bluuebunny/crossref_metadata_2025 huggingface dataset:
How to present quality of life outcomes after focal therapy: using validated instruments and novel statistical methods
Authors: Clements Matthew B.
Published: February 2022

Purpose of review

To provide an up-to-date summary of widely used patient-reported measures for focal therapy quality of life outcomes and review contemporary analytic methods and recommendations for data visualization.

Recent findings

Measures such as pad-use, or preferably validated instruments such as the International Consultation on Incontinence Questionnaire, MSKCC Prostate Quality of Life Survey, or Expanded Prostate Cancer Index (EPIC) should be used for urinary function assessment. Sexual Function can be assessed with the International Index of Erectile Function or EPIC, but researchers must be careful to account for patients that are not currently sexually active when analyzing outcomes. Measurement of baseline function is crucial for a meaningful understanding of post-treatment outcomes. When multiple measurements are collected, longitudinal models such as generalized estimating equations or linear mixed effects models are preferred. Whenever possible, the data visualization should mirror the hypothesis testing for clarity of interpretation, and use of restricted cubic splines or generalized additive models are preferred to illustrate non-linear trajectories in quality of life after treatment.

Advances in both the measurement of patient quality of life with validated instruments and statistical methods have allowed for a more complete understanding and reporting of outcomes, which can be applied to the evaluation of focal therapy for prostate cancer.
Health Care Experiences During Pregnancy and Parenting with an Opioid Use Disorder
Authors: Kim Jane , Busse Morgan , Kantrowitz-Gordon Ira , Altman Molly R.
Published: February 2022

Purpose:

The purpose of this study was to describe the experience of individuals with opioid use disorder (OUD) during the perinatal period.

Study Design and Methods:

We convened focus groups of patients with OUD who had been pregnant and were parenting. Participants who were 18 and older, English-speaking, self-identified as pregnant or parenting, and actively using opioids or in recovery from OUD were recruited using snowball and convenience sampling in resident treatment facilities and outpatient settings. Data were recorded, transcribed, and analyzed for themes.

Results:

Twenty-four participants were recruited, 10 of whom were actively receiving residential recovery services. Most participants had been pregnant from 4 weeks to 2 years prior to our focus group session; none reported being currently pregnant. Nineteen participants had custody of some, or all, of their children. They identified four key themes related to their care: (1) disrespectful care, (2) fear of accessing services, (3) inconsistencies in care received, and (4) limited health and social services.

Clinical Implications:

Participants reported overall negative interactions across different health care settings and lack of social resources to promote ongoing recovery and successful parenting. Nurses should be aware of the lasting impressions they have on their patients. Recognition of their own biases, person-first language, and partnership building skills with patients can help attenuate OUD stigma, promote positive nurse–patient relationships, and support new parents in recovery and infant bonding.
Use of Insoluble Dietary Fiber and Probiotics for Bowel Preparation Before Colonoscopy: A Prospective Study
Authors: Kudou Kensuke , Kimura Koich , Tsutsumi Ryosuke , Hashimoto Naotaka , Wada Hiroya , Ikeda Tetsuo
Published: February 2022

Background:

In screening colonoscopy, patients usually have to ingest large amounts of bowel-cleansing agents, including polyethylene glycol (PEG). This is difficult and has various side effects; thus, patients avoid undergoing a colonoscopy. We tested a novel bowel preparation method before colonoscopy using insoluble dietary fiber and probiotics (PB).

Methods:

This was a prospective clinical study conducted between October 2018 and March 2019 at a general hospital. Forty participants were randomly assigned to low-volume PEG solution diet (MoviPrep), wheat bran fiber (WBF) and probiotic Bifidobacterium animalis subsp. lactis GCL2505 (PB GCL2505), or standard-volume regimen (1.0 to 1.5 L of MoviPrep) (control group). The patient compliance and the quality of bowel preparation were evaluated.

Results:

Forty individuals aged 38 to 83 years were randomly assigned to the WBF with PB (n=20) and control (n=20) groups. All participants underwent bowel preparation before colonoscopy according to each protocol. The mean required volume of MoviPrep was significantly lower in the WBF with PB group than in the control group (582.5 vs. 1305 mL, P<0.0001). Successful bowel-cleansing rates were not significantly different between the 2 groups; however, the ratio of the Harefield Cleansing Scale grades C and D was significantly lower in the WBF with PB group than in the control group (P=0.0471).

