bluuebunny/crossref_metadata_2025 huggingface dataset:
In-vivo characterization of glutamine metabolism identifies therapeutic targets in clear cell renal cell carcinoma
Authors: Kaushik Akash K. , Burroughs Lindsey K. , Tarangelo Amy , Ragavan Mukundan , Wu Cheng-Yang , Li Xiangyi , Ahumada Kristen , Tcheuyap Vanina T. , Saatchi Faeze , Do Quyen N , Yong Cissy , Rosales Tracy , Stevens Christina , Rao Aparna , Faubert Brandon , Pachnis Panayotis , Zacharias Lauren G. , Vu Hieu , Cai Feng , Mathews Thomas P. , Slusher Barbara , Kapur Payal , Sun Xiankai , Merritt Matthew , Brugarolas James , DeBerardinis Ralph J.
Published: November 2022

Targeting metabolic vulnerabilities has been proposed as a therapeutic strategy in renal cell carcinoma (RCC). Here, we analyzed metabolism in patient-derived xenografts (tumorgrafts) from diverse forms of RCC. Tumorgrafts fromVHL-mutant clear cell RCC (ccRCC) retained metabolic features of human ccRCC and engage in oxidative and reductive glutamine metabolism. We used several approaches to suppress glutamine metabolism and test the effect on tumor growth. Genetic silencing of isocitrate dehydrogenase-1 or -2 impaired reductive labeling of TCA cycle intermediates and suppressed tumor growth. Glutaminase inhibition resulted in modest growth suppression and variable effects on glutamine metabolism in vivo. Infusions with [amide-15N]glutamine revealed persistent amidotransferase activity during glutaminase inhibition, and blocking these activities with the amidotransferase inhibitor JHU-083 also reduced tumor growth. We conclude that ccRCC tumorgrafts catabolize glutamine via multiple pathways, perhaps explaining why it has been challenging to achieve therapeutic responses in patients by inhibiting glutaminase.

Teaser

Glutamine fuels the TCA cycle and amidotransferase pathways in clear cell renal cell carcinoma.
Schwann cells promote sensory neuron excitability during development
Authors: Kantarci Husniye , Elvira Pablo D. , Thottumkara Arun P. , Iyer Manasi , Donovan Lauren J. , Dugan Micaela Quinn , Ambiel Nicholas , O’Connell Emma M. , Granados Alejandro , Zeng Hong , Saw Nay L. , Lutz Amanda Brosius , Sloan Steven A. , Gray Erin E. , Tran Khanh V. , Vichare Aditi , Yeh Ashley K. , Münch Alexandra E. , Huber Max , Agrawal Aditi , Morri Maurizio , Shamloo Mehrdad , Anderson Thomas Anthony , Tawfik Vivianne L. , Du Bois J. , Bradley Zuchero J.
Published: November 2022

Excitability—the ability to fire action potentials—is a signature feature of neurons. How neurons become excitable during development, and whether excitability is an intrinsic property of neurons or requires signaling from glial cells, remain unclear. Here we demonstrate that Schwann cells, the most abundant glia in the peripheral nervous system, promote somatosensory neuron excitability during development. We find that Schwann cells secrete prostaglandin E2, which is necessary and sufficient to induce developing somatosensory neurons to express normal levels of voltage-gated sodium channels and fire action potential trains. Inactivating this signaling pathway specifically in Schwann cells selectively impairs the maturation of nociceptor and proprioceptor somatosensory neuron subtypes, leading to corresponding sensory defects in thermoception, inflammatory pain, and proprioception. Our studies thus reveal a cell non-autonomous mechanism by which glia regulate neuronal excitability to enable the development of normal sensory functions.
Lomasomes and other fungal plasma membrane macroinvaginations have a tubular and lamellar genesis
Authors: Mazheika Igor S. , Kamzolkina Olga V.
Published: November 2022

