bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1
Authors: Leandro João , Khamrui Susmita , Suebsuwong Chalada , Chen Peng-Jen , Secor Cody , Dodatko Tetyana , Yu Chunli , Sanchez Roberto , DeVita Robert J. , Houten Sander M. , Lazarus Michael B.
Published: May 2022

In humans, a single enzyme 2-aminoadipic semialdehyde synthase (AASS) catalyzes the initial two critical reactions in the lysine degradation pathway. This enzyme evolved to be a bifunctional enzyme with both lysine 2-oxoglutarate reductase (LOR) and saccharopine dehydrogenase domains (SDH). Moreover, AASS is a unique drug target for metabolic genetic diseases such as glutaric aciduria type 1 that arise from deficiencies downstream in the lysine degradation pathway. While work has been done to elucidate the SDH domain structurally and to develop inhibitors, neither has been done for the LOR domain. Here, we purify and characterize LOR, show that AASS is rate-limiting upon high lysine exposure of mice, and present the crystal structure of the human LOR domain, which should enable future efforts to identify inhibitors of this novel drug target.
Probing the force-from-lipid mechanism with synthetic polymers
Authors: Jacobs Miranda L. , Steinkühler Jan , Lemley Audra , Larmore Megan J. , Gunnels Taylor F. , Ng Leo C. T. , Cologna Stephanie M. , DeCaen Paul G. , Kamat Neha P.
Published: May 2022

A central feature of mechanotransduction is the ability of mechanosensitive channels to respond to mechanical stimuli from the surrounding lipid bilayer. Accordingly, the mechanical properties of membranes should play an important role in modulating force transmission to embedded channels, yet the nature of this relationship remains unclear for a wide class of mechanosensitive channels across prokaryotic and eukaryotic systems. Here, we use a synthetic amphiphile to modulate the membrane mechanical properties of cell-derived vesicles and probe channel activation. Using precise membrane mechanical characterization approaches that have rarely been used in conjunction with electrophysiology techniques, we directly characterize three membrane properties and the activation threshold of theE. colimechanosensitive channel of large conductance (MscL). Our study reveals that decreases in the membrane area expansion modulus, KA, and bending rigidity, kc, correlate with increases in the pressure required to activate MscL and that this effect is reproducible with the mammalian channel, TREK-1. MD simulations demonstrate that polymer-mediated changes in interfacial tension is the best mechanism to describe these experimental results. Together, our results bolster theforce-from-lipidsmechanism by demonstrating the generality of the relationship between changes in specific membrane mechanical properties and the gating pressure of MscL and TREK-1. In addition, our results reveal the mechanical mechanism by which membrane amphiphiles alter the activity and sensitivity of mechanosensitive channels through changes in long-range force transmission.
Emergent coexistence in multispecies microbial communities
Authors: Chang Chang-Yu , Bajic Djordje , Vila Jean , Estrela Sylvie , Sanchez Alvaro
Published: May 2022

Microbial communities are highly diverse, and understanding the factors that promote and modulate this diversity is a major area of research in microbial ecology. Recent work has proposed a reductionist perspective to microbial coexistence, where pairwise coexistence between strains in isolation is required for their coexistence in a more complex community. In this view, species exclusion in pairwise co-culture would preclude their coexistence in a more complex community too. An alternative view is that coexistence is a more complex property of the entire community, requiring the presence of additional community members. If this view were correct, competitive exclusion in pairwise co-culture would not necessarily preclude species coexistence in more complex community contexts. Empirically testing these alternative hypotheses is complicated by the intractably high microbial diversity of most natural communities, and the challenges of reconstituting every pair of coexisting species under the exact same habitat where their community of origin was assembled. To address this challenge, we have experimentally reconstituted all possible pairwise co-cultures between stably coexisting species from 13 different, low-diversity microbial enrichment communities, which had previously been assembled in a well-controlled synthetic habitat. We find that, when isolated from the rest of their community members, most species pairs fail to coexist. This result highlights the importance of community context for microbial coexistence and indicates that pairwise exclusion may not reflect the ability of species to coexist in more complex, multispecies ecosystems.
The Adaptor Protein 2 (AP2) complex modulates habituation and behavioral selection across multiple pathways and time windows
Authors: Mouret Rodrigo Zúñiga , Greenbaum Jordyn P. , Doll Hannah M. , Brody Eliza M. , Iacobucci Emma L. , Roland Nicholas C. , Simamora Roy C. , Ruiz Ivan , Seymour Rory , Ludwick Leanne , Groneberg Antonia H. , Marques João C. , Laborde Alexandre , Rajan Gokul , Bene Filippo Del , Orger Michael B. , Jain Roshan A.
Published: May 2022

