bluuebunny/crossref_metadata_2025 huggingface dataset:
Shaping the BRCAness mutational landscape by alternative double-strand break repair, replication stress and mitotic aberrancies
Authors: Stok Colin , Kok Yannick P , van den Tempel Nathalie , van Vugt Marcel A T M
Published: March 2021

Tumours with mutations in the BRCA1/BRCA2 genes have impaired double-stranded DNA break repair, compromised replication fork protection and increased sensitivity to replication blocking agents, a phenotype collectively known as ‘BRCAness’. Tumours with a BRCAness phenotype become dependent on alternative repair pathways that are error-prone and introduce specific patterns of somatic mutations across the genome. The increasing availability of next-generation sequencing data of tumour samples has enabled identification of distinct mutational signatures associated with BRCAness. These signatures reveal that alternative repair pathways, including Polymerase θ-mediated alternative end-joining and RAD52-mediated single strand annealing are active in BRCA1/2-deficient tumours, pointing towards potential therapeutic targets in these tumours. Additionally, insight into the mutations and consequences of unrepaired DNA lesions may also aid in the identification of BRCA-like tumours lacking BRCA1/BRCA2 gene inactivation. This is clinically relevant, as these tumours respond favourably to treatment with DNA-damaging agents, including PARP inhibitors or cisplatin, which have been successfully used to treat patients with BRCA1/2-defective tumours. In this review, we aim to provide insight in the origins of the mutational landscape associated with BRCAness by exploring the molecular biology of alternative DNA repair pathways, which may represent actionable therapeutic targets in in these cells.
Detection of Uncoupled Circadian Rhythms in Individual Cells of Lemna minor using a Dual-Color Bioluminescence Monitoring System
Authors: Watanabe Emiri , Isoda Minako , Muranaka Tomoaki , Ito Shogo , Oyama Tokitaka
Published: March 2021

The plant circadian oscillation system is based on the circadian clock of individual cells. Circadian behavior of cells has been observed by monitoring the circadian reporter activity, such as bioluminescence of AtCCA1::LUC+. To deeply analyze different circadian behaviors in individual cells, we developed the dual-color bioluminescence monitoring system that automatically measured the luminescence of two luciferase reporters simultaneously at a single-cell level. We selected a yellow-green-emitting firefly luciferase (LUC+) and a red-emitting luciferase (PtRLUC) that is a mutant form of Brazilian click beetle ELUC. We used AtCCA1::LUC+ and CaMV35S::PtRLUC. CaMV35S::LUC+ was previously reported as a circadian reporter with a low-amplitude rhythm. These bioluminescent reporters were introduced into the cells of a duckweed, Lemna minor, by particle bombardment. Time series of the bioluminescence of individual cells in a frond were obtained using a dual-color bioluminescence monitoring system with a green-pass- and red-pass filter. Luminescence intensities from the LUC+ and PtRLUC of each cell were calculated from the filtered luminescence intensities. We succeeded in reconstructing the bioluminescence behaviors of AtCCA1::LUC+ and CaMV35S::PtRLUC in the same cells. Under prolonged constant light conditions, AtCCA1::LUC+ showed a robust circadian rhythm in individual cells in an asynchronous state in the frond, as previously reported. By contrast, CaMV35S::PtRLUC stochastically showed circadian rhythms in a synchronous state. These results strongly suggested the uncoupling of cellular behavior between these circadian reporters. This dual-color bioluminescence monitoring system is a powerful tool to analyze various stochastic phenomena accompanying large cell-to-cell variation in gene expression.
Larger pain extent is associated with greater pain intensity and disability but not with general health status or psychosocial features in patients with cervical radiculopathy
Authors: Lam Kwun , Peolsson Anneli , Soldini Emiliano , Löfgren Håkan , Wibault Johanna , Dedering Åsa , Öberg Birgitta , Zsigmond Peter , Barbero Marco , Falla Deborah
Published: March 2021

Pain as a result of cervical radiculopathy (CR) can be widespread, nondermatomal and individually specific, but the association between pain extent and other clinical features has never been explored. The objective of this study is to investigate whether pain extent relates to clinical variables including pain intensity in addition to health indicators including disability, general health, depression, somatic anxiety, coping strategies or self-efficacy.

An observational cohort study was conducted. Participants were recruited from 4 hospital spinal centres in Sweden. Pain extent was quantified from the pain drawings of 190 individuals with cervical disc disease, verified with magnetic resonance imaging (MRI) and compatible with clinical findings (examined by a neurosurgeon), that show cervical nerve root compression. Pain extent was evaluated in relation to neck pain, arm pain, and headache intensity. Multiple linear regression analysis were then used to verify whether pain extent was associated with other health indicators including disability, health-related quality of life, depression, somatic anxiety, coping strategies and self-efficacy.

Pain extent was directly related to neck, arm and headache pain intensity (all P < .01). Multiple linear regression revealed that pain extent was significantly associated only to the level of perceived disability (P < .01).

