bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural basis underlying specific biochemical activities of non-muscle tropomyosin isoforms
Authors: Selvaraj Muniyandi , Kokate Shrikant , Reggiano Gabriella , Kogan Konstantin , Kotila Tommi , Kremneva Elena , DiMaio Frank , Lappalainen Pekka , Huiskonen Juha T.
Published: May 2022

The actin cytoskeleton is critical for cell migration, morphogenesis, endocytosis, organelle dynamics, and cytokinesis. To support diverse cellular processes, actin filaments form a variety of structures with specific architectures and dynamic properties. Key proteins specifying actin filaments are tropomyosins. Non-muscle cells express several functionally non-redundant tropomyosin isoforms, which differentially control the interactions of other proteins, including myosins and ADF/cofilin, with actin filaments. However, the underlying molecular mechanisms have remained elusive. By determining the cryogenic electron microscopy structures of actin filaments decorated by two functionally distinct non-muscle tropomyosin isoforms, Tpm1.6 and Tpm3.2, we reveal that actin filament conformation remains unaffected upon binding. However, Tpm1.6 and Tpm3.2 follow different paths along the major groove of the actin filament, providing an explanation for their incapability to co-polymerize on actin filaments. The structures and biochemical work also elucidate the molecular basis underlying specific roles of Tpm1.6 and Tpm3.2 in myosin II activation and protecting actin filaments from ADF/cofilin-catalysed severing.
Partner-assisted artificial selection of a secondary function for efficient bioremediation
Authors: Zaccaria Marco , Sandlin Natalie , Soen Yoav , Momeni Babak
Published: May 2022

Microbial enzymes have a broad potential to address many current needs, such as detoxification of harmful toxins and waste, but their native performance often does not match specific applications of interest. In attempting to evolve strains for a specific need, one challenge is that our functions of interest may not confer a fitness effect on the producer. As a result, a conventional selection scheme cannot be used to improve such secondary functions. We propose an alternative approach, partner-assisted artificial selection (PAAS), in which an assisting population acts as an intermediate to create a feedback from the function of interest to the fitness of the producer. We use a simplified model to examine how well and under what conditions such a scheme leads to improved enzymatic function, focusing on degradation of a toxin as a case example. We find that selection for improved growth in this scheme successfully leads to improved degradation performance, even in the presence of other sources of stochasticity. We find that standard selection considerations apply in PAAS: a more restrictive bottleneck leads to stronger selection but adds uncertainty. We also examine how much stochasticity in other traits can be tolerated in PAAS. Our findings offer a roadmap for successful implementation of PAAS to evolve improved functions of interest such as detoxification of harmful compounds.
The cluster transfer function of AtNEET supports the ferredoxin-thioredoxin network of plant cells
Authors: Zandalinas Sara I. , Song Luhua , Nechushtai Rachel , Mendoza-Cozatl David G , Mittler Ron
Published: May 2022

NEET proteins are conserved 2Fe-2S proteins that regulate the levels of iron and reactive oxygen species in plant and mammalian cells. Previous studies of seedlings with constitutive expression of AtNEET, or its dominant-negative variant H89C (impaired in 2Fe-2S cluster transfer), revealed that disrupting AtNEET function causes oxidative stress, chloroplast iron overload, activation of iron-deficiency responses, and cell death. Because disrupting AtNEET function is deleterious to plants, we developed an inducible expression system to study AtNEET function in mature plants using a time-course proteomics approach. Here, we report that suppression of AtNEET cluster transfer function results in drastic changes in the expression of different members of the ferredoxin (Fd), Fd-thioredoxin (TRX) reductase (FTR), and TRX network of Arabidopsis, as well as in cytosolic cluster assembly proteins. In addition, the expression of Yellow Stripe-Like 6 (YSL6), involved in iron export from chloroplasts was elevated. Taken together, our findings reveal new roles for AtNEET in supporting the Fd-TFR-TRX network of plants, iron mobilization from the chloroplast, and cytosolic 2Fe-2S cluster assembly. In addition, we show that AtNEET function is linked to the expression of glutathione peroxidases (GPXs) which play a key role in the regulation of ferroptosis and redox balance in different organisms.

