bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of mitochondrial genome methylation using Nanopore single-molecule sequencing
Authors: Lüth Theresa , Klein Christine , Schaake Susen , Tse Ronnie , Pereira Sandro , Lass Joshua , Sinkkonen Lasse , Grünewald Anne , Trinh Joanne
Published: February 2021

The level and the biological significance of mitochondrial DNA (mtDNA) methylation in human cells is a controversial topic. Using long-read third-generation sequencing technology, mtDNA methylation can be detected directly from the sequencing data, which overcomes previously suggested biases, introduced by bisulfite treatment-dependent methods. We investigated mtDNA from whole blood-derived DNA and established a workflow to detect CpG methylation with Nanopolish. In order to obtain native mtDNA, we adjusted a whole-genome sequencing protocol and performed ligation library preparation and Nanopore sequencing. To validate the workflow, 897bp of methylated and unmethylated synthetic DNA samples at different dilution ratios were sequenced and CpG methylation was detected. Interestingly, we observed that reads with higher methylation in the synthetic DNA did not pass Guppy calling, possibly affecting conclusions about DNA methylation in Nanopore sequencing. We detected in all blood-derived samples overall low-level methylation across the mitochondrial genome, with exceptions at certain CpG sites. Our results suggest that Nanopore sequencing is capable of detecting low-level mtDNA methylation. However, further refinement of the bioinformatical pipelines including Guppy failed reads are recommended.
Pupil Size Reflects Exploration and Exploitation in Visual Search (and It’s Like Object-Based Attention)
Authors: Regnath Franziska , Mathôt Sebastiaan
Published: February 2021

The adaptive gain theory (AGT) posits that activity in the locus coeruleus (LC) is linked to two behavioral modes: exploitation, characterized by focused attention on a single task; and exploration, characterized by a lack of focused attention and frequent switching between tasks. Furthermore, pupil size correlates with LC activity, such that large pupils indicate increased LC firing, and by extension also exploration behavior. Most evidence for this correlation in humans comes from complex behavior in game-like tasks. However, predictions of the AGT naturally extend to a very basic form of behavior: eye movements. To test this, we used a visual-search task. Participants searched for a target among many distractors, while we measured their pupil diameter and eye movements. The display was divided into four randomly generated regions of different colors. Although these regions were irrelevant to the task, participants were sensitive to their boundaries, and dwelled within regions for longer than expected by chance. Crucially, pupil size increased before eye movements that carried gaze from one region to another. We propose that eye movements that stay within regions (or objects) correspond to exploitation behavior, whereas eye movements that switch between regions (or objects) correspond to exploration behavior.

Public Significance Statement

When people experience increased arousal, their pupils dilate. The adaptive-gain theory proposes that pupil size reflects neural activity in the locus coeruleus (LC), which in turn is associated with two behavioral modes: a vigilant, distractible mode (“exploration”), and a calm, focused mode (“exploitation”). During exploration, pupils are larger and LC activity is higher than during exploitation. Here we show that the predictions of this theory generalize to eye movements: smaller pupils coincide with eye movements indicative of exploitation, while pupils slightly dilate just before make eye movements that are indicative of exploration.
Comparing Methods for Species Tree Estimation With Gene Duplication and Loss
Authors: Willson James , Roddur Mrinmoy Saha , Warnow Tandy
Published: February 2021

Species tree inference from gene trees is an important part of biological research. One confounding factor in estimating species trees is gene duplication and loss which can lead to gene trees with multiple copies of the same gene. In recent years there have been several new methods developed to address this problem that have substantially improved on earlier methods; however, the best performing methods (ASTRAL-Pro, ASTRID-multi, and FastMulRFS) have not yet been directly compared. In this study, we compare ASTRAL-Pro, ASTRID-multi, and FastMulRFS under a wide variety of conditions. Our study shows that while all three have very good accuracy, nearly the same under many conditions, ASTRAL-Pro and ASTRID-multi are more reliably accurate than FastMuLRFS, and that ASTRID-multi is often faster than ASTRAL-Pro. The datasets generated for this study are freely available in the Illinois Data Bank athttps://databank.illinois.edu/datasets/IDB-2418574
Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation inDrosophila testis
Authors: Witt Evan , Shao Zhantao , Hu Chun , Krause Henry M. , Zhao Li
Published: February 2021

Dosage compensation (DC) is a mechanism by which X chromosome transcription is equalized in the somatic cells of both males and females. In male fruit flies, expression levels of the X-chromosome are increased two-fold to compensate for their single X chromosome. In testis, dosage compensation is thought to cease during meiosis, however, the timing and degree of the resulting transcriptional suppression is difficult to separate from global meiotic downregulation of each chromosome. To address this, we analyzed testis single-cell RNA-sequencing (scRNA-seq) data from twoDrosophila melanogasterstrains. We found evidence that the X chromosome is equally transcriptionally active as autosomes in somatic and pre-meiotic cells, and less transcriptionally active than autosomes in meiotic and post-meiotic cells. In cells experiencing dosage compensation, close proximity to MSL (male-specific lethal) chromatin entry sites (CES) correlates with increased X chromosome transcription. We found low or undetectable level of germline expression of mostmslgenes,mle, roX1androX2via sequencing or RNA-FISH, and no evidence of germline nuclearroX1/2localization. Our results suggest that, although DC occurs in somatic and premeiotic germ cells inDrosophilatestis, there might be non-canonical factors involved in the dosage compensation. The single-cell expression patterns and enrichment statistics of detected genes can be explored interactively in our database:https://zhao.labapps.rockefeller.edu/gene-expr/.
Drug Conjugates of Antagonistic RSPO4 Mutant For Simultaneous Targeting of LGR4/5/6 for Cancer Treatment
Authors: Cui Jie , Park Soohyun , Yu Wangsheng , Carmon Kendra , Liu Qingyun J.
Published: February 2021