Animals constantly perceive and integrate information across sensory modalities, and their nervous systems must select behavioral responses appropriate to the current situation and prior experience. Genetic factors supporting this behavioral flexibility are often disrupted in neuropsychiatric conditions, and our previous work revealed the disease-associatedap2s1gene critically supports habituation learning in acoustically-evoked escape behavior of zebrafish.ap2s1encodes a subunit of the AP2 endocytosis adaptor complex and has been linked to autism spectrum disorder, though its mechanism and direct behavioral importance have not been established. Here, we show that multiple subunits of the AP2 complex regulate acoustically-evoked behavior selection and habituation learning. Furthermore,ap2s1biases the choice between distinct escape behaviors in sensory modality-specific manners, and more broadly regulates action selection across different sensory contexts. Using tissue-specific and inducible transgenic rescue, we demonstrate that the AP2 complex functions acutely and in the nervous system to modulate acoustically-evoked habituation learning, suggesting several spatially and/or temporally distinct mechanisms through which AP2 regulates different aspects of escape behavior selection and performance. Altogether, we demonstrate that the AP2 complex coordinates action selection across stimulus modalities and contexts, providing a new vertebrate model for the role ofap2s1in human conditions including autism spectrum disorder.

SIGNIFICANCE STATEMENT

TheAP2S1gene has been linked to learning disabilities and autism spectrum disorders (ASD), though the mechanisms underlying its impact on human behavior are unknown. We explored how, when, and where this gene regulates vertebrate behavior, developing a zebrafish model to identify the roles and mechanisms through whichap2s1modulates behavior. We find thatap2s1regulates simple acoustically-evoked learning, as well as how individuals bias behavioral choice in a wide variety of contexts. We show thatap2s1acts at multiple distinct time periods and locations both within and outside of neuronal tissues, revealing the diverse mechanisms and pathways through which it modulates vertebrate behavior.
AGS3 antagonizes LGN to balance oriented cell divisions and cell fate choices in mammalian epidermis
Authors: Descovich Carlos Patiño , Lough Kendall J. , Jena Akankshya , Wu Jessica J , Yom Jina , Spitzer Danielle C. , Uppalapati Manuela , Kedziora Katarzyna M. , Williams Scott E.
Published: May 2022

Oriented cell divisions balance self-renewal and differentiation in stratified epithelia such as the skin epidermis. During peak epidermal stratification, the distribution of division angles among basal keratinocyte progenitors is bimodal, with planar and perpendicular divisions driving symmetric and asymmetric daughter cell fates, respectively. An apically-polarized, evolutionarily-conserved spindle orientation complex that includes the scaffolding protein LGN/Pins/Gpsm2 plays a central role in promoting perpendicular divisions and stratification, but little is known about the molecular regulation of planar divisions. Here, we demonstrate that the LGN paralog, AGS3/Gpsm1, is a novel negative regulator of LGN, and inhibits perpendicular divisions. Static and ex vivo live imaging reveal that AGS3 overexpression displaces LGN from the apical cortex and increases planar orientations, while AGS3 loss prolongs cortical LGN localization and leads to a perpendicular orientation bias. Genetic epistasis experiments in double mutants confirm that AGS3 operates through LGN. Finally, clonal lineage tracing shows that LGN and AGS3 promote asymmetric and symmetric fates, respectively, while also influencing differentiation through delamination. Collectively, these studies shed new light into how spindle orientation influences epidermal stratification.
Retigabine Suppresses Loss of Force in a Mouse Model of Hypokalemic Periodic Paralysis
Authors: Quiñonez Marbella , Cannon Stephen C.
Published: May 2022

Objective

The goal of this experimental study was to test the hypothesis that the potassium channel opener retigabine can prevent the episodic loss of force in hypokalemic periodic paralysis (HypoPP).

Methods

A knock-in mutant mouse model of HypoPP (Scn4a p.R669H) was used to determine whether pretreatment with retigabine suppressed the loss of force, or post-treatment hastened recovery of force for a low-K+ challenge in an ex vivo contraction assay.

Results

Retigabine completely prevents the loss of force induced by a 2 mM K+ challenge (protection) in our mouse model of HypoPP, with a 50% inhibitory concentration (IC50) of 0.8 µM. In comparison, the effective concentration for the KATP channel opener pinacidil was ten-fold higher. Application of retigabine also reversed the loss of force (rescue) for HypoPP muscle maintained in 2 mM K+.

Interpretation

Retigabine, a selective agonist of the KV7 family of potassium channels, is effective for the prevention of low-K+ induced attacks of weakness and to enhance recovery from an on-going loss of force in a mouse model of HypoPP. Substantial protection from the loss of force occurred in the low micromolar range, well within the therapeutic window for retigabine.
The abundances and occurrences of foliar microbes are poorly predicted by variation in plant traits and abiotic conditions
Authors: Harrison Joshua G. , Buerkle C. Alex
Published: May 2022