Highlight

Using proteomics analysis and an inducible expression system, the iron-sulfur cluster transfer function of AtNEET was found to support the ferredoxin-thioredoxin network of Arabidopsis.
Trans-generational physiological condition of embryos is conditioned by maternal thermal stress inOctopus maya
Authors: Domínguez-Castanedo Omar , Palomino-Cruz Daniela , Mascaró Maite , Rodríguez-Fuentes Gabriela , Juárez Oscar E. , Galindo-Sánchez Clara E. , Caamal-Monsreal Claudia , Torres Pavel Galindo , Díaz Fernando , Rosas Carlos
Published: May 2022

Current anthropogenic global warming generates profound metabolic alterations in marine ectotherm invertebrates capable of leading a wide range of these species to extinction. The most worrying and devastating consequence may be that the effect of thermal stress overpasses the individual generations. To evaluate the transgenerational effect of thermal stress on the cephalopodOctopus maya, this study experimentally tests morphology, respiratory metabolism, antioxidant mechanisms, and oxidative stress indicators of the embryos incubated at two temperatures (24 and 30°C) produced by females acclimated at 24 and 30°C. The results demonstrate that, regardless of their incubation temperature, embryos from females acclimated at 30°C are smaller, show more accelerated development, and higher respiratory rates than those from females acclimated at 24°C. These embryos confirmed a greater oxidative stress degree, as well as an increased amount of soluble carbonylated proteins and catalase activity as the main enzyme during the activation development stage (even the highest in the embryos incubated at 30°C). Finally, a collapse of the antioxidant defense system was observed, measured as lower both CAT activity and GSH concentrations. Additionally, soluble carbonylated proteins reduced and GST activity increased in embryos incubated at 30°C from females maintained at high temperatures in a clear deleterious and transgenerational effect of thermal stress on this octopus species.
Fat body-specific reduction of CTPS alleviates HFD-induced obesity
Authors: Liu Jingnan , Zhang Yuanbing , Zhou Youfang , Wang Qiao-Qi , Liu Ji-Long
Published: May 2022

High fat diet (HFD)-induced obesity is a multi-factorial disease including genetic, physiological, behavioral, and environmental components. Drosophila has emerged as a useful model of metabolic diseases. Cytidine 5′-triphosphate synthase (CTPS) is a key enzyme for the de novo synthesis of CTP, governing cellular level of CTP and phospholipid synthesis. We have demonstrated that CTPS show the capacity to assemble into large filaments termed cytoophidia, which are evolutionarily conserved in bacteria, archaea and eukaryotes. Here, we show that CTPS acts in fat body to regulate body weight and starvation resistant in Drosophila. HFD-induced obesity elevates CTPS transcription and elongates cytoophidia in larval adipocytes. Fat body-specific depletion of CTPS alleviated HFD-induced obesity including body weight gain, lipid storage and TAG level. Moreover, a dominant negative form of CTPS reduces lipid accumulation and down regulates lipogenic genes. Therefore, our data not only provide a functional link between CTPS and lipid homeostasis, but also highlight the potential application of manipulating CTPS in the treatment of HFD-induced obesity.
Short term tomato consumption alters the pig gut microbiome towards a more favorable profile
Authors: Goggans Mallory L. , Bilbrey Emma A. , Quiroz-Moreno Cristian , Francis David M. , Jacobi Sheila K. , Kovac Jasna , Cooperstone Jessica L.
Published: May 2022

Diets rich in fruits and vegetables have been shown to exert positive effects on the gut microbiome. However, little is known about the specific effect of individual fruits or vegetables on gut microbe profiles. This study aims to elucidate the effects of tomato consumption on the gut microbiome, as tomatoes account for 22% of vegetable consumption in Western diets, and their consumption has been associated with positive health outcomes. Using piglets as a physiologically relevant model of human metabolism, 20 animals were assigned either to a control or tomato powder supplemented diet (both macronutrient matched and isocaloric) for 14 days. The microbiome was sampled rectally at three time points: day 0 (baseline), day 7 (midpoint), and at day 14 (end of study). DNA was sequenced using shotgun metagenomics, and reads were annotated using MG-RAST. There were no differences in body weight or feed intake between our two treatment groups. There was a microbial shift which included a higher ratio of Bacteroidota to Bacillota (formerly known as Bacteroidetes and Firmicutes, respectively) and higher alpha-diversity in tomato-fed animals, indicating a shift to a more desirable phenotype. Analyses at both the phyla and genera levels showed global microbiome profile changes (PERMANOVA P ≤ 0.05) over time, but not with tomato consumption. These data suggest that short-term tomato consumption can beneficially influence the gut microbial profile, warranting further investigation in humans.