The plasma membrane of filamentous fungi forms large invaginations (>100-200 nm in diameter or length), which are especially pronounced in xylotrophic basidiomycetes. Typically, such macroinvaginations are either tubules or parietal vesicles. Vesicular macroinvaginations at the electron microscopic level correspond to classical lomasomes. There is an assumption that vesicular macroinvaginations/lomasomes may be involved in macrovesicular endocytosis, i.e., be scissored from the plasma membrane and be transported to the cytoplasm. The original aim of this study was to test for the presence of macroendocytosis in xylotrophic fungi using a fluorescent styryl label and time-lapse and Z-stacks microscopic technologies. However, the results were unexpected. It was found that most of the membrane structures labeled in fungal cells by the styryl fluorophore (analogue of FM4-64) is various types of macroinvaginations of the plasma membrane. All of these macroinvaginations are or go through a tube or lamella stage. Moreover, under specific conditions of a microscopic preparation, different types of invaginations are formed at different times – the longer the sample observation time, the greater may be the diameter of the tubes that form macroinvaginations. In addition, the morphology and successive formation of macroinvaginations mimics the endocytic pathway: different types of the invaginations can easily be mistaken for primary endocytic vesicles, endosomes, and vacuole-lysosomes. The paper qualitatively and quantitatively analyzes various types of macroinvaginations of the plasma membrane, suggests their biological functions, and discusses the presence and features of classical and macrovesicular endocytosis in fungi. This study is another step towards understanding the complex physiology of filamentous fungi associated with changes in plasma membrane tension, rapid changes in hyphae size, and endocytosis. In addition, this work is a presentation of a new tubular system in wood-decaying fungi, which takes its place among the already described tubular systems: vacuolar, mitochondrial, and endoplasmic-reticular.
Modality Independent or Modality Specific? Common Computations Underlie Confidence Judgements in Visual and Auditory Decisions
Authors: West Rebecca K , Harrison William J , Matthews Natasha , Mattingley Jason B , Sewell David K
Published: November 2022

Humans possess the ability to evaluate their confidence in a range of different decisions. In this study, we investigated the computational processes that underlie confidence judgements and the extent to which these computations are the same for perceptual decisions in the visual and auditory modalities. Participants completed two versions of a categorisation task with visual or auditory stimuli and made confidence judgements about their category decisions. In each modality, we varied both evidence strength, (i.e., the strength of the evidence for a particular category) and sensory uncertainty (i.e., the intensity of the sensory signal). We evaluated several classes of models which formalise the mapping of evidence strength and sensory uncertainty to confidence in different ways: 1) unscaled evidence strength models, 2) scaled evidence strength models, and 3) Bayesian models. Our model comparison results showed that across tasks and modalities, participants take evidence strength and sensory uncertainty into account in a way that is consistent with the scaled evidence strength class. Notably, the Bayesian class provided a relatively poor account of the data across modalities, particularly in the more complex categorisation task. Our findings suggest that a common process is used for evaluating confidence in perceptual decisions across domains, but that the parameter settings governing the process are tuned differently in each modality. Overall, our results highlight the impact of sensory uncertainty on confidence and the unity of metacognitive processing across sensory modalities.

Author Summary

In this study, we investigated the computational processes that describe how people derive a sense of confidence in their decisions. In particular, we determined whether the computations that underlie the evaluation of confidence for a visual decision are the same as those for an auditory decision. We tested a range of different models from 3 distinct classes which make different predictions about the computations that are used. We found that a single class of models provided the best account of confidence, suggesting a common process for evaluating confidence across sensory modalities. Even though these computations are governed by the same general process, our results suggest that the process is still fine-tuned within each modality.
More accurate analysis of maternal effect genes by siRNA electroporation into mouse oocytes
Authors: Yamamoto Takuto , Honda Shinnosuke , Ideguchi Issei , Suematsu Motoki , Ikeda Shuntaro , Minami Naojiro
Published: November 2022