Much effort has been made to understand why foliar microbes live where they do. However, whether foliar microbiome composition can be predicted is unknown. Here, we determine the limits of prediction using metabarcoding data of both fungal and bacterial assemblages that occur within (endophytes) and without (epiphytes) leaves from 59 plant taxa. We built random forest models for prevalent taxa and quantified the combined predictive power of 24 plant traits, 12 abiotic conditions and 7 additional features. As response variables, we considered microbial relative and absolute abundances, and occurrences. Most microbial taxa were too rare to effectively model, but model performance was generally poor even for the most prevalent and abundant taxa (modelR2was typically <0.1). Fungi were more tractable for modeling than bacteria. Models of Shannon’s diversity were moderately successful but those for richness were not. Taxa responded idiosyncratically and non-linearly to variation in the foliar habitat. When prevalent microbes were included as features in models, performance improved. Our results suggest that easily measurable aspects of the phyllosphere habitat are poor predictors of microbiome composition. These results pose a challenge for the study of microbial biogeography and we discuss possible ways forward.
Cytoplasmic TDP-43 accumulation drives changes in C-bouton number and size in a mouse model of sporadic Amyotrophic Lateral Sclerosis
Authors: Bak Anna Normann , Djukic Svetlana , Kadlecova Marion , Braunstein Thomas Hartig , Jensen Dennis Bo , Meehan Claire Francesca
Published: May 2022

An altered neuronal excitability of spinal motoneurones has consistently been implicated in Amyotrophic Lateral Sclerosis (ALS) leading to several investigations of synaptic input to these motoneurones. One such input that has repeatedly been shown to be affected is a population of large cholinergic synapses terminating mainly on the soma of the motoneurones referred to as C-boutons. Most research on these synapses during disease progression has used transgenic Superoxide Dismutase 1 (SOD1) mouse models of the disease which have not only produced conflicting findings, but also fail to recapitulate the key pathological feature seen in ALS; cytoplasmic accumulations of TAR DNA-binding protein 43 (TDP-43). Additionally, they fail to distinguish between slow and fast motoneurones, the latter of which have more C-boutons but are lost earlier in the disease.

To circumvent these issues, we quantified the frequency and volume of C-boutons on traced soleus and gastrocnemius motoneurones, representing predominantly slow and fast motor pools respectively. Experiments were performed using the TDP-43ΔNLS mouse model that carries a transgenic construct of TDP-43 devoid of its nuclear localization signal, preventing its nuclear import. This results in the emergence of pathological TDP-43 inclusions in the cytoplasm, modelling the main pathology seen in this disorder, accompanied by a severe and lethal ALS phenotype.

Our results confirmed changes in both the number and volume of C-boutons with a decrease in number on the more vulnerable, predominantly fast gastrocnemius motoneurones and an increase in number on the less vulnerable, predominantly slow soleus motoneurones. Importantly, these changes were only found in male mice. However, both sexes and motor pools showed a decrease in C-bouton volume. Our experiments confirm that cytoplasmic TDP-43 accumulation is sufficient to drive C-bouton changes.
Environmental DNA reveals invasive crayfish microbial associates and ecosystem-wide biodiversity before and after eradication
Authors: Ballare Kimberly M. , Worth Anna , Goodearly Tyler , Ruiz-Ramos Dannise V. , Beraut Eric , Nava Hailey , Fairbairn Colin , Wayne Robert K. , Shapiro Beth , Short Ginny , Meyer Rachel S.
Published: May 2022

Biodiversity monitoring in conservation projects is essential to understand environmental status and recovery. However, traditional field surveys can be expensive, time-consuming, biased towards visual detection, and focused on measuring a limited set of taxa. Environmental DNA (eDNA) methods provide a new approach to biodiversity monitoring that has the potential to sample a taxonomically broader set of organisms with similar effort, but many of these approaches are still in the early stages of development and testing. Here, we use multilocus eDNA metabarcoding to understand how the removal of invasive red swamp crayfish impacts local biodiversity of a desert oasis ecosystem, as well as to detect crayfish both directly and indirectly. We tracked crayfish DNA signatures, microbial DNA associated with crayfish, and biodiversity of plant, fungal, animal, and bacterial communities through time. We were unsuccessful in detecting crayfish directly in either control tanks or oases using targeted metabarcoding primers for invertebrates and eukaryotes, similar to previous studies which have shown variable levels of success in detecting crayfish from environmental samples. However, we were successful in discerning a suite of 90 crayfish-associated taxa to serve as candidate bioindicators of invasive presence using 16S and Fungal ITS2 metabarcoding. Ranking these 90 taxa by their geographic distribution in eDNA surveys and by evidence of crayfish-associations in the literature, we support 9 taxa to be high-ranking, and suggest they be prioritized in future biomonitoring. Biodiversity analyses from five metabarcode loci including plants, animals, and both prokaryotic and eukaryotic microbes showed that communities differed but that species richness remained relatively similar between oases through time. Our results reveal that, while there are limitations of eDNA approaches to detect crayfish and other invasive species, microbial bioindicators offer a largely untapped biomonitoring opportunity for invasive species management, adding a valuable resource to a conservation manager’s toolkit.
Metabolic shift toward ketosis in asocial cavefish increases social-like affinity
Authors: Iwashita Motoko , Tran Amity , Garcia Marianne , Cashon Jia , Burbano Devanne , Salgado Vanessa , Hasegawa Malia , Balmilero-Unciano Rhoada , Politan Kaylah , Wong Miki , Lee Ryan W.Y. , Yoshizawa Masato
Published: May 2022