IMPORTANCE

The composition of the microorganisms in the gut is a contributor to overall health, prompting the development of strategies to alter the microbiome composition. Studies have investigated the role of the diet on the microbiome, as it is a major modifiable risk factor contributing to health; however, little is known about the causal effects of consumption of specific foods on the gut microbiota. A more complete understanding of how individual foods impact the microbiome will enable more evidence-based dietary recommendations for long-term health. Tomatoes are of interest as the most consumed non-starchy vegetable and a common source of nutrients and phytochemicals across the world. This study aimed to elucidate the effect of short-term tomato consumption on the microbiome, using piglets as a physiologically relevant model to humans. We found that tomato consumption can positively affect the gut microbial profile, which warrants further investigation in humans.
Transcriptome analysis in the silkworm Bombyx mori overexpressing piRNA-resistant Masculinizer gene
Authors: Tomihara Kenta , Katsuma Susumu , Kiuchi Takashi
Published: May 2022

Dosage compensation is a process that produces a similar expression of sex-linked and autosomal genes. In the silkworm Bombyx mori with a WZ sex-determination system, the expression from the single Z in WZ females matches that of ZZ males due to the suppression of Z-linked genes in males. A primary maleness determinant gene, Masculinizer (Masc), is also required for dosage compensation. In females, P-element induced wimpy testis (PIWI) is complexed with the W chromosome-derived female-specific Feminizer (Fem) PIWI-interacting RNA (piRNA) and cleaves Masc mRNA. When Fem piRNA-resistant Masc cDNA (Masc-R) is overexpressed in both sexes, only female larvae are dead during the larval stage. In this study, transcriptome analysis was performed in neonate larvae to examine the effects of Masc-R overexpression on a global gene expression profile. Z-linked genes were globally repressed in Masc-R-overexpressing females due to force-driven dosage compensation. In contrast, Masc-R overexpression had little effect on the expression of Z-linked genes and the male-specific isoform of B. mori insulin-like growth factor II mRNA-binding protein in males, indicating that excessive Masc expression strengthens neither dosage compensation nor maleness in males. Fourteen genes were differentially expressed between Masc-R-overexpressing and control neonate larvae in both sexes, suggesting Masc functions other than dosage compensation and masculinization.

Highlights

Transcriptome analysis was performed in Masc-R-overexpressing neonate Bombyx mori larvae.

Z-linked genes were globally suppressed in Masc-R-overexpressing females.

Masc-R overexpression had little effect on BmImpM expression in males.

Several genes may be controlled by Masc-R regardless of sex.
Diffraction contrast in cryo-scanning transmission electron tomography reveals the boundary of hemozoin crystals in situ
Authors: Mullick Debakshi , Rechav Katya , Leiserowitz Leslie , Regev-Rudzki Neta , Dzikowski Ron , Elbaum Michael
Published: May 2022

Malaria is a potentially fatal infectious disease caused by the obligate intracellular parasite Plasmodium falciparum. The parasite infects human red blood cells (RBC) and derives nutrition by catabolism of hemoglobin. As amino acids are assimilated from the protein component, the toxic heme is released. Molecular heme is detoxified by rapid sequestration to physiologically insoluble hemozoin crystals within the parasite’s digestive vacuole (DV). Common antimalarial drugs interfere with this crystallization process, leaving the parasites vulnerable to the by-product of their own metabolism. A fundamental debate with important implications on drug mechanism regards the chemical environment of crystallization in vivo, whether aqueous or lipid. This issue had been addressed previously by cryogenic soft X-ray tomography. We employ cryo-scanning transmission electron tomography (CSTET) to probe parasite cells throughout the life cycle in a fully hydrated, vitrified state at higher resolution. During the acquisition of CSTET data, Bragg diffraction from the hemozoin provides a uniquely clear view of the crystal boundary at nanometer resolution. No intermediate medium, such as a lipid coating or shroud, could be detected surrounding the crystals. The present study describes a unique application of CSTET in the study of malaria. The findings can be extended to evaluate new drug candidates affecting hemozoin crystal growth.
Dandy Walker-like malformations in mutant mice demonstrate a role for PDGF-C/PDGFRα signalling in cerebellar development
Authors: Gillnäs Sara , Gallini Radiosa , He Liqun , Betsholtz Christer , Andrae Johanna
Published: May 2022

Formation of the mouse cerebellum is initiated in the embryo and continues for a few weeks after birth. Double mutant mice lacking platelet-derived growth factor-C and that are heterozygous for platelet-derived growth factor receptor alpha (Pdgfc-/-; PdgfraGFP/+) develop cerebellar hypoplasia and malformation with loss of cerebellar lobes in the posterior vermis. This phenotype is similar to those observed in Foxc1 mutant mice and the human syndrome Dandy Walker malformation. Pdgfc-Pdgfra mutant mice also display ependymal denudation in the 4th ventricle and gene expression changes in cerebellar meninges, which coincide with the first visible signs of cerebellar malformation. Our observations suggest that PDGF-C/PDGFRα signalling is a critical component of the network of molecular and cellular interactions that take place between the developing meninges and neural tissues, and which are required to build a fully functioning cerebellum.

