bluuebunny/crossref_metadata_2025 huggingface dataset:
Specialized pathogenic cells release Tc toxins using a type 10 secretion system
Authors: Sitsel Oleg , Wang Zhexin , Janning Petra , Kroczek Lara , Wagner Thorsten , Raunser Stefan
Published: February 2023

Disease-causing bacteria use a variety of secreted toxins to invade and subjugate their hosts. While the machinery responsible for secretion of many smaller toxins has already been established, it remains enigmatic for larger ones such as Tc toxins from human and insect pathogens, which approach the size of a prokaryotic ribosome. In the present study, we combine targeted genomic editing, proteomic profiling and cryo-electron tomography of the insect pathogenYersinia entomophagato reveal that a specialized subset of bacterial cells produces the Tc toxin YenTc as part of a complex toxin cocktail released into the environment by controlled cell lysis using a transcriptionally-coupled, pH-dependent type 10 secretion system (T10SS). Our results dissect the process of Tc toxin export by a T10SS in hitherto unprecedented detail, identifying that T10SSs operate via a previously unknown lytic mode of action, and establishing them as crucial players in the size-insensitive release of cytoplasmically folded toxins. With T10SSs directly embedded in Tc toxin operons of major human pathogens such asYersinia pestisandSalmonella enterica, we anticipate our findings to model an important aspect of pathogenesis in bacteria with a significant impact on global human health.
The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid
Authors: Bellegarda Celine , Zavard Guillaume , Moisan Lionel , Gray Ryan S. , Brochard-Wyart Françoise , Joanny Jean-François , Cantaut-Belarif Yasmine , Wyart Claire
Published: February 2023

The Reissner fiber (RF) is an acellular thread positioned in the midline of the central canal that aggregates thanks to the beating of numerous cilia from ependymal radial glial cells (ERGs) generating flow in the central canal of the spinal cord. RF together with cerebrospinal fluid (CSF)-contacting neurons (CSF-cNs) forms an axial sensory system detecting curvature. How RF, CSF-cNs and the multitude of motile cilia from ERGs interactin vivoappears critical for maintenance of RF and sensory functions of CSF-cNs to keep a straight body axis but is not well-understood. Usingin vivoimaging in larval zebrafish, we show that RF is under tension and resonates dorsoventrally. Focal RF ablations trigger retraction and relaxation of the fiber cut ends, with larger retraction speeds for rostral ablations. We built a mechanical model that estimates RF stress diffusion coefficient at 4 mm2/ s and reveals that tension builds up rostrally along the fiber. After RF ablation, CSF-cN spontaneous activity decreased and ciliary motility changed, suggesting physical interactions between RF and cilia projecting into the central canal. We observed that motile cilia were caudally-tilted and frequently interacted with RF. We propose that the numerous ependymal motile monocilia contribute to RF heterogenous tension via weak interactions. Our work demonstrates that under tension, the Reissner fiber dynamically interacts with motile cilia generating CSF flow and spinal sensory neurons.
Capturing and Detecting of Extracellular Vesicles Derived from SingleEscherichia coliMother Cells
Authors: Yokoyama Fumiaki , Kling André , Dittrich Petra S.
Published: February 2023

Cells have a phenotypic heterogeneity even in isogeneic populations. Differences in secretion of substances have been well-investigated with single mammalian cells. However, studies on the heterogeneity of secreted substances at the single-bacterial-cell level are challenging due to the small size, motility, and rapid proliferation of bacterial cells such asEscherichia coli. Here, we propose a microfluidic device to achieve an isolated culture of single bacterial cells and capture of extracellular vesicles (EVs) secreted from individuals. The device has winding channels to trap single rod-shapedE. colicells at their entrances. Isolated single mother cells grew constantly up to 24 h, while their daughter cells were removed by flow. The flow carried EVs of the trapped cells along the channel, whose surface was rendered positively charged to electrostatically capture negatively charged EVs, followed by staining with a lipophilic dye to detect EVs by microscopy. Our results underline that the amounts of segregated EVs vary among cells. Moreover, individual responses to perturbation using a membrane-perturbing antibiotic were observed in growth dynamics and EV secretion of living-alone bacteria. The proposed method can be applied to detect other secreted substances of interest, possibly paving the way for elucidating unknown heterogeneities in bacteria.
The song does not remain the same: daily singing of adult songbirds prevents passive changes in song structure independently of auditory feedback
Authors: Mizuguchi Daisuke , Sánchez-Valpuesta Miguel , Kim Yunbok , dos Santos Ednei B. , Kang HiJee , Mori Chihiro , Wada Kazuhiro , Kojima Satoshi
Published: February 2023