Social affinity and collective behavior are nearly ubiquitous in the animal kingdom, but many lineages feature evolutionarily asocial species. These solitary species may have evolved to conserve energy in food-sparse environments. However, the mechanism by which metabolic shifts regulate social affinity is not well investigated. In this study, we used the Mexican tetra (Astyanax mexicanus), which features riverine sighted surface (surface fish) and cave-dwelling populations (cavefish), to address the impact of metabolic shifts on asociality and other cave-associated behaviors in cavefish, including repetitive turning, sleeplessness, swimming longer distances, and enhanced foraging behavior. After one month of ketosis-inducing ketogenic diet feeding, asocial cavefish exhibited significantly higher social affinity, whereas social affinity regressed in cavefish fed the standard diet. The ketogenic diet also reduced repetitive turning and swimming in cavefish. No major behavioral shifts were found regarding sleeplessness and foraging behavior, suggesting that other evolved behaviors are not largely regulated by ketosis. We further examined the effects of the ketogenic diet via supplementation with extragenic ketone bodies, revealing that ketone bodies are pivotal molecules positively associated with social affinity. Our study indicated that fish that evolved to be asocial remain capable of exhibiting social affinity under ketosis, possibly linking the seasonal food availability and sociality.
Butyrate differentiates permissiveness to Clostridioides difficile infection and influences growth of diverse C. difficile isolates
Authors: Pensinger Daniel A. , Fisher Andrea T. , Dobrila Horia A. , Van Treuren William , Gardner Jackson O. , Higginbottom Steven K. , Carter Matthew M. , Schumann Benjamin , Bertozzi Carolyn R. , Anikst Victoria , Martin Cody , Robilotti Elizabeth V. , Chow JoMay , Buck Rachael H. , Tompkins Lucy S. , Sonnenburg Justin L. , Hryckowian Andrew J.
Published: May 2022

A disrupted “dysbiotic” gut microbiome engenders susceptibility to the diarrheal pathogen Clostridioides difficile by impacting the metabolic milieu of the gut. Diet, in particular the microbiota accessible carbohydrates (MACs) found in dietary fiber, is one of the most powerful ways to affect the composition and metabolic output of the gut microbiome. As such, diet is a powerful tool for understanding the biology of C. difficile and for developing alternative approaches for coping with this pathogen. One prominent class of metabolites produced by the gut microbiome are short chain fatty acids (SCFAs), the major metabolic end products of MAC metabolism. SCFAs are known decrease the fitness of C. difficile in vitro and that high intestinal SCFA concentrations are associated with reduced fitness of C. difficile in animal models of C. difficile infection (CDI). Here, we use controlled dietary conditions (8 diets that differ only by MAC composition) to show that C. difficile fitness is most consistently impacted by butyrate, rather than the other two prominent SCFAs (acetate and propionate), during murine model CDI. We similarly show that butyrate concentrations are lower in fecal samples from humans with CDI relative to healthy controls. Finally, we demonstrate that butyrate impacts growth in diverse C. difficile isolates. These findings provide a foundation for future work which will dissect how butyrate directly impacts C. difficile fitness and will lead to the development of diverse approaches distinct from antibiotics or fecal transplant, such as dietary interventions, for mitigating CDI in at-risk human populations.

IMPORTANCE

Clostridioides difficile is a leading cause of infectious diarrhea in humans and it imposes a tremendous burden on the healthcare system. Current treatments for C. difficile infection (CDI) include antibiotics and fecal microbiota transplant, which contribute to recurrent CDIs and face major regulatory hurdles, respectively. Therefore, there is an ongoing need to develop new ways to cope with CDI. Notably, a disrupted “dysbiotic” gut microbiota is the primary risk factor for CDI but we incompletely understand how a healthy microbiota resists CDI. Here, we show that a specific molecule produced by the gut microbiota, butyrate, is negatively associated with C. difficile burdens in humans and in a mouse model of CDI and that butyrate impedes the growth of diverse C. difficile strains in pure culture. These findings help to build a foundation for designing alternative, possibly diet-based, strategies for mitigating CDI in humans.
Purified cytosolic crystals from Bacillus thuringiensis as a novel active pharmaceutical ingredient (API)
Authors: Chicca Jeffrey , Cazeault Nicholas R. , Rus Florentina , Abraham Ambily , Garceau Carli , Li Hanchen , Atwa Samar M. , Flanagan Kelly , Soto Ernesto R. , Morrison Mary S. , Gazzola David , Hu Yan , Liu David R. , Nielsen Martin K. , Urban Joseph F. , Ostroff Gary R. , Aroian Raffi V.
Published: May 2022

Bacillus thuringiensis or Bt is a Gram-positive soil bacterium, widely and safely applied in the environment as an insecticide for combatting insect pests that damage crops and vector diseases. Dominant active ingredients made by Bt are insect-killing crystal (Cry) proteins released as crystalline inclusions upon bacterial sporulation. Some Bt Cry proteins, e.g., Cry5B, target nematodes (roundworms) and show exceptional promise as anthelmintics (cures for parasitic nematode diseases). We have recently described IBaCC (for Inactivated Bacteria with Cytosolic Crystal(s)) in which bioactive Bt Cry crystals (containing Cry5B) are fully contained within the cytosol of dead bacterial ghosts. Here we demonstrate that these IBaCC-trapped Cry5B crystals can be liberated and purified away from cellular constituents yielding Purified Cytosolic Crystals (PCC). Cry5B PCC contains ∼95% Cry5B protein out of the total protein content. Cry5B PCC is highly bioactive against parasitic nematode larvae and adults in vitro. Cry5B PCC is also highly active in vivo against experimental human hookworm and Ascaris infections in rodents. The process was scaled up to the 100 liter scale to produce PCC for a pilot study to treat two foals infected with the Ascarid, Parascaris spp. Single dose Cry5B PCC brought the fecal egg counts of both foals to zero. These studies describe the process for the scalable production of purified Bt crystals and define a new active pharmaceutical ingredient form of Bt Cry proteins.