Summary statement

Mice lacking PDGF-C develop cerebellar hypoplasia and malformation. In addition, the ventricular zone close to the rhombic lip suffer from ependymal denudation.
The Smc5/6 complex is a DNA loop extruding motor
Authors: Pradhan Biswajit , Kanno Takaharu , Igarashi Miki Umeda , Baaske Martin Dieter , Kei Wong Jan Siu , Jeppsson Kristian , Björkegren Camilla , Kim Eugene
Published: May 2022

Structural Maintenance of Chromosomes (SMC) protein complexes are essential for the spatial organization of chromosomes. While cohesin and condensin organize chromosomes by extruding DNA loops, the molecular functions of the third eukaryotic SMC complex, Smc5/6, remain largely unknown. Using single-molecule imaging, we reveal that Smc5/6 forms DNA loops by extrusion. Upon ATP-hydrolysis, Smc5/6 symmetrically reels DNA into loops at a force-dependent rate of 1 kilobase pairs per second. Smc5/6 extrudes loops in the form of a dimer, while monomeric Smc5/6 unidirectionally translocate along DNA. We also find that Nse5 and Nse6 (Nse5/6) subunits act as negative regulators of Smc5/6-mediated loop initiation and stability. Our findings reveal Smc5/6’s molecular functions, and establish loop extrusion as a conserved mechanism among eukaryotic SMC complexes.

One-Sentence Summary

Smc5/6 is a DNA-loop-extruding motor, establishing loop extrusion as a conserved mechanism among eukaryotic SMC complexes.
Human REM sleep controls neural excitability in support of memory formation
Authors: Lendner Janna D. , Mander Bryce A. , Schuh-Hofer Sigrid , Schmidt Hannah , Knight Robert T. , Walker Matthew P. , Lin Jack , Helfrich Randolph F.
Published: May 2022

Sleep oscillations provide a key substrate to facilitate memory processing, the underlying mechanism of which may involve the overnight homeostatic regulation of plasticity at a synaptic and whole-network level. However, there remains a lack of human data demonstrating if and how sleep enhances memory consolidation and associated neural homeostasis. We combined intracranial recordings and scalp electroencephalography (EEG) in humans to reveal a new role for rapid eye movement (REM) sleep in promoting the homeostatic recalibration of optimal excitation/inhibition-balance. Moreover, the extent of this REM-sleep homeostatic recalibration predicted the success of overnight memory consolidation, expressly the modulation of hippocampal— neocortical excitability favoring remembering rather than forgetting. The findings describe a novel, fundamental role of human REM sleep in maintaining neural homeostasis, thereby enhancing long-term memory.
neoMS: Attention-based Prediction of MHC-I Epitope Presentation
Authors: Mill Nil Adell , Bogaert Cedric , van Criekinge Wim , Fant Bruno
Published: May 2022

Personalised immunotherapy aims to (re-)activate the immune system of a given patient against its tumour. It relies extensively on the ability of tumour-derived neoantigens to trigger a T-cell immune reaction able to recognise and kill the tumour cells expressing them. Since only peptides presented on the cell surface can be immunogenic, the prediction of neoantigen presentation is a crucial step of any discovery pipeline. Limiting neoantigen presentation to MHC binding fails to take into account all other steps of the presentation machinery and therefore to assess the true potential clinical benefit of a given epitope. Indeed, research has uncovered that merely 5% of predicted tumour-derived MHC-bound peptides is actually presented on the cell surface, demonstrating that affinity-based approaches fall short from isolating truly actionable neoantigens. Here, we present neoMS, a MHC-I presentation prediction algorithm leveraging mass spectrometry-derived MHC ligandomic data to better isolate presented antigens from potentially very large sets. The neoMS model is a transformer-based, peptide-sequence-to-HLA-sequence neural network algorithm, trained on 386,647 epitopes detected in the ligandomes of 92 HLA-monoallelic datasets and 66 patient-derived HLA-multiallelic datasets. It leverages attention mechanisms in which the most relevant parts of both putative epitope and HLA alleles are isolated. This results in a positive predictive value of 0.61 at a recall of 40% on its patient-derived test dataset, considerably outperforming current alternatives. Predictions made by neoMS correlate with peptide identification confidence in mass spectrometry experiments and reliably identify binding motif preferences of individual HLA alleles thereby further consolidating the biological relevance of the model. Additionally, neoMS displays extrapolation capabilities, showing good predictive power for presentation by HLA alleles not present in its training dataset. Finally, it was found that neoMS results can help refine predictions of response to immune checkpoint inhibitor treatment in certain cancer indications. Taken together, these results establish neoMS as a considerable step forward in high-specificity isolation of clinically actionable antigens for immunotherapies.
Genes ruler for genomes, Gnodes, measures assembly accuracy in animals and plants
Authors: Gilbert Donald G.
Published: May 2022

