anticipated cost of obtaining EC; 4) Inadequate transportation options.

Conclusions

Interventions are warranted to address each of the four major reasons for treatment delay. The next stage of formative research will generate intervention strategies and assess the opportunities and challenges to implementation with community and health system stakeholders.
Association between psychological distress trajectories from adolescence to midlife and mental health during the pandemic: Evidence from two British birth cohorts
Authors: Moulton Vanessa , Sullivan Alice , Patalay Praveetha , Fitzsimons Emla , Henderson Morag , Bann David , Ploubidis George B.
Published: October 2021

Background

Some studies suggest worsening mental health in the early stages of the pandemic, for individuals with pre-existing mental health conditions the evidence is mixed. We examined whether different life-course trajectories of psychological distress from adolescence to midlife were associated with psychological distress, lower life satisfaction and feelings of loneliness at different stages during the pandemic.

Methods

This study is a secondary analysis of two nationally representative British Birth cohorts, the National Child Development Study (1958) and 1970 British Cohort Study, from birth to later mid-life. We used latent variable mixture models to identify pre-pandemic longitudinal trajectories of psychological distress and a modified poisson model with robust standard errors to estimate associations with mental health outcomes during the pandemic from May 2020 to March 2021.

Findings

Our analysis identified five distinct pre-pandemic trajectories of psychological distress in both cohorts. All trajectories with prior symptoms of psychological distress were associated with a greater relative risk of mental health outcomes during the pandemic. This was the case irrespective of age of onset, severity, longevity and proximal occurrence. Those who had experienced more than one prior episode of high psychological distress, and more recent occurrences, faced the greatest risk of poor mental health during the pandemic.

Interpretation

Whilst any prior episode of poor mental health put individuals at greater risk of severe mental health symptoms, those with chronic and more recent occurrence are likely to require greater mental health support.
Appearance of IgG to SARS-CoV-2 in saliva effectively indicates seroconversion in mRNA vaccinated immunocompromised individuals
Authors: Healy Katie , Pin Elisa , Chen Puran , Söderdahl Gunnar , Nowak Piotr , Mielke Stephan , Hansson Lotta , Bergman Peter , Smith C. I. Edvard , Ljungman Per , Valentini Davide , Blennow Ola , Österborg Anders , Gabarrini Giorgio , Al-Manei Khaled , Alkharaan Hassan , Sobkowiak Michal Jacek , Xu Xinling , Akber Mira , Loré Karin , Hellström Cecilia , Muschiol Sandra , Bogdanovic Gordana , Buggert Marcus , Ljunggren Hans-Gustaf , Hober Sophia , Nilsson Peter , Aleman Soo , Sällberg Chen Margaret
Published: October 2021

Background

Immunocompromised individuals are highly susceptible to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Whether vaccine-induced immunity in these individuals involves the oral cavity, a primary site of infection, is presently unknown.

Methods

Immunocompromised individuals (n=404) and healthy controls (n=82) participated in a prospective clinical trial encompassing two doses of the mRNA BNT162b2 vaccine. Immunocompromised individuals included primary immunodeficiencies (PID) and secondary immunodeficiencies caused by human immunodeficiency virus (HIV) infection, allogeneic hematopoietic stem cell transplantation (HSCT)/chimeric antigen receptor T cell therapy (CAR-T), solid organ transplantation (SOT), and chronic lymphocytic leukemia (CLL). Saliva and serum samples were collected at four time points from the first vaccine dose until 2 weeks after second dose. SARS-CoV-2 spike specific immunoglobulin G (IgG) responses were quantified by a multiplex bead-based assay in saliva and correlated to paired serum IgG titers determined by Elecsys® Anti-SARS-CoV-2 S assay.

Results

IgG responses to the SARS-CoV-2 spike full-length trimeric glycoprotein (Spike-f) and S1 subunit in saliva in the HIV and HSCT/CAR-T groups were comparable to healthy controls. In contrast, PID, SOT, and CLL patients all displayed weaker responses which were mainly influenced by disease parameters or immunosuppressants. Salivary IgG levels strongly correlated with serum IgG titers on days 21 and 35 (rho=0.8079 and 0.7768, p=<0.0001). Receiver operating characteristic curve analysis for the predictive power of salivary IgG yielded AUC=0.95, PPV=90.7% for the entire cohort on D35.

Conclusions

Saliva conveys humoral responses induced by BNT162b2 vaccination. The predictive power makes it highly suitable for screening low responding/vulnerable groups for revaccination.

Trial Registration

ClinicalTrials.govIdentifier:NCT04780659

Funding

Knut and Alice Wallenberg Foundation, Erling Perssons family foundation, Region Stockholm, Swedish Research Council, Karolinska Institutet, The Swedish Blood Cancer Foundation and the organization for PID patient group in Sweden, and Nordstjernan AB. Center for Medical Innovation (CIMED), the Swedish Medical Research Council and the Stockholm County Council (ALF).