Many songbirds learn to produce songs through vocal practice early in life and continue to sing numerous renditions of their learned songs daily throughout their lifetime. While it is well-known that adult songbirds sing as part of a mating ritual, the functions of singing behavior outside of reproductive contexts are not fully understood. Here, we demonstrate that adult singing outside of reproductive contexts serves to prevent passive changes in song performance. We suppressed the daily singing behavior of adult zebra finches produced in the solo context for two weeks using a reversible behavioral manipulation and examined the effect on song performance. Our results indicated that suppressing daily singing significantly decreased the pitch of song elements and both the amplitude and duration of song motifs. These findings suggest that adult song is not acoustically stable without singing, and that adult birds maintain their song performance by daily singing. Moreover, we found that the changes in song structure caused by singing suppression were substantially recovered within two weeks of free singing, even in deafened birds. Thus, the recovery of song performance does not necessarily require auditory feedback but is predominantly caused by singing behavior per se (i.e., the physical act of singing). Finally, unlike the auditory feedback-dependent song plasticity reported previously, the passive song changes caused by singing suppression were not significantly dependent on age. Taken together, our findings demonstrate that adult songbirds maintain song performance by preventing passive song changes through the physical act of daily singing throughout their life. Such daily singing likely functions as vocal training to maintain the neural and/or muscular system in optimal conditions for song performance in reproductive contexts, similar to how human singers and athletes practice daily to maintain their performance.
Cell-cycle status of male and female gametes during Arabidopsis reproduction
Authors: Voichek Yoav , Hurieva Bohdana , Michaud Caroline , Schmücker Anna , Vergara Zaida , Desvoyes Bénédicte , Gutierrez Crisanto , Nizhynska Viktoria , Jaegle Benjamin , Borg Michael , Berger Frédéric , Nordborg Magnus , Ingouff Mathieu
Published: February 2023

Fertilization inArabidopsis thalianais a highly coordinated process that begins with a pollen tube delivering the two sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization still remains elusive as DNA quantification and DNA replication assays have given conflicting results1–4. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all the phases of the cell cycle. We show that male and female gametes in Arabidopsis are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.
Dentate Neurogenesis Modulates Dorsal Hippocampal Excitation/Inhibition Balance Crucial for Cognitive Flexibility
Authors: Li Haowei , Tamura Risako , Hayashi Daiki , Asai Hirotaka , Koga Junya , Ando Shota , Yokota Sayumi , Kaneko Jun , Sakurai Keisuke , Sumiyoshi Akira , Yamamoto Tadashi , Hikishima Keigo , Tanaka Kazumasa Z. , McHugh Thomas J. , Hisatsune Tatsuhiro
Published: February 2023

Adult neurogenesis endows the hippocampus with unparalleled neural plasticity, essential for intricate cognitive functions. However, the manner in which sparse newborn neurons (NBNs) modulate neural activities and subsequently shape behavior remains enigmatic. Utilizing a newly engineered NBN-Tetanus Toxin mouse model, we non-invasively silenced NBNs and confirmed their crucial role in cognitive flexibility, as demonstrated through reversal learning in the Morris water maze and the Go/Nogo task in operant learning. Pairing task-based functional MRI (tb-fMRI) with operant learning revealed a dorsal hippocampal hyperactivation during Nogo task, implying that hippocampal hyperexcitability might underlie the observed behavioral deficits. Notably, resting-state fMRI (rs-fMRI) revealed enhanced functional connectivity between the dorsal and ventral dentate gyrus following NBN silencing. Further exploration of PV+ interneurons and mossy cells’ activities highlighted NBN’s integral part in preserving the excitation/inhibition balance within the hippocampus. Our findings emphasize how the neural plasticity driven by NBNs extensively modulates the hippocampus, sculpting cognitive flexibility.
Complex chemical signals dictate Ah receptor activation through the gut-lung axis
Authors: Dong Fangcong , Murray Iain A. , Annalora Andrew , Coslo Denise , Desai Dhimant , Gowda Krishne , Yang Jian , Wang Dingbowen , Koo Imhoi , Hao Fuhua , Amin Shantu G. , Patterson Andrew D. , Marcus Craig , Perdew Gary H.
Published: February 2023

The aryl hydrocarbon receptor (AHR) mediates intestinal barrier homeostasis. Many AHR ligands are also CYP1A1/1B1 substrates, which can result in the rapid clearance within the intestinal tract, limiting AHR activation. This led us to the hypothesis that there are dietary substrates of CYP1A1/1B1 that increase the half-life of potent AHR ligands. We examined the potential of urolithin A (UroA) as a CYP1A1/1B1 substrate to enhance AHR activity in vivo. UroA is a competitive substrate for CYP1A1/1B1 in an in vitro competition assay. A broccoli-containing diet promotes the gastric formation of the potent hydrophobic AHR ligand and CYP1A1/1B1 substrate, 5,11-dihydroindolo[3,2-b]carbazole (ICZ). Dietary exposure to UroA in a broccoli diet led to a coordinated increase in duodenal, cardiac, and pulmonary AHR activity, but no increase in activity in liver. Thus, CYP1A1 dietary competitive substrates can lead to intestinal “escape”, likely through the lymphatic system, increasing AHR activation in key barrier tissues.
Comparison of concurrent and asynchronous running kinematics and kinetics from marker-based motion capture and markerless motion capture under two clothing conditions
Authors: Kanko Robert M. , Outerleys Jereme B. , Laende Elise K. , Selbie W. Scott , Deluzio Kevin J.
Published: February 2023

