bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical network motifs can transduce and process oscillatory information
Authors: Reja Jamil , Fallon Tess K. , Leader Andrew M. , Azeloglu Evren U.
Published: December 2022

Biological networks that are formed through amalgamation of signaling pathways include recurrent configurations called network motifs. These statistically over-represented subgraphs are often formed through interconnected enzyme-substrate relationships that are known to result in highly dynamic downstream behavior, including oscillatory output. Such signals are abundant in biology: heartbeats, circadian rhythms, and cell cycles all exhibit characteristic frequencies. Though there has been great emphasis on how oscillations can be generated through network dynamics, little is known about oscillatory information processing or transduction capacity of network motifs. We employ ordinary differential equations-based dynamical modeling to understand how different network topologies impact oscillatory signal propagation through a multi-enzyme network. We model enzyme-substrate interactions of 20 commonly observed motifs using Michaelis-Menten kinetics. We then perform deterministic Monte Carlo simulations using a range of biologically relevant enzymatic parameters and input frequencies. From these simulations, we quantify signal propagation characteristics using cluster analysis, categorize different motif responses based on output characteristics, and identify potential mechanisms for oscillatory signal processing using parameter sensitivity analysis. We see that the input-output responses depend on network topology and enzyme kinetic parameters. Enzymatic motifs show median oscillatory suppression of 30-135 decibels, with three-node coherent feedforward loops showing the lowest propensity for oscillatory signal suppression. Motifs that contained negative feedback or four-node coherent feedforward loops had the biggest potential to act as AC-to-DC converters, translating oscillatory input signals into transient impulses or sustained continuous outputs, respectively. We conclude that enzyme networks can process and decode information within oscillatory inputs in a frequency- and network-dependent manner.
Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea
Authors: Koch Nicolás Mongiardino , Tilic Ekin , Miller Allison K. , Stiller Josefin , Rouse Greg W.
Published: December 2022

Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest trenches. Their reduced skeletons and limited number of phylogenetically-informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with twelve novel transcriptomes. Using a highly-curated dataset of 1,100 orthologues, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support, and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores, and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favor one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories.
Integrating defense and leaf economic spectrum traits in a tropical savanna plant
Authors: Mohanbabu Neha , Veldhuis Michiel P. , Jung Dana , Ritchie Mark E
Published: December 2022

Allocation to plant defense traits likely depends on resource supply, herbivory, and other plant functional traits such as the leaf economic spectrum (LES) traits. Yet, attempts to integrate defense and resource acquisitive traits remains elusive.

We assessed intraspecific correlations between different defense and LES traits in a widely distributed tropical savanna herb,Solanum incanum, a unique model species for studying allocations to physical, chemical, and structural defenses to mammalian herbivory.

In a multivariate trait space, the structural defenses - lignin and cellulose - were positively related to the resource conservative traits - low SLA and low leaf N. Phenolic content, a chemical defense, was positively associated with resource acquisitive traits - high SLA and high leaf N - while also being associated with an independent third component axis. Both principal components 1 and 3 were not associated with resource supply and herbivory intensity. In contrast, spine density - a physical defense - was orthogonal to the LES axis and positively associated with soil P and herbivory intensity.

Synthesis: These results suggest a hypothesized “pyramid” of trade-offs in allocation to defense along the LES and herbivory intensity axes. Therefore, future attempts to integrate defense traits with the broader plant functional trait framework needs a multifaceted approach that accounts for unique influences of resource acquisitive traits and herbivory intensity.
The Structural Layers of the Porcine Iris Exhibit Inherently Different Biomechanical Properties
Authors: Tan Royston K. Y. , Panda Satish K. , Braeu Fabian A. , Muralidharan Arumugam R. , Nongpiur Monisha E. , Chan Anita S. Y. , Aung Tin , Najjar Raymond P. , Girard Michaël J.A.
Published: December 2022

Purpose

To isolate the structural components of theex vivoporcine iris tissue and to determine their biomechanical properties.

Methods

The porcine stroma and dilator tissues were separated, and their dimensions were assessed using optical coherence tomography (OCT). The stroma underwent flow test (n= 32) to evaluate for permeability using Darcy’s Law (ΔP= 2000 Pa,A= 0.0391 mm2), and both tissues underwent stress relaxation experiments (ε = 0.5 with initial ramp of δε = 0.1) to evaluate for their viscoelastic behaviours (n= 28). Viscoelasticity was characterised by the parametersβ(half width of the Gaussian distribution), τm(mean relaxation time constant),E0(instantaneous modulus) andE∞(equilibrium modulus).

Results

For the stroma, the hydraulic permeability was 9.49 ± 3.05 × 10-6mm2/Pa·s, and the viscoelastic parameters wereβ= 2.50 ± 1.40, and τm= 7.43 ± 4.96 s, with the two moduli calculated to beE0= 14.14 ± 6.44 kPa andE∞= 6.08 ± 2.74 kPa. For the dilator tissue, the viscoelastic parameters wereβ= 2.06 ± 1.33 and τm= 1.28 ± 1.27 s, with the two moduli calculated to beE0= 9.16 ± 3.03 kPa andE∞= 5.54 ± 1.98 kPa.