GRAPHIC ABSTRACT
Human Satellite III long non-coding RNA imparts survival benefits to cancer cells
Authors: Chatterjee Manjima , Sengupta Sonali
Published: October 2021

Long non-coding RNAs are heterogeneous group of transcripts that lack coding potential and have crucial roles in gene regulations. Recent days have seen an increasing association of non-coding RNAs with human diseases, especially cancers. Satellite III (SatIII) lncRNAs are transcribed from pericentromeric heterochromatic region of the human chromosome. Though transcriptionally silent in normal conditions, SatIII is actively transcribed under condition of stress, mainly heat shock. SatII repeat, another component of pericentromeric region of human chromosome, has been associated with wide variety of epithelial cancer. Overexpression of Satellite RNAs induces breast cancer in mice. Though much is known about Satellite RNAs, which includes alpha satellites and SatII repeats, however little is known about SatIII in human cancers. Hence we directed our study to understand the role of human Satellite III repeats in cancerous conditions. In the present study, we show that colon and breast cancer cells transcribe SatIII independent of heat shock, in an HSF1-independent manner. Our study also reveals that, overexpression of SatIII RNA favours cancer cell survival by overriding chemo drug-induced cell death. Knockdown of SatIII sensitizes cells towards chemotherapeutic drugs. SatIII transcript knockdown restores the expression of p53 protein, which in turn facilitates cell death. Heat shock however helps SatIII to continue with its pro-cell survival function. Our results, therefore suggest SatIII to be an important regulator of human cancers. Induction of SatIII is not only a response to the oncogenic stress but also facilitates cancer progression by a distinct pathway that is different from heat stress pathway.
Functional characterisation of single nucleotide variants of the psychiatric risk gene cacna1c in the zebrafish
Authors: Banono Nancy Saana , Gawel Kinga , Mäki-Marttunen Tuomo , van der Ent Wietske , Kukula-Koch Wirginia , Fyhn Marianne , Einevoll Gaute T. , Andreassen Ole A. , Esguerra Camila V.
Published: October 2021

Several genome-wide association studies have associated CACNA1C variants with psychiatric disorders. The molecular mechanisms involved are poorly understood. Taking advantage of the zebrafish larva as a model, we investigated how two different mutations in cacna1c – sa10930 (nonsense mutation) and sa15296 (splice site mutation), affect neuronal function. We characterized changes in cacna1c mRNA, neurotransmitter levels and behaviour, as well as whole-brain activity using single electrode local field potential recordings. Both point mutations resulted in a significant reduction in cacna1c mRNA, as well as social behaviour and prepulse inhibition deficits. Whereas sa15296 mutants displayed abnormal locomotor and open-field behaviour, we observed normal behaviour in the sa10930 mutants. Brain recordings from both mutants had lower spectral power while sa15296 displayed significant seizure-like activity. Finally, sa10930 homozygotes showed increased dopamine and serotonin levels, decreased gamma-aminobutyric acid (GABA) levels, and unchanged glutamate levels while homozygous sa15296 larvae showed increased levels of serotonin and glutamate, and unaffected levels of GABA and dopamine. Our work provides new insights into the functional role of CACNA1C in behavioural, electrophysiological and biochemical traits linked to psychiatric disorders. We show a functional role for the non-coding mutation (sa15296) in the cacna1c in vivo animal model. Consistent with existing hypotheses, our data suggest that disruption of gene expression, neurotransmission, and cortical excitability are involved in CACNA1C-related mechanisms of psychiatric disorders.
Training data composition affects performance of protein structure analysis algorithms
Authors: Derry Alexander , Carpenter Kristy A. , Altman Russ B.
Published: October 2021

The three-dimensional structures of proteins are crucial for understanding their molecular mechanisms and interactions. Machine learning algorithms that are able to learn accurate representations of protein structures are therefore poised to play a key role in protein engineering and drug development. The accuracy of such models in deployment is directly influenced by training data quality. The use of different experimental methods for protein structure determination may introduce bias into the training data. In this work, we evaluate the magnitude of this effect across three distinct tasks: estimation of model accuracy, protein sequence design, and catalytic residue prediction. Most protein structures are derived from X-ray crystallography, nuclear magnetic resonance (NMR), or cryo-electron microscopy (cryo-EM); we trained each model on datasets consisting of either all three structure types or of only X-ray data. We find that across these tasks, models consistently perform worse on test sets derived from NMR and cryo-EM than they do on test sets of structures derived from X-ray crystallography, but that the difference can be mitigated when NMR and cryo-EM structures are included in the training set. Importantly, we show that including all three types of structures in the training set does not degrade test performance on X-ray structures, and in some cases even increases it. Finally, we examine the relationship between model performance and the biophysical properties of each method, and recommend that the biochemistry of the task of interest should be considered when composing training sets.
Identification and expression analysis of Shaker K+ channel genes in millet (Setaria italica) under abiotic stresses
Authors: Zhang Ben , Wang Hui , Guo Yue , Wang Xiaoxia , Lv Mengtao , Yang Pu , Zhang Lizhen
Published: October 2021