Conclusions:

The intake of WBF and GCL2505 before colonoscopy reduces the required PEG quantities while maintaining bowel-cleansing quality. This novel, minimally invasive pretreatment method makes colonoscopy more accessible contributing to the prevention and early treatment of colorectal cancer.
Dominant remodelling of cattle rumen microbiome by Schedonorus arundinaceus (tall fescue) KY-31 carrying a fungal endophyte
Authors: Khairunisa Bela Haifa , Susanti Dwi , Loganathan Usha , Teutsch Christopher D. , Campbell Brian T. , Fiske David , Wilkinson Carol A. , Aylward Frank O. , Mukhopadhyay Biswarup
Published: February 2022

Tall fescue KY-31 is an important primary forage for beef cattle. It carries a fungal endophyte that produces ergovaline, the main cause of tall fescue toxicosis that leads to major revenue loss for livestock producers. The MaxQ, an engineered cultivar, hosts an ergovaline nonproducing strain of the fungus and consequently is nontoxic. However, it is less attractive economically. It is not known how rumen microbiome processes these two forages towards nutrient generation and ergovaline transformation. We have analysed the rumen microbiome compositions of cattle that grazed MaxQ with an intervening KY-31 grazing period using the 16S rRNA-V4 element as an identifier and found that KY-31 remodelled the microbiome substantially, encompassing both cellulolytic and saccharolytic functions. The effect was not evident at the whole microbiome levels but was identified by analysing the sessile and planktonic fractions separately. A move from MaxQ to KY-31 lowered the Firmicutes abundance in the sessile fraction and increased it in planktonic part and caused an opposite effect for Bacteroidetes, although the total abundances of these dominant rumen organisms remained unchanged. The abundances of

Fibrobacter

, which degrades less degradable fibres, and certain cellulolytic Firmicutes such as

Pseudobutyrivibrio

and

Butyrivibrio

2, dropped in the sessile fraction, and these losses were apparently compensated by increased occurrences of

Eubacterium

and specific

Ruminococcaceae

and

Lachnospiraceae

. A return to MaxQ restored the original Firmicutes and Bacteroidetes distributions. However, several KY-31 induced changes, such as the low abundance of

Fibrobacter

and

Butyrivibrio

two remained in place, and their substitutes maintained significant presence. The rumen microbiome was distinct from previously reported faecal microbiomes. In summary, KY-31 and MaxQ were digested in the cattle rumen with distinct consortia and the KY-31-specific features were dominant. The study also identified candidate ergovaline transforming bacteria. It highlighted the importance of analysing sessile and planktonic fractions separately.
EXPERIMENTAL INVESTIGATION OF PULSE STERILIZATION OF VIRAL INFECTION
Authors: Chumakov Volodymyr , Ostryzhnyi Mykhailo , Kharchenko Oksana , Naumenko Krystina , Zagorodnya Svitlana , Muraveinyk Vasiliy , Tarasevich Aleksandr
Published: February 2022

The results of experimental investigations of the effect of high-intensity pulsed UV radiation on the influenza virus type A (H1N1) are presented. The research methodology is developed and the structure of the experiments is described. An end-face plasma accelerator was used as a radiation source, which provides a power pulsed discharge in an open atmosphere. The high efficiency of inactivation of the infectiousness of the virus was shown within a short period of time. The possibility of providing urgent 100% sterilization of a viral infection has been shown for the first time. A model for calculating the efficiency of pulse sterilization has been developed. The prospects for the application of pulse sterilization technology to combat coronavirus infection are considered.
Performance of polygenic risk scores in screening, prediction, and risk stratification
Authors: Hingorani AD. , Gratton J. , Finan C. , Schmidt AF. , Patel R. , Sofat R. , Kuan V. , Langenberg C. , Hemingway H. , Morris JK. , Wald NJ.
Published: February 2022

Background

The clinical value of polygenic risk scores has been questioned. We sought to clarify performance in population screening, individual risk prediction and population risk stratification by analysing 926 polygenic risk scores for 310 diseases from the Polygenic Score (PGS) Catalog.

Methods

Polygenic risk scores in the PGS Catalog are reported using hazard ratios or odds ratios per standard deviation, or the area under the receiver operating characteristic curve sometimes expressed as theC-index. We used this information to produce estimates of performance in: (a)population screening— by calculating the detection rate (DR5) for a 5% false positive rate (FPR) and the population odds of becoming affected given a positive result (OAPR); (b)individual risk prediction— by calculating the individual odds of becoming affected for a person with a particular polygenic score; and (c)population risk stratification— by calculating the odds of becoming affected for groups of individuals in different portions of a polygenic risk score distribution. We use coronary artery disease and breast cancer as illustrative examples.

Findings

Population screening performance: The medianDR5for all polygenic risk scores and all diseases studied was 11% [interquartile range 8 − 18%]. The medianDR5was 12% [9 − 19] for polygenic risk scores for CAD and 10% [9 − 12] for breast cancer, with populationOAPRsof 1:8 and 1: 21 respectively, with background 10-year odds of 1:19 and 1:41 respectively, which are typical for these diseases at age 50.Individual risk prediction: The corresponding 10-year odds of becoming affected for individuals aged 50 with a polygenic risk score at the 2.5th, 25th, 75thand 97.5thcentile were 1:54, 1:29, 1:15, and 1:8 for CAD and 1:91, 1:56, 1:34, and 1:21 for breast cancer.Population risk stratification: At age 50, stratifying into quintile groups of CAD risk yielded 10-year odds of 1: 41 and 1: 11 for the lowest and highest quintile groups respectively. The 10-year odds was 1: 7 for the upper 2.5% of the polygenic risk score distribution for CAD, a group that contributed 7% of cases. The corresponding estimates for breast cancer were 1: 72 and 1: 26 for lowest and highest quintiles; and 1:19 for the upper 2.5% of the distribution, which contributed 6% of cases.