Increased pain extent in people with CR is associated with higher headache, neck and arm pain intensity, and disability but not measures of general health, depression, somatic anxiety, coping strategies or self-efficacy.
Clinical and radiologic characteristics of radiologically missed miliary tuberculosis
Authors: Choe Jooae , Jung Kyung Hwa , Park Joung-Ha , Kim Sung-Han , Kim Mi Young
Published: March 2021

While chest CT provides important clue for diagnosis of miliary tuberculosis (TB), patients are occasionally missed on initial CT, which might delay the diagnosis. This study was to evaluate the clinical and radiological characteristics of radiologically missed miliary TB.

Total 117 adult patients with microbiologically confirmed miliary TB in an intermediate TB-burden country were included. ‘Missed miliary TB’ were defined as the case in which miliary TB was not mentioned as a differential diagnosis in the initial CT reading. Clinical characteristics and radiologic findings including the predominant nodule size, demarcation of miliary nodules and disease extent on CT were retrospectively evaluated. Findings were compared between the missed and non-missed miliary TB groups. Multivariable analyses were performed to determine independent risk factors of missed miliary TB.

Of 117 patients with miliary TB, 13 (11.1%) were classified as missed miliary TB; these patients were significantly older than those with non-missed miliary TB (median age, 71 vs 57 years, P = .024). There was a significant diagnostic delay in the missed miliary TB group (P < .001). On chest CT, patients with missed miliary TB had a higher prevalence of ill-defined nodules (84.6% vs 14.4%; P < .001), miliary nodule less than 2 mm showing granular appearance (69.2% vs 12.5%; P < .001), and subtle disease extent (less than 25% of whole lung field, 46.2% vs 8.7%; P < .001). Multivariable analysis revealed that only CT findings including ill-defined nodule (Odd ratios [OR], 15.64; P = .002) and miliary nodule less than 2 mm (OR, 10.08; P = .007) were independently associated with missed miliary TB.

Approximately 10% of miliary TB could be missed on initial chest CT, resulting in a delayed diagnosis and treatment. Caution is required in patients with less typical CT findings showing ill-defined miliary nodules less than 2 mm showing granular appearance and follow-up CT might have a benefit.
The differences in plasma/serum ghrelin levels between obstructive sleep apnea-hypopnea patients and controls
Authors: Sun Meng-Ling , Niu Xun , Xiao Xi-Yue , Chen Xiong
Published: March 2021

Background:

The association between obstructive sleep apnea-hypopnea syndrome (OSAHS) and plasma/serum ghrelin levels remains controversial. We performed a meta-analysis to evaluate the difference in plasma/serum ghrelin levels between OSAHS patients and controls.

Methods:

Database of PubMed, SCI, and Elsevier were searched entirely. Two independents identified eligible studies of ghrelin levels in OSAHS patients. ReviewManager (version 5.3) was adopted for data synthesis.

Results:

The meta-analysis A pooled the comparison of ghrelin concentrations in OSAHS patients and controls, which included 7 studies and involving 446 participants. The result of the meta-analysis A indicated that plasma/serum ghrelin levels were no significant differences between the OSAHS group and the control group (standard mean difference (SMD) = 0.08, 95% confidence interval (CI) = −0.12 to 0.28, P = .43). As a supplementary, meta-analysis B pooled the comparison of plasma/serum ghrelin levels in OSAHS patients before and after continuous positive airway pressure (CPAP) therapy, which included 155 participants from 4 studies, it revealed that plasma/serum ghrelin levels were no significant differences between before and after CPAP therapy (SMD = 0.12, 95%CI = −0.07 to 0.31, P = .22).

Conclusion:

The meta-analysis A demonstrated that plasma/serum ghrelin levels were no significant differences between the OSAHS group and the control group. The meta-analysis B showed plasma/serum ghrelin levels have no significant changes after CPAP therapy in OSAHS patients.
18F-FDG PET/CT imaging for aggressive melanotic schwannoma of the L3 spinal root
Authors: Shen Xun-Ze , Wang Wei , Luo Zhou-Ye
Published: March 2021

Rationale:

Melanotic schwannoma (MS) is an unusual variant of a nerve sheath neoplasm that accounts for less than 1% of all primary peripheral nerve sheath tumors. Fluorine-18 fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) has unique value in detecting malignant MS lesions. To date, only 4 cases of MS with hepatic metastasis have been reported. Herein, we report the fifth case, which is the first reported patient with MS of Asian ethnicity with hepatic metastasis.

Patient concerns:

A 29-year-old woman with a 1-day history of backache was admitted to our hospital. PET/CT showed a paravertebral heterogeneous soft tissue mass along the spinal nerve at the L2-L3 level with strong FDG uptake, and a nodule with increased FDG uptake in the lateral lobe of the left liver.