As markerless motion capture is increasingly used to measure three-dimensional human pose, it is important to understand how markerless results can be interpreted alongside historical marker-based data and how they are impacted by clothing. We compared concurrent running kinematics and kinetics between marker-based and markerless motion capture, and between two markerless clothing conditions. Thirty adults ran on an instrumented treadmill wearing motion capture clothing while concurrent marker-based and markerless data were recorded, and ran a second time wearing athletic clothing (shorts and t-shirt) while markerless data were recorded. Differences calculated between the concurrent signals from both systems, and also between each participant’s mean signals from both asynchronous clothing conditions were summarized across all participants using root-mean-square differences. Most kinematic and kinetic signals were visually consistent between systems and markerless clothing conditions. Between systems, joint center positions differed by 3 cm or less, sagittal plane joint angles differed by 5° or less, and frontal and transverse plane angles differed by 5°-10°. Joint moments differed by 0.3 Nm/kg or less between systems. Differences were sensitive to segment coordinate system definitions, highlighting the effects of these definitions when comparing against historical data or other motion capture modalities.
The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct
Authors: Getz Eric W. , Lanclos V. Celeste , Kojima Conner Y. , Cheng Chuankai , Henson Michael W. , Schön Max Emil , Ettema Thijs J. G. , Faircloth Brant C. , Thrash J. Cameron
Published: February 2023

Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning Order level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to thePelagibacteralesis highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to thePelagibacterales. We used a new isolate genome, recently released single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with recruitment of metagenomes spanning open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade, and support the contention that this group represents a taxonomic Family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa.

IMPORTANCE

One goal of marine microbiologists is to uncover the roles various microorganisms are playing in biogeochemical cycles. Success in this endeavor relies on differentiating groups of microbes and circumscribing their relationships. An early-diverging group (subclade V) of the most abundant bacterioplankton, SAR11, has recently been proposed as a separate lineage that does not share a most recent common ancestor. But beyond phylogenetics, little has been done to evaluate how these organisms compare with SAR11. Our work leverages dozens of new genomes to demonstrate the similarities and differences between subclade V and SAR11. In our analysis, we also establish that subclade V is synonymous with a group of bacteria established from 16S rRNA gene sequences, AEGEAN-169. Subclade V/AEGEAN-169 has clear metabolic distinctions from SAR11 and their shared traits point to remarkable convergent evolution if they do not share a most recent common ancestor.
Oxygen intrusions sustain aerobic nitrite-oxidizing bacteria in anoxic marine zones
Authors: Buchanan Pearse J. , Sun Xin , Weissman JL , McCoy Daniel , Bianchi Daniele , Zakem Emily
Published: February 2023

Anaerobic metabolisms are thought to dominate nitrogen cycling in anoxic marine zones (AMZs). However, thriving populations of aerobic nitrite-oxidizing bacteria (NOB) in AMZs challenge this assumption and remain unexplained. Using theory and modelling, we show how periodic oxygen intrusions sustain aerobic NOB in AMZs alongside more competitive aerobic heterotrophs. Ecological theory, supported by genomics and numerical simulations, frames NOB as opportunists exploiting a fleeting supply of oxygen. Consistent within situobservations, we show that simulated NOB contribute substantially (>40%) to oxygen consumption at AMZ boundaries, which implies that NOB may provide a unique stabilizing feedback to AMZs. Fine-scale ocean currents increase the metabolic diversity in AMZs, which could stabilize AMZ volume under climate change.

One-Sentence Summary

Fleeting whiffs of oxygen to the ocean ‘s anoxic zones increase microbial diversity and alter biogeochemical cycling.
Quantitative Time-Course Analysis of Osmotic and Salt Stress inArabidopsis thalianausing Short Gradient Multi-CV FAIMSpro BoxCar DIA
Authors: Gallo M.C. Rodriguez , Li Q. , Talasila M. , Uhrig RG
Published: February 2023

A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple composition voltage (CV) HighFieldAsymetric WaveformIonMobilitySpectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply-quantify theArabidopsis thalianaseedling proteome. Using a BoxCarDIA acquisition workflow with a −30 −50 −70 CV FAIMSpro setting we are able to consistently quantify >5000Arabidopsisseedling proteins over a 21-minute gradient, facilitating the analysis of ~42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring inArabidopsisseedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ~9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants.
Joint testing of rare variant burden scores using non-negative least squares
Authors: Ziyatdinov Andrey , Mbatchou Joelle , Marcketta Anthony , Backman Joshua , Gaynor Sheila , Zou Yuxin , Joseph Tyler , Geraghty Benjamin , Herman Joseph , Watanabe Kyoko , Ghosh Arkopravo , Kosmicki Jack , Locke Adam ,   Regeneron Genetics Center, Thornton Timothy , Kang Hyun Min , Ferreira Manuel , Baras Aris , Abecasis Goncalo , Marchini Jonathan
Published: February 2023