LGR4-6 (Leucine-rich repeating containing, G-protein-coupled receptors 4, 5, and 6) are three related receptors with distinct roles in organ development and stem cell survival. All three receptors are upregulated in gastrointestinal cancers to different levels, and LGR5 has been shown to be enriched in cancer stem cells. Antibody-drug conjugates (ADCs) targeting LGR5 showed robust antitumor effect in vivo but could not eradicate tumors due to plasticity of LGR5-positive cancer cells. As LGR5-negative cells often express LGR4 or LGR6 or both, we reasoned that simultaneous targeting of all three LGRs may provide a more effective approach. R-spondins (RSPOs) bind to LGR4-6 with high affinity and potentiate Wnt signaling. We identified an RSPO4 mutant (Q65R) that retains potent LGR binding but no longer potentiates Wnt signaling. The RSPO4 mutant was fused to the N-terminus of human IgG1-Fc to create a peptibody which was then conjugated with cytotoxins monomethyl auristatin or duocarmycin by site-specific conjugation. The resulting peptibody drug conjugates (PDCs) showed potent cytotoxic effects on cancer cell lines expressing any LGR in vitro and suppressed tumor growth in vivo without inducing intestinal enlargement or other adverse effects. These results suggest that RSPO-derived PDCs may provide a novel approach to the treatment of cancers with high LGR expression.
Objective pupillometry shows that perceptual styles covary with autistic-like personality traits
Authors: Tortelli Chiara , Turi Marco , Burr David C. , Binda Paola
Published: February 2021

We measured the modulation of pupil-size (in constant lighting) elicited by observing transparent surfaces of black and white moving dots, perceived as a cylinder rotating about its vertical axis. The direction of rotation was swapped periodically by flipping stereo-depth of the two surfaces. Pupil size modulated in synchrony with the changes in front-surface color (dilating when black). The magnitude of pupillary modulation was larger for participants with higher Autism-Spectrum Quotient (AQ), consistent with a local style of perception, with attention focused on the front surface. The modulation with surface color, and its correlation with AQ, was equally strong when participants passively viewed the stimulus. No other indicator, including involuntary pursuit eye-movements, covaried with AQ. These results reinforce our previous report with a similar bistable stimulus (Turi, Burr, & Binda, 2018), and go on to show that bistable illusory motion is not necessary for the effect, or its dependence on AQ.
Targeting interleukin-1 for reversing fat browning and muscle wasting in infantile nephropathic cystinosis
Authors: Cheung Wai W , Hao Sheng , Zheng Ronghao , Wang Zhen , Gonzalez Alex , Zhou Ping , Hoffman Hal M , Mak Robert H
Published: February 2021

Background

Ctns−/−mice, a mouse model of infantile nephropathic cystinosis, exhibit hypermetabolism with adipose tissue browning and profound muscle wasting. Inflammatory cytokines such as IL-1 trigger inflammatory cascades and play an important role in the pathogenesis of cachexia. Anakinra is an FDA-approved IL-1 receptor antagonist that blocks IL-1 signaling and may provide targeted novel therapy.

Methods

Ctns−/−mice were bred toIl6−/−andIl1β−/−mice.Ctns−/−mice and wild type control were treated with anakinra (2.5 mg.kg.day, IP) or saline as vehicle for 6 weeks. We quantitated total fat mass and studied expression of molecules regulating adipose tissue browning. We measured gastrocnemius weight, total lean mass content, muscle function (grip strength and rotarod activity), muscle fiber size, muscle fatty infiltration and expression of molecules regulating muscle metabolism. We also evaluated the effects of anakinra on the muscle transcriptome.

Results

Il-1β deficiency or treatment with anakinra normalized food intake and weight gain, fat and lean mass content, metabolic rate and muscle function inCtns−/−mice. Anakinra also diminished molecular perturbations of energy homeostasis in adipose tissue and muscle, specifically, aberrant expression of beige adipose cell biomarkers (UCP-1, CD137, Tmem26 and Tbx1) and molecules implicated in adipocyte tissue browning (Cox2/Pgf2α, Tlr2, Myd88 and Traf6) in inguinal white adipose tissue inCtns−/−mice. Moreover, anakinra normalized gastrocnemius weight and fiber size as well as attenuated muscle fat infiltration inCtns−/−mice. This was accompanied by correction of the increased muscle wasting signaling pathways (increased protein content of ERK1/2, JNK, p38 MAPK and NF-κB p65 and gene expression of Atrogin-1 and Myostatin) and the decreased myogenesis process (decreased gene expression of MyoD and Myogenin) in gastrocnemius ofCtns−/−mice. Finally, anakinra normalized or attenuated 12 of those top 20 differentially expressed muscle genes inCtns−/−mice.