Diagnosis:

A puncture biopsy of the L3 bony destruction and surrounding soft tissue mass was performed. The final diagnosis was spinal MS with hepatic metastasis.

Interventions:

The patient underwent 6 courses of systemic chemotherapy.

Outcomes:

The patient did not receive further treatment for half a year after the end of chemotherapy and recovered well.

Lessons:

Unlike conventional schwannomas, which are completely benign, MS has an unpredictable prognosis. It is thought to have low malignant potential, and the malignant type tends to metastasize. FDG PET/CT has a unique and important value in the differential diagnosis of benign and malignant lesions, in detecting occult metastases, monitoring the treatment response, and assessing the prognosis of MS.
“PEM Pals”—Cultivating a Learning Community During the Pandemic
Authors: Goldman Michael P. , Rudd Alexis V. , Auerbach Marc A.
Published: March 2021

Objectives

The current pandemic has pushed medical educators to rethink traditional learning constructs as residents are experiencing fewer patient contacts in the pediatric emergency department (PED). Especially for those bound for a career in pediatric emergency medicine (PEM), we designed a curriculum to proactively address this emerging learning gap, incorporating a wellness “check-in” at the beginning of each session. The objective of this report is to share the themes of this wellness check-ins with those engaged in pediatric emergency medicine education and mentorship. Additionally, we share our curricular approach as we plan to continue PEM Pals after the pandemic restrictions are lifted.

Methods

“PEM Pals” is a twice-weekly video conference meeting made up of pediatric residents with an expressed interest in PEM and those residents currently on rotation in the pediatric emergency department. Following a flipped classroom model, participants complete a presession learning activity and then core PEM topics are covered through literature review, case discussions, and telesimulations. Each meeting begins with a wellness “check-in.” Themes generated from these check-ins were member checked by our core learning contingent.

Results

Nine residents make up our core learning contingent and we have had 11 “PEM Pals” sessions since March 2020. Three themes emerged from the wellness check-ins. The first was each postgraduate year's unique concern over professional transitions. The second was a pervasive sense of guilt. And the third was a grave concern about their ability to support and be supported from their personal communities.

Conclusions

The goal of our curriculum was to supplement an anticipated knowledge gap. Through use of a wellness “check-in,” we elicited important themes for PEM educational leaders to consider as they mentor pediatric residents toward a career in PEM during the pandemic.
The effect of stimulus duration on preferences for gain adjustments when listening to speech
Authors: Whitmer William M. , Caswell-Midwinter Benjamin , Naylor Graham
Published: March 2021

Objectives

In the personalisation of hearing aid fittings, gain is often adjusted to suit patient preferences using live speech. When using brief sentences as stimuli, the minimum gain adjustments necessary to elicit consistent preferences (‘preference thresholds’) were previously found to be much greater than typical adjustments in current practice. The current study examined the role of duration on preference thresholds.

Design

Participants heard 2, 4 and 6-s segments of a continuous monologue presented successively in pairs. The first segment of each pair was presented at each individual’s real-ear or prescribed gain. The second segment was presented with a ±0-12 dB gain adjustment in one of three frequency bands. Participants judged whether the second was “better”, “worse” or “no different” from the first.

Study Sample

Twenty-nine adults, all with hearing-aid experience.

Results

The minimum gain adjustments needed to elicit “better” or “worse” judgments decreased with increasing duration for most adjustments. Inter-participant agreement and intra-participant reliability increased with increasing duration up to 4 s, then remained stable.

Conclusions

Providing longer stimuli improves the likelihood of patients providing reliable judgments of hearing-aid gain adjustments, but the effect is limited, and alternative fitting methods may be more viable for effective hearing-aid personalisation.
Association between SARS-CoV-2 Transmissibility, Viral Load, and Age in Households
Authors: Lyngse Frederik Plesner , Mølbak Kåre , Træholt Franck Kristina , Nielsen Claus , Skov Robert Leo , Voldstedlund Marianne , Cohen Arieh S. , Kirkeby Carsten Thure
Published: March 2021

Aim

The objective of this nationwide study was to investigate the association between SARS-CoV-2 transmissibility, viral load, and age of primary cases in Danish households.

Background

Spread in households represents a major mode of transmission of SARS-CoV-2. In order to take proper action against the spread of the disease, it is important to have a better understanding of transmission in the household domain—including the role of viral load of primary cases.

Methods

The study was designed as an observational cohort study, using detailed administrative register data. We included the full population of Denmark and all SARS-CoV-2 tests (August 25, 2020 to February 10, 2021) to estimate transmissibility in house-holds comprising 2-6 people. RT-PCR Cycle threshold (Ct) values were used as a proxy for viral load.

