bluuebunny/crossref_metadata_2025 huggingface dataset:
RhoA/ROCK2 signalling is enhanced by PDGF-AA in fibro-adipogenic progenitor cells in DMD
Authors: Fernández-Simón Esther , Suárez-Calvet Xavier , Carrasco-Rozas Ana , Piñol-Jurado Patricia , López-Fernández Susana , Bech Serra Joan Josep , de la Torre Carolina , de Luna Noemí , Gallardo Eduard , Jordi-Díaz-Manera
Published: April 2021

The lack of dystrophin expression in Duchenne muscular dystrophy (DMD) leads to muscle necrosis and replacement of muscle tissue by fibro-adipose tissue. Although the role of some growth factors in the process of fibrogenesis has been previously studied, the pathways that are activated by PDGF-AA in muscular dystrophies have not been described so far. Herein we report the effects of PDGF-AA on the fibrotic process in muscular dystrophies by performing a quantitative proteomic study in DMD isolated fibro-adipogenic precursor cells (FAPs) treated with PDGF-AA. In vitro studies showed that RhoA/ROCK2 pathway is activated by PDGF-AA and induces the activation of FAPs. The inhibition of RhoA/ROCK signalling pathway by C3-exoenzyme or fasudil attenuated the effects of PDGF-AA. The blocking effects of RhoA/ROCK pathway were analysed in the dba/2J-mdx murine model with fasudil. Grip strength test showed an improvement in the muscle function and histological studies demonstrated reduction of the fibrotic area. Our results suggest that blockade of RhoA/ROCK could attenuate the activation of FAPs and could be considered a potential therapeutic approach for muscular dystrophies.
Epigenomic profiling of stem cells within the pilosebaceous unit identifies PRDM16 as a regulator of sebaceous gland homeostasis
Authors: Rehimi Rizwan , Crispatzu Giuliano , Chacón-Martínez Carlos Andrés , Bleckwehl Tore , Mantellato Giada , Gözüm Gökcen , Clément-Ziza Mathieu , Wickström Sara A. , Niemann Catherin , Niessen Carien , Rada-Iglesias Alvaro
Published: April 2021

The epidermis consists of different compartments such as the hair follicle (HF), sebaceous gland (SG) and interfollicular epidermis (IFE), each containing distinct stem cell (SC) populations. However, with the exception of the SCs residing within the HF bulge, other epidermal SC populations remain less well understood. Here we used an epigenomic strategy that combines H3K27me3 ChIP-seq and RNA-seq profiling to identify major regulators of pilosebaceous unit (PSU) SC located outside the bulge. When applied to the bulk of PSU SC isolated from mouse skin our approach identified both previously known and potentially novel non-bulge PSU SC regulators. Among the latter, we found that PRDM16 was predominantly enriched within the Junctional Zone (JZ), which harbors SC that contribute to renewal of the upper HF and the SG. To investigate PRDM16 function in the PSU SC, we generated an epidermal-specificPrdm16Knock-out mouse model (K14-Cre-Prdm16fl/fl). Notably, SG homeostasis was disturbed upon loss of PRDM16 resulting in enlarged SGs, and excessive sebum production, resembling some of the features associated with human acne and sebaceous hyperplasia. Importantly, PRDM16 is essential to shut down proliferation in differentiating sebocytes. Overall, our study provides a list of putative novel regulators of PSU SC outside the bulge and identifies PRDM16 as a major regulator of SG homeostasis.
Feature selectivity explains mismatch signals in mouse visual cortex
Authors: Muzzu Tomaso , Saleem Aman B.
Published: April 2021

Sensory experience is often dependent on one’s own actions, including self-motion. Theories of predictive coding postulate that actions are regulated by calculating prediction error, which is the difference between sensory experience and expectation based on self-generated actions. Signals consistent with prediction error have been reported in mouse visual cortex (V1) when visual flow coupled to running is unexpectedly perturbed. Here, we show that such signals can be elicited by visual stimuli uncoupled with the animal’s running. We recorded the activity of mouse V1 neurons while presenting drifting gratings that unexpectedly stopped. We found strong responses to visual perturbations, which were enhanced during running. If these perturbation responses are signals about sensorimotor mismatch, they should be largest for front-to-back visual flow expected from the animals’ running. Responses, however, did not show a bias for front-to-back visual flow. Instead, perturbation responses were strongest in the preferred orientation of individual neurons and perturbation responsive neurons were more likely to prefer slow visual speeds. Our results therefore indicate that prediction error signals can be explained by the convergence of known motor and sensory signals in visual cortex, providing a purely sensory and motor explanation for purported mismatch signals.
Comparative toxicogenomics of glyphosate and Roundup herbicides by mammalian stem cell-based genotoxicity assays and molecular profiling in Sprague-Dawley rats
Authors: Mesnage Robin , Ibragim Mariam , Mandrioli Daniele , Falcioni Laura , Tibaldi Eva , Belpoggi Fiorella , Brandsma Inger , Bourne Emma , Savage Emanuel , Mein Charles A , Antoniou Michael N
Published: April 2021