Gnodes is a Genome Depth Estimator for animal and plant genomes, also a genome size estimator. It calculates genome sizes based on DNA coverage of assemblies, using unique, conserved gene spans for its standard depth. Results of this tool match the independent measures from flow cytometry of genome size quite well in tests with plants and animals. Tests on a range of model and non-model animal and plant genome assemblies give reliable and accurate results, in contrast to less reliable K-mer histogram methods. The problem of half-sized assemblies of duplication-rich Daphnia is addressed. A 20-year old Arabidopsis genome discrepancy is resolved in favor of 157Mb as measured with flow-cytometry. Not all genome DNA samples contain a genome, examples and reasons for this are discussed. The T2T completed human genome assembly of 2022 is complete by Gnodes measures, with about 5% uncertainty. With full genome DNA, Gnodes measures within 10%, usually within 5%, of flow cytometry, indicating they are both measuring the same content. Public URL: http://eugenes.org/EvidentialGene/other/gnodes/
Active licking shapes cortical taste coding
Authors: Neese Camden , Bouaichi Cecilia G. , Needham Tom , Bauer Martin , Bertram Richard , Vincis Roberto
Published: May 2022

Neurons in the gustatory cortex (GC) represent taste through time-varying changes in their spiking activity. The predominant view is that the neural firing rate represents the sole unit of taste information. It is currently not known whether the phase of spikes relative to lick timing is used by GC neurons for taste encoding. To address this question, we recorded spiking activity from >500 single GC neurons in male and female mice permitted to freely lick to receive four liquid gustatory stimuli and water. We developed a set of data analysis tools to determine the ability of GC neurons to discriminate gustatory information and then to quantify the degree to which this information exists in the spike rate versus the spike timing or phase relative to licks. These tools include machine learning algorithms for classification of spike trains and methods from geometric shape and functional data analysis. Our results show that while GC neurons primarily encode taste information using a rate code, the timing of spikes is also an important factor in taste discrimination. A further finding is that taste discrimination using spike timing is improved when the timing of licks is considered in the analysis. That is, the interlick phase of spiking provides more information than the absolute spike timing itself. Overall, our analysis demonstrates that the ability of GC neurons to distinguish among tastes is best when spike rate and timing is interpreted relative to the timing of licks.

Significance Statement

Neurons represent information from the outside world via changes in their number of action potentials (spikes) over time. This study examines how neurons in the mouse gustatory cortex (GC) encode taste information when gustatory stimuli are experienced through the active process of licking. We use electrophysiological recordings and data analysis tools to evaluate the ability of GC neurons to distinguish tastants and then to quantify the degree to which this information exists in the spike rate versus the spike timing relative to licks. We show that the neuron’s ability to distinguish between tastes is higher when spike rate and timing are interpreted relative to the timing of licks, indicating that the lick cycle is a key factor for taste processing.
Discretized representations in V1 predict suboptimal orientation discrimination
Authors: Corbo Julien , Erkat O. Batuhan , McClure John P. , Khdour Hussein , Polack Pierre-Olivier
Published: May 2022

Neuronal population activity in sensory cortices is the substrate for perceptual decisions. Yet, we still do not understand how neuronal information content in sensory cortices relates to behavioral reports. To reconcile neurometric and psychometric performance, we recorded the activity of V1 neurons in mice performing a Go/NoGo orientation discrimination task. We found that, around the discrimination threshold, V1 does not represent the orientation of the stimuli as canonically expected. Instead, it forms categorical representations characterized by a relocation of activity at task-relevant domains of the orientation representational space. The relative neuronal activity at those discrete domains accurately predicted the probabilities of the animals’ decisions. Our results thus suggest that the categorical integration of discretized feature representations from sensory cortices explains perceptual decisions.
Disrupted Decision-Making: EcoHIV Inoculation Following a History of Cocaine Use
Authors: McLaurin Kristen A. , Li Hailong , Mactutus Charles F. , Harrod Steven B. , Booze Rosemarie M.
Published: May 2022