Results

We identified 63,657 primary cases and 139,882 household members of which 21% tested positive by RT-PCR within a 1-14 day period after the primary case. There was an approximately linear association between Ct value of the sample and transmissibility, implying that cases with samples having a higher viral load were more transmissible than cases with samples having a lower viral load. However, even for primary cases with relatively high sample Ct values, the transmissibility was not negligible, e.g., for primary cases with a sample Ct value of 38, we found that 13% of the primary cases had at least one secondary household case. Moreover, 34% of all secondary cases were found in households with primary cases having sample Ct values >30. An increasing transmissibility with age of the primary cases for adults (≥20 years) and a decreasing transmissibility with age for children (<20 years) were found.

Conclusions

Although primary cases with sample high viral loads (low Ct values) were associated with higher SARS-CoV-2 transmissibility, we found no obvious cut-off for sample Ct values to eliminate transmissibility and a substantial amount of household transmission occurred in households where the primary cases had high sample Ct values (low viral load), The study further showed that transmissibility increases with age. These results have important public health implications, as they suggest that contact tracing should prioritize cases according to Ct values and age, and underline the importance of quick identification and isolation of cases. Furthermore, the study highlights that households can serve as a transmission bridge by creating connections between otherwise separate domains.
SARS-CoV-2 Load does not Predict Transmissibility in College Students
Authors: Tian Di , Lin Zhen , Kriner Ellie M. , Esneault Dalton J. , Tran Jonathan , DeVoto Julia C. , Okami Naima , Greenberg Rachel , Yanofsky Sarah , Ratnayaka Swarnamala , Tran Nicholas , Livaccari Maeghan , Lampp Marla , Wang Noel , Tim Scott , Norton Patrick , Scott John , Hu Tony Y. , Garry Robert , Delafontaine Patrice , Hamm Lee , Yin Xiao-Ming
Published: March 2021

SARS-CoV2 is highly contagious and the global spread has caused significant medical, social and economic impacts. Other than vaccination, effective public health measures, including contact tracing, isolation and quarantine, is critical for deterring viral transmission, preventing infection progression and resuming normal activities. Viral transmission is affected by many factors but the viral load and vitality could be among the most important ones. Although in vitro culture studies have indicated that the amount of virus isolated from infected people determines the successful rate of virus isolation, whether the viral load carried at the individual level would affect the transmissibility was not known. We aimed to determine whether the Ct value, a measurement of viral load by RT-PCR assay, could differentiate the spreader from the non-spreader in a population of college students. Our results indicate that while at the population level the Ct value is lower, suggesting a higher viral load, in the symptomatic spreaders than the asymptomatic non-spreaders, there is a significant overlap in the Ct values between the two groups. Thus Ct values, or the viral load, at the individual level could not predict the transmissibility. Our studies also suggest that a sensitive method to detect the presence of virus is needed to identify asymptomatic persons who may carry a low viral load but can still be infectious.
An Explainable Artificial Intelligence based Prospective Framework for COVID-19 Risk Prediction
Authors: Sharma Vishal , Piyush  , Chhatwal Samarth , Singh Bipin
Published: March 2021

Given the spread of COVID-19 to vast geographical regions and populations, it is not feasible to undergo or recommend the RT-PCR based tests to all individuals with flu-like symptoms. The reach of RT-PCR based testing is still limited due to the high cost of the test and huge population in few countries. Thus, alternative methods for COVID-19 infection risk prediction can be useful. We built an explainable artificial intelligence (AI) based integrated web-based prospective framework for COVID-19 risk prediction. We employed a two-step procedure for the non-clinical prediction of COVID19 infection risk. In the first step we assess the initial risk of COVID19 infection based on carefully selected parameters associated with COVID-19 positive symptoms from recent research. Generally, X-ray scans are cheaper and easily available in most government and private health centres. Therefore, based on the outcome of the computed initial risk in first step, we further provide an optional prediction using the chest X-ray scans in the second step of our proposed AI based prospective framework. Since there is a bottleneck to undergo an expensive RT-PCR based confirmatory test in economically backward nations, this is a crucial part of our explainable AI based prospective framework. The initial risk assessment outcome is analysed in combination with the advanced deep learning-based analysis of chest X-ray scans to provide an accurate prediction of COVID-19 infection risk. This prospective web-based AI framework can be employed in limited resource settings after clinical validation in future. The cost and time associated with the adoption of this prospective AI based prospective framework will be minimal and hence it will be beneficial to majority of the population living in low-income settings such as small towns and rural areas that have limited access to advanced healthcare facilities.
Evaluation of sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing
Authors: Banada Padmapriya , Elson David , Daivaa Naranjargal , Park Claire , Desind Samuel , Montalvan Ibsen , Kwiatkowski Robert , Chakravorty Soumitesh , Alland David , Xie Yingda L.
Published: March 2021