Whether glyphosate-based herbicides (GBHs) are more potent than glyphosate alone at activating cellular mechanisms, which drive carcinogenesis remains controversial. As GBHs are more cytotoxic that glyphosate, we reasoned they may also be more capable of activating carcinogenic pathways. We tested this hypothesis by comparing the effects of glyphosate with Roundup GBHs bothin vitroandin vivo. First, glyphosate was compared with representative GBHs namely MON 52276 (EU), MON 76473 (UK) and MON 76207 (USA) using the mammalian stem cell-based ToxTracker system. Here, MON 52276 and MON 76473, but not glyphosate and MON 76207, activated oxidative stress and unfolded protein responses. Second, molecular profiling of liver was performed in female Sprague-Dawley rats exposed to glyphosate or MON 52276 (both at 0.5, 50, 175 mg/kg bw/day glyphosate) for 90 days. MON 52276 but not glyphosate increased hepatic steatosis and necrosis. MON 52276 and glyphosate altered the expression of genes in liver reflecting TP53 activation by DNA damage and circadian rhythm regulation. Genes most affected in liver were similarly altered in kidneys. Small RNA profiling in liver showed decreased amounts of miR-22 and miR-17 from MON 52276 ingestion. Glyphosate decreased mir-30 while miR-10 levels were increased. DNA methylation profiling of liver revealed 5,727 and 4,496 differentially methylated CpG sites between the control and glyphosate and MON 52276 exposed animals respectively. Apurinic/apyrimidinic DNA damage formation in liver was increased with glyphosate exposure. Altogether, our results show that Roundup formulations cause more biological changes linked with carcinogenesis than glyphosate.
Revealing intraosseous blood flow in the human tibia with ultrasound
Authors: Salles Sebastien , Shepherd Jami , Vos Hendrik J. , Renaud Guillaume
Published: April 2021

Intraosseous blood circulation is thought to have a critical role in bone growth and remodeling, fracture healing, and bone disorders. However, it is rarely considered in clinical practice due to the absence of a suitable non-invasive in vivo measurement technique. In this work, we assessed blood perfusion in tibial cortical bone simultaneously with blood flow in the superficial femoral artery with ultrasound imaging in 5 healthy volunteers. After suppression of stationary signal with Singular-Value-Decomposition, pulsatile blood flow in cortical bone tissue is revealed, following the heart rate measured in the femoral artery. Using a method combining transverse oscillations and phase-based motion estimation, two-dimensional vector flow was obtained in the cortex of the tibia. After spatial averaging over the cortex, the peak blood velocity along the long axis of the tibia was measured four times larger than the peak blood velocity across the bone cortex. This suggests that blood flow in central (Haversian) canals is larger than in perforating (Volkmann’s) canals, as expected from the intracortical vascular organization in humans. The peak blood velocity indicates a flow from the endosteum to the periosteum and from the heart to the foot for all subjects. Because aging and the development of bone disorders are thought to modify the direction and velocity of intra-cortical blood flow, their quantification is crucial. This work reports for the first time an in vivo quantification of the direction and velocity of blood flow in human cortical bone.
Diagnostic classification based on DNA methylation profiles using sequential machine learning approaches
Authors: Wojewodzic M. W. , Lavender J. P.
Published: April 2021

Aberrant methylation patterns in human DNA have great potential for the discovery of novel diagnostic and disease progression biomarkers. In this paper, we used machine learning algorithms to identify promising methylation sites for diagnosing cancerous tissue and to classify patients based on methylation values at these sites.

We used genome-wide DNA methylation patterns from both cancerous and normal tissue samples, obtained from the Genomic Data Commons consortium and trialled our methods on three types of urological cancer. A decision tree was used to identify the methylation sites most useful for diagnosis.

The identified locations were then used to train a neural network to classify samples as either cancerous or non-cancerous. Using this two-step approach we found strong indicative biomarker panels for each of the three cancer types.

These methods could likely be translated to other cancers and improved by using non-invasive liquid methods such as blood instead of biopsy tissue.
Filling gaps: fishing, genetics, and conservation of groupers, especially the comb grouper (badejo) (Mycteroperca acutirostris), in SE Brazil (2013-2020)
Authors: Begossi Alpina , Salivonchyk Svetlana , Glamuzina Branko , Alves-Pereira Alessandro , Araújo Batista Carlos Eduardo De , Priolli Regina H. G.
Published: April 2021

There are large gaps in our knowledge of the biology of important fish consumed by people in tropical countries, which makes conservation difficult. Small-scale fisheries are difficult to study and regulate, especially in countries with no systematic species monitoring. It is even more difficult to estimate the influence of these fisheries on vulnerable fish species and to diagnose possible damage to local fish populations. In this study, 490 individuals ofbadejo, or comb grouper (Mycteropeca acutirostris), were observed at the Posto 6 fishery in Copacabana, Rio de Janeiro, for the periods of 2013-2014 and 2018-2020. A pattern of decreasing catches was observed for comb grouper. Therefore, provided that the fishing gear and the number of fish have remained the same, the apparent decrease in comb grouper needs to be further investigated. The results provide information regarding the reproduction of comb grouper, with major spawning season around spring (September-December) and additional spawning during April in SE Brazil. Samples from 96 groupers along the coast of Brazil were obtained, and genetic analyses were conducted. The genetic information obtained for grouper species enabled us to determine the relative genetic proximity ofM. acutirostrisandMycteroperca bonaciand to obtain information that can be useful for aquaculture and conservation.
Axonal CB1 receptors mediate inhibitory bouton formation via cAMP increase
Authors: Liang Jian , Kruijssen Dennis LH , Verschuuren Aniek CJ , Voesenek Bas JB , Benavides Feline , Gonzalez Maria Sáez , Ruiter Marvin , Wierenga Corette J
Published: April 2021