Interpretation

Polygenic risk scores perform poorly in population screening, individual risk prediction, and population risk stratification.

Funding

British Heart Foundation; UK Research and Innovation; National Institute of Health and Care Research.
A Multi-Component Telehealth Intervention to Improve Oncofertility Care Delivery among Young Cancer Patients: A Pilot Study
Authors: Yang Emily , Dornisch Anna , Nerb Laura , Helsten Teresa , Kaiser Bonnie N. , Aristizabal Paula , Armenian Saro , Torno Lilibeth L. , Baca Nicole M. , Genensen Mark C. , Su H. Irene , Romero Sally A. D.
Published: February 2022

Purpose

Oncofertility care for pediatric, adolescent, and young adult cancer patients remains under-implemented across adult and pediatric oncology settings. We pilot tested an electronic health record (EHR)-enabled multi-component oncofertility intervention (including screening, referral, and fertility consult) in an adult academic oncology program and systematically assessed intervention fit to pediatric and community oncology programs.

Methods

Using surveys (n=33), audits (n=143), and interviews (n=21) guided by implementation science frameworks, we pilot tested the EHR-enabled intervention for oncofertility care in young cancer patients at an adult oncology program and evaluated implementation outcomes. We interviewed healthcare providers from seven regional oncology and fertility programs about intervention fit to their clinical contexts.

Results

We recruited 33 healthcare providers from an adult oncology setting and 15 healthcare providers from seven additional oncology and fertility settings. At the adult oncology setting, the intervention was found to be appropriate, acceptable, and feasible and improved the screening of fertility needs (from 30% pre- to 51% post-intervention), yet some patients did not receive appropriate referrals to fertility consults. Providers across all settings suggested content and context modifications, such as adding options to the intervention or allowing the screening component to pop up at a second visit, to improve and adapt the intervention to better fit their clinical care contexts.

Conclusions

We found that the EHR-enabled intervention increased the rate of goal-concordant oncofertility care delivery at an adult oncology program. We also identified facilitators, barriers, and needed adaptations to the intervention required for implementation and scaling up across diverse oncology settings.
Avoiding false positive SARS-CoV-2 rapid antigen test results with point-of-care molecular testing on residual test buffer
Authors: LeBlanc Jason J , McCracken Gregory R. , Goodall Barbara , Hatchette Todd F , Barrett Lisa , Ross John , Davidson Ross J , Patriquin Glenn
Published: February 2022

Objectives

Antigen-based rapid diagnostic tests (Ag-RDTs) have been widely used for the detection of SARS-CoV-2 during the Covid-19 pandemic. In settings of low disease prevalence, such as asymptomatic community testing, national guidelines recommend molecular confirmation of positive Ag-RDT results. This often requires patients to be recalled for repeat specimen recollection and subsequent testing in reference laboratories. This project assessed the use of a point-of-care molecular method for SARS-CoV-2 detection on-site at a volunteer-led asymptomatic community testing site, using the residual test buffer (RTB) from positive Ag-RDTs.

Methods

The Abbott COVID-19 ID NOW assay was performed on RTB from two Ag-RDTs: the Abbott Panbio COVID-19 Ag Rapid Test Device and the BTNX Rapid Response COVID-19 Antigen Rapid Test Device. All RTBs were tested using real-time RT-PCR at a reference laboratory using the ThermoFisher TaqPath COVID-19 Combo kit which was used to assign positive Ag-RDTs results as true or false positives. Analytical specificity of the ID NOW was assessed with a panel of various respiratory organisms.

Results

Of 419 positive Ag-RDTs from 5148 tests performed, ID NOW testing of the RTB was positive in 100% of the samples characterized as true positives by RT-PCR. No SARS-CoV-2 detections by ID NOW were observed from 10 specimens characterized as false positive Ag-RDTs, or from contrived specimens with various respiratory organisms.

Conclusions

The use of on-site molecular testing on RTB provides a suitable option for rapid confirmatory testing of positive Ag-RDTs, thereby obviating the need for specimen recollection for molecular testing at local reference laboratories.
Omicron and Alpha P680H block SARS-CoV2 spike protein from accessing cholinergic inflammatory pathway via α9-nAChR mitigating the risk of MIS-C
Authors: Santiago Ulises , Camacho Carlos J.
Published: February 2022