Sensitive, accessible, and biosafe sampling methods for COVID-19 reverse-transcriptase polymerase chain reaction (RT-PCR) assays are needed for frequent and widespread testing. We systematically evaluated diagnostic yield across different sample collection and transport workflows, including the incorporation of a viral inactivation buffer. We prospectively collected nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal and oral swabs were placed in both viral transport media (VTM) and eNAT™, a sterilizing transport buffer, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert) test. The sensitivity of each sampling strategy was compared using a composite positive standard. Overall, swab specimens collected in eNAT showed superior sensitivity compared to swabs in VTM (70% vs 57%, P=0.0022). Direct saliva 90.5%, (95% CI: 82%, 95%), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50%, P<0.001) or eNAT (67.8%, P=0.0012) and oral swabs in VTM (50%, P<0.0001) or eNAT (56%, P<0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert test; however, no single sample matrix identified all positive cases.
Network Theory Reveals Principles of Spliceosome Structure and Dynamics
Authors: Kaur Harpreet , van der Feltz Clarisse , Sun Yichen , Hoskins Aaron A.
Published: March 2021

Cryo-EM has revolutionized structural biology of the spliceosome and dozens of distinct spliceosome structures representing much of the splicing cycle have now been determined. However, comparison of these structures is challenging due to extreme compositional and conformational dynamics of the splicing machinery and the thousands of intermolecular interactions created or dismantled as splicing progresses. We have used network theory to quantitatively analyze the dynamic interactions of splicing factors throughout the splicing cycle by constructing structure-based networks from every protein-protein, protein-RNA, and RNA-RNA interaction found in eight different spliceosome structures. Our networks reveal that structural modules comprising the spliceosome are highly dynamic with factors oscillating between modules during each stage along with large changes in the algebraic connectivities of the networks. Overall, the spliceosome’s connectivity is focused on the active site in part due to contributions from non-globular proteins and components of the NTC. Many key components of the spliceosome including Prp8 and the U2 snRNA exhibit large shifts in both eigenvector and betweenness centralities during splicing. Other factors show transiently high betweenness centralities only at certain stages thereby suggesting mechanisms for regulating splicing by briefly bridging otherwise poorly connected network nodes. These observations provide insights into the organizing principles of spliceosome architecture and provide a framework for comparative network analysis of similarly complex and dynamic macromolecular machines.
Kinetic structure of recycling vesicle pool at the Calyx of Held synapse under in vivo-like activities
Authors: Liu Zili , Zhu Ying , Hu Yubing , Sun Jianyuan
Published: March 2021

Synaptic transmission at mammalian central synapses has ongoing background activity at physiological temperature. The recycling vesicle pool, with proper kinetics, ensures sustained synaptic transmission. However, the kinetic structure of recycling vesicle pool has never been quantitatively analyzed before, and most studies were performed at room temperature and under resting conditions. With the combination of presynaptic capacitance measurement and postsynaptic EPSC recording on calyx of Held synapses at physiological temperature, we studied vesicle recycling under sustained presynaptic stimulation. The kinetics of vesicle reuse was revealed by impeding transmitter refilling with folimycin. We kinetically dissected the recycling vesicle pool as sequentially connected sub-pools and depicted the complete kinetic structure. The sizes and transition rates among these sub-pools were dynamically regulated by neuronal activity, in order to ensure efficient synaptic transmission. Our work highlights the impact of the vesicle recycling machinery on stable and reliable synaptic transmission under variable levels of neuronal activity.

Impact statement

The recycling pool of vesicles are kinetically dissected as four populated pools ensuring stable and reliable synaptic transmission
Disinfection of SARS-CoV-2 contaminated surfaces of personal items with UVC-LED disinfection boxes
Authors: Bormann M. , Alt M. , Schipper L. , van de Sand L. , Otte M. , Meister T. L. , Dittmer U. , Witzke O. , Steinmann E. , Krawczyk A.
Published: March 2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is transmitted from person-to-person by close contact, small aerosol respiratory droplets and potentially via contact with contaminated surfaces. Here, we investigated the effectiveness of commercial UVC-LED disinfection boxes in inactivating SARS-CoV-2 contaminated surfaces of personal items. We contaminated glass, metal and plastic samples representing the surfaces of personal items such as smartphones, coins or credit cards with SARS-CoV-2 formulated in an organic matrix mimicking human respiratory secretions. For disinfection, the samples were placed at different distances from UVC emitting LEDs inside commercial UVC-LED disinfection boxes and irradiated for different time periods (up to 10 minutes). High viral loads of SARS-CoV-2 were effectively inactivated on all surfaces after 3 minutes of irradiation. Even 10 seconds of UVC-exposure strongly reduced viral loads. Thus, UVC-LED boxes proved to be an effective method for disinfecting SARS-CoV-2 contaminated surfaces that are typically found on personal items.
Evaluating the role of reference-genome phylogenetic distance on evolutionary inference
Authors: Prasad Aparna , Lorenzen Eline D , Westbury Michael V
Published: March 2021