Experience-dependent formation and removal of synapses are essential throughout life. For instance, GABAergic synapses are removed to facilitate learning, and strong excitatory activity is accompanied by formation of inhibitory synapses. We recently discovered that active dendrites trigger the growth of inhibitory synapses via CB1 receptor-mediated endocannabinoid signaling, but the underlying mechanism remained unclear. Using two-photon microscopy to monitor the formation of individual inhibitory boutons, we found that CB1 receptor activation mediated formation of inhibitory boutons and promoted their subsequent stabilization. Inhibitory bouton formation did not require neuronal activity and was independent of Gi/oprotein signaling, but was directly induced by elevating cAMP levels using forskolin and by activating Gsproteins using DREADDs. Our findings reveal that axonal CB1 receptors signal via unconventional downstream pathways and that inhibitory bouton formation is triggered by an increase in axonal cAMP levels. Our results demonstrate a novel role for axonal CB1 receptors in axon-specific, and context-dependent, inhibitory synapse formation.
A multifaceted role of progranulin in regulating amyloid-beta dynamics and responses
Authors: Du Huan , Wong Man Ying , Zhang Tingting , Santos Mariela Nunez , Hsu Charlene , Zhang Junke , Yu Haiyuan , Luo Wenjie , Hu Fenghua
Published: April 2021

Haploinsufficiency of progranulin (PGRN) is a leading cause of frontotemporal lobar degeneration (FTLD). PGRN polymorphisms are associated with Alzheimer’s disease (AD). PGRN is highly expressed in the microglia near Aβ plaques and influences plaque dynamics and microglial activation. However, the detailed mechanisms remain elusive. Here we report that PGRN deficiency reduces human APP and Aβ levels in the young male but not female mice. PGRN deficient microglia exhibit increased expression of markers associated with microglial activation, including CD68, Galectin-3, TREM2 and GPNMB, specifically near Aβ plaques. In addition, PGRN loss leads to up-regulation of lysosome proteins and an increase in the nuclear localization of TFE3, a transcription factor involved in lysosome biogenesis. Cultured PGRN deficient microglia show enhanced nuclear translocation of TFE3 and inflammation in response to Aβ fibril treatment. Taken together, our data revealed a sex- and age-dependent effect of PGRN on amyloid metabolism and a role of PGRN in regulating lysosomal activities and inflammation in plaque-associated microglia, which may contribute to the disease mechanism associated with PGRN polymorphisms in AD.
Longitudinal characterization of neuroanatomical changes in the Fischer 344 rat brain during normal aging and between sexes
Authors: Fowler Caitlin , Goerzen Dana , Madularu Dan , Devenyi Gabriel A. , Chakravarty M. Mallar , Near Jamie
Published: April 2021

Animal models are widely used to study the pathophysiology of disease and to evaluate the efficacy of novel interventions, crucial steps towards improving disease outcomes in humans. The Fischer 344 (F344) wildtype rat is a common experimental background strain for transgenic models of disease and is also one of the most frequently used models in aging research. Despite frequency of use, characterization of neuroanatomical change with age has not been performed in the F344 rat. To this end, we present a comprehensive longitudinal examination of morphometric change in 73 brain regions and at a voxel-wise level during normative aging in a mixed-sex cohort of F344 rats. We identified age- and sex-related changes in regions such as the cortex, hippocampus, cingulum, caudoputamen, and nucleus accumbens, which are implicated in memory and motor control circuits frequently affected by aging and neurodegenerative disease. These findings provide a baseline for neuroanatomical changes associated with aging in male and female F344 rats, to which data from transgenic models or other background strains can be compared.

HIGHLIGHTS

In vivomagnetic resonance imaging reveals altered neuroanatomy in aging Fischer rats

Linear and curvilinear age effects exist in both grey and white matter structures

Sex differences are primarily seen in grey matter structures

This study clarifies normal aging trajectories across 73 brain regions in both sexes

Improved understanding of normal aging will inform future pathological aging studies
Target enrichment improves phylogenetic resolution in the genusZanthoxylum(Rutaceae) and indicates both incomplete lineage sorting and hybridization events
Authors: Reichelt Niklas , Wen Jun , Pätzold Claudia , Appelhans Marc S
Published: April 2021

Background and aims

ZanthoxylumL. is the only pantropical genus within Rutaceae, with a few species native to temperate eastern Asia and North America. Efforts using Sanger sequencing failed to resolve the backbone phylogeny ofZanthoxylum. In this study, we employed target enrichment high-throughput sequencing to improve resolution. Gene trees were examined for concordance and sectional classifications ofZanthoxylumwere evaluated. Off-target reads were investigated to identify putative single-copy markers for bait refinement, and low-copy markers for evidence of putative hybridization events.