Potassium (K+) is one of the essential nutrients for plant, which is involved in plant growth and development and abiotic stress tolerance. The absorption and transport of K+ depends on Shaker K+ channels. Foxtail millet is a Poaceae crop with strong drought stress-tolerant. In this study, we identified ten Shaker K+ channel genes in foxtail millet. Phylogenetic analysis, prediction of conserved motif, and gene structure analysis classified these genes into five groups. The transcription level of these genes under different abiotic stress treatments (cold, heat, NaCl, PEG) and ABA treatment were analyzed by quantitative real-time PCR. Each gene displayed its own regulation pattern under different treatments, suggests these channels play important role in plant adaptation to different environment conditions.
Experience resetting in reinforcement learning facilitates exploration–exploitation transitions during a behavioral task for primates
Authors: Sakamoto Kazuhiro , Okuzaki Hidetake , Sato Akinori , Mushiake Hajime
Published: October 2021

The exploration–exploitation trade-off is a fundamental problem in re-inforcement learning. To study the neural mechanisms involved in this problem, a target search task in which exploration and exploitation phases appear alternately is useful. Monkeys well trained in this task clearly understand that they have entered the exploratory phase and quickly acquire new experiences by resetting their previous experiences. In this study, we used a simple model to show that experience resetting in the exploratory phase improves performance rather than decreasing the greediness of action selection, and we then present a neural network-type model enabling experience resetting.
Investigation of Dengue Fever Outbreak in a Rural Area of Islamabad, Pakistan: A Case Control Study
Authors: Khan Fawad Khalid , Akram Khurram Shahzad , Chaudhry Ambreen , Bullo Mir Hassan , Hussain Zakir , Baig Mirza Amir , Mehmood Amjad , Baig Zeeshan Iqbal
Published: October 2021

Background

In the second week of October 2019, five suspected cases of dengue fever were reported from union council Sohan, Islamabad rural (population 45,747) to the health department, Islamabad Capital Territory (ICT). Outbreak investigation was conducted with the objectives to identify risk factors and recommend control measures.

Methods

Outbreak investigation was conducted from 17th October to 25th November 2019. A case was defined as, “fever and two or more of the following signs/symptoms; headache, retro-orbital pain, joint/bone pain, myalgia and petechial rash with NS1 test (Nonstructural Protein 1) positive during 8th October to 25th November 2019 among residents of Sohan”. Age and sex-matched controls were recruited from the same neighborhood. All cases were positive for NS1 antigen. Blood samples from five suspected cases were collected and tested for laboratory confirmation.

Results

A total of 547 households were surveyed and 85 cases were identified. The mean age was 34.4 years + 16.05 (range 3-71 years). The attack rate was 0.19% whereas the most affected age group was the 45-54 years (AR 0.43%). Males were predominantly affected (n=48 56.5%). Among all cases, 32% (n=27)) had stagnant water inside or around their houses (aOR 2.65, CI 1.20-5.83, P=0.005), 33% (n=28) were using mosquito repellent (aOR 0.35, CI 0.17-0.70, P<0.001), 31% (n=26) used indoor residual spray insecticide (aOR 0.48, CI 0.24-0.97, P=0.041), and 73% (n=62) used full protective clothing (aOR 0.17, CI 0.05-0.58, P<0.001). All five blood samples were tested positive for NS-1 antigen.

Conclusion

The presence of accumulated rainwater in pools and empty receptacles around houses acted as breeding grounds for Aedes aegypti mosquitos and was the most probable cause of this outbreak. Following our recommendations, the health department-initiated mosquito breeding sites control activities through residual insecticide spray and advocacy on the use of protective measures against mosquito bites.
Humoral cross-reactivity towards SARS-CoV-2 in young children with acute respiratory infection with low-pathogenicity coronaviruses
Authors: Dhochak Nitin , Agrawal Tanvi , Shaman Heena , Khan Naseem Ahmed , Kumar Prawin , Kabra Sushil K , Medigeshi Guruprasad R , Lodha Rakesh
Published: October 2021