NON-TECHNICAL IMPORTANCE PARAGRAPH

Bacillus thuringiensis crystal proteins are widely and safely used as insecticides. Recent studies show they also can cure gastrointestinal parasitic worm (nematode) infections when ingested. However, reproducible, scalable, and practical techniques for purifying these proteins have been lacking. Here, we address this severe limitation and present scalable and practical methods for large-scale purification of potently bioactive B. thuringiensis crystals and crystal proteins. The resultant product, called Purified Cytosolic Crystals (PCC), is highly compatible with ingestible drug delivery and formulation. Furthermore, there are growing applications in agriculture and insect control where access to large quantities of purified crystal proteins are desirable and where these methods will find great utility.
Machine Learning for Identifying Data-Driven Subphenotypes of Incident Post-Acute SARS-CoV-2 Infection Conditions with Large Scale Electronic Health Records: Findings from the RECOVER Initiative
Authors: Zhang Hao , Zang Chengxi , Xu Zhenxing , Zhang Yongkang , Xu Jie , Bian Jiang , Morozyuk Dmitry , Khullar Dhruv , Zhang Yiye , Nordvig Anna S. , Schenck Edward J. , Shenkman Elizabeth A. , Rothman Russel L. , Block Jason P. , Lyman Kristin , Weiner Mark G. , Carton Thomas W. , Wang Fei , Kaushal Rainu
Published: May 2022

The post-acute sequelae of SARS-CoV-2 infection (PASC) refers to a broad spectrum of symptoms and signs that are persistent, exacerbated, or newly incident in the post-acute SARS-CoV-2 infection period of COVID-19 patients. Most studies have examined these conditions individually without providing concluding evidence on co-occurring conditions. To answer this question, this study leveraged electronic health records (EHRs) from two large clinical research networks from the national Patient-Centered Clinical Research Network (PCORnet) and investigated patients’ newly incident diagnoses that appeared within 30 to 180 days after a documented SARS-CoV-2 infection. Through machine learning, we identified four reproducible subphenotypes of PASC dominated by blood and circulatory system, respiratory, musculoskeletal and nervous system, and digestive system problems, respectively. We also demonstrated that these subphenotypes were associated with distinct patterns of patient demographics, underlying conditions present prior to SARS-CoV-2 infection, acute infection phase severity, and use of new medications in the post-acute period. Our study provides novel insights into the heterogeneity of PASC and can inform stratified decision-making in the treatment of COVID-19 patients with PASC conditions.
Understanding Post-Acute Sequelae of SARS-CoV-2 Infection through Data-Driven Analysis with Longitudinal Electronic Health Records: Findings from the RECOVER Initiative
Authors: Zang Chengxi , Zhang Yongkang , Xu Jie , Bian Jiang , Morozyuk Dmitry , Schenck Edward J. , Khullar Dhruv , Nordvig Anna S. , Shenkman Elizabeth A. , Rothman Russel L. , Block Jason P. , Lyman Kristin , Weiner Mark , Carton Thomas W. , Wang Fei , Kaushal Rainu
Published: May 2022

Recent studies have investigated post-acute sequelae of SARS-CoV-2 infection (PASC) using real-world patient data such as electronic health records (EHR). Prior studies have typically been conducted on patient cohorts with small sample sizes1 or specific patient populations2,3 limiting generalizability. This study aims to characterize PASC using the EHR data warehouses from two large national patient-centered clinical research networks (PCORnet), INSIGHT and OneFlorida+, which include 11 million patients in New York City (NYC) and 16.8 million patients in Florida respectively. With a high-throughput causal inference pipeline using high-dimensional inverse propensity score adjustment, we identified a broad list of diagnoses and medications with significantly higher incidence 30-180 days after the laboratory-confirmed SARS-CoV-2 infection compared to non-infected patients. We found more PASC diagnoses and a higher risk of PASC in NYC than in Florida, which highlights the heterogeneity of PASC in different populations.
Neuroanatomical and Functional Consequences of Oxytocin Treatment at Birth
Authors: Kenkel William M. , Ortiz Richard J. , Yee Jason R. , Perkeybile Allison M. , Kulkarni Praveen , Carter C. Sue , Cushing Bruce S. , Ferris Craig F.
Published: May 2022