Sequence homology between neurotoxins and the site encompassing the furin cleavage site 680SPRRAR685 in the spike protein (S) of CoV2 suggested that this site could interact with nicotinic acetylcholine receptors (nAChRs). Molecular dynamics simulations confirm robust structural similarity between wild-type (WT) CoV2 and the binding motif of α-conotoxin to α9 nAChR, which is known to modulate IL-1β in immune cells. We show that the structural integrity of this binding motif is eliminated by Alpha P681H mutation, reemerged in Delta variant P681R, and disappeared again with Omicron N679H/P681H. Interactions between the toxin-mimic CoV2 motif and α9-nAChR are expected to trigger the release of pro-inflammatory cytokines an effect that is mollified by Alpha and Omicron. Clinical features of this interaction site are relevant because, contrary to most regions in the S protein, the furin binding site does not appear to trigger an immune response prior to cleavage, indicating that the cholinergic pathway should be activated in the respiratory tract and nasal mucosa where α9-nAChR co-localizes with the virus. The correlation of changes on this motif by the different variants closely matches the reported cases of Multisystem Inflammatory Syndrome in Children by the CDC, and predicts significant mitigation of MIS-C with the Omicron variant. Our findings strongly motivate further study of this cholinergic pathway as one source of the cytokine storm triggered by CoV2.
Biophysical fitness landscape of the SARS-CoV-2 Delta variant receptor binding domain
Authors: Patrick Casey , Upadhyay Vaibhav , Lucas Alexandra , Mallela Krishna M.G.
Published: February 2022

Among the five known SARS-CoV-2 variants of concern, Delta is the most virulent leading to severe symptoms and increased number of deaths. Our study seeks to examine how the biophysical parameters of the Delta variant correlate to the clinical observations. Receptor binding domain (RBD) is the first point of contact with the human host cells and is the immunodominant form of the spike protein. Delta variant RBD contains two novel mutations L452R and T478K. We examined the effect of single mutations as well as the double mutation on RBD expression in human Expi293 cells, RBD stability using urea and thermal denaturation, and RBD binding to angiotensin converting enzyme 2 (ACE2) receptor and to neutralizing antibodies using isothermal titration calorimetry. Delta variant RBD showed significantly higher expression compared to the wild-type RBD, and the increased expression is due to L452R mutation. Despite their non-conservative nature, none of the mutations significantly affected RBD structure and stability. All mutants showed similar binding affinity to ACE2 and to Class 1 antibodies (CC12.1 and LY-CoV016) as that of the wild-type. Delta double mutant L452R/T478K showed no binding to Class 2 antibodies (P2B-2F6 and LY-CoV555) and a hundred-fold weaker binding to a Class 3 antibody (REGN10987), and the decreased antibody binding is determined by the L452R mutation. These results indicate that the immune escape from neutralizing antibodies, rather than receptor binding, is the main biophysical parameter determining the fitness landscape of the Delta variant RBD and is determined by the L452R mutation.
Generalization in Sensorimotor Networks Configured with Natural Language Instructions
Authors: Riveland Reidar , Pouget Alexandre
Published: February 2022

Abstract

One of humans’ most fundamental cognitive feats is the ability to interpret linguistic instructions in order to perform novel tasks without any explicit experience with the task. Yet, the computations that the brain might use to accomplish such a feat remains poorly understood. Here we use the latest advances in Natural Language Processing to create a neural model of generalization based on linguistic instructions. Models are trained on a set of commonly studied psychophysical tasks, and receive instructions embedded by a pre-trained language model. Our best models can perform a previously unseen task with a performance of 83% correct on average based solely on linguistic instructions (i.e. 0-shot learning). We found that language scaffolds sensorimotor representations such that activity for interrelated tasks share a common geometry with the semantic representations of instructions, allowing language to cue the proper composition of practiced skills in unseen settings. Finally, we show how this model can generate a linguistic description of a novel task it has identified using only motor feedback, which can subsequently guide a partner model to perform the task. Our models offer several experimentally testable predictions outlining how linguistic information must be represented in order to facilitate flexible and general cognition in the human brain.
Neuromuscular embodiment of feedback control elements in Drosophila flight
Authors: Whitehead Samuel C. , Leone Sofia , Lindsay Theodore , Meiselman Matthew R. , Cowan Noah , Dickinson Michael , Yapici Nilay , Stern David L. , Shirangi Troy , Cohen Itai
Published: February 2022

While insects like Drosophila are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units—prominent components of the fly’s steering muscles system—modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.
Genetic Algorithm with Rank Selection optimises robust parameter estimation for systems biology models
Authors: Douilhet Gemma , Niranjan Mahesan , Vallejo Andres , Clayton Kalum , Davies James , Sirvent Sofia , Pople Jenny , Ardern-Jones Michael R , Polak Marta E
Published: February 2022

The ability to reliably predict and infer cellular responses to environmental exposures would offer a major advance in the investigation of immune regulation in health and disease. One possible approach is the use of in silico modelling. Design of such a mathematical kinetic model would be based on existing knowledge of a biological system and utilise a partial data set to parameterise. However, the process of parameter estimation, key for the accuracy of the model, is difficult to conduct by hand, and thus a computational alternative is necessary. We report the utility of Genetic Algorithm with Rank Selection (GARS) as a parameter estimation tool on multiple biological models, including heat shock, signal transduction via ERK, circadian rhythm and NFκB systems, where it showed strong accuracy and superiority to the Extended Kalman Filter method, Algebraic Difference Equations, and MATLAB fminsearch approaches. GARS parameter estimation is a valuable tool for biological data because it reliably infers system behaviour from partial data sets, allowing for the prediction of cellular responses to environmental exposures.
SOL3D: Soft-lithography on 3D vat polymerised moulds for fast, versatile, and accessible high-resolution fabrication of customised multiscale cell culture devices with complex designs
Authors: Hagemann Cathleen , Bailey Matthew C. D. , Carraro Eugenia , Lionello Valentina Maria , Khokhar Noreen , Suklai Pacharaporn , Moreno-Gonzalez Carmen , O’Toole Kelly , Konstantinou George , Joshi Sudeep , Giagnorio Eleonora , Bergholt Mads , Imbert Albane , Tedesco Francesco Saverio , Serio Andrea
Published: February 2022