SARS-CoV-2 infection in children frequently leads to only asymptomatic and mild infections. It has been suggested that frequent infections due to low-pathogenicity coronaviruses in children, imparts immunity against SARS-CoV-2 in this age group. From a prospective birth cohort study prior to the pandemic, we identified children (n=42) with proven low-pathogenicity coronavirus infections. Convalescent sera from these samples had antibodies against the respective seasonal CoVs as demonstrated by immunofluorescence assay. We tested these samples for neutralization of SARS-CoV-2 using virus microneutralization assay. Forty serum samples showed no significant neutralization of SARS-CoV-2, while 2 samples showed inconclusive results. These findings suggest that the antibodies generated in low-pathogenicity coronavirus infections offer no protection from SARS-CoV-2 infection in young children.
Frailty trajectories in the oldest old: Is the level or the rate of change more predictive of mortality?
Authors: Stolz Erwin , Mayerl Hannes , Hoogendijk Emiel O.
Published: October 2021

BACKGROUND

It is unclear whether frailty index (FI) change captures mortality risk better than and independently of the current FI level, i.e. whether a regular FI assessment among older adults provides additional insights for mortality risk stratification or not.

METHODS

We used data from the LASA 75-PLUS-study, which monitored health among 508 older adults (75+) between 2016-2019 every 9 months. Joint models for longitudinal and time-to-event data were used to assess the impact of both current FI and within-person FI change during the last year on mortality risk.

RESULTS

20% of the participants died during 4.5 years of follow-up. Adding within-person FI change to the current FI model improved model fit and it showed that FI increases during the last year were associated with a strong increase in mortality risk. Consequently, the effect of the current FI decreased considerably and became statistically non-significant.

CONCLUSIONS

The rate of FI change was more important than the current FI level for short-term mortality prediction among the oldest old, which highlights the benefits of regular frailty assessments.
Presaccadic attention enhances contrast sensitivity, but not at the upper vertical meridian
Authors: Hanning Nina M. , Himmelberg Marc M. , Carrasco Marisa
Published: October 2021

Human visual performance is not only better at the fovea and decreases with eccentricity, but also has striking radial asymmetries around the visual field: At a fixed eccentricity, it is better along (1) the horizontal than vertical meridian and (2) the lower than upper vertical meridian. These asymmetries are not alleviated by covert exogenous or endogenous attention, but have been studied exclusively during eye fixation. However, a major driver of everyday attentional orienting is saccade preparation, during which visual attention automatically shifts to the future eye fixation. This presaccadic shift of attention is considered strong and compulsory, and relies on fundamentally different neural computations and substrates than covert attention. Given these differences, we investigated whether presaccadic attention can compensate for the ubiquitous performance asymmetries observed during eye fixation. Our data replicate polar performance asymmetries during fixation and document the same asymmetries during saccade preparation. Crucially, however, presaccadic attention enhanced contrast sensitivity at the horizontal and lower vertical meridian, but not at the upper vertical meridian. Thus, instead of attenuating polar performance asymmetries, presaccadic attention exacerbates them.
Collagen Pre-strain Discontinuity at the Cartilage - Bone Interface
Authors: Badar Waqas , Ali Husna , Brooker Olivia N , Newham E. , Snow Tim , Terrill Nicholas J , Tozzi Gianluca , Fratzl Peter , Knight Martin M , Gupta Himadri S
Published: October 2021

The bone-cartilage unit (BCU) is a universal feature in diarthrodial joints, which is mechanically-graded and subjected to shear and compressive strains. Changes in the BCU have been linked to osteoarthritis progression. Here we report existence of a physiological internal strain gradient (pre-strain) across the BCU at the ultrastructural scale of the extracellular matrix constituents, specifically the collagen fibril. We use X-ray scattering that probes changes in the axial periodicity of fibril-level D-stagger of tropocollagen molecules in the matrix fibrils, as a measure of microscopic pre-strain. We find that mineralized collagen nanofibrils in the calcified plate are in tensile pre-strain relative to the underlying trabecular bone. This behaviour contrasts with the previously accepted notion that fibrillar pre-strain (or D-stagger) in collagenous tissues always reduces with mineralization, via reduced hydration and associated swelling pressure. Within the calcified part of the BCU, a finer-scale gradient in pre-strain (0.6% increase over ∼50μm) is observed. The increased fibrillar pre-strain is linked to prior research reporting large tissue-level residual strains under compression. The findings may have biomechanical adaptative significance: higher in-built molecular level resilience/damage resistance to physiological compression, and disruption of the molecular-level pre-strains during remodelling of the BCI may be potential factors in osteoarthritis-based degeneration.
Brain stimulation competes with ongoing oscillations for control of spike timing in the primate brain
Authors: Krause Matthew R. , Vieira Pedro G. , Thivierge Jean-Philippe , Pack Christopher C.
Published: October 2021