Independently, chronic cocaine use and HIV-1 viral protein exposure induce neuroadaptations in the frontal-striatal circuit; how the frontal-striatal circuit responds to HIV-1 infection following chronic drug use, however, has remained elusive. After establishing a history of both sucrose and cocaine self-administration, a pretest-posttest experimental design was utilized to evaluate preference judgment, a simple form of decision-making dependent upon the integrity of frontal- striatal circuit function. During the pretest assessment, male rats exhibited a clear preference for cocaine, whereas female animals preferred sucrose. Two posttest evaluations (3 Days and 6 Weeks Post Inoculation) revealed that, independent of biological sex, inoculation with chimeric HIV (EcoHIV), but not saline, disrupted decision-making. Prominent structural alterations in frontal-striatal circuit dysfunction were evidenced by synaptodendritic alterations in pyramidal neurons in the medial prefrontal cortex. Thus, the EcoHIV rat affords a biological system to model how the frontal-striatal circuit responds to HIV-1 infection following chronic drug use.
Cysteine Restriction-Specific Effects of Sulfur Amino Acid Restriction on Lipid Metabolism
Authors: Nichenametla Sailendra N , Mattocks Dwight AL , Cooke Diana , Midya Vishal , Malloy Virginia L , Mansilla Wilfredo , Øvrebø Bente , Turner Cheryl , Bastani Nasser E , Sokolová Jitka , Pavlíková Markéta , Richie John P , Shoveller Anna K , Refsum Helga , Olsen Thomas , Vinknes Kathrine J , Kožich Viktor , Ables Gene P
Published: May 2022

Decreasing dietary intake of methionine exerts robust anti-adiposity effects in rodents but modest effects in humans. Since cysteine can be synthesized from methionine, animal diets are formulated by decreasing methionine and eliminating cysteine. Such diets exert both methionine restriction (MR) and cysteine restriction (CR), i.e., sulfur amino acid restriction (SAAR). Contrarily, human diets used in clinical studies did not eliminate cysteine and thus might have exerted only MR. Epidemiological studies positively correlate body adiposity with plasma cysteine but not with methionine, suggesting that CR, but not MR, is responsible for the antiadiposity effects of SAAR in rodents. Whether this is true, and if so, the underlying mechanisms are unknown. Using multiple diets with variable concentrations of methionine and cysteine, we demonstrate that the anti-adiposity effects of SAAR are due to CR. CR increased serinogenesis (serine biosynthesis from non-glucose substrates) by diverting substrates from glyceroneogenesis, essential for fatty acid/triglyceride cycling. Molecular data suggest that the CR results in glutathione depletion, which induces Nrf2 and downstream targets Phgdh (the serine biosynthetic enzyme) and Pepck-M. Using multiple mouse models, we show that the magnitude of SAAR-induced changes in molecular markers depends on dietary fat concentration (60 fat>10% fat), gender (males>females), and age-at-onset (young>adult). Our findings are translationally relevant as we found a negative correlation of plasma serine with triglycerides and metabolic syndrome criteria in a cross-sectional epidemiological study. SAAR-like diets with high polyunsaturated fatty acids increased plasma serine in a short-term human feeding study. Serinogenesis might be a potential target to correct hypertriglyceridemia.
Solubility-aware protein binding peptide design using AlphaFold
Authors: Kosugi Takatsugu , Ohue Masahito
Published: May 2022

New protein–protein interactions (PPIs) are being identified, but PPIs have different physicochemical properties compared with conventional targets, making it difficult to use small molecules. Peptides offer a new modality to target PPIs, but designing appropriate peptide sequences by computation is challenging. Recently, AlphaFold and RosettaFold have made it possible to predict protein structures from amino acid sequences with ultra-high accuracy, enabling de novo protein design. We designed peptides likely to have PPI as the target protein using the “binder hallucination” protocol of AfDesign, a de novo protein design method using AlphaFold. However, the solubility of the peptides tended to be low. Therefore, we designed a solubility loss function using solubility indices for amino acids and developed a solubility-aware AfDesign binder hallucination protocol. The peptide solubility in sequences designed using the new protocol increased with the weight of the solubility loss function; moreover, they captured the characteristics of the solubility indices. Moreover, the new protocol sequences tended to have higher affinity than random or single residue substitution sequences when evaluated by docking binding affinity. Our approach shows that it is possible to design peptide sequences that can bind to the interface of PPI while controlling solubility.
The ClpP Peptidase Forcefully Grips Protein Substrates
Authors: Walker Steven D. , Olivares Adrian O.
Published: May 2022

ATPases Associated with diverse cellular Activities (AAA+) proteases power the maintenance of protein homeostasis by coupling ATP hydrolysis to mechanical protein unfolding, translocation, and ultimately degradation. Though ATPase activity drives a large portion of the mechanical work these molecular machines perform, how the peptidase contributes to the forceful denaturation and processive threading of substrates remains unknown. Here, using single-molecule optical trapping, we examine the mechanical activity of the Caseinolytic Peptidase P (ClpP) from Escherichia coli in the absence of a partner ATPase and in the presence of an activating small molecule acyldepsipeptide. We demonstrate that ClpP grips protein substrate under mechanical loads exceeding 40 pN, which are greater than those observed for the AAA+ unfoldase ClpX and the AAA+ protease complexes ClpXP and ClpAP. We further characterize substrate-ClpP bond lifetimes and rupture forces under varying loads. We find that the resulting slip bond behavior does not depend on ClpP peptidase activity. Additionally, we find that unloaded bond lifetimes between ClpP and protein substrate are on a timescale relevant to unfolding times (up to ∼160 s) for difficult to unfold model substrate proteins. These direct measurements of the substrate-peptidase bond under load define key properties required by AAA+ proteases to mechanically unfold and degrade protein substrates.