Conclusion

We have established a new protocol to evaluate the biomechanical properties of the structural layers of the iris. Overall, the stroma was permeable and exhibited smaller moduli than those of the dilator muscle. An improved characterisation of iris biomechanics may form the basis to further our understanding of angle closure glaucoma.
BCG vaccination of healthcare workers does not reduce SARS-CoV-2 infections nor infection severity or duration: a randomised placebo-controlled trial
Authors: Claus Juana , Doesschate Thijs ten , Gumbs Cheyenne , van Werkhoven Cornelis H. , van der Vaart Thomas W. , Janssen Axel B. , Smits Gaby , van Binnendijk Rob , van der Klis Fiona , van Baarle Debbie , Paganelli Fernanda L. , Leavis Helen , Verhagen Lilly M. , Joosten Simone A. , Bonten Marc J.M. , Netea Mihai G. , van de Wijgert Janneke H. H. M.
Published: December 2022

Background

Bacillus Calmette-Guerin (BCG) vaccination has been hypothesised to reduce SARS-CoV-2 infection, severity, and/or duration via trained immunity induction.

Methods

Healthcare workers (HCWs) in 9 Dutch hospitals were randomised to BCG or placebo vaccination (1:1) in March/April 2020 and followed for one year. They reported daily symptoms, SARS-CoV-2 test results, and healthcare-seeking behaviour via a smartphone application, and donated blood for SARS-CoV-2 serology at two time points.

Results

1,511 HCWs were randomised and 1,309 analysed (665 BCG and 644 placebo). Of the 298 infections detected during the trial, 74 were detected by serology only. The SARS-CoV-2 incidence rates were 0.25 and 0.26 per person-year in the BCG and placebo groups, respectively (incidence rate ratio=0.95; 95% confidence interval 0.76-1.21; p=0.732). Only three participants required hospitalisation for COVID-19. The proportions of participants with asymptomatic, mild, or mild-to-moderate infections, and the mean infection durations, did not differ between randomisation groups. Unadjusted and adjusted logistic regression and Cox proportional hazards models showed no differences between BCG and placebo vaccination for any of these outcomes either. The percentage of participants with seroconversion (7.8% versus 2.8%; p=0.006) and mean anti-S1 antibody concentration (13.1 versus 4.3 IU/ml; p=0.023) were higher in the BCG than placebo group at 3 months but not at 6 or 12 months post-vaccination.

Conclusions

BCG vaccination of HCWs did not reduce SARS-CoV-2 infections nor infection duration or severity (on a scale from asymptomatic to moderate). In the first 3 months after vaccination, BCG vaccination may enhance SARS-CoV-2 antibody production during SARS-CoV-2 infection.
Suicide after leaving the UK Armed Forces 1996-2018: a cohort study
Authors: Rodway Cathryn , Ibrahim Saied , Westhead Jodie , Bojanić Lana , Turnbull Pauline , Appleby Louis , Bacon Andy , Dale Harriet , Harrison Kate , Kapur Nav
Published: December 2022

Background

There are comparatively few international studies investigating suicide in military veterans and no recent UK studies. We aimed to investigate the rate, timing, and risk factors for suicide in personnel who left the UK Armed Forces (UKAF) over a 22-year period.

Methods and findings

We conducted a retrospective cohort study of suicide in personnel who left the regular UKAF between 1996 and 2018 by linking national databases of discharged personnel and suicide deaths. Of the 458,058 individuals who left the UKAF, 1,086 (0.2%) died by suicide. The overall rate of suicide in veterans was not greater than the general population (SMR [95% CI] 94 [88-99]). However, suicide risk was two to four times higher in male and female veterans aged under 25 years than in the same age groups in the general population (age-specific mortality ratios ranging from 160 to 409). Male veterans aged 35 years and older were at reduced risk of suicide (age-specific mortality ratios 47 to 80). Male sex, Army service, discharge between the ages of 16 and 34 years, being untrained on discharge, and length of service under 10 years were associated with increased suicide risk. Factors associated with reduced risk included being married, a higher rank and deployment on combat operations. The rate of contact with specialist NHS mental health services (273/1,086, 25%) was lowest in the youngest age groups (10% for 16–19-year-olds; 23% for 20–24-year-olds).