Birth is a critical period for the developing brain, a time when surging hormone levels help prepare the fetal brain for the tremendous physiological changes it must accomplish upon entry into the ‘extrauterine world’. A number of obstetrical conditions warrant manipulations of these hormones at the time of birth, but we know little of their possible consequences on the developing brain. One of the most notable birth signaling hormones is oxytocin, which is administered to roughly 50% of laboring women in the United States prior to / during delivery. Previously, we found evidence for behavioral, epigenetic, and neuroendocrine consequences in adult prairie vole offspring following maternal oxytocin treatment immediately prior to birth. Here, we examined the neurodevelopmental consequences in adult prairie vole offspring following maternal oxytocin treatment immediately. Control prairie voles and those exposed to 0.25 mg/kg oxytocin were scanned as adults using anatomical and functional MRI, with neuroanatomy and brain function analyzed as voxel-based morphometry and resting state functional connectivity, respectively. Overall, anatomical differences brought on by oxytocin treatment, while widespread, were generally small, while differences in functional connectivity, particularly among oxytocin-exposed males, were larger. Analyses of functional connectivity based in graph theory revealed that oxytocin-exposed males in particular showed markedly increased connectivity throughout the brain and across several parameters, including closeness and degree. These results are interpreted in the context of the organizational effects of oxytocin exposure in early life and these findings add to a growing literature on how the perinatal brain is sensitive to hormonal manipulations at birth.
Ecological Dynamics Imposes Fundamental Challenges in Microbial Source Tracking
Authors: Wang Xu-Wen , Wu Lu , Dai Lei , Yin Xiaole , Zhang Tong , Weiss Scott T. , Liu Yang-Yu
Published: May 2022

Quantifying the contributions of possible environmental sources (“sources”) to a specific microbial community (“sink”) is a classical problem in microbiology known as microbial source tracking (MST). Solving the MST problem will not only help us understand how microbial communities were formed, but also have far-reaching applications in pollution control, public health, and forensics. Numerous computational methods, referred to as MST solvers hereafter, have been developed in the past and applied to various real datasets to demonstrate their utility across different contexts. Yet, those MST solvers do not consider microbial interactions and priority effects in microbial communities. Here, we revisit the performance of several representative MST solvers. We show compelling evidence that solving the MST problem using existing MST solvers is impractical when ecological dynamics plays a role in community assembly. In particular, we clearly demonstrate that the presence of either microbial interactions or priority effects will render the MST problem mathematically unsolvable for any MST solver. We further analyze data from fecal microbiota transplantation studies, finding that the state-of-the-art MST solvers fail to identify donors for most of the recipients. Finally, we perform community coalescence experiments to demonstrate that the state-of-the-art MST solvers fail to identify the sources for most of the sinks. Our findings suggest that ecological dynamics imposes fundamental challenges in solving the MST problem using computational approaches.
Two therapeutic CRISPR/Cas9 gene editing approaches revert FTD/ALS cellular pathology caused by aC9orf72repeat expansion mutation in patient derived cells
Authors: Sckaff M , Gill K , Sachdev A , Birk AM , Aladesuyi Arogundade O , Watry HL , Keough KC , Tsai Y-C , Ziegle J , Conklin BR , Clelland CD
Published: May 2022

CRISPR gene editing holds promise to cure or arrest genetic disease, if we can find and implement curative edits reliably, safely and effectively. Expansion of a hexanucleotide repeat inC9orf72is the leading known genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). We evaluated three approaches to editing the mutantC9orf72gene for their ability to correct pathology in neurons derived from patient iPSCs: excision of the repeat region, excision of the mutant allele, and excision of regulatory region exon 1A. All three approaches normalized RNA abnormalities and TDP-43 pathology, but only repeat excision and mutant allele excision completely eliminated pathologic dipeptide repeats. Our work sheds light on the complex regulation of theC9orf72gene and suggests that because of sense and anti-sense transcription, silencing a single regulatory region may not reverse all pathology. Our work also provides a roadmap for evaluating CRISPR gene correction using patient iPSCs.
Transcriptional signature pattern in black, blue and purple wheat and impact on seed pigmentation and other associated features: Comparative transcriptomics, genomics and metabolite profiling
Authors: Sharma Saloni , Kumar Ashish , Singh Dalwinder , Kumari Anita , Kapoor Payal , Kaur Satveer , Sheoran Bhawna , Garg Monika
Published: May 2022

Anthocyanin biosynthesis in plants is complex, especially in a polyploid monocot wheat plant. Using whole-genome sequencing, transcriptomics, and LC-MS/MS, we investigated anthocyanin production in pigmented (black, blue, and purple) wheat seeds. According to differential gene expression profiling, 2AS-MYC, 7DL-MYB, WD40 regulatory genes controls purple pericarp coloration, 4DL-MYC, 2AS-MYC, 7DL-MYB, WD40 controls blue aleurone coloration, and 4DL-MYC, 7DL-MYB, WD40 controls black aleurone colour. We believe that at least one MYC and MYB isoform is sufficient to regulate the anthocyanin synthesis in pericarp or aleurone. Based upon the reduced expressions of the genes belonging to the 4D, SSR molecular marker mapping, variant calling using genome sequencing and IGV browser gene structure visualization, it was inferred that the advanced black and blue wheat lines were substitution lines (4E{4D}), with very small recombinations. Pericarp anthocyanin profiling is controlled by a mutation in chromosome 2AS of purple wheat, and environmental variations more influence pigmented pericarp trait. The expression patterns of anthocyanin structural and other genes varied in different colored wheat, corroborating differences in agronomical metrics.
Condensates of disordered proteins have small-world network structures and interfaces defined by expanded conformations
Authors: Farag Mina , Cohen Samuel R. , Borcherds Wade M. , Bremer Anne , Mittag Tanja , Pappu Rohit V.
Published: May 2022