Methods

We developed a custom bait set for target enrichment of 745 exons inZanthoxylumand applied it to 45Zanthoxylumspecies and oneTetradiumspecies as the outgroup. Illumina reads were processed via the HybPhyloMaker pipeline. Phylogenetic inferences were conducted using coalescent and concatenated methods. Concordance was assessed using quartet sampling. Off-target reads were assembled and putative single- and low-copy genes were extracted. Additional phylogenetic analyses were performed based on these alignments.

Key results

Four major clades are supported withinZanthoxylum: the African clade, theZ. asiaticumclade, the Asian-Pacific-Australian clade, and the American-eastern Asian clade. While overall support has improved, regions of conflict are similar to those previously observed. Gene tree discordances indicate a hybridization event in the ancestor of the Hawaiian lineage, and incomplete lineage sorting for the American backbone. Off-target putative single-copy genes largely confirm on-target results, and putative low-copy genes provide additional evidence for hybridization in the Hawaiian lineage. Only two of the five sections ofZanthoxylumare resolved as monophyletic.

Conclusion

Target enrichment is suitable to assess phylogenetic relationships inZanthoxylum. Our phylogenetic analyses reveal that current sectional classifications need revision. Quartet tree concordance indicates several instances of reticulate evolution. Off-target reads are proven useful to identify additional phylogenetically informative regions for bait refinement or gene tree based approaches.
Phase- and State-Dependent Modulation of Breathing Pattern by preBötzinger Complex Somatostatin Expressing Neurons
Authors: de Sousa Abreu Raquel P. , Bondarenko Evgeny , Feldman Jack L.
Published: April 2021

As neuronal subtypes are increasingly categorized, delineating their functional role is paramount. The preBötzinger Complex (preBötC) subpopulation expressing the neuropeptide somatostatin (SST) is classified as mostly excitatory, inspiratory-modulated and not rhythmogenic. We further characterized their phenotypic identity; 87% were glutamatergic and the balance were glycinergic and/or GABAergic. We then used optogenetics to investigate their modulatory role in both anesthetized and freely moving mice. In anesthetized mice, short photostimulation (100 ms) of preBötC SST+neurons modulated breathing-related variables in a combinatory phase- and state-dependent manner; changes in inspiratory duration, inspiratory peak amplitude (Amp), and phase were different at higher (≥2.5 Hz) vs. lower (<2.5 Hz) breathing frequency. Moreover, we observed a biphasic effect of photostimulation during expiration that is probabilistic, i.e., photostimulation given at the same phase in consecutive cycles can evoke opposite responses (lengthening vs. shortening of the phase). This unexpected probabilistic state- and phase-dependent responses to photostimulation exposed properties of the preBötC that were not predicted and cannot be readily accounted for in current models of preBötC pattern generation. In freely moving mice, prolonged photostimulation decreasedfin normoxia, hypoxia, or hypercapnia, and increased Amp and produced a phase advance, which was similar to the results in anesthetized mice whenf≥2.5 Hz. We conclude that preBötC SST+neurons are a key mediator of the extraordinary and essential lability of breathing pattern.

Key points summary

We transfected preBötzinger Complex (preBötC) somatostatin-expressing (SST+) neurons, which modulate respiratory pattern, but are not rhythmogenic, with channelrhodopsin to investigate phase- and state-dependent modulation of breathing pattern in anesthetized and freely behaving mice in normoxia, hypoxia, and hypercapnia.

In anesthetized mice, photostimulation of preBötC SST+neurons during inspiration increased inspiratory duration and amplitude regardless of baseline breathing frequency,f.

In anesthetized mice with lowf(<2.5 Hz), photostimulation of preBötC SST+neurons during expiration evoked either phase advance or phase delay, whereas in anesthetized mice with highf(≥2.5 Hz) and in freely behaving mice in normoxia, hypoxia, or hypercapnia, photostimulation always evoked phase advance.

Phase- and state-dependency is a function of overall breathing network excitability.

Thef-dependent probabilistic modulation of breathing pattern by preBötC SST+neurons was unexpected, requiring reconsideration of current models of preBötC function, which neither predict nor can readily account for such responses.
Persistence and anti-persistence in treadmill walking
Authors: Kozlowska Klaudia , Latka Miroslaw , West Bruce J.
Published: April 2021

Background

Long-range persistent correlations in stride time (ST) and length (SL) are the fundamental traits of treadmill gait. Our recent work showed that the ST and SL time series’ statistical properties originated from the superposition of large-scale trends and small-scale fluctuations (residuals). Trends served as the control manifolds about which ST and SL fluctuated. The scaling exponents of the residuals were slightly smaller than 0.5.

Research question

Do random changes in treadmill belt speed affect the trend properties and scaling exponents of ST/SL residuals?

Methods

We used Multivariate Adaptive Regression Splines (MARS) to determine gait trends during a walk on a treadmill whose belt speed was perturbed by a strong random noise. Then, we calculated the scaling exponents of MARS residuals with the madogram estimator.