STATEMENT OF SIGNIFICANCE

Energy-dependent proteases drive essential protein degradation to maintain cellular homeostasis and to rapidly regulate protein levels in response to changes in cellular environment. Using single-molecule optical tweezers, several studies demonstrate that the molecular process of degradation involves the mechanical unfolding and translocation of protein substrates by the ATP hydrolyzing enzyme component of these protease complexes. This study provides evidence that the chambered peptidase component of these molecular machines also contributes to the mechanical process of degradation by gripping substrate under load in a manner independent of peptide hydrolysis. Our results suggest that the peptidase actively contributes to the biophysical mechanisms underlying processive protein degradation by energy-dependent proteolytic machines.
Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures
Authors: Charon Justine , Kahlke Tim , Larsson Michaela E. , Abbriano Raffaela , Commault Audrey , Burke Joel , Ralph Peter , Holmes Edward C.
Published: May 2022

Unicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the diversity within, and effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions on virus evolution. We assessed the diversity of RNA viruses in eight microalgal cultures including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimised to detect highly divergent RNA viruses, we identified ten RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae and Partitiviridae, greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae, commonly associated with microalgal hosts, were also identified. This study highlights that a great diversity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterisation and to investigate the effects of viral infections on microalgal physiology, biology and growth, considering their environmental and industrial roles.

Importance

In comparison to animals or plants, our knowledge of the diversity of RNA viruses infecting microbial algae – the microalgae – is minimal. Yet describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economical levels because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte and euglena major clades of algae. This work identified ten new divergent RNA virus species, belonging to RNA virus families as diverse as the double-stranded Totiviridae, Endornaviridae, Partitiviridae and the single-stranded Marnaviridae. By expanding the known diversity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.
Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation
Authors: Shukla Harsh , Suryamohan Kushal , Khan Anubhab , Mohan Krishna , Perumal Rajadurai C. , Mathew Oommen K. , Menon Ramesh , Dixon Mandumpala Davis , Muraleedharan Megha , Kuriakose Boney , Michael Saju , Krishnankutty Sajesh P. , Zachariah Arun , Seshagiri Somasekar , Ramakrishnan Uma
Published: May 2022

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of their genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140□Mb, with 19□scaffolds, corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous assemblies which will improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 tRNAs and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to tiger’s apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of non-invasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.
Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics
Authors: Bittremieux Wout , Avalon Nicole E. , Thomas Sydney P. , Kakhkhorov Sarvar A. , Aksenov Alexander A. , P. Gomes Paulo Wender , Aceves Christine M. , Caraballo-Rodríguez Andrés Mauricio , Gauglitz Julia M. , Gerwick William H. , Huan Tao , Jarmusch Alan K. , Kaddurah-Daouk Rima F. , Kang Kyo Bin , Kim Hyun Woo , Kondić Todor , Mannochio-Russo Helena , Meehan Michael J. , Melnik Alexey V. , Nothias Louis-Felix , O’Donovan Claire , Panitchpakdi Morgan , Petras Daniel , Schmid Robin , Schymanski Emma L. , van der Hooft Justin J. J. , Weldon Kelly C. , Yang Heejung , Xing Shipei , Zemlin Jasmine , Wang Mingxun , Dorrestein Pieter C.
Published: May 2022

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of public MS/MS spectra. Annotations were propagated based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
Evolution of personality and locomotory performance traits during a late Pleistocene island colonization in a treefrog
Authors: Bisconti Roberta , Carere Claudio , Costantini David , Liparoto Anita , Chiocchio Andrea , Canestrelli Daniele
Published: May 2022