Gene-based burden tests are a popular and powerful approach for analysis of exome-wide association studies. These approaches combine sets of variants within a gene into a single burden score that is then tested for association. Typically, a range of burden scores are calculated and tested across a range of annotation classes and frequency bins. Correlation between these tests can complicate the multiple testing correction and hamper interpretation of the results. We introduce a new method called the Sparse Burden Association Test (SBAT) that tests the joint set of burden scores under the assumption that causal burden scores act in the same effect direction. The method simultaneously assesses the significance of the model fit and selects the set of burden scores that best explain the association at the same time. Using simulated data, we show that the method is well calibrated and highlight some scenarios where the test outperforms existing gene-based tests. We apply the method to 73 quantitative traits from the UK Biobank which further illustrates the power of the method. This test is implemented in the REGENIE software.
The most probable ancestral sequence reconstruction yields proteins without systematic bias in thermal stability or activity
Authors: Sennett Michael A. , Beckett Brian C. , Theobald Douglas L.
Published: February 2023

Ancestral sequence resurrection (ASR) is the inference of extinct biological sequences from extant sequences, the most popular of which are based on probabilistic models of evolution. ASR is becoming a popular method for studying the evolution of enzyme characteristics. The properties of ancestral enzymes are biochemically and biophysically characterized to gain some knowledge regarding the origin of some enzyme property. Current methodology relies on resurrection of the single most probable (SMP) sequence and is systematically biased. Previous theoretical work suggests this will result in a thermostability bias in resurrected SMP sequences, and even the activity, calling into question inferences derived from ancestral protein properties. We experimentally test the potential stability bias hypothesis by resurrecting 40 malate and lactate dehydrogenases. Despite the methodological bias in resurrecting an SMP protein, the measured biophysical and biochemical properties of the SMP protein are not biased in comparison to other, less probable, resurrections. In addition, the SMP protein property seems to be representative of the ancestral probability distribution. Therefore, the conclusions and inferences drawn from the SMP protein are likely not a source of bias.

Significance

Ancestral sequence resurrection (ASR) is a powerful tool for: determining how new protein functions evolve; inferring the properties of an environment in which species existed; and protein engineering applications. We demonstrate, using lactate and malate dehydrogenases (L/MDHs), that resurrecting the single most probable sequence (SMP) from a maximum likelihood phylogeny does not result in biased activity and stability relative to sequences sampled from the posterior probability distribution. Previous studies using experimentally measured phenotypes of SMP sequences to make inferences about the environmental conditions and the path of evolution are likely not biased in their conclusions. Serendipitously, we discover ASR is also a valid tool for protein engineering because sampled reconstructions are both highly active and stable.
O-GlcNAcylation regulates neurofilament-light assembly and function and is perturbed by Charcot-Marie-Tooth disease mutations
Authors: Huynh Duc T. , Hu Jimin , Schneider Jordan R. , Tsolova Kalina N. , Soderblom Erik J. , Watson Abigail J. , Chi Jen-Tsan , Evans Chantell S. , Boyce Michael
Published: February 2023

The neurofilament (NF) cytoskeleton is critical for neuronal morphology and function. In particular, the neurofilament-light (NF-L) subunit is required for NF assemblyin vivoand is mutated in subtypes of Charcot-Marie-Tooth (CMT) disease. NFs are highly dynamic, and the regulation of NF assembly state is incompletely understood. Here, we demonstrate that human NF-L is modified in a nutrient-sensitive manner by O-linked-β-N-acetylglucosamine (O-GlcNAc), a ubiquitous form of intracellular glycosylation. We identify five NF-L O-GlcNAc sites and show that they regulate NF assembly state. Interestingly, NF-L engages in O-GlcNAc-mediated protein-protein interactions with itself and with the NF component α-internexin, implying that O-GlcNAc is a general regulator of NF architecture. We further show that NF-L O-GlcNAcylation is required for normal organelle trafficking in primary neurons, underlining its functional significance. Finally, several CMT-causative NF-L mutants exhibit perturbed O-GlcNAc levels and resist the effects of O-GlcNAcylation on NF assembly state, indicating a potential link between dysregulated O-GlcNAcylation and pathological NF aggregation. Our results demonstrate that site-specific glycosylation regulates NF-L assembly and function, and aberrant NF O-GlcNAcylation may contribute to CMT and other neurodegenerative disorders.
Dynamic walking behavior during odor trail-following in locusts
Authors: Traner Mike , Raman Barani
Published: February 2023