Conclusions

Anakinra attenuates adipose tissue browning and muscle wasting inCtns−/−mice. IL-1 receptor blockade may represent a novel targeted treatment for cachexia in patients with infantile nephropathic cystinosis.
Elephant seal muscle cells adapt to sustained glucocorticoid exposure by shifting their metabolic phenotype
Authors: Torres-Velarde Julia Maria , Kolora Sree Rohit Raj , Khudyakov Jane I. , Crocker Daniel E. , Sudmant Peter H. , Vázquez-Medina José Pablo
Published: February 2021

Elephant seals experience natural periods of prolonged food deprivation while breeding, molting, and undergoing postnatal development. Prolonged food deprivation in elephant seals increases circulating glucocorticoids without inducing muscle atrophy, but the cellular mechanisms that allow elephant seals to cope with such conditions remain elusive. We generated a cellular model and conducted transcriptomic, metabolic, and morphological analyses to study how seal cells adapt to sustained glucocorticoid exposure. Seal muscle progenitor cells differentiate into contractile myotubes with a distinctive morphology, gene expression profile, and metabolic phenotype. Exposure to dexamethasone at three ascending concentrations for 48h modulated the expression of 6 clusters of genes related to structural constituents of muscle and pathways associated with energy metabolism and cell survival. Knockdown of the glucocorticoid receptor (GR) and downstream expression analyses corroborated that GR mediates the observed effects. Dexamethasone also decreased cellular respiration, shifted the metabolic phenotype towards glycolysis, and induced mitochondrial fission and dissociation of mitochondria-ER interactions without decreasing cell viability. Knockdown of DDIT4, a GR target involved in the dissociation of mitochondria-ER membranes, recovered respiration and modulated antioxidant gene expression. These results show that adaptation to sustained glucocorticoid exposure in elephant seal myotubes involves a metabolic shift toward glycolysis, which is supported by alterations in mitochondrial morphology and a reduction in mitochondria-ER interactions, resulting in decreased respiration without compromising cell survival.
Optical regulation of endogenous RhoA reveals selection of cellular responses by signal amplitude
Authors: Ju Jeongmin , Lee Hae Nim , Ning Lin , Ryu Hyunjoo , Zhou Xin X. , Chun Hyeyeon , Lee Yong Woo , Lee-Richerson Austin I. , Jeong Cherlhyun , Lin Michael Z. , Seong Jihye
Published: February 2021

How protein signaling networks respond to different input strengths is an important but poorly understood problem in cell biology. For example, the small GTPase RhoA regulates both focal adhesion (FA) growth or disassembly, but whether RhoA serves as a switch selecting between cellular outcomes, or if outcomes are simply modulated by additional factors in the cell, is not clear. Here, we develop a photoswitchable RhoA guanine exchange factor, psRhoGEF, to precisely control endogenous RhoA activity. We also develop a FRET-based biosensor to allow visualization of RhoA activity together with psRhoGEF control. Using these new optical tools, we discover that low levels of RhoA activation preferentially induce FA disassembly in a Src-dependent manner, while high levels induce both FA growth and disassembly in a ROCK-dependent manner. Thus, rheostatic control of RhoA activation with photoswitchable RhoGEF reveals that cells can use signal amplitude to produce multiple responses to a single biochemical signal.
Rational Design of Programmable Monodisperse Semi-Synthetic Protein Nanomaterials Containing Engineered Disulfide Functionality
Authors: Bhandari Pavankumar Janardhan , Sandanaraj Britto S
Published: February 2021

The reversible nature of disulfide functionality has been exploited to design intelligent materials such as nanocapsules, micelles, vesicles, inorganic nanoparticles, peptide and nucleic acid nanodevices. However, to our knowledge, there are no reports on design of semi-synthetic protein assemblies containing an engineered disulfide bond. Towards that end, herein, we disclose a new chemical methodology for the construction redox-sensitive protein assemblies using monodisperse facially amphiphilic protein-dendron bioconjugates. The disulfide functionality is strategically placed between the dendron and protein domains. The custom designed bioconjugates self-assembled into nanoscopic objects of a defined size dictated by the nature of dendron domain. The stimuli-responsive behavior of the protein assemblies is demonstrated using a suitable redox trigger.
Impact of cobas PCR Media Freezing on SARS-CoV-2 Viral RNA Integrity and Whole Genome Sequencing Analyses
Authors: Benoit Patrick , Point Floriane , Gagnon Simon , Kaufmann Daniel E. , Tremblay Cécile , Harrigan Richard Paul , Hardy Isabelle , Coutlée François , Lapierre Simon Grandjean
Published: February 2021

SARS-CoV-2 whole genome sequencing is an important molecular biology tool performed to support many aspects of the response to the pandemic. Freezing of primary clinical nasopharyngeal swab samples and shipment to reference laboratories is usually required since RNA sequencing is rarely available in routine clinical microbiology laboratories where initial diagnosis and support to outbreak investigations occur. The cobas PCR Media transport medium developed by Roche facilitates high throughput analyses on cobas multianalyzer PCR platforms. There is no data on the stability of SARS-CoV-2 RNA after freezing and thawing of clinical samples in this transport medium, but potential denaturing of the molecular template could impair test results. Our objective was to compare the quality and results of SARS-CoV-2 genomic sequencing when performed on fresh or frozen samples in cobas PCR Media. Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. Genomic coverage and sequencing depth did not significantly differ between fresh and frozen samples (n=10). For samples with lower viral inoculum and PCR cycle threshold above 30, sequencing quality scores and detection of single nucleotide polymorphisms did not differ either. Freezing of cobas PCR Media does not negatively affect the quality of SARS-CoV-2 RNA sequencing results and it is therefore a suitable transport medium for outsourcing sequencing analyses to reference laboratories. Those results support secondary use of diagnostic nasopharyngeal swab material for viral sequencing without requirement for additional clinical samples.
COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model
Authors: Alser Mohammed , Kim Jeremie S. , Alserr Nour Almadhoun , Tell Stefan W. , Mutlu Onur
Published: February 2021