The formation of membraneless biomolecular condensates is driven by macromolecules with sticker-and-spacer architectures that undergo phase separation coupled to percolation (PSCP). Driving forces for PSCP are governed by the interplay between reversible inter-sticker crosslinks and solvation preferences of spacers. Here, we introduce molecular and mesoscale descriptions of structures within, outside, and at the interfaces of condensates that are formed by prion-like low complexity domains (PLCDs), which are exemplars of intrinsically disordered, linear multivalent proteins. Our studies are based on simulations that accurately describe sequence-specific phase behaviors of PLCDs. We find that networks of reversible, intermolecular, inter-sticker crosslinks organize PLCDs into small-world topologies within condensates. These topologies result from distinct conformational preferences within dense, dilute, and interfacial regions. Specifically, the degree of conformational expansion varies non-monotonically, being most expanded at the interface and most compact in the dilute phase with molecules preferring to be oriented perpendicular to condensate interfaces. This contrasts with dense and dilute phases where molecules are randomly oriented relative to one another. Our results demonstrate that even simple condensates, with only one type of macromolecule, feature inhomogeneous spatial organizations of molecules and interfacial features that likely prime them for being locations of biochemical activity.
A comprehensive assay of social motivation reveals sex-differential roles of ASC-associated genes and oxytocin
Authors: Maloney Susan E. , Sarafinovska Simona , Weichselbaum Claire , McCullough Katherine B. , Swift Raylynn G. , Liu Yating , Dougherty Joseph D.
Published: May 2022

Social motivation is critical to the development of healthy social functioning. Autism spectrum condition (ASC) is characterized in part by challenges with social communication and social interaction. The root of these challenges is hypothesized to be a deficit in social motivation, specifically in one or more subcomponents (e.g. social reward reward seeking or social orienting). Current social behavior assays lack the ability to quantitatively measure both social reward seeking and social orienting simultaneously. We have developed an automated socially-rewarded operant conditioning task coupled with video tracking, to quantify effort to achieve access to a social partner and concurrent social orienting behavior in mice. We established that adult wildtype mice will work for access to a social partner, that male mice exhibit greater social motivation compared to females, and there is high test-retest reliability in the task across multiple days. We then benchmarked the method with two test-case manipulations. We first tested a mouse model of Phelan-McDermid syndrome, a neurodevelopmental disorder associated with ASC. TheseShank3Bmutants failed to show social reward seeking and exhibited reduced social orienting. Next, we demonstrated that oxytocin receptor antagonism decreased social motivation in wildtype mice, consistent with its role in social reward circuitry. Intriguingly, only male mice were vulnerable toShank3Bmutation, while females were more vulnerable to oxytocin blockade, a double dissociation suggesting separate circuits for social motivation in male and female brain. Overall, we believe this method provides a valuable addition to the assessment of social phenotypes in rodent models of ASC and the mapping of potentially sex-specific social motivation circuits in the brain.
UHMK1 is a novel splicing regulatory kinase
Authors: Arfelli Vanessa C. , Chang Yun-Chien , Bagnoli Johannes W. , Kerbs Paul , Ciamponi Felipe E. , Paz Laissa M. S. , Massirer Katlin B. , Enard Wolfgang , Kuster Bernhard , Greif Philipp A. , Archangelo Leticia Fröhlich
Published: May 2022

The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif (UHM), a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in the 3’ splice site recognition during the early steps of spliceosome assembly. Although UHMK1 phosphorylates these splicing factors in vitro, the involvement of UHMK1 in RNA processing has not previously been demonstrated. Here, we identify novel putative substrates of this kinase and evaluate UHMK1 contribution to overall gene expression and splicing, by integrating global phosphoproteomics, RNA-seq, and bioinformatics approaches. Upon UHMK1 modulation, 163 unique phosphosites were differentially phosphorylated in 117 proteins, of which 106 are novel potential substrates of this kinase. Gene Ontology (GO) analysis showed enrichment of terms previously associated with UHMK1 function, such as mRNA splicing, cell cycle, cell division and microtubule organization. The majority of the annotated RNA-related proteins are components of the spliceosome, but are also involved in several steps of gene expression. Comprehensive analysis of splicing showed that UHMK1 affected over 200 alternative splicing events. Moreover, splicing reporter assay further supported UHMK1 function on splicing. Overall, RNA-seq data demonstrated that UHMK1 knockdown had a minor impact on gene expression and pointed to UHMK1 function in epithelial-mesenchymal transition. Finally, the functional assays demonstrated that UHMK1 modulation affects proliferation, colony formation, and migration of the cells. Taken together, our data implicate UHMK1 as a splicing regulatory kinase, connecting protein regulation through phosphorylation and gene expression in key cellular processes.
Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates
Authors: Trivedi Vikas D. , Sullivan Sean F. , Choudhury Debika , Endalur Gopinarayanan Venkatesh , Hart Taylor , Nair Nikhil U.
Published: May 2022