One of the important subsets of odor sources used in olfactory navigation is surface-bound sources, which can broadly take the form of point sources or trails. Odor trails, in particular, have been observed to be highly relevant components of olfactory-based navigation for species as broadly distributed as dogs and ants. Here, we present an automated treadmill setup capable of dynamically printing odor trails of arbitrary lengths and configurations, and with closed-loop control of speed based on the subject’s movement. We used this setup to characterize trail-following behavior in locusts (Schistocerca americana). The free-moving behavior of the locusts is more naturalistic and is richer in plumbable data than many traditional assays. We reveal broad classes of behavioral walking motifs and their dynamic transitions as locusts pursue or avoid an odor trail. Furthermore, we show how these motifs vary across individuals, with the identity of the odorant and with respect to the sex of the organism. Our dataset and analyses provide a first demonstration that this model organism is capable of robust odor trail following, and provides a comprehensive analysis of the dynamic motifs that underlie this behavioral capability.
Isoform-specific targeting properties of the protocadherin CDHR5 control its apical delivery to promote brush border assembly
Authors: Matoo Samaneh , Graves Maura J. , Choi Myoung Soo , El Sheikh Idris Rawnag A. , Acharya Prashun , Thapa Garima , Nguyen Tram , Atallah Sarah Y. , Tipirneni Ashna K. , Stevenson Phillip J. , Crawley Scott W.
Published: February 2023

Transporting epithelial cells of the gut and kidney interact with their luminal environment through a densely-packed collection of apical microvilli known as the brush border. Proper brush border assembly depends on the intermicrovillar adhesion complex (IMAC), a protocadherin-based adhesion complex found at the distal tips of microvilli that mediates adhesion between neighboring protrusions to promote their organized packing. Loss of the IMAC adhesion molecule Cadherin-related family member 5 (CDHR5) correlates with poor prognosis of colon cancer patients, though the functional properties of this protocadherin have not been thoroughly explored in relevant cell systems. Here, we show that the two dominant CDHR5 splice isoforms expressed in enterocytes interact to form an apparentcis-oligomer that is competent to target to the apical domain to drive microvillar elongation. The two isoforms exhibited distinct sequence-dependent apical targeting properties, with one isoform requiring its cytoplasmic tail. Library screening identified the Ezrin-associated scaffolds EBP50 and E3KARP as cytoplasmic binding partners for CDHR5. Consistent with this, loss of EBP50 disrupted proper brush border assembly with cells exhibiting markedly reduced apical IMAC levels. Together, our results shed light on the apical targeting determinants of CDHR5 and further define the interactome of the IMAC involved in brush border assembly.
DR-BERT: A Protein Language Model to Annotate Disordered Regions
Authors: Nambiar Ananthan , Forsyth John Malcolm , Liu Simon , Maslov Sergei
Published: February 2023

Despite their lack of a rigid structure, intrinsically disordered regions in proteins play important roles in cellular functions, including mediating protein-protein interactions. Therefore, it is important to computationally annotate disordered regions of proteins with high accuracy. Most popular tools use evolutionary or biophysical features to make predictions of disordered regions. In this study, we present DR-BERT, a compact protein language model that is first pretrained on a large number of unannotated proteins before being trained to predict disordered regions. Although it does not use any explicit evolutionary or biophysical information, DR-BERT shows a statistically significant improvement when compared to several existing methods on a gold standard dataset. We show that this performance is due to the information learned during pretraining and DR-BERT’s ability to use contextual information. A web application for using DR-BERT is available athttps://huggingface.co/spaces/nambiar4/DR-BERTand the code to run the model can be found athttps://github.com/maslov-group/DR-BERT.
A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma
Authors: Banu Matei A. , Dovas Athanassios , Argenziano Michael G. , Zhao Wenting , Grajal Henar Cuervo , Higgins Dominique M.O. , Sperring Colin P. , Pereira Brianna , Ye Ling F. , Mahajan Aayushi , Humala Nelson , Furnari Julia L. , Upadhyayula Pavan S. , Zandkarimi Fereshteh , Nguyen Trang T. T. , Wu Peter B. , Hai Li , Karan Charles , Razavilar Aida , Siegelin Markus D. , Kitajewski Jan , Bruce Jeffrey N. , Stockwell Brent R. , Sims Peter A. , Canoll Peter D.
Published: February 2023

Glioma cells hijack developmental transcriptional programs to control cell state. During neural development, lineage trajectories rely on specialized metabolic pathways. However, the link between tumor cell state and metabolic programs is poorly understood in glioma. Here we uncover a glioma cell state-specific metabolic liability that can be leveraged therapeutically. To model cell state diversity, we generated genetically engineered murine gliomas, induced by deletion of p53 alone (p53) or with constitutively active Notch signaling (N1IC), a pathway critical in controlling cellular fate. N1IC tumors harbored quiescent astrocyte-like transformed cell states while p53 tumors were predominantly comprised of proliferating progenitor-like cell states. N1IC cells exhibit distinct metabolic alterations, with mitochondrial uncoupling and increased ROS production rendering them more sensitive to inhibition of the lipid hydroperoxidase GPX4 and induction of ferroptosis. Importantly, treating patient-derived organotypic slices with a GPX4 inhibitor induced selective depletion of quiescent astrocyte-like glioma cell populations with similar metabolic profiles.
Modulation of quantitative trait loci forArabidopsis thalianaseed performance by the maternal and germination environment
Authors: Snoek Basten L. , Serin Elise A. R. , Nijveen Harm , Willems Leo A. J. , Rienstra Juriaan A. , van Zanten Martijn , Hilhorst Henk W. M. , Ligterink Wilco
Published: February 2023

The quality of seeds contributes to plant performance, especially during germination and in the young seedling stage, and hence affects the economic value of seed crops. A seed’s innate quality is determined during seed development and the following seed maturation phase. It is tightly controlled by the genetic make-up of the mother plant and further shaped by the environmental conditions of the mother plant. The interaction between genotype and environment can result in substantial quantitative variation in seed traits like dormancy and viability.