Motivation

Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited number of daily COVID-19 tests performed in every country, simulating the COVID-19 spread along with the potential effect of each mitigation strategy currently remains one of the most effective ways in managing the healthcare system and guiding policy-makers. We introduceCOVIDHunter, a flexible and accurate COVID-19 outbreak simulation model that evaluates the current mitigation measures that are applied to a region and provides suggestions on what strength the upcoming mitigation measure should be. The key idea of COVIDHunter is to quantify the spread of COVID-19 in a geographical region by simulating the average number of new infections caused by an infected person considering the effect of external factors, such as environmental conditions (e.g., climate, temperature, humidity) and mitigation measures.

Results

Using Switzerland as a case study, COVIDHunter estimates that the policy-makers need to keep the current mitigation measures for at least 30 days to prevent demand from quickly exceeding existing hospital capacity. Relaxing the mitigation measures by 50% for 30 days increases both thedailycapacity need for hospital beds anddailynumber of deaths exponentially by an average of 23.8 ×, who may occupy ICU beds and ventilators for a period of time. Unlike existing models, the COVIDHunter model accurately monitors and predicts the daily number of cases, hospitalizations, and deaths due to COVID-19. Our model is flexible to configure and simple to modify for modeling different scenarios under different environmental conditions and mitigation measures.

Availability

https://github.com/CMU-SAFARI/COVIDHunter

Contact

alserm@ethz.ch,omutlu@ethz.ch

Supplementary information

Supplementary data is available atBioinformaticsonline.
Hepatocyte nuclear factor 4a and glucocorticoid receptor coordinately regulate lipid metabolism in mice fed a high-fat-high-sugar diet
Authors: Lu Hong , Lei Xiaohong , Guo Shangdong , Winkler Rebecca , John Savio , Kumar Devendra , Li Wenkuan , Alnouti Yazen
Published: February 2021

Hepatocyte nuclear factor 4α (HNF4α) and glucocorticoid receptor (GR), master regulators of liver metabolism, are down-regulated in fatty liver diseases. The present study was aimed to elucidate the role of down-regulation of HNF4α and GR in fatty liver and hyperlipidemia. Adult mice with liver-specific heterozygote and knockout (knockout) of HNF4α were fed a low-fat diet (LFD) or a high-fat-high-sugar diet (HFHS) for 15 days. Compared to LFD-fed mice, HFHS-fed wildtype mice had hepatic induction of lipid catabolic genes and down-regulation of lipogenic genes. Compared to HFHS-fed wildtype mice, HNF4α heterozygote mice had down-regulation of lipid catabolic genes, induction of lipogenic genes, and increased hepatic and blood levels of lipids, whereas HNF4α knockout mice had mild hypolipidemia, down-regulation of lipid-efflux genes, but induction of genes for uptake/storage of lipids. Sterol-regulatory-element-binding protein-1c (SREBP-1C), a master lipogenic regulator, was induced in HFHS-fed HNF4α heterozygote mice. In reporter assays, HNF4α potently inhibited the transactivation of mouse and human SREBP-1C promoter by liver X receptor. Surprisingly, nuclear GR proteins were gene-dosage-dependently decreased in HNF4α heterozygote and knockout mice. HFHS-fed mice with liver-specific knockout of GR had increased hepatic lipids and induction of SREBP-1C and PPARγ. In reporter assays, GR and HNF4α synergistically/additively induced lipid catabolic genes. Phosphorylation of AMP-activated protein kinase (AMPK), a key GR modulator, was dramatically decreased in HNF4α knockout mice. Thus, cooperative induction of lipid catabolic genes and suppression of lipogenic genes by HNF4α and GR, modulated by AMPK, may mediate the early resistance to HFHS-induced fatty liver and hyperlipidemia.
Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2)
Authors: Karmakar Shilpita , Ramirez Oscar , Paul Kiran V. , Gupta Abhishek K. , Botti Valentina , de los Mozos Igor Ruiz , Neuenkirchen Nils , Ross Robert J. , Neugebauer Karla M. , Pillai Manoj M.
Published: February 2021