Conclusions

Suicide risk in veterans is not high but there are important differences according to age, with higher risk in young men and women. We found a number of factors which increased the risk of suicide but deployment was associated with reduced risk. Our focus should be on improving and maintaining access to mental health care and social supports for young service leavers, as well as implementing general suicide prevention measures for all veterans.
Mental Health in Ireland During the Covid Pandemic: Evidence from Two Longitudinal Surveys
Authors: Madden David
Published: December 2022

Using data from the Growing Up in Ireland Covid survey, this study examines the evolution of mental health as measured in December 2020, nine months into the pandemic, compared to observations pre pandemic for two cohorts of people. A deterioration in mental health was observed for both cohorts and particularly for younger women of the 1998 cohort. The increase in the rate of depression predominantly occurred due to an overall decline in mental health rather than being concentrated amongst those already vulnerable (in the sense of being near the depression threshold). There was little, if any, change in the socioeconomic gradient associated with mental health and virtually no gradient at all was observed pre or post pandemic for the 1998 cohort. Mobility analysis revealed that not only did females from the 1998 cohort show greater transitions into depression, they also appeared to transition into more extreme levels of depression.

JEL Codes

I14, I31.

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Background

The Covid pandemic arrived in Ireland on February 29, 2020. In the following weeks various restrictions were introduced to stem the spread of the disease. Anxiety over the spread of the disease and over the restrictions introduced had an adverse effect upon mental health. This study examines the change in mental health for two groups: young adults aged around 23 at the time of onset of Covid (the 1998 cohort) and a sample of principal carers (PCs) of children who were aged 13 at the onset of Covid (the 2008 cohort).

Methods

Data were obtained from the two cohorts of the longitudinal Growing Up In Ireland (GUI) survey. The sample included 1953 young adults (from the 1998 cohort) and 3547 principal carers (from the 2008 cohort). Mental health as measured by the Centre for Epidemiological Studies Depression - 8 scale was obtained for the last pre-Covid wave and for the Covid wave (surveyed in December 2020). Observations for which CES-D8 was not available in either pre or post Covid waves were excluded. Post-Covid sampling weights were applied.

Results

Relative to the last pre-Covid survey, mental health, as measured by CES-D8 deteriorated for both the young adults of the 1998 cohort and the PCs of the 2008 cohort. For young adults, the deterioration was more pronounced for females. There was no observable socioeconomic gradient for poor mental health amongst young adults, both pre and post Covid. For mothers from the 2008 cohort, a gradient was observed pre-Covid with poorer mental health for lower-income, less well-educated mothers. This gradient was less pronounced post-Covid, the levelling-off arising from a greater deterioration in mental health for higher-income and better-educated PCs.

Conclusion

Both observed cohorts showed a significant deterioration in mental health post Covid. For young adults the effect was more pronounced among females.
Laboratory-Developed Test Orders in an Academic Health System
Authors: Rychert Jenna , Schmidt Robert L. , Genzen Jonathan R
Published: December 2022

Importance

The Verifying Accurate Leading-edge IVCT Development Act, if enacted, would create a unified regulatory oversight system for all in vitro clinical tests, including laboratory-developed tests.

Objective

To determine the frequency of use of laboratory-developed tests in an academic medical center system.

Design

Quality improvement study analyzing 2021 test order data.

Setting

Academic medical center (hospital, outpatient clinics, and cancer center) and non-profit national reference laboratory.

Main Outcome(s) and Measure(s)

Main outcome, not applicable; non-interventional study of retrospective data. Measures include assay type, assay methodology, compliance status (i.e., Food and Drug Administration cleared, approved, and/or authorized assay, laboratory-developed test, and standard method), test order volume, inpatient versus outpatient setting, and provider medical specialty.

Results

Of the 3,016,928 tests ordered in 2021, 2,831,489 (93.9%) were Food and Drug Administration cleared, approved, and/or authorized assays, 116,583 (3.9%) were laboratory-developed tests, and 68,856 (2.3%) were standard methods. Laboratory-developed tests were more commonly ordered in the outpatient versus inpatient setting and represented a higher proportion of the test volume at the cancer center compared to University Hospital (5.6% vs 3.6% respectively). The top 167 laboratory-developed test assays accounted for 90% of the laboratory-developed test volume (104,996 orders). Among the 20 most frequently ordered laboratory-developed tests were mass spectrometry assays and tests used in the care of immunocompromised patients. Internal/family medicine placed the greatest number of orders (1,044,642) and ordered one of the lowest proportions of laboratory-developed tests (3.2%). Non-infectious disease molecular testing made up 8.8% of laboratory-developed tests ordered.

Conclusions

Laboratory-developed tests made up a small percentage of the total laboratory tests ordered within the academic health system studied. Regulatory reform proposals should consider the need for both safety and availability of laboratory-developed tests in clinical laboratory settings.

KEY POINTS

Question

How frequently are laboratory developed tests (LDTs) used in an academic medical center (AMC) setting?

Findings

In this quality improvement study looking at test orders in 2021, 93.9% of test orders were for FDA cleared, approved, or authorized assays, 3.9% were for LDTs, and 2.3% were for standard methods. The top 167 LDT assays accounted for 90% of the LTD volume.