Cell culture devices, such as microwells and microfluidic chips, are designed to increase the complexity of cell-based models whilst retaining control over culture conditions and have become indispensable platforms for biological systems modelling. From microtopography, microwells, plating devices and microfluidic systems to larger constructs for specific applications such as live imaging chamber slides, a wide variety of culture devices with different geometries have become indispensable in biology laboratories. However, while their application in biological projects is increasing exponentially, due to a combination of the techniques and tools required for their manufacture, and the physical science background sometimes needed, the design and fabrication of such devices directly by biological labs remains a relatively high investment in terms of costs, use of facilities, needed collaborations and time. Whilst commercially available systems are available, these are also often costly, and importantly lack the potential for customisation by each single lab. This combination of factors still limits widespread application of microfabricated custom devices in most biological wet labs.

Capitalising on recent important advancements in the fields of bioengineering and microfabrication, and taking advantage of low-cost, high-resolution desktop resin 3D printers combined with PDMS soft lithography, we have developed an optimised low-cost and highly reproducible microfabrication pipeline, capable of generating a wide variety of customisable devices for cell culture and tissue engineering in an easy, fast reproducible way for a fraction of the cost of conventional microfabrication or commercial alternatives. This protocol is designed specifically to be a resource for biological labs with little to none prior exposure to these fields technique and enables the manufacture of complex devices across the µm to cm scale.

We provide a ready-to-go pipeline for the efficient treatment of resin-based 3D printed constructs for PDMS curing, using a combination of curing steps, washes and surface treatments. Together with the extensive characterisation of the fabrication pipeline, we show the utilization of this system to a variety of applications and use cases relevant to biological experiments, ranging from micro topographies for cell alignments to complex multi-part hydrogel culturing systems.

This methodology can be easily adopted by any wet lab, irrespective of prior expertise or resource availability and will enable the wide adoption of tailored microfabricated devices across many fields of biology.
Spatiotemporal growth pattern during plant nutation implies fast dynamics for cell wall mechanics and chemistry: a multiscale study in Averrhoa carambola
Authors: Rivière Mathieu , Peaucelle Alexis , Derr Julien , Douady Stéphane
Published: February 2022

Nutation is the most striking and ubiquitous example of the rhythmic nature of plant development. Although there is a consensus that this wide oscillatory motion is driven by growth, its internal mechanisms have not been fully elucidated yet. In this work, we study the specific case of nutation in compound leaves in the archetypal Averrhoa carambola plant. We quantify the macroscopic growth kinematics with time lapse imaging, image analysis and kinematics modeling. We further characterize the mechanical and chemical properties of the cell wall with atomic force microscopy and immunolabelling. Our data first reveal that the differential growth driving nutation is localized and peaks where the average growth drops. We then show this specific spatiotemporal growth profile is compatible with local contraction events. At the cell wall level, differential growth is further colocalized with an asymmetry of the cell wall elastic modulus, and with an asymmetric distribution of homogalacturonans (HG). Our results not only back up the hypothesis of HG being involved in plant growth, but also build up on it by suggesting a dynamic nature for this process.

Significance Statement

Nutation is an oscillatory motion displayed by many organs of growing plants. Most works on nutation focus on its relation to external stimuli attempting to explain its origins. By contrast, its internal physiological mechanisms remain to be fully explored. Here we propose an experimental and multiscale characterization of undisturbed nutation. We determine the macroscopic growth profile and show it is compatible with cell expansion but also local contractions in the tissues. At the microscopic level, we reveal that both the rigidity and composition of the cell wall are asymmetrically distributed where nutation occurs. The combination of results on both scales brings contributions to the understanding of interplay between global movement, local growth, cell wall mechanics and cell wall biochemistry.
A SARS-CoV-2 peptide vaccine which elicits T-cell responses in mice but does not protect against infection or disease
Authors: Baxter Victoria K. , Anderson Elizabeth J. , Taft-Benz Sharon A. , Olsen Kelly , Sambade Maria , Gentry Kaylee M. , Beck Wolfgang , Garness Jason , Woods Allison , Fini Misha , Carpenter Brandon , Smith Christof C. , Heise Mark T. , Vincent Benjamin , Rubinsteyn Alex
Published: February 2022