Musashi 2 (MSI2) is an RNA binding protein (RBP) that regulates asymmetric cell division and cell fate decisions in normal and cancer stem cells. MSI2 appears to repress translation by binding to 3’ untranslated regions (3’UTRs) of mRNA, but the identity of functional targets remains unknown. Here we used iCLIP to identify direct RNA binding partners of MSI2 and integrated these data with polysome profiling to obtain insights into MSI2 function. iCLIP revealed specific MSI2 binding to thousands of target mRNAs largely in 3’UTRs, but translational differences were restricted to a small fraction of these transcripts, indicating that MSI2 regulation is not triggered by simple binding. Instead, the functional targets identified here were bound at higher density and contain more “U/TAG” motifs compared to targets bound non-productively. To further distinguish direct and indirect targets, MSI2 was acutely depleted. Surprisingly, only 50 transcripts were found to undergo translational induction on acute MSI2 loss. Eukaryotic elongation factor 3A (EIF3A) was determined to be an immediate, direct target. We propose that MSI2 down-regulation of EIF3A amplifies these effects on the proteome. Our results also underscore the challenges in defining functional targets of RBP since mere binding does not imply a discernible functional interaction.
Tn7-CRISPR-Cas12K elements manage pathway choice using truncated repeat-spacer units to target tRNA attachment sites
Authors: Hsieh Shan-Chi , Peters Joseph E.
Published: February 2021

CRISPR-Cas systems provide a defense against mobile elements. These defense systems have been naturally coopted multiple times for guide RNA-directed transposition by Tn7-like transposons. Elements associated with a type I-F CRISPR-Cas system categorize guide RNAs, maintaining a standard CRISPR array capable of acquiring new spacers targeting other mobile elements while maintaining a special guide RNA allowing integration into a conserved site in the chromosome called an attachment site. We show here that Tn7-like elements associated with a type V-K (Cas12K-based) system use a similar strategy to target diverse tRNA genes as attachment sites. These guides are encoded as truncated minimal repeat-spacer units and are found in distinct locations. Multiple pieces of information support that V-K guide RNAs are acquired using a type I-D adaptation system, but remain private to the V-K transposition process. This catalog of Cas12K elements and naturally occurring insertions will help future work engineering precision integration systems.
Huntingtin CAG expansion impairs germ layer patterning in synthetic human gastruloids through polarity defects
Authors: Galgoczi Szilvia , Ruzo Albert , Markopoulos Christian , Yoney Anna , Phan-Everson Tien , Haremaki Tomomi , Metzger Jakob J. , Etoc Fred , Brivanlou Ali H.
Published: February 2021

Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by an expansion of the CAG repeats in the Huntingtin gene (HTT). While HD has been shown to have a developmental component, how early during human embryogenesis the HTT-CAG expansion can cause embryonic defects remains unknown. Here, we demonstrate a specific and highly reproducible CAG length-dependent phenotypic signature in a synthetic model for human gastrulation derived from human embryonic stem cells (hESCs). Specifically, we observed a reduction in the extension of the ectodermal compartment that is associated with enhanced ACTIVIN signaling. Surprisingly, rather than a cell-autonomous effect, tracking the dynamics of TGFβ signaling demonstrated that HTT-CAG expansion perturbs the spatial restriction of ACTIVIN response. This is due to defects in the apicobasal polarization in the context of the polarized epithelium of the gastruloid, leading to ectopic subcellular localization of TGFβ receptors. This work refines the earliest developmental window for the prodromal phase of HD to the first two weeks of human development as modeled by our gastruloids.
Derived loss of signal complexity and plasticity in a genus of weakly electric fish
Authors: Saenz David E. , Gu Tingting , Ban Yue , Winemiller Kirk O. , Markham Michael R.
Published: February 2021

Signal plasticity can maximize the usefulness of costly animal signals such as the electric organ discharges (EODs) of weakly electric fishes. Some species of the order Gymnotiformes rapidly alter their EOD amplitude and duration in response to circadian cues and social stimuli. How this plasticity is maintained across related species with different degrees of signal complexity is poorly understood. In one genus of weakly electric gymnotiform fish (Brachyhypopomus) only one species,B. bennetti, produces a monophasic signal while all other species emit complex biphasic or multiphasic EOD waveforms produced by two overlapping but asynchronous action potentials in each electric organ cell (electrocyte). One consequence of this signal complexity is the suppression of low-frequency signal content that is detectable by electroreceptive predators. In complex EODs, reduction of the EOD amplitude and duration during daytime inactivity can decrease both predation risk and the metabolic cost of EOD generation. We compared EOD plasticity and its underlying physiology inBrachyhypopomusfocusing onB. bennetti. We found thatB. bennettiexhibits minimal EOD plasticity, but that its electrocytes retained vestigial mechanisms of biphasic signaling and vestigial mechanisms for modulating the EOD amplitude. These results suggest that this species represents a transitional phenotypic state within a clade where signal complexity and plasticity were initially gained and then lost. We discuss potential the roles of signal mimicry, species recognition, and sexual selection in maintaining the monophasic EOD phenotype in the face of detection by electroreceptive predators.
Repurposing of Synaptonemal Complex Proteins for Kinetochores in Kinetoplastida
Authors: Tromer Eelco C. , Wemyss Thomas A. , Waller Ross F. , Akiyoshi Bungo
Published: February 2021