Meaning

In vitro diagnostic reform efforts will impact many LDTs assays with relatively low order volumes in AMC settings.
Distribution of mutation rates challenges evolutionary predictability
Authors: Sun T. Anthony , Lind Peter A.
Published: December 2022

Natural selection is commonly assumed to act on extensive standing genetic variation. Yet, accumulating evidence highlights the role of mutational processes creating this genetic variation: to become evolutionarily successful, adaptive mutants must not only reach fixation, but also emerge in the first place,i.e.have a high enough mutation rate relative to the population size.

Here, we use numerical simulations to investigate how mutational biases impact our ability to observe rare mutational pathways in the laboratory and to predict outcomes in experimental evolution. We find the number of available mutations and the unevenness of their mutation rates to increase, sometimes impractically, the experimental effort required to discover all of them. Thus, most experimental studies lack power to directly observe the full range of adaptive mutations.

Modelling mutation rates as a distribution, we show that a substantially larger target size ensures that a pathway mutates more commonly. Therefore, we predict that commonly mutated pathways are conserved between closely related species, contrary to rare pathways. This approach formalizes our proposal that most mutations have a lower mutation rate than the average mutation rate measured experimentally. We suggest that the extent of genetic variation is overestimated when based on the average mutation rate.
Characterization of the mIF4G domains in the RNA surveillance protein Upf2
Authors: Colón Edgardo M. , Haddock Luis A. , Lasalde Clarivel , Lin Qishan , Ramírez-Lugo Juan S. , González Carlos I.
Published: December 2022

Thirty percent of all mutations causing human diseases generate mRNAs with premature termination codons (PTCs). Recognition and degradation of these PTC-containing mRNAs is carried out by the mechanism known as nonsense-mediated mRNA decay (NMD). Upf2 is a scaffold protein known to be a central component of the NMD surveillance pathway. It harbors three middle domain of eukaryotic initiation factor 4G (mIF4G) domains in its N-terminal potentially important in regulating the surveillance pathway. In this study, we defined regions within the mIF4G-1 and mIF4G-2 that are required for proper function of NMD and translation termination inSaccharomyces cerevisiaeUpf2. In addition, we narrowed down the activity of these regions to an aspartic acid (D59) in mIF4G-1 which is important for NMD activity and translation termination accuracy. Taken together, these studies suggest that inherent charged residues within mIF4G-1 of Upf2 play a role in the regulation of the NMD surveillance mechanism inS. cerevisiae.
SARS-CoV-2 vaccine-breakthrough infections (VBIs) by Omicron (B.1.1.529) variant and consequences in structural and functional impact
Authors: Abduljaleel Zainularifeen , Melebari Sami , Dehlawi Saied , Udhaya Kumar S , Aziz Syed A. , Dannoun Anas Ibrahim , Malik Shaheer M. , George Priya Doss C
Published: December 2022

This study investigated the efficacy of existing vaccinations against hospitalization and infection due to the Omicron variant of COVID-19, particularly for those who received two doses of Moderna or Pfizer vaccines and one dose of a vaccine by Johnson & Johnson or who were vaccinated more than five months previously. A total of 36 variants in Omicron’s spike protein, targeted by all three vaccinations, have made antibodies less effective at neutralizing the virus. Genotyping of SARS-CoV-2 viral sequencing revealed clinically significant variants such as E484K in three genetic mutations (T95I, D614G, and del142-144). One woman displayed two of these mutations, indicating a potential risk of infection following successful immunization, as recently reported by Hacisuleyman (2021). We examined the effects of mutations on domains (NID, RBM, and SD2) found at the interfaces of spike domains Omicron B.1.1529, Delta/B.1.1529, Alpha/B.1.1.7, VUM B.1.526, B.1.575.2, and B.1.1214 (formerly VOI Iota). We tested the affinity of Omicron for hACE2 and found that the wild and mutant spike proteins were using atomistic molecular dynamics simulations. According to binding free energies calculated during mutagenesis, hACE2 bound Omicron spike more strongly than SARS-CoV-2 wild strain. T95I, D614G, and E484K are three substitutions that significantly contribute to the RBD, corresponding to hACE2 binding energies and a doubling of Omicron spike proteins’ electrostatic potential. Omicron appears to bind hACE2 with greater affinity, increasing its infectivity and transmissibility. The spike virus was designed to strengthen antibody immune evasion through binding while boosting receptor binding by enhancing IgG and IgM antibodies that stimulate humanβ-cell, as opposed to the wild strain, which has more vital stimulation of both antibodies.
Genetic analysis of the rice jasmonate receptors reveals specialized function forOsCOI2
Authors: Nguyen Hieu Trang , Cheaib Mohamad , Fournel Marie , Rios Maelle , Gantet Pascal , Laplaze Laurent , Guyomarc’h Soazig , Riemann Michael , Heitz Thierry , Petitot Anne-Sophie , Champion Antony
Published: December 2022

COI1-mediated perception of jasmonate is critical for plant development and responses to environmental stresses. Monocots such as rice have two groups ofCOIgenes due to gene duplication:OsCOI1aandOsCOI1bthat are functionally equivalent to the dicotyledonsCOI1on one hand andOsCOI2whose function remains unclear.