Engineering synthetic heterotrophy (i.e., growth on non-native substrates) is key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored inSaccharomyces cerevisiae(yeast) over several decades – yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that “extrinsic” factors – specifically, upstream genes that direct flux of pentoses into central carbon metabolism – are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., flux balancing, directed evolution, functional genomics, and network modeling) is largely unnecessary. We posit that the need for extensive engineering espoused by prior works is a consequence of unfortunate (albeit avoidable) antagonism between engineering and cellular objectives. We also found that deletion of endogenous genes to promote growth demonstrate inconsistent outcomes that are genetic-context- and condition-dependent. For the most part, these knockouts also lead to deleterious pleiotropic effects that decrease the robustness of strains against inhibitors and stressors associated with bioprocessing. Thus, at best, perturbation of “intrinsic” factors (e.g., native metabolic, regulatory genes) results in incremental and inconsistent benefits. At worst, they are detrimental. Overall, this work provides insight into the limitations and pitfalls to realizing efficient synthetic heterotrophy using traditional/systems metabolic engineering approaches, demonstrates the innate adaptability of yeast for metabolism of non-native substrates, and provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.
Super-exponential growth and stochastic size dynamics in rod-like bacteria
Authors: Cylke Callaghan , Banerjee Shiladitya
Published: May 2022

Proliferating bacterial cells exhibit stochastic growth and size dynamics but the regulation of noise in bacterial growth and morphogenesis remains poorly understood. A quantitative understanding of morphogenetic noise control, and how it changes under different growth conditions, would provide better insights into cell-to-cell variability and intergenerational fluctuations in cell physiology. Using multigenerational growth and width data of singleEscherichia coliandCaulobacter crescentuscells, we deduce the equations governing growth and size dynamics of rod-like bacterial cells. Interestingly, we find that bothE. coliandC. crescentuscells deviate from exponential growth within the cell cycle. In particular, the exponential growth rate increases during the cell cycle, irrespective of nutrient or temperature conditions. We propose a mechanistic model that explains the emergence of super-exponential growth from autocatalytic production of ribosomes, coupled to the rate of cell elongation and surface area synthesis. Using this new model and statistical inference on large datasets, we construct the Langevin equations governing cell size and size dynamics ofE. colicells in different growth conditions. The single-cell level model predicts how noise in intragenerational and intergenerational processes regulate variability in cell morphology and generation times, revealing quantitative strategies for cellular resource allocation and morphogenetic noise control in different growth conditions.
A survey of mapping algorithms in the long-reads era
Authors: Sahlin Kristoffer , Baudeau Thomas , Cazaux Bastien , Marchet Camille
Published: May 2022

It has been ten years since the first publication of a method dedicated entirely to mapping third-generation sequencing long-reads. The unprecedented characteristics of this new type of sequencing data created a shift, and methods moved on from theseed-and-extendframework previously used for short reads to aseed-and-chainframework due to the abundance of seeds in each read. As a result, the main novelties in proposed long-read mapping algorithms are typically based on alternative seed constructs or chaining formulations. Dozens of tools now exist, whose heuristics have considerably evolved with time. The rapid progress of the field, synchronized with the frequent improvements of data, does not make the literature and implementations easy to keep up with. Therefore, in this survey article, we provide an overview of existing mapping methods for long reads with accessible insights into methods. Since mapping is also very driven by the implementations themselves, we join an original visualization tool to understand the parameter settings (http://bcazaux.polytech-lille.net/Minimap2/) for the chaining part.
Transplantation Elicits a Clonally Diverse CD8+T Cell Response that is Comprised of Potent CD43+Effectors
Authors: Cohen Gregory A. , Kallarakal Melissa A. , Jayaraman Sahana , Ibukun Francis I. , Tong Katherine P. , Orzolek Linda D. , Larman H. Benjamin , Krummey Scott M.
Published: May 2022

CD8+T cells mediate acute rejection of allografts, which threatens the long-term survival of transplanted organs. The factors that govern differentiation of graft-directed effector CD8+T cells could lead to targeted approaches to limit acute rejection. Using MHC Class I tetramers, we found that allogeneic CD8+T cells were present at an elevated precursor frequency in naïve mice, only modestly increased in number after grafting, and maintained high T cell receptor diversity throughout the immune response. While antigen-specific effector CD8+T cells poorly express the canonical effector marker KLRG-1, expression of the activated glycoform of CD43 defined potent effectors after transplantation. Activated CD43+effector T cells maintained high expression of ICOS in the presence of CTLA-4 Ig, and dual CTLA-4 Ig/anti-ICOS treatment prolonged graft survival. These data demonstrate that graft-specific CD8+T cells have a distinct response profile relative to anti-pathogen CD8+T cells, and that CD43 and ICOS are critical surface receptors that define potent effector CD8+T cell populations that form after transplantation.