Chromosome segregation in eukaryotes is driven by a macromolecular protein complex called the kinetochore that connects centromeric DNA to microtubules of the spindle apparatus. Kinetochores in well-studied model eukaryotes consist of a core set of proteins that are broadly conserved among distant eukaryotic phyla. In contrast, unicellular flagellates of the class Kinetoplastida have a unique set of kinetochore components. The evolutionary origin and history of these kinetochores remains unknown. Here, we report evidence of homology between three kinetoplastid kinetochore proteins KKT16–18 and axial element components of the synaptonemal complex, such as the SYCP2:SYCP3 multimers found in vertebrates. The synaptonemal complex is a zipper-like structure that assembles between homologous chromosomes during meiosis to promote recombination. Using a sensitive homology detection protocol, we identify divergent orthologues of SYCP2:SYCP3 in most eukaryotic supergroups including other experimentally established axial element components, such as Red1 and Rec10 in budding and fission yeast, and the ASY3:ASY4 multimers in land plants. These searches also identify KKT16–18 as part of this rapidly evolving protein family. The widespread presence of the SYCP2-3gene family in extant eukaryotes suggests that the synaptonemal complex was likely present in the last eukaryotic common ancestor. We found at least twelve independent duplications of the SYCP2-3gene family throughout the eukaryotic tree of life, providing opportunities for new functional complexes to arise, including KKT16–18 inTrypanosoma brucei. We propose that kinetoplastids evolved their unique kinetochore system by repurposing meiotic components of the chromosome synapsis and homologous recombination machinery that were already present in early eukaryotes.
Systems-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact onStreptomycesdevelopment
Authors: Du Chao , Willemse Joost , Erkelens Amanda M. , Carrion Victor J. , Dame Remus T. , van Wezel Gilles P.
Published: February 2021

Bacterial chromosome structure is organized by a diverse group of proteins collectively referred to as nucleoid-associated proteins (NAPs). Many NAPs have been well studied in Streptomyces, including Lsr2, HupA, HupS, and sIHF. Here, we show that SCO1839 represents a novel family of Actinobacteria NAPs and recognizes a consensus sequence consisting of GATC followed by (A/T)T. The protein was designated Gbn forGATC-bindingNAP. Deletion ofgbnled to alterations in development and antibiotic production inStreptomyces coelicolor. Chromatin immunoprecipitation sequencing (ChIP-Seq) detected more than 2800 binding regions, encompassing some 3600 GATCWT motifs, which comprise 55% of all such motifs in theS. coelicolorgenome. DNA binding of Gbn in vitro increased DNA stiffness but not compaction, suggesting a role in regulation rather than chromosome organization. Transcriptomics analysis showed that Gbn binding generally leads to reduced gene expression. The DNA binding profiles were nearly identical between vegetative and aerial growth. Exceptions are SCO1311 and SCOt32, for a tRNA editing enzyme and a tRNA that recognises the rare leucine codon CUA, respectively, which nearly exclusively bound during vegetative growth. Taken together, our data show that Gbn is a highly pleiotropic NAP that impacts growth and development in streptomycetes.

IMPORTANCE

A large part of the chemical space of bioactive natural products is derived from Actinobacteria. Many of the biosynthetic gene clusters for these compounds are cryptic, in others words, they are expressed in nature but not in the laboratory. Understanding the global regulatory networks that control gene expression is key to the development of approaches to activate this biosynthetic potential. Chromosome structure has a major impact on the control of gene expression. In bacteria, the organization of chromosome structure is mediated by a diverse group of proteins referred to collectively as nucleoid-associated proteins (NAPs), which play an important role in the control of gene expression, nucleoid structure and DNA repair. We here present the discovery of a novel and extremely pleiotropic NAP, which we refer to as Gbn. Gbn is a sporulation-specific protein that occurs only in the Actinobacteria and binds to GATC sequences, with a subtle but broad effect on global gene expression. The discovery of Gbn is a new step towards better understanding of how gene expression and chromosome structure is governed in antibiotic-producing streptomycetes.
Trophic resources of the edaphic microarthropods: a worldwide review of the empirical evidence
Authors: Velazco Víctor Nicolás , Saravia Leonardo Ariel , Coviella Carlos Eduardo , Falco Liliana Beatriz
Published: February 2021

Ecosystem sustainable use requires reliable information about its biotic and abiotic structure and functioning. Accurate knowledge of trophic relations is central for the understanding of ecosystem dynamics, which in turn, is essential for food web stability analyzes and the development of sustainable practices. There is a rapid growth in the knowledge on how belowground biodiversity regulates the structure and functioning of terrestrial ecosystems. Although, the available information about trophic relationships is hard to find and fragmented. This gathering the information available worldwide about the food resources of soil mesofauna. From the 3105 hits of the initial search on food resources of soil microarthropods, only a total of 196 published works related particular species, genera, and families to particular trophic resources, the majority of them dealing with soils of the Palearctic region. From the 196 publications we extracted 3009 records relating specific taxonomic groups to their trophic resources, 20% mention saprophytic fungi as a food resource, 16% cite microfauna, 11% mention bacteria, 10% litter and 5% cite Mycorrhizal fungi. The available information was highly skewed, the 73.71% comes from Acari, and within these, 50.62% correspond just to Sarcoptiformes. For Collembola, the literature is scarce, the majority coming from Arthropleona. This review highlights the general lack of information relating species, genera, and families of the soil mesofauna to specific trophic resources. It also highlights that available research mostly comes from European sites, with the use of trophic resources by the mesofauna of the majority of the soils in other parts of the world still largely unknown.
An MILP Model for Corn Planting and Harvest Scheduling Considering Storage Capacity and Growing Degree Units
Authors: Khalilzadeh Zahra , Wang Lizhi
Published: February 2021