Transcranial alternating current stimulation (tACS) is commonly used to enhance brain rhythms, in the hopes of improving behavioral performance. Unfortunately, these interventions often yield highly variable results. Here, we identify a key source of this variability by recording from single neurons in alert non-human primates. We find that, rather than enhancing rhythmic activity, tACS appears to compete with the brain’s endogenous oscillations for control of spike timing. Specifically, when the strength of stimulation is weak relative to endogenous oscillations, tACS actually decreases the rhythmicity of spiking. However, when stimulation is comparatively stronger, tACS imposes its own rhythm on spiking activity. Thus the effect of tACS depends categorically on the strength of neural entrainment to endogenous oscillations, which varies greatly across behavioral states and brain regions. Without carefully considering these factors, attempts to impose external rhythms on specific brain regions may often yield precisely the opposite of the intended effect.
Topographic connectivity and cellular profiling reveal detailed input pathways and functionally distinct cell types in the subthalamic nucleus
Authors: Jeon Hyungju , Lee Hojin , Kwon Dae-Hyuk , Kim Jiwon , Tanaka-Yamamoto Keiko , Feng Linqing , Park Hyeran , Lim Yong Hoon , Cho Zang-Hee , Paek Sun Ha , Kim Jinhyun
Published: October 2021

The subthalamic nucleus (STN) controls psychomotor activity and is an efficient therapeutic deep brain stimulation target in Parkinson’s disease patients. Despite evidence indicating position-dependent therapeutic effects and distinct functions within the STN, input circuit and cellular profile in the STN remain largely unclear. Using advanced neuroanatomical techniques, we constructed a comprehensive connectivity map of the indirect and hyperdirect pathways in both the mouse and human STN. Our detailed circuit- and cellular-level connectivity revealed a topographically graded organization with three convergent types of indirect and hyperdirect-pathways. Furthermore, we identified two functional types of glutamatergic STN neurons (parvalbumin, PV +/- neurons) segregated with a topographical distribution. Glutamatergic PV+ STN neurons contribute to burst firing. We confirmed synaptic connectivity from indirect and hyperdirect pathways to both PV+ and PV-. These data suggest a complex interplay of information integration within the basal ganglia underlying coordinated movement control and therapeutic effects.
Characterization of Cell-Induced Astigmatism in High-Resolution Imaging
Authors: de Mercado Rick Rodrigues , van Hoorn Hedde , de Valois Martin , Backendorf Claude , Eckert Julia , Schmidt Thomas
Published: October 2021

High-resolution and super-resolution techniques become more frequently used in thick, inhomogeneous samples. In particular for imaging life cells and tissue in which one wishes to observe a biological process at minimal interference and in the natural environment, sample inhomogeneities are unavoidable. Yet sample-inhomogeneities are paralleled by refractive index variations, for example between the cell organelles and the surrounding medium, that will result in the refraction of light, and therefore lead to sample-induced astigmatism. Astigmatism in turn will result in positional inaccuracies of observations that are at the heart of all super-resolution techniques. Here we introduce a simple model and define a figure-of-merit that allows one to quickly assess the importance of astigmatism for a given experimental setting. We found that astigmatism caused by the cell’s nucleus can easily lead to aberrations up to hundreds of nanometers, well beyond the accuracy of all super-resolution techniques. The astigmatism generated by small objects, like bacteria or vesicles, appear to be small enough to be of any significance in typical super-resolution experimentation.
Encounter networks from collective mitochondrial dynamics support the emergence of effective mtDNA genomes in plant cells
Authors: Giannakis Konstantinos , Chustecki Joanna M. , Johnston Iain G.
Published: October 2021

Mitochondria in plant cells form strikingly dynamic populations of largely individual organelles. Each mitochondrion contains on average less than a full copy of the mitochondrial DNA (mtDNA) genome. Here, we asked whether mitochondrial dynamics may allow individual mitochondria to ‘collect’ a full copy of the mtDNA genome over time, by facilitating exchange between individuals. Akin to trade on a social network, exchange of mtDNA fragments across organelles may lead to the emergence of full ‘effective’ genomes in individuals over time. We characterise the collective dynamics of mitochondria in Arabidopsis thaliana hypocotyl cells using a recent approach combining single-cell timelapse microscopy, video analysis, and network science. We then use a quantitative model to predict the capacity for the sharing and accumulation of genetic information through the networks of encounters between mitochondria. We find that biological encounter networks are strikingly well predisposed to support the collection of full genomes over time, outperforming a range of other networks generated from theory and simulation. Using results from the coupon collector’s problem, we show that the upper tail of the degree distribution is a key determinant of an encounter network’s performance at this task and discuss how features of mitochondrial dynamics observed in biology facilitate the emergence of full effective genomes.
Host phylogeny and ecological associations best explainWolbachiahost shifts in scale insects
Authors: Sanaei Ehsan , Albery Gregory F , Yeoh Yun Kit , Lin Yen-Po , Cook Lyn G , Engelstädter Jan
Published: October 2021