Making use of naturally occurring variation within theArabidopsis thalianagermplasm, we studied the interaction between seed production environments and the genetic architecture of mother plants on diverse seed quality traits. An Arabidopsis Bayreuth-0 x Shahdara recombinant inbred line (RIL) population was grown in four different seed production environments: high temperature, high light, low phosphate, and control conditions. The seeds harvested from the mother plants that were exposed to these environments from flowering until seed harvest were subsequently subjected to germination assays under standard and mild stress conditions (cold, heat, osmotic stress and added phytohormone ABA). Quantitative trait locus (QTL) analysis identified many environmental-sensitive QTLs (QTL x E) as well as several interactions between the maternal and germination environments. Variation in the number and position of the QTLs was largely determined by the germination conditions, however effects of the maternal environment were clearly present regarding the genomic location as well as significance of the individual QTLs.

Together, our findings uncover the extensive environmental modulation of the genetic influence on seed performance and how this is shaped by the genetic make-up of the mother plant. Our data provides a systems-view of the complex genetic basis of genotype-by-environment interactions determining seed quality.
Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity
Authors: Liu Zhi , Lee Dong-Sung , Liang Yuqiong , Zheng Ye , Dixon Jesse R
Published: February 2023

Chromatin conformation reorganization is emerging as an important layer of regulation for gene expression and lineage specification. Yet, how lineage-specific transcription factors contribute to the establishment of cell type-specific 3D chromatin architecture in the immune cells remains unclear, especially for the late stages of T cell subset differentiation and maturation. Regulatory T cells (Treg) are mainly generated in the thymus as a subpopulation of T cells specializing in suppressing excessive immune responses. Here, by comprehensively mapping 3D chromatin organization during Treg cell differentiation, we show that Treg-specific chromatin structures were progressively established during its lineage specification, and highly associated with Treg signature gene expression. Additionally, the binding sites of Foxp3, a Treg lineage specifying transcription factor, were highly enriched at Treg-specific chromatin loop anchors. Further comparison of the chromatin interactions between wide-type Tregs versus Treg cells from Foxp3 knock-in/knockout or newly-generated Foxp3 domain-swap mutant mouse revealed that Foxp3 was essential for the establishment of Treg-specific 3D chromatin architecture, although it was not dependent on the formation of the Foxp3 domain-swapped dimer. These results highlighted an underappreciated role of Foxp3 in modulating Treg-specific 3D chromatin structure formation.
Evaluation of antimicrobial activity of Kefir drink against Escherichia coli, Salmonella typhimurium and Shigella flexneri
Authors: Cortéz Zaira Cecilia Gutiérrez , Rubén Tescucano Alonso C. Alonso , Almeida Villegas Jorge Angel , González Gabriel Martínez
Published: February 2023

Objective

Evaluate the antimicrobial activity of the Kefir drink againstEscherichia coli, Salmonella typhimurium and Shigella flexneri

Method

The Kefir used in the investigation was acquired in Toluca, State of Mexico. We performed a reactivation of Kefir with pasteurized milk and analyzed 3 carbohydrates (honey, sugar and piloncillo) at different concentrations and times, 80, 100, 120% and 24, 48 and 72 hours respectively. Isolated cultivable microorganisms were characterized by phenotypic, biochemical and mass spectroscopy techniques. The initial and final pH were determined during the study time. The antimicrobial activity was carried out by extracting the metabolites present in the ferment with the Kirby-Bauer method, in addition the direct ferment was evaluated, to determine if there was inhibition with theEscherichia coli (ATCC 11229) strains,Salmonella typhimurium(ATCC 14028) andShigella flexneri(ATCC 12022).

Results

It was observed that in the three carbohydrates used at a concentration of 120% and at a time of 72 h, a lower pH was obtained (3.51 to 3.64) compared to their initial concentration (6.50 to 6.64). From the metabolites extracted in the different ferments, no inhibition halo was obtained with the strains analyzed. However, when using direct ferments, it was observed that in the carbohydrates used (sugar, honey, piloncillo) there was the presence of an inhibiting halo or the growth of colonies other than those evaluated. The isolated cultivable microorganisms were:Pichia kudriavzevii(yeast);Enterococcussp (gram-positive coconut) andLactobacillussp (gram-positive bacillus).