In order to assess the function ofOsCOI2and its functional redundancy withCOI1genes, we developed a series of rice mutants in the 3 genesOsCOI1a, OsCOI1bandOsCOI2by CRISPR Cas9 and characterized their phenotype and responses to jasmonate.

Characterization ofOsCOI2uncovered important roles in root, leaf and flower development. In particular, we show that crown root growth inhibition by jasmonate relies onOsCOI2and notOsCOI1aorOsCOI1bin rice, revealing a major function for the non-canonicalOsCOI2in jasmonate-dependent control of rice root growth.

Collectively, these results point to a specialized function ofOsCOI2in the regulation of plant development in rice and indicate that sub-functionalisation of jasmonate receptors has occurred in the monocot phylum.
Mean Dimension of Generative Models for Protein Sequences
Authors: Feinauer Christoph , Borgonovo Emanuele
Published: December 2022

Abstract

Generative models for protein sequences are important for protein design, mutational effect prediction and structure prediction. In all of these tasks, the introduction of models which include interactions between pairs of positions has had a major impact over the last decade. More recently, many methods going beyond pairwise models have been developed, for example by using neural networks that are in principle able to capture interactions between more than two positions from multiple sequence alignments. However, not much is known about the inter-dependency patterns between positions in these models, and how important higher-order interactions involving more than two positions are for their performance. In this work, we introduce the notion of mean dimension for generative models for protein sequences, which measures the average number of positions involved in interactions when weighted by their contribution to the total variance in log probability of the model. We estimate the mean dimension for different model classes trained on different protein families, relate it to the performance of the models on mutational effect prediction tasks and also trace its evolution during training. The mean dimension is related to the performance of models in biological prediction tasks and can highlight differences between model classes even if their performance in the prediction task is similar. The overall low mean dimension indicates that well-performing models are not necessarily of high complexity and encourages further work in interpreting their performance in biological terms.
EEG Changes during Odor Perception and Discrimination
Authors: Morozova Marina , Bikbavova Alsu , Bulanov Vladimir , Lebedev Mikhail A.
Published: December 2022

Brain-Computer Interfaces (BCIs) are devices designed for communication between the central nervous system and a computer. The communication can occur through different sensory modalities, and most commonly visual and auditory systems are used. We suggest that BCIs can be expanded by the incorporation of olfactory modality. To probe the modulation of EEG activity by odorants, we implemented two olfactory tasks: one that required attention to perception of odors, and the second one where participants discriminated consecutively presented odors. EEG recordings were conducted in 13 healthy participants while they performed the tasks following computer-generated verbal instructions. Respiratory activity was recorded to relate EEG modulations to the breath cycle. Theta activity responses were observed over the frontal EEG leads approximately 2 s after the inhalation. This theta activity was different depending on whether or not the inhaled air contained an odorant, and cognitive load also had an effect. We conclude that the frontal theta rhythm is reflective of the neural processing of odors. As such, it could be incorporated in the olfactory-based BCIs which take odors either as inputs or outputs. These BCIs could improve olfactory training needed for conditions like anosmia and hyposmia, and mild cognitive impairment.
Genome-wide analysis of dry (Tamar) Date palm fruit color
Authors: Younuskunju Shameem , Mohamoud Yasmin A. , Mathew Lisa Sara , Mayer Klaus F. X. , Suhre Karsten , Malek Joel A.
Published: December 2022

Date palm (Phoenix dactylifera) fruit are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. Genetic studies of some Date palm traits have been performed, including for date palm sex-determination, sugar content and fresh fruit colour. In this study, we used genome sequences and image data of 199 dry date fruit (Tamar) samples collected from 14 countries to identify genetic loci associated with the color of this fruit stage. Here, we find loci across multiple linkage groups (LG) associated with dry fruit color phenotype. We recover the previously identified VIR genotype associated with fresh fruit yellow or red color and new associations with the lightness and darkness of dry fruit. This study will add resolution to our understanding of the date palm fruit color phenotype especially at the most commercially important tamar stage.
Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer
Authors: Dondi Arthur , Lischetti Ulrike , Jacob Francis , Singer Franziska , Borgsmüller Nico , Coelho Ricardo ,   Tumor Profiler Consortium, Heinzelmann-Schwarz Viola , Beisel Christian , Beerenwinkel Niko
Published: December 2022

Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients presenting with omental metastasis and increase the PacBio sequencing depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, of which over 52,000 are novel. Isoform-level analysis accounting for non-coding isoforms reveals 20% overestimation of protein-coding gene expression on average. We also detect cell type-specific isoform and poly-adenylation site usage in tumor and mesothelial cells, and find that mesothelial cells transition into cancer-associated fibroblasts in the metastasis, partly through the TGF-β/miR-29/Collagen axis. Furthermore, we identify gene fusions, including an experimentally validatedIGF2BP2::TESPA1fusion, which is misclassified as highTESPA1expression in matched short-read data, and call mutations confirmed by targeted NGS cancer gene panel results. With these findings, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.
MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root
Authors: Sharma Nilesh Kumar , Gupta Santosh Kumar , Irulappan Vadivelmurugan , Yadav Shalini , Francis Aleena , Senthil-Kumar Muthappa , Chattopadhyay Debasis
Published: December 2022