Wolbachiaare among the most prevalent and widespread endosymbiotic bacteria on earth.Wolbachia’ s success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch to new host species. Whilst much progress has been made in elucidating the phenotypes induced byWolbachia, our understanding ofWolbachiahost shifting is still very limited: we lack answers to even fundamental questions concerningWolbachia’s routes of transfer and the importance of factors influencing host shifts. Here, we investigate the diversity and host-shift patterns ofWolbachiain scale insects, a group of arthropods with intimate associations with other insects that make them well-suited to studying host shifts. Using Illumina pooled amplicon sequencing ofWolbachia-infected scale insects and their direct associates we determined the identity of allWolbachiastrains, revealing that 32% of samples were multiply infected (with up to five distinct strains per species). We then fitted a Generalised Additive Mixed Model (GAMM) to our data to estimate the influence of factors such as the host phylogeny and the geographic distribution of each species onWolbachiastrain sharing among scale insect species. The model predicts no significant contribution of host geography but strong effects of host phylogeny, with high rates ofWolbachiasharing among closely related species and a sudden drop-off in sharing with increasing phylogenetic distance. We also detected the sameWolbachiastrain in scale insects and several intimately associated species (ants, wasps, beetles, and flies). This indicates putative host shifts and potential routes of transfers via these associates and highlights the importance of ecological connectivity inWolbachiahost-shifting.
Polyamine elevation and nitrogen stress are toxic hallmarks of chronic sleep loss in Drosophila melanogaster
Authors: Bedont Joseph , Kolesnik Anna , Malik Dania , Weljie Aalim , Sehgal Amita
Published: October 2021

Chronic sleep loss profoundly impacts health in ways coupled to metabolism; however, much existing literature links sleep and metabolism only on acute timescales. To explore the impact of chronically reduced sleep, we conducted unbiased metabolomics on heads from three Drosophila short-sleeping mutants. Common features included elevated ornithine and polyamines; and lipid, acyl-carnitine, and TCA cycle changes suggesting mitochondrial dysfunction. Biochemical studies of overall, circulating, and excreted nitrogen in sleep mutants demonstrate a specific defect in eliminating nitrogen, suggesting that elevated polyamines may function as a nitrogen sink. Both supplementing polyamines and inhibiting their synthesis with RNAi regulated sleep in control flies. Finally, both polyamine-supplemented food and high-protein feeding were highly toxic to sleep mutants, suggesting their altered nitrogen metabolism is maladaptive. Together, our results suggest polyamine accumulation specifically, and nitrogen stress in general, as potential mechanisms linking chronic sleep loss to adverse health outcomes.
Responses to Temperatures of DifferentDrosophilaSpecies
Authors: Huda Ainul , Vaden Thomas J. , Omelchenko Alisa A. , Castaneda Allison N. , Ni Lina
Published: October 2021

Temperature is a critical environmental variable that affects the distribution, survival, and reproduction of most animals. Although temperature receptors have been identified in different animals, how these receptors respond to temperatures is largely unknown. Here we use modified single-fly thermotactic assays to analyze movements and temperature preferences of nineDrosophilaspecies. The ability/inclination to move varies among these species and at different temperatures. Importantly, different species prefer various ranges of temperatures. While wild-typeD. melanogasterflies avoid the warm temperature in the warm avoidance assay and the cool temperature in the cool avoidance assay,D. bipectinataandD. yakubaavoid neither warm nor cool temperatures andD. biarmipesandD. mojavensisdo not avoid the warm temperature in the warm avoidance assay. These results demonstrate thatDrosophilaspecies have different mobilities and temperature preferences, thereby benefiting the research on molecular mechanisms of temperature responsiveness.

Summary statement

The ability to move and the preference for temperatures vary among fly species when flies are exposed to steep temperature gradients.
Characterization of wheat lacking B-type starch granules
Authors: Saccomanno Benedetta , Berbezy Pierre , Findlay Kim , Shoesmith Jennifer , Uauy Cristobal , Viallis Bruno , Trafford Kay
Published: October 2021