When a high-quality genome assembly of a target species is unavailable, an option to avoid the costlyde novoassembly process is a mapping-based assembly. However, mapping shotgun data to a distant relative may lead to biased or erroneous evolutionary inference. Here, we used short-read data from a mammal and a bird species (beluga and rowi kiwi) to evaluate whether reference genome phylogenetic distance can impact downstream demographic (PSMC) and genetic diversity (heterozygosity, runs of homozygosity) analyses. We mapped to assemblies of species of varying phylogenetic distance (conspecific to genome-wide divergence of >7%), andde novoassemblies created using cross-species scaffolding. We show that while reference genome phylogenetic distance has an impact on demographic analyses, it is not pronounced until using a reference genome with >3% divergence from the target species. When mapping to cross-species scaffolded assemblies, we are unable to replicate the original beluga demographic analyses, but can with the rowi kiwi, presumably reflecting the more fragmented nature of the beluga assemblies. As for genetic diversity estimates, we find that increased phylogenetic distance has a pronounced impact; heterozygosity estimates deviate incrementally as phylogenetic distance increases. Moreover, runs of homozygosity are removed when mapping to any non-conspecific assembly. However, these biases can be reduced when mapping to a cross-species scaffolded assembly. Taken together, our results show that caution should be exercised when selecting the reference genome for mapping assemblies. Cross-species scaffolding may offer a way to avoid a costly, traditionalde novoassembly, while still producing robust, evolutionary inference.
The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions
Authors: Benoît Moury , Jean-Marc Audergon , Sylvie Baudracco-Arnas , Safa Ben Krima , François Bertrand , Nathalie Boissot , Mireille Buisson , Valérie Caffier , Mélissa Cantet , Sylvia Chanéac , Carole Constant , François Delmotte , Catherine Dogimont , Juliette Doumayrou , Frédéric Fabre , Sylvain Fournet , Valérie Grimault , Thierry Jaunet , Isabelle Justafré , Véronique Lefebvre , Denis Losdat , Marcel Thierry C. , Josselin Montarry , Morris Cindy E. , Mariem Omrani , Manon Paineau , Sophie Perrot , Marie-Laure Pilet-Nayel , Youna Ruellan
Published: March 2021

Abstract

Understanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no or minor parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.
CHRM1 is a Druggable Melanoma Target Whose Endogenous Activity is Determined by Inherited Genetic Variation in DOPA Production
Authors: Doepner Miriam , Natale Christopher A. , Lee In Young , Venkat Swati , Kim Sung Hoon , Katzenellenbogen John A. , Katzenellenbogen Benita S. , Feigin Michael E. , Ridky Todd W.
Published: March 2021

Melanoma risk is 30 times higher in people with lightly pigmented skin compared to those with darkly pigmented skin. Here we show that this difference results from more than melanin pigment and its ultraviolet radiation (UVR) shielding effect. Using primary human melanocytes representing the full human skin pigment continuum and several preclinical melanoma models, we show that cell-intrinsic differences between dark and light melanocytes regulate melanocyte proliferative capacity, overall cellular differentiation state, and susceptibility to malignant transformation,independently of melanin and UV exposure.We determined that these differences result from dihydroxyphenylalanine (DOPA), a melanin precursor synthesized at higher levels in melanocytes from dark skin. Although DOPA was not previously known to have specific signaling activity, we used both high throughput pharmacologic and geneticin vivoCRISPR screens to determine that DOPA limits melanocyte and melanoma cell proliferation by directly inhibiting the muscarinic acetylcholine receptor M1 (CHRM1), a G Protein-Coupled Receptor (GPCR) not previously known to bind DOPA, nor to affect melanoma pathobiology. Pharmacologic CHRM1 antagonism in melanoma leads to depletion of c-Myc and FOXM1, both of which are proliferation drivers associated with aggressive melanoma. In preclinical mouse melanoma models using both immune deficient and syngeneic immune competent mice, pharmacologic inhibition of CHRM1 or FOXM1 inhibited tumor growth. CHRM1 and FOXM1 may be new therapeutic targets for melanoma.
SPOT: a web-tool enabling Swift Profiling Of Transcriptomes
Authors: Farr Elias , Sattler Julia M. , Frischknecht Friedrich
Published: March 2021

The increasing number of single cell and bulk RNAseq data sets describing complex gene expression profiles in different organisms, organs or cell types calls for an intuitive tool allowing rapid comparative analysis. Here we present Swift Profiling Of Transcriptomes (SPOT) as a web tool that allows not only differential expression analysis but also fast ranking of genes fitting transcription profiles of interest. Based on a heuristic approach the spot algorithm ranks the genes according to their proximity to the user-defined gene expression profile of interest. The best hits are visualized as a table, bar chart or dot plot and can be exported as an Excel file. While the tool is generally applicable, we tested it on RNAseq data from malaria parasites that undergo multiple stage transformations during their complex life cycle as well as on data from multiple human organs during development and cell lines infected by the SARS-CoV-2 virus. SPOT should enable non-bioinformaticians to easily analyse their own and any available dataset.
Closer appendage spacing augments metachronal swimming speed by promoting tip vortex interactions
Authors: Ford Mitchell P. , Santhanakrishnan Arvind
Published: March 2021