We vaccinated BALB/c mice with peptides derived from the SARS-CoV-2 proteome selectedin silicoto elicit T-cell responses and/or B-cell responses against linear epitopes. These peptides were administered in combination with either of two adjuvants, poly(I:C) and the STING agonist BI-1387466. Antibody responses against predicted linear epitopes were not observed but both adjuvants consistently elicited T-cell responses to the same peptides, which were primarily from the set chosen for predicted T-cell immunogenicity. The magnitude of T-cell responses was significantly higher with BI-1387466 compared with poly(I:C). Neither adjuvant group, however, provided any protection against infection with the murine adapted virus SARS-CoV-2-MA10 or from disease following infection. In light of more recent evidence for protection from severe disease mediated by CD8+ T-cells, we suspect that the epitopes selected for vaccination were not presented by infected murine cells.
Single-cell analysis reveals the range of transcriptional states of circulating human neutrophils
Authors: Wigerblad Gustaf , Cao Qilin , Brooks Stephen , Naz Faiza , Gadkari Manasi , Jiang Kan , Gupta Sarthak , O’Neil Liam , Dell’Orso Stefania , Kaplan Mariana J. , Franco Luis M.
Published: February 2022

Neutrophils are the most abundant leukocytes in human blood and are essential components of innate immunity. Until recently, neutrophils were considered homogeneous and transcriptionally inactive cells, but both concepts are being challenged. To date, neutrophils have been characterized based on discrete parameters including cell-surface markers, buoyancy, maturation status, or tissue localization. Single-cell RNA sequencing (scRNA-seq) offers an unbiased view of cells along a continuum of transcriptional states. However, the use of scRNA-seq to characterize neutrophils has proven technically difficult, explaining in part the paucity of published single-cell data on neutrophils. We have found that modifications to the data analysis pipeline, rather than to the existing scRNA-seq chemistries, can significantly increase the detection of human neutrophils in scRNA-seq. We have then applied a modified pipeline to the study of human peripheral blood neutrophils. Our findings indicate that circulating human neutrophils are transcriptionally heterogeneous cells, which can be classified into one of four transcriptional clusters that are reproducible among healthy human subjects. We demonstrate that peripheral blood neutrophils shift from relatively immature (Nh0) cells, through a transitional phenotype (Nh1), into one of two endpoints defined by either relative transcriptional inactivity (Nh2) or high expression of type I interferon-inducible genes (Nh3). Transitions among states are characterized by the expression of specific transcription factors. By simultaneously measuring surface proteins and intracellular transcripts at the single-cell level, we show that these transcriptional subsets are independent of the canonical surface proteins that are commonly used to define and characterize human neutrophils. These findings provide a new view of human neutrophil heterogeneity, with potential implications for the characterization of neutrophils in health and disease.
Novel and Reported Compensatory Mutations in rpoABC Associate Specifically with Predominant Mycobacterium tuberculosis Rifampicin Resistance Marker rpoB:S450L
Authors: Conkle-Gutierrez D , Ramirez-Busby SM , Gorman BM , Elghraoui A , Hoffner S , Elmaraachli W , Valafar F
Published: February 2022

Background

Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a pulmonary disease caused by Mycobacterium tuberculosis. However antibiotic resistance to RIF is prevalent despite an apparent fitness cost. RIF resistance is primarily caused by mutations in the RIF resistance determining region in the rpoB gene, at the cost of slower growth in rich media. Compensatory mutations in the genes rpoA and rpoC have been shown to alleviate this fitness cost. These compensatory mutations may explain how RIF resistant strains have spread so rapidly. However, the effect of compensation on transmission is still unclear, partly because of uncertainty over which rpoABC mutations compensate for which RIF resistance markers.

Objectives

We performed an association study on a globally representative set of 4309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations.

Results and Conclusions

Only 20.0% (216/1079) of RIF resistant isolates carried previously reported high-probability compensatory mutations, suggesting existence of other compensatory mutations. Using a strict phylogenetic approach, we identified 18 novel putative compensatory mutations in rpoC, rpoB, and rpoA. Novel and previously reported compensatory mutations were strongly associated with the RIFR marker rpoB:S450L, suggesting compensation may be specific to particular RIFR markers. These findings will aid identification of RIF-resistant M. tuberculosis strains with restored fitness. Such strains pose a greater risk of causing resistant outbreaks.
Trunk neural crest migratory position and asymmetric division predict terminal differentiation
Authors: Alhashem Zain , Camargo-Sosa Karen , Kelsh Robert N , Linker Claudia
Published: February 2022

The generation of complex structures during embryogenesis requires the controlled migration and differentiation of cells from distant origins. How migration and differentiation are coordinated and impact each other to form functional structures is not fully understood. Neural crest cells migrate extensively giving rise to many cell types. In the trunk, neural crest migrate collectively forming chains comprised of cells with distinct migratory identities: one leader cell at the front of the group directs migration, while followers track the leader forming the body of the chain. Herein we analysed the relationship between trunk neural crest migratory identity and terminal differentiation. We found that trunk neural crest migration and fate allocation is coherent. Leader cells that initiate movement give rise to the most distal derivativities. Interestingly, the asymmetric division of leaders separates migratory identity and fate. The distal daughter cell retains the leader identity and clonally forms the Sympathetic Ganglia. The proximal sibling migrates as a follower and gives rise to Schwann cells. The sympathetic neuron transcription factor phox2bb is strongly expressed by leaders from early stages of migration, suggesting that specification and migration occur concomitantly and in coordination. Followers divide symmetrically and their fate correlates with their position in the chain.
PERK Signaling Promotes Mitochondrial Elongation By Remodeling Membrane Phosphatidic Acid
Authors: Perea Valerie , Cole Christian , Lebeau Justine , Dolina Vivian , Baron Kelsey R. , Madhavan Aparajita , Kelly Jeffery W. , Grotjahn Danielle A. , Wiseman R. Luke
Published: February 2022

Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are linked in the onset and pathogenesis of numerous diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria during ER stress. The PERK signaling arm of the unfolded protein response (UPR) has emerged as a prominent ER stress-responsive signaling pathway that regulates diverse aspects of mitochondrial biology. Here, we show that PERK activity also promotes adaptive remodeling of mitochondrial membrane phosphatidic acid (PA) to induce protective mitochondrial elongation during ER stress. We find that PERK activity is required for ER stress-dependent increases in both cellular PA and YME1L-dependent degradation of the intramitochondrial PA transporter PRELID1. Together, these processes lead to the accumulation of PA on the outer mitochondrial membrane where it induces mitochondrial elongation by inhibiting mitochondrial fission. Our results establish a new role for PERK in the adaptive remodeling of mitochondrial phospholipids and demonstrate that PERK-dependent PA regulation functions to adapt organellar shape in response to ER stress.
Functional stemness-related genes revealed by single-cell profiling of naïve and stimulated human CD34+ cells from CB and mPB
Authors: Dong Guoyi , Xu Xiaojing , Li Yue , Ouyang Wenjie , Zhao Weihua , Gu Ying , Li Jie , Liu Tianbin , Zeng Xinru , Zou Huilin , Wang Shuguang , Liu Sixi , Sun Hai-Xi , Liu Chao
Published: February 2022

Hematopoietic stem cells (HSCs) from different sources show varied repopulating capacity, and HSCs lose their stemness after long-time ex vivo culture. However, the underlying mechanisms of the stemness differences because of the cell sources and the culture stimulation are not fully understood. Here, we applied single-cell RNA-seq (scRNA-seq) to analyze the naïve and stimulated human CD34+ cells from cord blood (CB) and mobilized peripheral blood (mPB). We collected over 16,000 single-cell data to construct a comprehensive trajectory inference map and characterized the HSCs population on the hierarchy top, which is under quiescent state. Then we compared HSCs in CB to those in mPB and HSCs of naïve samples to those of cultured samples, and identified stemness-related genes (SRGs) associated with culture time (CT-SRGs) and cell source (CS-SRGs), respectively. Interestingly, CT-SRGs and CS-SRGs share genes enriched in the signaling pathways such as mRNA catabolic process, Translational initiation, Ribonucleoprotein complex biogenesis and Cotranslational protein targeting to membrane, suggesting dynamic protein translation and processing may be a common requirement for stemness maintenance. Meanwhile, CT-SRGs are enriched in pathways involved in glucocorticoid and corticosteroid response that affect HSCs homing and engraftment. In contrast, CS-SRGs specifically contain genes related purine and ATP metabolic process which is important to initiate hematopoiesis. Finally, we presented an application through a small-scale drug screening using Connectivity Map (CMap) against CT-SRGs and found a small molecule cucurbitacin I, targeting STAT3/JAK2, can efficiently expand HSCs ex vivo while maintaining its stemness. These results indicate SRGs revealed by scRNA-seq can provide helpful insights to understand the stemness differences under diverse circumstances, and CT-SRGs can be a valuable database to identify candidates enhancing functional HSCs expansion during ex vivo culture.
Maternal and/or direct supplementation with a combination of a casein hydrolysate and yeast β-glucan on post-weaning performance and intestinal health in the pig
Authors: Conway Eadaoin , O’Doherty John V. , Mukhopadhya Anindya , Dowley Alison , Vigors Stafford , Maher Shane , Ryan Marion T. , Sweeney Torres
Published: February 2022

A 2 × 2 factorial experiment was conducted to investigate the effect of maternal supplementation from day 83 of gestation and/or direct supplementation from weaning of a bovine casein hydrolysate plus a yeast β-glucan (CH-YBG) on pig performance and intestinal health on day ten post-weaning. Twenty cross bred gilts (Large White × Landrace) were randomly assigned to one of two dietary groups (n = 10 gilts/group): basal diet (basal sows) and basal diet supplemented with CH-YBG (supplemented sows) from day 83 of gestation until weaning (2g/sow/day). At weaning, 120 pigs (6 pigs/sow) were selected. The two dam groups were further divided, resulting in four experimental groups (10 replicates/group; 3 pigs/pen) as follows: 1) BB (basal sows + basal pigs); 2) BS (basal sows + supplemented pigs); 3) SB (supplemented sows + basal pigs); 4) SS (supplemented sows + supplemented pigs). Supplemented pigs were offered 0.5g CH-YBG/kg of feed for 10 days post-weaning. On day 10 post-weaning, 1 pig/pen was humanely sacrificed and samples were taken from the gastrointestinal tract for analysis. Pigs weaned from supplemented sows (SS, SB) had reduced faecal scores and incidence of diarrhoea (P<0.05) compared to pigs weaned from basal sows (BB, BS), with SS pigs not displaying the transient rise in faecal scores seen in the other three groups from day 3 to day 10 post-weaning (P<0.05). Pigs weaned from supplemented sows had reduced feed intake (P<0.05), improved feed efficiency (P<0.05), increased butyrate concentrations (P<0.05), increased abundance of Lactobacillus (P<0.05) and decreased abundance of Enterobacteriaceae and Campylobacteraceae (P<0.05) compared to pigs weaned from basal sows. In conclusion, a combination of both maternal and direct supplementation with CH-YBG is the desirable feeding strategy to ameliorate the post-weaning challenge in pig production systems.
Coursing hyenas and stalking lions: the potential for inter- and intraspecific interactions
Authors: Barker Nancy A. , Joubert Francois G. , Kasaona Marthin , Shatumbu Gabriel , Stowbunenko Vincent , Alexander Kathleen A. , Slotow Rob , Getz Wayne M.
Published: February 2022