Recent empirical and theoretical studies suggest that personality and locomotory performance traits are crucial components of the dispersal syndromes, and that they can evolve during a dispersal process. Island colonisation is one the best characterized processes in dispersal biogeography, and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales. However, the effect of island colonization on personality and performance traits of natural populations has been little explored, and no studies have addressed these processes in the context of late-Pleistocene range expansions. Here, we investigated the contribution of island colonisations triggered by post-glacial range expansions to intraspecific variation in personality and locomotory performance traits. We compared boldness, exploration, jumping performance, and stickiness abilities, in three equidistant populations of the Tyrrhenian tree frogHyla sarda, two from the source area and one from the colonised island. Individuals from the colonised population were significantly bolder than individuals from the source area, as they emerged sooner from a shelter (p=0.028), while individuals from the source area showed markedly higher jumping and stickiness performance (both p<0.001). We discuss these results in the context of the major microevolutionary processes at play during range expansion, including selection, spatial sorting, and founder effects. However, irrespective of the processes contributing the most, our results clearly indicate that late Pleistocene climatic changes have had major consequences not just on species’ range dynamics, but also on the spatial patterns of phenotypic variation within species, including personality and locomotory traits variation.
Recapitulation of the embryonic transcriptional program in insect pupae
Authors: Ozerova Alexandra M , Gelfand Mikhail S.
Published: May 2022

Metamorphosis of holometabolous insects is predominantly a motionless stage, when no active feeding is observed and the body is enclosed into the pupa. These physiological properties as well as undergoing processes resemble embryogenesis since at the pupal stage organs and systems of the imago are formed. Therefore recapitulation of the embryonic expression program during pupa development could be hypothesized. To assess this hypothesis at the transcriptome level, we have performed a comprehensive analysis of the developmental datasets available in the public domain. Indeed, for most datasets, the pupal gene expression resembles the embryonic rather than the larval pattern, interrupting gradual changes of the transcriptome. Moreover, changes in the transcriptome profile during the pupa-to-imago transition are positively correlated with those at the embryo-to-larvae transition, suggesting that similar expression programs are activated. Gene sets that change their expression level during the larval stage and revert it to the embryonic-like state during the metamorphosis are enriched with genes associated with metabolism and development.
The neurodevelopmental genesalan shepardandNeurogliancontribute to female mate preference in AfricanDrosophila melanogaster
Authors: Roy Paula R. , Castillo Dean M.
Published: May 2022

Mate choice is a key trait that determines fitness for most sexually reproducing organisms, with females often being the choosy sex. Female preference often results in strong selection on male traits that can drive rapid divergence of traits and preferences between lineages, leading to reproductive isolation. Despite this fundamental property of female mate choice, very few loci have been identified that contribute to mate choice and reproductive isolation. We used a combination of population genetics, quantitative complementation tests, and behavioral assays to demonstrate thatalan shepardandNeurogliancontribute to female mate choice, and could contribute to partial reproductive isolation between populations ofDrosophila melanogaster. Our study is among the first to identify genes that contribute to female mate preference in this historically important system, where female preference is an active premating barrier to reproduction. The identification of loci that are primarily known for their roles in neurodevelopment provides intriguing questions of how female mate preference evolves in populations via changes in sensory system and higher learning brain centers.
MHC-II molecules present RhoC-derived peptides on the surface of tumour cells
Authors: Thomas Pavana , Srivastava Sweta
Published: May 2022

RhoC is an important regulator of metastasis and tumour progression across various tumour models. Since RhoC has been found to have no major contribution towards normal embryogenic development, it has emerged as a suitable therapeutic target for effective cancer treatment. Recent evidence has shown that Rho-based peptide vaccines have favourable outcomes in prostate cancer patients, by bringing about activation of CD4+ T-cells. Antigen presentation on the surface of cells is brought about by the MHC-I/MHC-II complex. This work provides conclusive evidence to show that the seemingly cytosolic protein, RhoC, is in fact, present on the surface of tumour cells. This report goes on to prove that the presentation of RhoC peptides is brought about in association with MHC-II, becoming the first piece of scientific evidence to report this phenomenon.
Identification of representative trees in random forests based on a new tree-based distance measure
Authors: von Holt Björn-Hergen Laabs , Westenberger Ana , König Inke R.
Published: May 2022

In life sciences random forests are often used to train predictive models. However, gaining any explanatory insight into the mechanics leading to a specific outcome is rather complex, which impedes the implementation of random forests into clinical practice. By simplifying a complex ensemble of decision trees to a single most representative tree, it is assumed to be possible to observe common tree structures, the importance of specific features and variable interactions. Thus, representative trees could also help to understand interactions between genetic variants. Intuitively, representative trees are those with the minimal distance to all other trees, which requires a proper definition of the distance between two trees. Thus, we developed a new tree-based distance measure, which incorporates more of the underlying tree structure than other metrics. We compared our new method with the existing metrics in an extensive simulation study and applied it to predict the age at onset based on a set of genetic risk factors in a clinical data set. In our simulation study we were able to show the advantages of our weighted splitting variable approach. Our real data application revealed that representative trees are not only able to replicate the results from a recent genome-wide association study, but also can give additional explanations of the genetic mechanisms. Finally, we implemented all compared distance measures in R and made them publicly available in the R package timbR (https://github.com/imbs-hl/timbR).