Conclusions

Kefir ferments made with different carbohydrates, came to present a degree of inhibition only as a consortium against Gram-negative microorganisms analyzed.
The impacts of contemporary logging after 250 years of deforestation and degradation on forest-dependent threatened species
Authors: Ward Michelle , Ashman Kita , Lindenmayer David , Legge Sarah , Kindler Gareth , Cadman Timothy , Fletcher Rachel , Whiterod Nick , Lintermans Mark , Zylstra Philip , Stewart Romola , Thomas Hannah , Blanch Stuart , Watson James E.M.
Published: February 2023

Despite the importance of safeguarding forests and woodlands for achieving global climate and biodiversity agendas, logging continues across most forested countries. Forestry advocates often claim logging has minimal impacts, but rarely consider the cumulative threat deforestation and degradation has had, and continue to have, on species. Using New South Wales (Australia) as a case study, we quantify the extent of deforestation and degradation from 1750 – current. Using these estimates of overall loss as a baseline, we then quantify the relative extent of contemporary (2000 – 2022) logging and the condition of the remaining native forest and woodland (quantified by measuring the similarity of a current ecosystem to a historical reference state with high ecological integrity). Using these data, we measure the impacts on distinct vegetation types and on 484 terrestrial forest-dependent now-threatened species. We show that more than half (29 million ha) of pre-1750 (pre-European colonization of Australia) native forest and woodland vegetation in NSW has been lost. Of the remaining 25 million ha, 9 million ha is degraded. We found contemporary degradation from logging affected 244 forest-dependent now-threatened species that had already been affected by this historical deforestation and degradation, but the impacts varied across species and vegetation types. We found that 70 now-threatened species that were impacted by historical deforestation and degradation and continue to be impacted by logging, now have ≤50% of their pre-1750 extent remaining that is intact (with three species now having <20%). By quantifying the historical impacts of deforestation and degradation, our research sets the impact of contemporary degradation from logging in perspective and highlights shortfalls in current environmental assessments that fail to consider appropriate baselines when reporting on overall impact. Future land management decisions need to consider not only the extent of remaining habitat based on pre-1750 extents, but also its condition.

Article impact statement

The impact of logging needs to be placed in perspective by considering past losses and degradation due to human land use decisions.
Mitochondrial Transport in Symmetric and Asymmetric Axons with Multiple Branching Junctions: A Computational Study
Authors: Kuznetsov Ivan A. , Kuznetsov Andrey V.
Published: February 2023

We explore the impact of multiple branching junctions in axons on the mean age of mitochondria and their age density distributions in demand sites. The study looked at mitochondrial concentration, mean age, and age density distribution in relation to the distance from the soma. We developed models for a symmetric axon containing 14 demand sites and an asymmetric axon containing 10 demand sites. We examined how the concentration of mitochondria changes when an axon splits into two branches at the branching junction. We also studied whether mitochondria concentrations in the branches are affected by what proportion of mitochondrial flux enters the upper branch and what proportion of flux enters the lower branch. Additionally, we explored whether the distributions of mitochondria mean age and age density in branching axons are affected by how the mitochondrial flux splits at the branching junction. When the mitochondrial flux is split unevenly at the branching junction of an asymmetric axon, with a greater proportion of the flux entering the longer branch, the average age of mitochondria (system age) in the axon increases. Our findings elucidate the effects of axonal branching on mitochondria age. Mitochondria aging is the focus of this study as recent research suggests it may be involved in neurodegenerative disorders, such as Parkinson’s disease.
APLNR marks a cardiac progenitor derived with human induced pluripotent stem cells
Authors: Lam Yin-Yu , Chan Chun-Ho , Geng Lin , Wong Nicodemus , Keung Wendy , Cheung Yiu-Fai
Published: February 2023

Cardiomyocytes can be readily derived from human induced pluripotent stem cell (hiPSC) lines, yet its efficacy varies across different batches of the same and different hiPSC lines. To unravel the inconsistencies of in vitro cardiac differentiation, we utilized single cell transcriptomics on hiPSCs undergoing cardiac differentiation and identified cardiac and extra-cardiac lineages throughout differentiation. We further identified APLNR as a surface marker for in vitro cardiac progenitors and immunomagnetically isolated them. Differentiation of isolated in vitro APLNR+cardiac progenitors derived from multiple hiPSC lines resulted in predominantly cardiomyocytes accompanied with cardiac mesenchyme. Transcriptomic analysis of differentiating in vitro APLNR+cardiac progenitors revealed transient expression of cardiac progenitor markers before further commitment into cardiomyocyte and cardiac mesenchyme. Analysis of in vivo human and mouse embryo single cell transcriptomic datasets have identified APLNR expression in early cardiac progenitors of multiple lineages. This platform enables generation of in vitro cardiac progenitors from multiple hiPSC lines without genetic manipulation, which has potential applications in studying cardiac development, disease modelling and cardiac regeneration.
Aberration modeling in deep learning for volumetric reconstruction of light-field microscopy
Authors: Zhou You , Jin Zhouyu , Zhao Qianhui , Xiong Bo , Cao Xun
Published: February 2023