The physicochemical and agronomic properties of a new form of bread wheat, lacking B-type starch granules (BlessT) were assessed. Three BlessT mutant lines, made by combining homoeologous deletions ofBGC1, a gene responsible for the control of B-granule content were compared with two sibling lines with normal starch phenotype and the parent line, cv. Paragon. Quantification of starch granule size and number in developing grain confirmed the lack of small, B-type starch granules throughout development in BlessT. Most starch, flour, grain and loaf characteristics did not vary between BlessT and the wild type sibling controls. However, BlessT starches had higher water absorption, reduced grain hardness and higher protein content, and dough made from BlessT flour required more water and had increased elasticity. Despite the lack of B-granules, BlessT lines do not display a significant decrease in total starch content suggesting that it should be possible to produce commercial wheat varieties that lack B-type starch granules without compromising yield. These findings support the potential utility of this novel type of wheat as a specialist crop in applications ranging from bread making and alcohol production to improved industrial starch products.
Volatile social environments can favour investments in quality over quantity of social relationships
Authors: Aubier Thomas G. , Kokko Hanna
Published: October 2021

Cooperation does not occur in a vacuum: interactions develop over time in social groups that undergo demographic changes. Intuition suggests that stable social environments favour developing few but strong reciprocal relationships (a ‘focused’ strategy), while volatile social environments favour the opposite: more but weaker social relationships (a ‘diversifying’ strategy). We model reciprocal investments under a quality-quantity tradeoff for social relationships. We find that volatility, counterintuitively, can favour a focused strategy. This result becomes explicable through applying the theory of antagonistic pleiotropy, originally developed for senescence, to social life. Diversifying strategies show superior performance later in life, but with costs paid at young ages while the social network is slowly being built. Under volatile environments, many individuals die before reaching sufficiently old ages to reap the benefits. Social strategies that do well early in life are then favoured: a focused strategy leads individuals to form their first few social bonds quickly and to make strong use of existing bonds. Our model highlights the importance of pleiotropy and population age structure for the evolution of cooperative strategies and other social traits, and shows that it is not sufficient to reflect on the fate of survivors only, when evaluating the benefits of social strategies.
THE SPLICING FACTOR PTBP1 REPRESSES TP63 γ ISOFORM PRODUCTION IN SQUAMOUS CELL CARCINOMA
Authors: Taylor William , Reboutier David , Paillard Luc , Méreau Agnès , Audic Yann
Published: October 2021

The TP63 gene encodes the transcription factor p63. It is frequently amplified or overexpressed in squamous cell carcinomas. Owing to alternative splicing, p63 has multiple isoforms called α, β, γ and δ. The regulatory functions of p63 may be isoform-specific. The α isoform inhibits the epithelial to mesenchymal transition (EMT) and controls apoptosis, while the γ isoform promotes EMT. Here, we observed in TCGA data that a high ratio of the TP63γ isoform to the other isoforms is a pejorative factor for the survival of patients with head and neck squamous cell carcinoma (HNSCC). We therefore addressed the regulation of the γ isoform. In several tissues (GTEX data), the expression of the RNA-binding protein PTBP1 (polypyrimidine tract binding protein 1) is negatively correlated with the abundance of TP63γ. Accordingly, we demonstrated that PTBP1 depletion in HNSCC cell lines leads to an increase in abundance of the γ isoform. By RNA immunoprecipitation and in vitro interaction assays, we showed that PTBP1 directly binds to TP63 pre-mRNA in close proximity to the TP63γ-specific exon. The region around the TP63γ-specific exon was sufficient to elicit a PTBP1-dependent regulation of alternative splicing in a splice reporter minigene assay. Finally, we demonstrated that the regulation of TP63γ production by PTBP1 is conserved in amphibians, revealing that it encounters a strong evolutionary pressure. Together, these results identify TP63γ as a prognostic marker in HNSCC, and identify PTBP1 as a direct negative regulator of its production.
Dynamic DNA methylation changes in the COMT gene promoter region in response to mental stress and its modulation by transcranial direct current stimulation
Authors: Wiegand Ariane , Blickle Arne , Brückmann Christof , Weller Simone , Nieratschker Vanessa , Plewnia Christian
Published: October 2021

Changes in epigenetic modifications present a mechanism how environmental factors like the experience of stress can alter gene regulation. While stress-related disorders have consistently been associated with differential DNA methylation, little is known about the time scale in which these alterations emerge. We investigated dynamic DNA methylation changes in whole blood of 42 healthy male individuals in response to a stressful cognitive task, its association with concentration changes in cortisol and its modulation by transcranial direct current stimulation (tDCS). We observed a continuous increase in COMT promotor DNA methylation which correlated with higher saliva cortisol levels and was still detectable one week later. However, this lasting effect was suppressed by concurrent activity-enhancing anodal tDCS to the dorsolateral prefrontal cortex. Our findings support the significance of gene-specific DNA methylation in whole blood as potential biomarkers for stress-related disorders. Moreover, they suggest alternative molecular mechanisms possibly involved in lasting behavioral effects of tDCS.
Oligogenic combinations of rare variants influence specific phenotypes in complex disorders
Authors: Pounraja Vijay Kumar , Girirajan Santhosh
Published: October 2021