Numerous species of aquatic invertebrates, including crustaceans, swim by oscillating multiple closely spaced appendages. The coordinated, out-of-phase motion of these appendages, known as “metachronal paddling”, has been well-established to improve swimming performance relative to synchronous paddling. Invertebrates employing this propulsion strategy cover a wide range of body sizes and shapes, but the ratio of appendage spacing (G) to the appendage length (L) has been reported to lie in a comparatively narrow range of 0.2 <G/L≤ 0.65. The functional role ofG/Lon metachronal swimming performance is unknown. We hypothesized that for a given Reynolds number and stroke amplitude, hydrodynamic interactions promoted by metachronal stroke kinematics with smallG/Lcan increase forward swimming speed. We used a dynamically scaled self-propelling robot to comparatively examine swimming performance and wake development of metachronal and synchronous paddling under varyingG/L, phase lag, and stroke amplitude.G/Lwas varied from 0.4 to 1.5, with the expectation that whenG/Lis large, there should be no performance difference between metachronal and synchronous paddling due to a lack of interaction between vortices that form on the appendages. Metachronal stroking at non-zero phase lag withG/Lin the biological range produced faster swimming speeds than synchronous stroking. AsG/Lincreased and as stroke amplitude decreased, the influence of phase lag on the swimming speed of the robot was reduced. For smallerG/L, vortex interactions between adjacent appendages generated a horizontally-oriented wake and increased momentum fluxes relative to largerG/L, which contributed to increasing swimming speed. We find that while metachronal motion augments swimming performance for closely spaced appendages (G/L< 1), moderately spaced appendages (1.0 ≤G/L≤ 1.5) can benefit from metachronal motion only when the stroke amplitude is large.
Complementary Phenotyping of Maize Root Architecture by Root Pulling Force and X-Ray Computed Tomography
Authors: Shao Mon-Ray , Jiang Ni , Li Mao , Howard Anne , Lehner Kevin , Mullen Jack L. , Gunn Shayla L. , McKay John K. , Topp Christopher N
Published: March 2021

The root system is critical for the survival of nearly all land plants and a key target for improving abiotic stress tolerance, nutrient accumulation, and yield in crop species. Although many methods of root phenotyping exist, within field studies one of the most popular methods is the extraction and measurement of the upper portion of the root system, known as the root crown, followed by trait quantification based on manual measurements or 2D imaging. However, 2D techniques are inherently limited by the information available from single points of view. Here, we used X-ray computed tomography to generate highly accurate 3D models of maize root crowns and created computational pipelines capable of measuring 71 features from each sample. This approach improves estimates of the genetic contribution to root system architecture, and is refined enough to detect various changes in global root system architecture over developmental time as well as more subtle changes in root distributions as a result of environmental differences. We demonstrate that root pulling force, a high-throughput method of root extraction that provides an estimate of root biomass, is associated with multiple 3D traits from our pipeline. Our combined methodology can therefore be used to calibrate and interpret root pulling force measurements across a range of experimental contexts, or scaled up as a stand-alone approach in large genetic studies of root system architecture.
Nemertean, brachiopod and phoronid neuropeptidomics reveals ancestral spiralian signalling systems
Authors: Thiel Daniel , Yañez Guerra Luis A. , Franz-Wachtel Mirita , Hejnol Andreas , Jékely Gáspár
Published: March 2021

Neuropeptides are diverse signalling molecules in animals commonly acting through G-protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive diversification in bilaterians and the relationships of many peptide-receptor systems have been clarified. However, we lack a detailed picture of neuropeptide evolution in lophotrochozoans as in-depth studies only exist for molluscs and annelids. Here we analyse peptidergic systems in Nemertea, Brachiopoda and Phoronida. We screened transcriptomes from thirteen nemertean, six brachiopod and four phoronid species for proneuropeptides and neuropeptide GPCRs. With mass spectrometry from the nemerteanLineus longissimus, we validated several predicted peptides and identified novel ones. Molecular phylogeny combined with peptide-sequence and gene-structure comparisons allowed us to comprehensively map spiralian neuropeptide evolution. We found most mollusc and annelid peptidergic systems also in nemerteans, brachiopods and phoronids. We uncovered previously hidden relationships including the orthologies of spiralian CCWamides to arthropod agatoxin-like peptides and of mollusc APGWamides to RGWamides from annelids, with orthologues systems in nemerteans, brachiopods and phoronids. We found that pleurin neuropeptides previously only found in molluscs are also present in nemerteans and brachiopods. We also identified cases of gene family duplications and losses. These include a protostome-specific expansion of RFamide/Wamide signalling, a spiralian expansion of GnRH-related peptides, and duplications of vasopressin/oxytocin before the divergence of brachiopods, phoronids and nemerteans. This analysis expands our knowledge of peptidergic signalling in spiralians and protostomes. Our annotated dataset of nearly 1,300 proneuropeptide sequences and 600 GPCRs presents a useful resource for further studies of neuropeptide signalling in protostomes.
Mass Dynamics 1.0: A streamlined, web-based environment for analyzing, sharing and integrating Label-Free Data
Authors: Bloom Joseph , Triantafyllidis Aaron , Burton (Ngov) Paula , Infusini Giuseppe , Webb Andrew
Published: March 2021