Results

Except for the ST at the lowest treadmill speedv= 0.8 m/s, the normalized trend duration was at least three times greater than that for the unperturbed walk. The Cauchy distribution scale parameter, which served as a measure of the width of SL and ST trend slope distributions, was atv= 1.2 m/s, almost 50% and 25% smaller than the unperturbed values. The differences were even greater atv= 1.6 m/s: 73% and 83%. For all speeds, the ST and SL MARS residuals were strongly anti-persistent. Atv= 1.2 m/s, the corresponding scaling exponents were equal to 0.37±0.10 and 0.25±0.09. Apart from ST atv= 0.8 m/s, the ST/SL scaling indices were close to 0.5.

Significance

Persistence of gait parameters is closely related to the properties of their trends. Longer trends with a gentle slope and strong anti-persistence of ST/SL residuals are the manifestations or tight control required during the perturbed treadmill walk.
Multi-Trait Machine and Deep Learning Models for Genomic Selection using Spectral Information in a Wheat Breeding Program
Authors: Sandhu Karansher S. , Patil Shruti S. , Pumphrey Michael O. , Carter Arron H.
Published: April 2021

Prediction of breeding values and phenotypes is central to plant breeding and has been revolutionized by the adoption of genomic selection (GS). Use of machine and deep learning algorithms applied to complex traits in plants can improve prediction accuracies in the context of GS. Spectral reflectance indices further provide information about various physiological parameters previously undetectable in plants. This research explores the potential of multi-trait (MT) machine and deep learning models for predicting grain yield and grain protein content in wheat using spectral information in GS models. This study compares the performance of four machine and deep learning-based uni-trait (UT) and MT models with traditional GBLUP and Bayesian models. The dataset consisted of 650 recombinant inbred lines from a spring wheat breeding program, grown for three years (2014-2016), and spectral data were collected at heading and grain filling stages. MT-GS models performed 0-28.5% and −0.04-15% superior to the UT-GS models for predicting grain yield and grain protein content. Random forest and multilayer perceptron were the best performing machine and deep learning models to predict both traits. These two models performed similarly under UT and MT-GS models. Four explored Bayesian models gave similar accuracies, which were less than machine and deep learning-based models, and required increased computational time. Green normalized difference vegetation index best predicted grain protein content in seven out of the nine MT-GS models. Overall, this study concluded that machine and deep learning-based MT-GS models increased prediction accuracy and should be employed in large-scale breeding programs.

Core Ideas

Potential for combining high throughput phenotyping, machine and deep learning in breeding.

Multi-trait models exploit information from secondary correlated traits efficiently.

Spectral information improves genomic selection models.

Deep learning can aid plant breeders owing to increased data generated in breeding programs
Auditory processing remains sensitive to environmental experience during adolescence
Authors: Anbuhl Kelsey L. , Yao Justin D. , Hotz Robert A. , Mowery Todd M. , Sanes Dan H.
Published: April 2021

Development is a time of great opportunity. A heightened period of neural plasticity contributes to dramatic improvements in perceptual, motor, and cognitive skills. However, developmental plasticity poses a risk: greater malleability of neural circuits exposes them to environmental factors that may impede behavioral maturation. While these risks are well-established prior to sexual maturity (i.e., critical periods), the degree of neural vulnerability during adolescence remains uncertain. To address this question, we induced a transient period of hearing loss (HL) spanning adolescence in the gerbil, confirmed by assessment of circulating sex hormones, and asked whether behavioral and neural deficits are diminished. Wireless recordings were obtained from auditory cortex neurons during perceptual task performance, and within-session behavioral and neural sensitivity were compared. We found that a transient period of adolescent HL caused a significant perceptual deficit (i.e., amplitude modulation detection thresholds) that could be attributed to degraded auditory cortex processing, as confirmed with both single neuron and population-level analyses. In contrast, perceptual deficits did not occur when HL of the same duration was induced in adulthood. To determine whether degraded auditory cortex encoding was attributable to an intrinsic change, we obtained auditory cortex brain slices from adolescent HL animals, and recorded synaptic and discharge properties from auditory cortex pyramidal neurons. There was a clear and novel phenotype, distinct from critical period HL: excitatory postsynaptic potential amplitudes were elevated in adolescent HL animals, whereas inhibitory postsynaptic potentials were unchanged. This is in contrast to critical period deprivation, where there are large changes to synaptic inhibition. Taken together, these results show that diminished adolescent sensory experience can cause long-lasting behavioral deficits that originate, in part, from a dysfunctional cortical circuit.