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localized multicopper oxidase family enzymes LACCASES (LACs) catalyze the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of severalLACgenes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to targetLAC4andLAC17Lout of twenty annotatedLACs in chickpea. CamiR397 and its target genes are expressed in root. Overexpression of CamiR397 reduced expression ofLAC4andLAC17Land lignin deposition in chickpea root xylem causing reduction in xylem diameter. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing (miR397OX) and STTM397 chickpea lines showed sensitivity and tolerance, respectively, to drought. Infection with a fungal pathogenMacrophomina phaseolina, responsible for dry root rot disease in chickpea, induced local lignin deposition andLACgene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to dry root rot. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and dry root rot in an agriculturally important crop chickpea.
Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell-eye evolution
Authors: Liu Xu , Sigwart Julia D. , Sun Jin
Published: December 2022

Mollusca is the second-largest animal phylum with over 100,000 species among eight distinct taxonomic classes. Across 1000 living species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess “shell eyes”, true eyes with a lens and retina that are embedded within the dorsal shells, which represent the most recent evolution of animal eyes. The phylogeny of major chiton clades is mostly well established, in a set of superfamily and higher-level taxa supported by various approaches including multiple gene markers, mitogenome-phylogeny and phylotranscritomic approaches as well as morphological studies. However, one critical lineage has remained unclear:Schizochitonwas controversially suggested as a potential independent origin of chiton shell eyes. Here, with the draft genome sequencing ofSchizochiton incisus(superfamily Schizochitonoidea) plus assembly of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. Phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. A consistent robust topology was generated with protein coding genes using different models and methods. Our results support Schizochitonoidea is a sister group to other Chitonoidea in Chitonina, in agreement with established classification. This suggests that the earliest origin of shell eyes is in Schizochitonoidea, which were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding on the evolution of Polyplacophora.
Deuterated buprenorphine retains pharmacodynamic properties of buprenorphine and resists metabolism to the active metabolite norbuprenorphine in rats
Authors: Janganati Venumadhav , Salazar Paloma , Parks Brian J. , Gorman Gregory S. , Prather Paul L. , Peterson Eric C. , Alund Alexander W. , Moran Jeffery H. , Crooks Peter A. , Brents Lisa K.
Published: December 2022

An active metabolite of buprenorphine (BUP), called norbuprenorphine (NorBUP), is implicated in neonatal opioid withdrawal syndrome when BUP is taken during pregnancy. Therefore, reducing or eliminating metabolism of BUP to NorBUP is a novel strategy that will likely lower total fetal exposure to opioids and thus improve offspring outcomes. Precision deuteration alters pharmacokinetics of drugs without altering pharmacodynamics. Here, we report the synthesis and testing of deuterated buprenorphine (BUP-D2). We determined opioid receptor affinities of BUP-D2 relative to BUP with radioligand competition receptor binding assays, and the potency and efficacy of BUP-D2 relative to BUP to activate G-proteins via opioid receptors with [35S]GTPγS binding assays in homogenates containing the human mu, delta, or kappa opioid receptors. The antinociceptive effects of BUP-D2 and BUP were compared using the warm-water tail withdrawal assay in rats. Blood concentration versus time profiles of BUP, BUP-D2, and NorBUP were measured in rats following intravenous BUP-D2 or BUP injection. The synthesis provided a 48% yield and the product was ≥99% deuterated. Like BUP, BUP-D2 had sub-nanomolar affinity for opioid receptors. BUP-D2 also activated opioid receptors and induced antinociception with equal potency and efficacy as BUP. The maximum concentration and the area under the curve of NorBUP in the blood of rats that received BUP-D2 were over 19- and 10-fold lower, respectively, than in rats that received BUP. These results indicate that BUP-D2 retains key pharmacodynamic properties of BUP and resists metabolism to NorBUP and therefore holds promise as an alternative to BUP.