Label Free Quantification (LFQ) of shotgun proteomics data is a popular and robust method for the characterization of relative protein abundance between samples. Many analytical pipelines exist for the automation of this analysis and some tools exist for the subsequent representation and inspection of the results of these pipelines. Mass Dynamics 1.0 (MD 1.0) is a web based analysis environment that can analyze and visualize LFQ data produced by software such as Maxquant. Unlike other tools, MD 1.0 utilizes cloud-based architecture to enable researchers to store their data, enabling researchers to not only automatically process and visualize their LFQ data but annotate and share their findings with collaborators and, if chosen, to easily publish results to the community. With a view toward increased reproducibility and standardisation in proteomics data analysis and streamlining collaboration between researchers, MD 1.0 requires minimal parameter choices and automatically generates quality control reports to verify experiment integrity. Here, we demonstrate that MD 1.0 provides reliable results for protein expression quantification, emulating Perseus on benchmark datasets over a wide dynamic range.

The MD 1.0 platform is available globally via:https://app.massdynamics.com/.

Contact

webb@wehi.edu.au
A novel, anatomy-similar in vitro model of 3D airway epithelial for anti-coronavirus drug discovery
Authors: Zhang Yaling , Ma Dingailu , Zhang David Jitao , Liu Xin’an , Zhu Qihui , Wang Li , Gao Lu
Published: March 2021

SARS-CoV-2 and its induced COVID-19 remains as a global health calamity. Severe symptoms and high mortality, caused by cytokine storm and acute respiratory distress syndrome in the lower respiratory airway, are always associated with elderly individuals and those with comorbidities; whereas mild or moderate COVID-19 patients have limited upper respiratory flu-like symptoms. There is an urgent need to investigate SARS-CoV-2 and other coronaviruses replication and immune responses in human respiratory systems. The human reconstituted airway epithelial air-liquid interface (ALI) models are the most physiologically relevant model for the investigation of coronavirus infection and virus-triggered innate immune signatures. We established ALI models representing both the upper and the lower respiratory airway to characterize the coronavirus infection kinetics, tissue pathophysiology, and innate immune signatures from upper and lower respiratory tract perspective. Our data suggested these in vitro ALI models maintain high physiological relevance with human airway tissues. The coronavirus induced immune response observed in these upper and lower respiratory airway models are similar to what has been reported in COVID-19 patients. The antiviral efficacy results of a few promising anti-coronavirus drugs in these models were consistent with previous reports and could be valuable for the human dose prediction. Taken together, our study demonstrates the importance of 3D airway epithelial ALI model for the understanding of coronavirus pathogenesis and the discovery and development of anti-coronavirus drugs.
Identification of a fully dechlorinated product of chlordecone in soil microcosms and enrichment cultures
Authors: Lomheim Line , Flick Robert , Rambinaising Suly , Gaspard Sarra , Edwards Elizabeth A.
Published: March 2021

Anaerobic microcosms constructed with soil from Guadeloupe, amended with electron donor (ethanol and acetone) and incubated for more than a decade, transformed chlordecone (CLD) into a suite of progressively more dechlorinated products, including a fully dechlorinated carboxylated indene product. This fully dechlorinated transformation product has never before been observed and indicates that complete dechlorination of CLD is possible. The carboxylated indene was detected by LC-MS and structure was confirmed by LC-MS/MS using a Q-Exactive Orbitrap mass spectrometer.
Laboratory Yeast Strains Rely On Oxidative Phosphorylation For Efficient ATP Production
Authors: Moharir Akshay , Gay Lincoln , Babst Markus
Published: March 2021

Even though it is a well-accepted fact that the energy metabolism of yeast is likely to impact all cellular activities, surprising little is known about the ATP homeostasis of particular yeast strains that are commonly used in cell biological studies. Therefore, we determined key parameters such as oxygen consumption and fermentation rates of the lab strain SEY6210. Our data indicated that even at high glucose concentrations, SEY6210 produces 30-50% of cellular ATP from oxidative phosphorylation. Loss of respiration, either by disrupting ATP synthase function or by growth in anaerobic conditions, was not fully compensated by fermentation and as a result affected energy intensive processes such as the maintenance of the plasma membrane proton gradient and the associated import of nutrients.