Abstract Figure

Summary of experimental design and main findings.
Within-cycle instantaneous frequency profiles report oscillatory waveform dynamics
Authors: Quinn Andrew J. , Lopes-dos-Santos Vítor , Huang Norden , Liang Wei-Kuang , Juan Chi-Hung , Yeh Jia-Rong , Nobre Anna C. , Dupret David , Woolrich Mark W.
Published: April 2021

Non-sinusoidal waveform is emerging as an important feature of neuronal oscillations. However, the role of single cycle shape dynamics in rapidly unfolding brain activity remains unclear. Here, we develop an analytical framework that isolates oscillatory signals from time-series using masked Empirical Mode Decomposition to quantify dynamical changes in the shape of individual cycles (along with amplitude, frequency and phase) using instantaneous frequency. We show how phase-alignment, a process of projecting cycles into a regularly sampled phase-grid space, makes it possible to compare cycles of different durations and shapes. ‘Normalised shapes’ can then be constructed with high temporal detail whilst accounting for differences in both duration and amplitude. We find that the instantaneous frequency tracks non-sinusoidal shapes in both simulated and real data. Notably, in local field potential recordings of mouse hippocampal CA1, we find that theta oscillations have a stereotyped slow-descending slope in the cycle-wise average, yet exhibiting high variability on a cycle-by-cycle basis. We show how Principal Components Analysis allows identification of motifs of theta cycle waveform that have distinct associations to cycle amplitude, cycle duration and animal movement speed. By allowing investigation into oscillation shape at high temporal resolution, this analytical framework will open new lines of enquiry into how neuronal oscillations support moment-by-moment information processing and integration in brain networks.
Borf: Improved ORF prediction inde-novoassembled transcriptome annotation
Authors: Signal Beth , Kahlke Tim
Published: April 2021

ORF prediction inde-novoassembled transcriptomes is a critical step for RNA-Seq analysis and transcriptome annotation. However, current approaches do not appropriately account for factors such as strand-specificity and incompletely assembled transcripts. Strand-specific RNA-Seq libraries should produce assembled transcripts in the correct orientation, and therefore ORFs should only be annotated on the sense strand. Additionally, start site selection is more complex than appreciated as sequences upstream of the first start codon need to be correctly annotated as 5’ UTR in completely assembled transcripts, or part of the main ORF in incomplete transcripts. Both of these factors influence the accurate annotation of ORFs and therefore the transcriptome as a whole. We generated fourde-novotranscriptome assemblies of well annotated species as a gold-standard dataset to test the impact strand specificity and start site selection have on ORF prediction in real data. Our results show that prediction of ORFs on the antisense strand in data from stranded RNA libraries results in false-positive ORFs with no or very low similarity to known proteins. In addition, we found that up to 23% of assembled transcripts had no stop codon upstream and in-frame of the first start codon, instead comprising a sequence of upstream codons. We found the optimal length cutoff of these upstream sequences to accurately classify these transcripts as either complete (upstream sequence is 5’ UTR) or 5’ incomplete (transcript is incompletely assembled and upstream sequence is part of the ORF). Here, we present Borf, the better ORF finder, specifically designed to minimise false-positive ORF prediction in stranded RNA-Seq data and improve annotation of ORF start-site prediction accuracy. Borf is written in Python3 and freely available athttps://github.com/betsig/borf.
Marine food webs are more complex but less stable in sub-Antarctic than in Antarctic regions
Authors: Rodriguez Iara Diamela , Marina Tomás Ignacio , Schloss Irene Ruth , Saravia Leonardo Ariel
Published: April 2021

Food web structure plays an important role in determining ecosystem stability against perturbations. High-latitude marine ecosystems are being affected by environmental stressors and biological invasions. In the West Antarctic Peninsula these transformations are mainly driven by climate change, while in the sub-Antarctic region by anthropogenic activities. Understanding the differences between these areas is necessary to monitor the changes that are expected to occur in the upcoming decades. Here, we compared the structure and stability of Antarctic (Potter Cove) and sub-Antarctic (Beagle Channel) marine food webs. We compiled species trophic interactions (predator-prey) and calculated complexity, structure and stability metrics. Even if both food webs presented the same connectance, we found important differences between them. The Beagle Channel food web is more complex, but less stable and sensitive to the loss of its most connected species, while the Potter Cove food web presented lower complexity and greater stability against perturbations.
Many ways to stick the landing: novel righting strategies allow spotted lanternfly nymphs to land on diverse substrates
Authors: Kane Suzanne Amador , Bien Theodore , Contreras-Orendain Luis , Ochs Michael F. , Hsieh S. Tonia
Published: April 2021

Unlike large animals, insects and other very small animals are so unsusceptible to impact-related injuries that they can use falling for dispersal and predator evasion. Reorienting to land upright can mitigate lost access to resources and predation risk. Such behaviors are critical for the spotted lanternfly (SLF) (Lycorma delicatula), an invasive, destructive insect pest spreading rapidly in the US. High-speed video of SLF nymphs released under different conditions showed that these insects self-right using both active midair righting motions previously reported for other insects, and novel post-impact mechanisms that take advantage of their ability to experience near-total energy loss on impact. Unlike during terrestrial self-righting, in which an animal initially at rest on its back uses appendage motions to flip over, SLF nymphs impacted the surface at varying angles and then self-righted during the rebound using coordinated body rotations, foot-substrate adhesion, and active leg motions. These previously-unreported strategies were found to promote disproportionately upright, secure landings on both hard, flat surfaces and tilted, compliant host plant leaves. Our results highlight the importance of examining biomechanical phenomena in ecologically-relevant contexts, and show that, for small animals, the post-impact bounce period can be critical for achieving an upright landing.
Plasticity of the gastrocnemius elastic system in response to decreased work and power demand during growth
Authors: Cox SM , DeBoef A , Salzano MQ , Katugam K , Piazza SJ , Rubenson J
Published: April 2021