Optical aberration is a crucial issue in optical microscopes, which fundamentally limits the practical imaging performance. As a commonly encountered one, spherical aberration is introduced by the refractive index mismatches between samples and environments, which will cause problems like low contrast, blurring, and distortion in imaging. Light-field microscopy (LFM) has recently emerged as a powerful tool for fast volumetric imaging. The appearance of spherical aberration in LFM will cause large changes of the point spread function (PSF) and thus greatly affects the imaging performance. Here, we propose the aberration-modeling view-channel-depth (AM-VCD) network for LFM reconstruction, which can well mitigate the influence of large spherical aberration. By quantitatively estimating the spherical aberration in advance and modeling it in the network training, the AM-VCD can obtain aberration-corrected high-speed visualization of three-dimensional (3D) processes with uniform spatial resolution and real-time reconstruction speed. Without any hardware modification, our method provides a convenient way to directly observe the 3D dynamics of samples in solution. We demonstrate the capability of AM-VCD under a large refractive index mismatch with volumetric imaging of a large-scale fishbone of largemouth bass. We further investigate the capability of AM-VCD in real-time volumetric imaging of dynamic zebrafish for tracking neutrophil migration.
A compact regulatory RNA element in mouse Hsp70 mRNA
Authors: Wang Wenshuai , Liu Fei , Ugalde Maria Vera , Pyle Anna Marie
Published: February 2023

Hsp70 performs molecular chaperone functions by assisting in folding newly synthesized or misfolded proteins, thereby counteracting various cell stresses and preventing multiple diseases including neurodegenerative disorders and cancer. It is well established that Hsp70 upregulation during post-heat shock stimulus is mediated by cap-dependent translation. However, the molecular mechanisms of Hsp70 expression during heat shock stimulus remains elusive, even though the 5’ end of Hsp70 mRNA may form a compact structure to positively regulate protein expression in the mode of cap-independent translation. The minimal truncation which can fold to a compact structure was mapped and its secondary structure was characterized by chemical probing. The predicted model revealed a highly compact structure with multiple stems. Including the stem where the canonical start codon is located, several stems were identified to be vital for RNA folding, thereby providing solid structural basis for future investigations on the function of this RNA structure on Hsp70 translation during heat shock.
The La Crosse virus class II fusion glycoproteinijloop contributes to infectivity and cholesterol-dependent entry
Authors: Thannickal Sara A. , Spector Sophie N. , Stapleford Kenneth A.
Published: February 2023

Arthropod-borne viruses (arboviruses) are an emerging and evolving global public health threat with little to no antiviral treatments. La Crosse virus (LACV) from theBunyaviralesorder is responsible for pediatric encephalitis cases in the United States, yet little is known about the infectivity of LACV. Given the structural similarities between class II fusion glycoproteins of LACV and chikungunya virus (CHIKV), an alphavirus from theTogaviridaefamily, we hypothesized that LACV would share similar entry mechanisms to CHIKV. To test this hypothesis, we performed cholesterol-depletion and repletion assays and used cholesterol modulating compounds to study LACV entry and replication. We found that LACV entry was cholesterol-dependent while replication was less affected by cholesterol manipulation. In addition, we generated single point mutants in the LACVijloop that corresponded to known CHIKV residues important for virus entry. We found that a conserved histidine and alanine residue in the Gcijloop impaired virus infectivity and attenuate LACVin vitroandin vivo. Finally, we took an evolution-based approach to explore how the LACV glycoprotein evolution in mosquitoes and mice. We found multiple variants that cluster in the Gc glycoprotein head domain, supporting the Gc glycoprotein as a target for LACV adaptation. Together, these results begin to characterize the mechanisms of LACV infectivity and how the LACV glycoprotein contributes to infectivity and pathogenesis.

Importance

Vector-borne arboviruses are significant health threats leading to devastating disease worldwide. This emergence and the fact that there are little to no vaccines or antivirals targeting these viruses highlights the need to study how arboviruses replicate at the molecular level. One potential antiviral target is the class II fusion glycoprotein. Alphaviruses, flaviviruses, and bunyaviruses encode a class II fusion glycoprotein that contain strong structural similarities in the tip of domain II. Here we show that the bunyavirus La Crosse virus uses similar mechanisms to entry as the alphavirus chikungunya virus and residues in theijloop are important for virus infectivity. These studies show that genetically diverse viruses use similar mechanisms through concerned structure domains, suggesting these may be a target for broad-spectrum antivirals to multiple arbovirus families.
Inoculum-dependent bactericidal activity of aMycobacterium tuberculosisMmpL3 inhibitor
Authors: Berube Bryan , Deshpande Aditi , Bhagwat Amala , Parish Tanya
Published: February 2023

Indolcarboxamides are a promising series of anti-tubercular agents which targetMycobacterium tuberculosisMmpL3, the exporter of trehalose monomycolate, a key cell wall component. We determined the kill kinetics of the lead indolcarboxamide NITD-349 and determined that while kill was rapid against low density cultures, bactericidal activity was inoculum-dependent. A combination of NITD-349 with isoniazid (which inhibits mycolate synthesis) had an increased kill rate; this combination prevented the appearance of resistant mutants, even at higher inocula.