Abstract

Corn planting and harvest scheduling is an important problem due to having a significant impact on corn yield, balancing the capacities for harvest, transport, and storage operations. Different corn hybrids also have different planting window and poor planting and harvest schedules may cause erratic weekly harvest quantities and logistical and productivity issues. In the 2021 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the historical daily growing degree units (GDU) of two sites and provided planting window, required GDUs, and harvest quantity of corn hybrids planted in these two sites. Then, participants of this challenge were asked to schedule planting and harvesting dates of corn hybrids under two storage capacity scenarios so that facilities are not over capacity in harvesting weeks and have consistent weekly harvest quantities. The two storage capacity scenarios include: (1) planting and harvest scheduling given the maximum storage capacity, and (2) planting and harvest scheduling without maximum storage capacity to determine the lowest possible capacity for each site. In this paper, we propose two mixed integer linear programming (MILP) models for solving this problem considering both the storage capacity and the uncertainty in GDUs. Our results indicate that our proposed models can provide optimal planting and harvest scheduling under different GDU possibilities which ensures consistent weekly harvest quantities that are below the maximum capacity.
Cold adapted desiccation-tolerant bacteria isolated from polar soils presenting high resistance to anhydrobiosis
Authors: Nóbrega Felipe , Duarte Rubens T. D. , Torres-Ballesteros Adriana M. , Queiroz Luciano Lopes , Whyte Lyle G. , Pellizari Vivian H.
Published: February 2021

Life on Earth is strictly dependent on liquid water. In polar terrestrial environments, water exists in solid state during almost the entire year. Polar microorganisms have not only to adjust their metabolism to survive at subzero temperatures, but also need to cope with extremely dry conditions. We investigated the presence of desiccation-adapted bacteria in Arctic permafrost and Antarctic surface soils and characterized their survivability to dryness. We selected desiccation tolerant cells by treating the soils with chloroform prior to cultivation, in order to mimic the stress of low water activity for long periods. From over 1000 colonies from different samples, 23 unique strains were selected and identified as members of phylaFirmicutes, ProteobacteriaandActinobacteria. About 60% of the strains survived after 50 days in anhydrobiosis. The competence to withstand desiccation varied between close related strains isolated from different locations, bringing the question if environmental conditions may play a role in the observed desiccation tolerance. Survivability was also affected by the solution in which the cells were suspended before drying; R2B medium being more protective than water. This is the first time that chloroform was used to select desiccation tolerant microorganisms from polar soils. The collection of polar microorganisms described herein opens the possibility of further experiments aiming to investigate the resistance mechanisms of polar anhydrobionts. Desiccation tolerance is fundamental to the survivability of microorganisms to the space environment and at the surface of thin-atmosphere planets like Mars. Therefore, the selected strains may open a road to better understand the limits of cold adapted life on Earth and beyond, and compare mechanisms of resistance with anhydrobionts from divergent extreme environments.
Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants
Authors: Liu Zhuoming , Wu Hua , Egland Kristi A. , Gilliland Theron C. , Dunn Matthew D. , Luke Thomas C. , Sullivan Eddie J. , Klimstra William B. , Bausch Christoph L. , Whelan Sean P. J.
Published: February 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with amino-acid substitutions and deletions in spike protein (S) can reduce the effectiveness of monoclonal antibodies (mAbs) and may compromise immunity induced by vaccines. We report a polyclonal, fully human, anti-SARS-CoV-2 immunoglobulin produced in transchromosomic bovines (Tc-hIgG-SARS-CoV-2) hyperimmunized with two doses of plasmid DNA encoding the SARS-CoV-2 Wuhan strain S gene, followed by repeated immunization with S protein purified from insect cells. The resulting Tc-hIgG-SARS-CoV-2, termed SAB-185, efficiently neutralizes SARS-CoV-2, and vesicular stomatitis virus (VSV) SARS-CoV-2 chimerasin vitro. Neutralization potency was retained for S variants including S477N, E484K, and N501Y, substitutions present in recent variants of concern. In contrast to the ease of selection of escape variants with mAbs and convalescent human plasma, we were unable to isolate VSV-SARS-CoV-2 mutants resistant to Tc-hIgG-SARS-CoV-2 neutralization. This fully human immunoglobulin that potently inhibits SARS-CoV-2 infection may provide an effective therapeutic to combat COVID-19.
The Human walking kinematic model combined with upper and lower limb movement
Authors: Chen Xin , Hong Bin , Lin Zhangxi , Hou Jing , Lv ShunYa , Gao Zhendong
Published: February 2021

The purpose of this study is to build a relatively complete human walking kinematic model. This model is combined with the rolling-foot model (lower limb) and multi-rod swinging model (upper limb) connected by COM. We calculated the velocity of COM and other critical joints of the upper limb by marker point capture experiment using the high-speed camera. This research shows that the hand joint velocity measured through the experiment can achieve high coincidence with that calculated by the theoretical model given specific inputs. Moreover, the common pattern of upper limb angles is also studied for an accurate description. The proposed kinematic model is expected to forecast desired motion intention for better compliance by the rehabilitation and assistive robots.
The impact of mobility network properties on predicted epidemic dynamics in Dhaka and Bangkok
Authors: Brown Tyler S. , Engø-Monsen Kenth , Kiang Mathew V. , Mahmud Ayesha S. , Maude Richard J. , Buckee Caroline O.
Published: February 2021