Resource partitioning promotes coexistence among guild members, and carnivores reduce interference competition through behavioural mechanisms that promote spatio-temporal separation. We analyzed sympatric lion and spotted hyena movements and activity patterns to ascertain the mechanisms facilitating their coexistence within semi-arid and wetland ecosystems. We identified recurrent high-use (revisitation) and extended stay (duration) areas within home ranges, and correlated environmental variables with movement-derived measures of inter- and intraspecific interactions. Spatial overlaps among lions and hyenas occurred at edges of home ranges, around water-points, along pathways between patches of high-use areas, and expanded during the wet season. Lions shared more of their home ranges with spotted hyenas in arid ecosystems, but shared more of their ranges with conspecifics in mesic environments. Despite shared space use, we found evidence for subtle temporal differences in the nocturnal movement and activity patterns between the two predators, suggesting a fine localized-scale avoidance strategy. Revisitation frequency and duration within home ranges were influenced by interspecific interactions, subsequent to land cover categories and diel cycles. Intraspecific interactions were also important for lions and, for hyenas, moon illumination and ungulates attracted to former anthrax carcass sites in Etosha, with distance to water in Chobe/Linyanti. Recursion and duration according to locales of competitor probabilities were similar among female lions and both sexes of hyenas, but different for male lions. Our results suggest that lions and spotted hyenas mediate the potential for interference competition through subtle differences in temporal activity, fine-scale habitat use differentiation, and localized reactive-avoidance behaviours. These findings enhance our understanding of the potential effects of interspecific interactions among large carnivore space-use patterns within an apex predator system, and show adaptability across heterogeneous and homogeneous environments. Future conservation plans should emphasize the importance of inter- and intraspecific competition within large carnivore communities, particularly moderating such effects within increasingly fragmented landscapes.
Quantifying the phenotypic information in mRNA abundance
Authors: Maltz Evan , Wollman Roy
Published: February 2022

Quantifying the dependency between mRNA abundance and downstream cellular phenotypes is a fundamental open problem in biology. Advances in multimodal single cell measurement technologies provide an opportunity to apply new computational frameworks to dissect the contribution of individual genes and gene combinations to a given phenotype. Using an information theory approach, we analyzed multimodal data of the expression of 83 genes in the Ca2+signaling network and the dynamic Ca2+response in the same cell. We found that the overall expression levels of these 83 genes explain approximately 60% of Ca2+signal entropy. The average contribution of each single gene was 16%, revealing a large degree of redundancy between genes. Using different heuristics we estimated the dependency between the size of a gene set and its information content, revealing that on average a set of 53 genes contains 90% of the information about Ca2+signaling within the cellular transcriptional state. Our results provide the first direct quantification of information content about complex cellular phenotype that exists in mRNA abundance measurements.
Complex effects of chytrid parasites on the growth of the cyanobacteriumPlanktothrix rubescensacross interacting temperature and light gradients
Authors: Wierenga Joren , Thomas Mridul K. , Ranjan Ravi , Ibelings Bas W.
Published: February 2022

Chytrids are important drivers of aquatic ecosystems as phytoplankton parasites. The interaction between these parasites and their hosts are shaped by abiotic factors such as temperature and light. Here, we performed a full-factorial experiment to study how temperature and light interact to affect the dynamics of the bloom-forming toxic cyanobacteriumPlanktothrix rubescensand its chytrid parasite. We used a dynamic host-parasite model to explore how temperature and light affect long term dynamics. At low temperatures, chytrids do not survive. Higher light and temperature levels stimulated both phytoplankton and chytrid growth, with complex effects on their dynamics. Model exploration indicates that increasing temperature and light shifts equilibrium outcomes fromP. rubescenspersisting alone to stable coexistence and then to limit cycles. This provides an alternative biological explanation for whyP. rubescensis mainly found in the relatively cold and dark lake metalimnion – it may enable avoidance of its parasite. Our study emphasizes the importance of investigating how abiotic factors interact with biotic interactions to drive complex outcomes.