GRAPHICAL ABSTRACT
Structure of VanS from Vancomycin-Resistant Enterococci: A Sensor Kinase with Weak ATP Binding
Authors: Grasty Kimberly C. , Guzik Claudia , D’Lauro Elizabeth J. , Padrick Shae B. , Beld Joris , Loll Patrick J.
Published: December 2022

The VanRS two-component system regulates the resistance phenotype of vancomycin-resistant enterococci (VRE). VanS is a sensor histidine kinase that responds to the presence of vancomycin by autophosphorylating and subsequently transferring the phosphoryl group to the response regulator, VanR. The phosphotransfer activates VanR as a transcription factor, which initiates the expression of resistance genes. Structural information about VanS proteins has remained elusive, hindering the molecular-level understanding of their function. Here, we present X-ray crystal structures for the catalytic and ATP-binding (CA) domains of two VanS proteins, derived from VRE types A and C. Both proteins adopt the canonical Bergerat fold that has been observed for CA domains of other prokaryotic histidine kinases. We attempted to determine structures for the nucleotide-bound forms of both proteins; however, despite repeated efforts, these forms could not be crystallized, prompting us to measure the proteins’ binding affinities for ATP. Unexpectedly, both CA domains displayed low affinities for the nucleotide, withKDvalues in the low millimolar range. Since theseKDvalues are comparable to intracellular ATP concentrations, this weak substrate binding could reflect a way of regulating expression of the resistance phenotype.
Cell polarity opposes Jak-STAT mediated Escargot activation that drives intratumor heterogeneity in aDrosophilatumor model
Authors: Chatterjee Deeptiman , Cong Fei , Wang Xian-Feng , Costa Caique Almeida Machado , Huang Yi-Chun , Deng Wu-Min
Published: December 2022

In proliferating neoplasms, microenvironment-derived selective pressures promote tumor heterogeneity by imparting diverse capacities for growth, differentiation and invasion. However, what makes a tumor cell respond to signaling cues differently from a normal cell is not well understood. In theDrosophilaovarian follicle cells, apicobasal-polarity loss induces heterogenous epithelial multilayering. When exacerbated by oncogenic-Notch expression, this multilayer displays an increased consistency in the occurrence of morphologically distinguishable cells adjacent to the polar follicle cells. Polar cells release the Jak-STAT ligand Unpaired (Upd), in response to which, neighboring polarity-deficient cells exhibit a precursor-like transcriptomic state. Using single-cell transcriptomics, we discovered the ectopic activation of the Snail-family transcription factor Escargot (Esg) in these cells. We also characterized similar relationship between Upd and Esg during early follicular development, where the establishment of polarity determines follicle-cell differentiation. Overall, our results indicate that epithelial-cell polarity acts as a gatekeeper against microenvironmental selective pressures that drive heterogeneity.
Ultrafast molecular dynamics observed within a dense protein condensate
Authors: Galvanetto Nicola , Ivanović Miloš T. , Chowdhury Aritra , Sottini Andrea , Nüesch Mark F. , Nettels Daniel , Best Robert B. , Schuler Benjamin
Published: December 2022

Many biological macromolecules can phase-separate in the cell and form highly concentrated condensates. The mesoscopic dynamics of these assemblies have been widely characterized, but their behavior at the molecular scale has remained more elusive. Here we investigate condensates of two highly charged disordered human proteins as a characteristic example of liquid-liquid phase separation. The dense phase is 1000 times more concentrated and has 300 times higher bulk viscosity than the dilute phase. However, single-molecule spectroscopy in individual droplets reveals that the polypeptide chains are remarkably dynamic, with sub-microsecond reconfiguration times. We rationalize this behavior with large-scale all-atom molecular-dynamics simulations, which reveal an unexpectedly similar short-range molecular environment in the dense and dilute phases, suggesting that local biochemical processes and interactions can remain exceedingly rapid in phase-separated systems.
Improved Yield for the Enzymatic Synthesis of Radiolabeled Nicotinamide Adenine Dinucleotide
Authors: Eller Jared , Goyal Shivansh , Cambronne Xiaolu A.
Published: December 2022

Labeled β-nicotinamide adenine dinucleotide (NAD) analogs have been critical for uncovering new biochemical connections and quantitating enzymatic activity. They function as tracers for enzymology, flux analyses, and in situ measurements. Nevertheless, there is limited availability of specific types of analogs, especially radiolabeled NAD analogs. Here, we describe an improved enzymatic synthesis reaction for32P-NAD+with a yield of 98% ± 1%, using lowered concentrations of reactants and standard equipment. This represents the highest reported yield for the enzymatic synthesis of NAD+to date. With the high yield we were able to directly use the reaction product to generate derivatives, such as32P-NADP. The high-yield enzymatic synthesis is versatile for a broad variety of labels and NAD derivatives. Its advantages include lowered concentrations of reactants, providing sufficient amounts of product for downstream applications, and minimizing intermediate purification steps.
Impact of growth-promoting alternatives on weight gain and gut microbial diversity and activity in piglets
Authors: Palanee Jason , Gagnon Nathalie , Lauzon Karoline , Méthot Steve , Blais Mylène , Talbot Guylaine , Guay Frédéric , Lessard Martin , Yergeau Étienne , Poulin-Laprade Dominic
Published: December 2022