Genetic studies of complex disorders such as autism and intellectual disability (ID) are often based on enrichment of individual rare variants or their aggregate burden in affected individuals compared to controls. However, these studies overlook the influence of combinations of rare variants that may not be deleterious on their own due to statistical challenges resulting from rarity and combinatorial explosion when enumerating variant combinations, limiting our ability to study oligogenic basis for these disorders. We present a framework that combines the apriori algorithm and statistical inference to identify specific combinations of mutated genes associated with complex phenotypes. Our approach overcomes computational barriers and exhaustively evaluates variant combinations to identify non-additive relationships between simultaneously mutated genes. Using this approach, we analyzed 6,189 individuals with autism and identified 718 combinations significantly associated with ID, and carriers of these combinations showed lower IQ than expected in an independent cohort of 1,878 individuals. These combinations were enriched for nervous system genes such asNINandNGF, showed complex inheritance patterns, and were depleted in unaffected siblings. We found that an affected individual can carry many oligogenic combinations, each contributing to the same phenotype or distinct phenotypes at varying effect sizes. We also used this framework to identify combinations associated with multiple comorbid phenotypes, including mutations ofCOL28A1andMFSD2Bfor ID and schizophrenia andABCA4, DNAH10andMC1Rfor ID and anxiety/depression. Our framework identifies a key component of missing heritability and provides a novel paradigm to untangle the genetic architecture of complex disorders.

SIGNIFICANCE

While rare mutations in single genes or their collective burden partially explain the genetic basis for complex disorders, the role of specific combinations of rare variants is not completely understood. This is because combinations of rare variants are rarer and evaluating all possible combinations would result in a combinatorial explosion, creating difficulties for statistical and computational analysis. We developed a data mining approach that overcomes these limitations to precisely quantify the influence of combinations of two or more mutated genes on a specific clinical feature or multiple co-occurring features. Our framework provides a new paradigm for dissecting the genetic causes of complex disorders and provides an impetus for its utility in clinical diagnosis.
Short ‘1.2× genome’ infectious clone initiates deltavirus replication in Boa constrictor cells
Authors: Szirovicza Leonora , Hetzel Udo , Kipar Anja , Hepojoki Jussi
Published: October 2021

Human hepatitis D virus (HDV), discovered in 1977, represented the sole known deltavirus for decades. The dependence on hepatitis B virus (HBV) co-infection and its glycoproteins for infectious particle formation led to the assumption that deltaviruses are human-only pathogens. However, since 2018, several reports have described identification of HDV-like agents from various hosts but without co-infecting hepadnaviruses. Indeed, we demonstrated that Swiss snake colony virus 1 (SwSCV-1) uses arenaviruses as the helper for infectious particle formation, thus shaking the dogmatic alliance with hepadnaviruses for completing deltavirus life cycle. In vitro systems enabling helper virus-independent replication are key for studying the newly discovered deltaviruses. Others and we have successfully used constructs containing multimers of the deltavirus genome for the replication of various deltaviruses via transfection in cell culture. Here, we report the establishment of deltavirus infectious clones with 1.2× genome inserts bearing two copies of the genomic and antigenomic ribozymes. We used SwSCV-1 as the model to compare the ability of the previously reported “2× genome” and the “1.2× genome” plasmid constructs/infectious clones to initiate replication in cell culture. Using immunofluorescence, qRT-PCR, immuno- and northern blotting, we found the 2× and 1.2× genome clones to similarly initiate deltavirus replication in vitro and both induced a persistent infection of snake cells. We hypothesize that duplicating the ribozymes facilitates the cleavage of genome multimers into unit-length pieces during the initial round of replication. The 1.2× genome constructs enable easier introduction of modifications required for studying deltavirus replication and cellular interactions.

IMPORTANCE

Hepatitis D virus (HDV) is a satellite virus infecting humans with strict association to hepatitis B virus (HBV) co-infection because HBV glycoproteins can mediate infectious HDV particle formation. For decades, HDV was the sole representative of deltaviruses, which had led to hypotheses suggesting that it evolved in humans, the only known natural host. Recent sequencing studies have led to the discovery of HDV-like sequences across a wide range of species, representing a paradigm shift in deltavirus evolution. Molecular biology tools such as infectious clones, which enable initiation of deltavirus infection without helper virus, are key to demonstrate that the recently found deltaviruses are capable of independent replication. Such tools will enable identification of the potential helper viruses. Here, we report a 1.2× genome copy strategy for designing plasmid-based infectious clones to study deltaviruses and to demonstrate that plasmid delivery into cultured snake cells sufficiently initiates replication of different deltaviruses.