Elastic energy storage and release can enhance performance that would otherwise be limited by the force-velocity constraints of muscle. While functional influence of a biological spring depends on tuning between components of an elastic system (the muscle, spring, driven mass, and lever system), we do not know whether elastic systems systematically adapt to functional demand. To test whether altering work and power generation during maturation alters the morphology of an elastic system, we prevented growing guinea fowl (Numida Meleagris) from jumping. At maturity, we compared the jump performance of our treatment group to that of controls and measured the morphology of the gastrocnemius elastic system. We found that restricted birds jumped with lower jump power and work, yet there were no significant between-group differences in the components of the elastic system. Further, subject-specific models revealed no difference in energy storage capacity between groups, though energy storage was most sensitive to variations in muscle properties (most significantly operating length and least dependent on tendon stiffness). We conclude that the gastrocnemius elastic system in the guinea fowl displays little to no plastic response to decreased demand during growth and hypothesize that neural plasticity may explain performance variation.
The Bouma law accounts for crowding in fifty observers
Authors: Kurzawski Jan W. , Burchell Augustin , Thapa Darshan , Winawer Jonathan , Majaj Najib J. , Pelli Denis G.
Published: April 2021

Abstract

Crowdingis the failure to recognize an object due to surrounding clutter. Our visual crowding survey measured 13 crowding distances (or “critical spacings”) twice in each of 50 observers. The survey included three eccentricities (0, 5, and 10 deg), four cardinal meridians, two orientations (radial and tangential), and two fonts (Sloan and Pelli). The survey also tested foveal acuity, twice. Remarkably, fitting a two-parameter model, the well- known Bouma law — crowding distance grows linearly with eccentricity — explains 82% of the variance for all 13 × 50 measured log crowding distances, cross-validated. An enhanced Bouma law, with factors for meridian, crowding orientation, target kind, and observer, explains 94% of the variance, again cross-validated. These additional factors reveal several asymmetries, consistent with previous reports, which can be expressed as crowding- distance ratios: 0.62 horizontal:vertical, 0.79 lower:upper, 0.78 right:left, 0.55 tangential:radial, and 0.78 Sloan font:Pelli font. Across our observers, peripheral crowding is independent of foveal crowding and acuity. Evaluation of the Bouma factorb(the slope of the Bouma law) as a biomarker of visual health would be easier if there were a way to compare results across crowding studies that use different methods. We define astandardized Bouma factor b’that corrects for differences from Bouma’s 25 choice alternatives, 75% threshold criterion, and linearly symmetric flanker placement. For radial crowding on the right meridian, the standardized Bouma factorb’is 0.24 for this study, 0.35 for Bouma (1970), and 0.30 for the geometric mean across five representative modern studies, including this one, showing good agreement across labs, including Bouma’s. We found that guaranteeing fixation by gaze-contingent display halved the standard deviation across observers of the estimated logb. The reduction in standard deviation is explained by a “peeking” model in which the observer looked near an anticipated target location in 50% ofunmonitored-fixation trials. Individual differences are robust, as evidenced by the much larger 0.08 SD of logbacross observers than the 0.03 SD of test-retest within observers. Crowding’s ease of measurement enhances its promise as a biomarker for dyslexia and visual health.
Exploring Proteomes of RobustYarrowia lipolyticaIsolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation
Authors: Walker Caleb , Dien Bruce , Giannone Richard J. , Slininger Patricia , Thompson Stephanie R. , Trinh Cong T.
Published: April 2021

Yarrowia lipolyticais an oleaginous yeast exhibiting robust phenotypes beneficial for industrial biotechnology. The phenotypic diversity found within the undomesticatedY. lipolyticaclade from various origins illuminates desirable phenotypic traits not found in the conventional laboratory strain CBS7504, which include xylose utilization, lipid accumulation, and growth on undetoxified biomass hydrolysates. Currently, the related phenotypes of lipid accumulation and degradation when metabolizing non-preferred sugars (e.g., xylose) associated with biomass hydrolysates are poorly understood, making it difficult to control and engineer inY. lipolytica. To fill this knowledge gap, we analyzed the genetic diversity of five undomesticatedY. lipolyticastrains and identified singleton genes and genes exclusively shared by strains exhibiting desirable phenotypes. Strain characterizations from controlled bioreactor cultures revealed that the undomesticated strain YB420 used xylose to support cell growth and maintained high lipid levels while the conventional strain CBS7504 degraded cell biomass and lipids when xylose was the sole remaining carbon source. From proteomic analysis, we identified carbohydrate transporters, xylose metabolic enzymes and pentose phosphate pathway proteins stimulated during the xylose uptake stage for both strains. Furthermore, we distinguished proteins in lipid metabolism (e.g., lipase, NADPH generation, lipid regulators, β-oxidation) activated by YB420 (lipid maintenance phenotype) or CBS7504 (lipid degradation phenotype) when xylose was the sole remaining carbon source. Overall, the results relate genetic diversity of undomesticatedY. lipolyticastrains to complex phenotypes of superior growth, sugar utilization, lipid accumulation and degradation in biomass hydrolysates.