In swine husbandry, weaning is a critical event for piglets which causes environmental, nutritional, and psychological stresses, with consequences such as intestinal dysbiosis. To counteract this issue, producers resorted to the use of in-feed antimicrobials to prevent post-weaning diarrhea and to promote growth for increased animal performance. However, the use of antibiotic for growth promotion was banned in many countries. In-feed supplements have great potential as alternative strategies. This study evaluated the effect on gut microbial activity, microbiome, and animal performance of combinations of peri-weaning feeding strategies such as bovine colostrum, medium-chain fatty acids and yeast extract. We quantified weight gain, intestinal pH, volatile fatty acids, and characterized the gut microbiota on ileum, cecum, and colon digestates. Overall, the feed supplements had limited impact on weight gain and volatile fatty acids production. However, the combined treatments have demonstrated a modulatory effect on gut microbiota which supports a potential role as an alternative to growth-promoting antibiotic in the swine industry.
Robust SARS-CoV-2 antibody and T cell immunity following three COVID-19 vaccine doses in inflammatory bowel disease patients receiving anti-TNF or alternative treatments
Authors: Zhang Eva , Nguyen Thi H O , Allen Lilith F , Kedzierski Lukasz , Rowntree Louise C , Chang So Young , Zhang Wuji , Habel Jennifer R , Foo Isabelle J , Menon Tejas , Mitchell Jeni , Leong Rupert W , Bond Katherine A , Williamson Deborah A , Kedzierska Katherine , Christensen Britt
Published: December 2022

BACKGROUND AND AIMS

Vaccine-mediated immune responses in patients with inflammatory bowel disease (IBD) may be influenced by IBD therapies. We investigated in-depth humoral and T-cell responses to SARS-CoV-2 vaccination in IBD patients following three COVID-19 vaccine doses.

METHODS

Immune responses of 100 SARS-CoV-2-uninfected IBD patients on varying treatments were compared to healthy controls (n=35). Anti-S1/2 and anti-RBD SARS-CoV-2-specific antibodies, CD4+and CD8+T-cell responses were measured at baseline and at five time-points after COVID-19 vaccination.

RESULTS

Anti-S1/2 and anti-RBD antibody concentrations at ∼1 month after second dose vaccination were significantly lower in anti-TNF-treated patients compared to non-TNF IBD patients and healthy controls (126.4 vs 262.1 and 295.5, p<0.0001). Anti-S1/2 antibodies remained reduced in anti-TNF treated patients before and after the third dose (285.7 vs 365.3,p=0.03), although anti-RBD antibodies reached comparable titres to non-TNF patients. Anti-RBD antibodies were higher in the vedolizumab group than controls after second dose (4.2 vs 3.6, p=0.003). Anti-TNF monotherapy was associated with increased CD4+and CD8+T-cell activation compared to combination anti-TNF patients after second dose, but comparable after third dose. Overall, IBD patients demonstrated similar CD4+/CD8+T-cell responses compared to healthy controls regardless of treatment regimen.

CONCLUSIONS

Anti-TNFs impaired antibody concentrations when compared to non-TNF patients and controls after two vaccine doses. These differences were not observed after the third vaccine dose. However, vaccine induced SARS-CoV-2-specific T cell responses are robust in anti-TNF-treated patients. Our study supports the need for timely booster vaccination particularly in anti-TNF treated patients to minimise the risk of severe SARS-CoV-2 infection.
Avoidance learning reduces intricate covariation between boldness and foraging behavior in a generalist predator
Authors: Kuo Chi-Yun , Chin Hao-En , Wu Yu-Che
Published: December 2022

Many predators avoid unprofitable prey by learning to use visual features of the prey as reliable indicators of quality. Despite a rich literature on avoidance learning, we are still in the process of understanding how individuals might change their behavior towards unprofitable prey as information accumulates, the individual-level variation in avoidance foraging behavior, and whether learning would preserve or reduce this variation. In this study, we investigated how avoidance foraging behavior varied in a generalist lizard predator in relation to sex, population of origin, and boldness and tested the effects of learning on the variation in avoidance foraging behavior. We collected data on boldness and avoidance foraging behavior in individuals from two allopatric populations and compared variation in behavior at the beginning and end of learning experiments, in which individuals were presented with normal- and bitter-tasting prey that also differed consistently in color. We found that even though bitter prey elicited strong negative responses, lizards overall did not avoid consuming fewer such prey with learning. Instead, lizards learned to prioritize on palatable prey as they acquired more information. Our data revealed intricate covariation between boldness and avoidance foraging behavior, and the form of this covariation varied between populations, sex, and prey color. Learning overall reduced individual variation in foraging behavior, as well as the degree of covariation with boldness. Our findings highlighted the nuanced manners in which avoidance foraging behavior might manifest and suggested that learning could quickly mitigate fitness difference due to variation in behavior.

Lay Summary

Predators can learn to avoid unprofitable prey using certain visual cues or signals, but avoidance foraging behavior can manifest in more subtle ways than simply “to eat or not to eat”. We reported changes in foraging sequence and priority in a generalist lizard predator after learning and found that the nature of these changes depended on sex, population of origin, boldness, and prey color. We also found that learning made individuals more similar in behavior.