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Properties of city-level commuting networks are expected to influence epidemic potential of cities and modify the speed and spatial trajectory of epidemics when they occur. In this study, we use aggregated mobile phone user data to reconstruct commuter mobility networks for Bangkok (Thailand) and Dhaka (Bangladesh), two megacities in Asia with populations of 16 and 21 million people, respectively. We model the dynamics of directly-transmitted infections (such as SARS-CoV2) propagating on these commuting networks, and find that differences in network structure between the two cities drive divergent predicted epidemic trajectories: the commuting network in Bangkok is composed of geographically-contiguous modular communities and epidemic dispersal is correlated with geographic distance between locations, whereas the network in Dhaka has less distinct geographic structure and epidemic dispersal is less constrained by geographic distance. We also find that the predicted dynamics of epidemics vary depending on the local topology of the network around the origin of the outbreak. Measuring commuter mobility, and understanding how commuting networks shape epidemic dynamics at the city level, can support surveillance and preparedness efforts in large cities at risk for emerging or imported epidemics.
Fingerprinting and behavioural prediction rest on distinct functional systems of the human connectome
Authors: Mantwill Maron , Gell Martin , Krohn Stephan , Finke Carsten
Published: February 2021

The prediction of inter-individual behavioural differences from neuroimaging data is a rapidly evolving field of research, focusing on individualised methods to describe human brain organisation on the single-subject level. One method that harnesses such individual signatures is functional connectome fingerprinting, which can reliably identify individuals from large study populations. While connectome fingerprints have been previously associated with individual cognitive function, these associations rest on indirect evidence.

Contrasting with these previous reports, here we systematically investigate the link between connectome fingerprints and the prediction of behaviour on different levels of brain network organisation (individual edges, network interactions, topographical organisation, and edge variability), using 339 resting-state fMRI datasets from the Human Connectome Project.

Our analysis revealed a significant divergence between connectivity signatures that discriminate between individuals and those predictive of behaviour on all levels of network organisation. Across different parcellation schemes, thresholds and prediction algorithms, we consistently find fingerprints in higher-order multimodal association cortices, while neural correlates of behaviour display a more variable topological distribution. Furthermore, we find the standard deviation of connections between subjects to be significantly higher in fingerprinting than in prediction, making inter-individual connection variability a possible separating marker.

These results demonstrate that participant identification and behavioural prediction involve highly distinct functional systems of the human connectome, suggesting that connectome fingerprints are not as functionally relevant as previously believed. The present study thus calls for a re-evaluation of the significance of functional connectivity fingerprints in personalized medicine.
A non-structural pure enzyme protein forms a LCST type of stimuli-responsive and reversible hydrogel with novel structure and catalytic activity
Authors: Nie J. , Zhang X. , Liu Y. , Schroer M.A. , Wang W. , Ren J. , Svergun D.I. , Zeng A.-P.
Published: February 2021

Hydrogels have a wide range of applications such as in biomedicine, cosmetics and soft electronics. Compared to polymer hydrogels based on covalent bonding, protein hydrogels offer distinct advantages owing to their biocompatibility and better access to molecular engineering. However, pure and natural protein hydrogels have been seldom reported except for structural proteins like collagen and silk fibrin. Here, we report the unusual ability and mechanism of a unique natural enzyme, lipoate-protein ligase A (LplA) ofE. colito self-assemble into a stimuli-responsive and reversible hydrogel of the low critical solution temperature (LCST) type. This is the first globular and catalytic protein found to form a hydrogel in response to temperature, pH and the presence of ions. Protein structure based analysis reveals the key residues responsible for the gel formation and mutational studies confirms the essential roles of hydrogen bonding between the C-terminal domains and electrostatic interactions in the N-terminal domains. Characterization of phase transitions of wild type LplA and its mutants using small angle X-ray scattering (SAXS) yields details of the gelation process from initial dimer formation over a pre-gel-state to full network development. Further electron microscopic analyses and modeling of SAXS data suggest an unusual interlinked ladder-like structure of the macroscopic crosslinking network with dimers as ladder steps. The unique features of this first reported protein hydrogel may open up hitherto inaccessible applications, especially those taking advantage of the inherent catalytic activity of LplA.
Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor
Authors: Zhuang Youwen , Krumm Brian , Zhang Huibing , Zhou X. Edward , Wang Yue , Huang Xi-Ping , Liu Yongfeng , Cheng Xi , Jiang Yi , Jiang Hualiang , Zhang Cheng , Yi Wei , Roth Bryan L. , Zhang Yan , Xu H. Eric.
Published: February 2021

Dopamine is an essential neurotransmitter, which functions are mediated by five G protein-coupled receptors, dopamine D1 to D5 receptors (D1R-D5R) in mammals. Among them, D1R is the most abundantly expressed dopamine receptor in the CNS and is the central receptor mediating excitatory dopamine signaling in multiple dopaminergic pathways. Dysregulation of D1R signaling has been directly linked to Parkinson’s disease (PD), schizophrenia, and drug abuse. Due to its fundamental functions in human diseases, D1R has long been the subject of intensive drug development effort toward the treatment of neuropsychiatric diseases. Here, we report the structures of D1R-Gs complex bound to endogenous agonist dopamine and synthetic agonist SKF81297, both with positive allosteric modulator LY3154207. These structures reveal the basis of dopamine recognition, the binding and potential allosteric regulation of DRD1 PAM LY3154207, and provide structural templates for design of subtype-selective D1R ligand for drug discovery targeting DRD1 for treating various CNS diseases.