IMPORTANCE

Yarrowia lipolyticais an important industrial oleaginous yeast due to its robust phenotypes for effective conversion of inhibitory lignocellulosic biomass hydrolysates into neutral lipids. While lipid accumulation has been well characterized in this organism, its interconnected lipid degradation phenotype is poorly understood during fermentation of biomass hydrolysates. Our investigation into the genetic diversity of undomesticatedY. lipolyticastrains, coupled with detailed strain characterization and proteomic analysis, revealed metabolic processes and regulatory elements conferring desirable phenotypes for growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates by these natural variants. This study provides a better understanding of the robust metabolism ofY. lipolyticaand suggests potential metabolic engineering strategies to enhance its performance.
Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles
Authors: Gaulke Christopher A , Schmeltzer Emily R , Dasenko Mark , Tyler Brett M. , Thurber Rebecca Vega , Sharpton Thomas J
Published: April 2021

Shotgun metagenomic sequencing has transformed our understanding of microbial community ecology. However, preparing metagenomic libraries for high-throughput DNA sequencing remains a costly, labor-intensive, and time-consuming procedure, which in turn limits the utility of metagenomes. Several library preparation procedures have recently been developed to offset these costs, but it is unclear how these newer procedures compare to current standards in the field. In particular, it is not clear if all such procedures perform equally well across different types of microbial communities, or if features of the biological samples being processed (e.g., DNA amount) impact the accuracy of the approach. To address these questions, we assessed how five different shotgun DNA sequence library preparation methods, including the commonly used Nextera®Flex kit, perform when applied to metagenomic DNA. We measured each method’s ability to produce metagenomic data that accurately represents the underlying taxonomic and genetic diversity of the community. We performed these analyses across a range of microbial community types (e.g., soil, coral-associated, mouse-gut-associated) and input DNA amounts. We find that the type of community and amount of input DNA influence each method’s performance, indicating that careful consideration may be needed when selecting between methods, especially for low complexity communities. However, cost-effective preparation methods we assessed are generally comparable to the current gold standard Nextera®DNA Flex kit for high-complexity communities. Overall, the results from this analysis will help expand and even facilitate access to metagenomic approaches in future studies.

IMPORTANCE

Metagenomic library preparation methods and sequencing technologies continue to advance rapidly, allowing researchers to characterize microbial communities in previously underexplored environmental samples and systems. However, widely-accepted standardized library preparation methods can be cost-prohibitive. Newly available approaches may be less expensive, but their efficacy in comparison to standardized methods remains unknown. In this study, we compared five different metagenomic library preparation methods. We evaluated each method across a range of microbial communities varying in complexity and quantity of input DNA. Our findings demonstrate the importance of considering sample properties, including community type, composition, and DNA amount, when choosing the most appropriate metagenomic library preparation method.
HCV spread kinetics reveal varying contributions of transmission modes to infection dynamics
Authors: Durso-Cain Karina , Kumberger Peter , Schälte Yannik , Fink Theresa , Dahari Harel , Hasenauer Jan , Uprichard Susan L. , Graw Frederik
Published: April 2021

Hepatitis C virus (HCV) is capable of spreading within a host by two different transmission modes: cell-free and cell-to-cell. Although viral dissemination and diffusion of viral particles facilitates the infection of distant cells, direct cell-to-cell transmission to uninfected neighboring cells is thought to shield the virus from immune recognition. However, the contribution of each of these transmission mechanisms to HCV spread is unknown. To dissect the contribution of these different transmission modes to HCV spread, we measured HCV lifecycle kinetics and used an in vitro spread assay to monitor HCV spread kinetics after low multiplicity of infection in the absence and presence of a neutralizing antibody that blocks cell-free spread. By analyzing these data with a spatially-explicit mathematical model that describes viral spread on a single-cell level, we quantified the contribution of cell-free and cell-to-cell spread to the overall infection dynamics and show that both transmission modes act synergistically to enhance the spread of infection. Thus, the simultaneous occurrence of both transmission modes likely represents an advantage for HCV that may contribute to the efficient establishment of chronic infection. Notably, the relative contribution of each viral transmission mode appeared to vary dependent on different experimental conditions and suggests that viral spread is optimized according to the environment. Together, our analyses provide insight into the transmission dynamics of HCV and reveal how different transmission modes impact each other.

Importance

Hepatitis C Virus can spread within a host by diffusing viral particles or direct cell-to-cell transfer of viral material between infected and uninfected cells. To which extend these cell-free and cell-to-cell transmission modes contribute to HCV spread, establishment of chronicity and antiviral escape is still unknown. By combiningin vitroexperimental HCV spread data with a multi-scale mathematical model we have disentangled the contribution and interplay of cell-free and cell-to-cell transmission modes during HCV infection. Our analysis revealed synergistic effects between the two transmission modes, with the relative contribution of each transmission mode varying dependent on the experimental conditions. This highlights the adaptability of the virus and suggests that transmission modes might be optimized dependent on the environment, which could contribute to viral persistence.