Maternal RNAs and proteins accumulate in mouse oocytes and control the initial stages of development. The DNA in sperm combines with protamine, which is exchanged after fertilization with maternal histones, including H3.3, but the effect of H3.3 on post-fertilization development has been unclear. In this study, we established an electroporation method to introduce H3.3 siRNA into germinal vesicle (GV)-stage oocytes without removing cumulus cells. In the traditional microinjection method, cumulus cells attached to oocytes must be removed; however, we confirmed that artificially removing cumulus cells from oocytes reduced fertilization rates, and oocytes originally free of cumulus cells had reduced developmental competence. When H3.3 siRNA was introduced at the GV stage, H3.3 was still present in the maternal pronucleus and second polar body, but not in the paternal pronucleus, resulting in embryonic lethality after fertilization. This indicates that the H3.3 protein was not incorporated into the paternal pronucleus because it was repeatedly translated and degraded in a relatively short time. On the other hand, H3.3 protein incorporated into the maternal genome in the GV stage escaped degradation and remained in the maternal pronucleus after fertilization. This new method of electroporation into GV-stage oocytes without removing cumulus cells is not skill intensive and is essential for the accurate analysis of maternal effect genes.

In brief

For analysis of maternal factors contained in the oocyte, suppression of genes within the oocyte is necessary. In this paper, siRNA was introduced into oocytes by electroporation, showing that maternal mRNA was suppressed efficiently.
The molecular basis of phenotypic plasticity evolves in response to environmental predictability
Authors: Leung Christelle , Grulois Daphné , Quadrana Leandro , Chevin Luis-Miguel
Published: November 2022

Phenotypic plasticity, the response of a given genotype to its environment of development, is a ubiquitous feature of life, enabling organisms to cope with variation in their environment. Theoretical studies predict that, under stationary environmental variation, the level of plasticity should evolve to match the predictability of selection at the timing of development. However, we still lack critical empirical evidence on the extent to which selection on phenotypic plasticity cascades down from higher phenotypic levels to their underlying molecular basis. Here, we used experimental evolution under controlled environmental fluctuations, to test whether the evolution of phenotypic plasticity in responses to environmental predictability (ρ2) occurred across biological levels, going from DNA methylation to gene expression to cell morphology. Transcriptomic results indicate clear effects of salinity andρ2×salinity interaction on gene expression, thus identifying sets of genes involved in plasticity and its evolution. These transcriptomic effects were independent of DNA methylation changes incis. However we did findρ2-specific responses of DNA methylation to salinity change, albeit weaker than for gene expression. Overall, we found consistent evolution of reduced plasticity in less predictable environments for DNA methylation, gene expression, and cell morphology. Our results provide the first clear empirical signature of plasticity evolution at multiple levels in response to environmental predictability, and highlight the importance of experimental evolution to address predictions from evolutionary theory, as well as investigate the molecular basis of plasticity evolution.
CRISPR/FnCas12a-mediated efficient multiplex and iterative genome editing in bacterial plant pathogens without donor DNA templates
Authors: Yan Fang , Wang Jingwen , Zhang Sujie , Lu Zhenwan , Li Shaofang , Ji Zhiyuan , Song Congfeng , Chen Gongyou , Xu Jin , Feng Jie , Zhou Xueping , Zhou Huanbin
Published: November 2022

CRISPR-based genome editing technology is revolutionizing prokaryotic research, but it has been rarely studied in bacterial plant pathogens. Here, we have developed a targeted genome editing method with no requirement of donor templates for convenient and efficient gene knockout inXanthomonas oryzaepv.oryzae(Xoo), one of the most important bacterial pathogens on rice, by employing the heterogenous CRISPR/Cas12a fromFrancisella novicidaand NHEJ proteins fromMycobacterium tuberculosis.FnCas12a nuclease generated both small and large DNA deletions at the target sites as well as it enabled multiplex genome editing, gene cluster deletion and plasmid cure in theXooPXO99Astrain. Accordingly, a non-TAL effector-free polymutant strain PXO99AD25E, which lacks all 25Xopgenes involved inXoopathogenesis, has been engineered through iterative genome editing. Whole-genome sequencing analysis indicated that FnCas12a did not have a noticeable off-target effect. In addition, we revealed that these strategies are also suitable for targeted genome editing in another bacterial plant pathogenPseudomonas syringaepv.tomato(Pst). We believe that our bacterial genome editing method will greatly expand the CRISPR study on microorganisms and advance our understanding of the physiology and pathogenesis ofXoo.
Assessment of long-term trends in a threatened grassland bird community using daily bird lists
Authors: Bharadwaj Akshay , Mhamane Sarang , Bangal Priti , Menon Tarun , Isvaran Kavita , Quader Suhel
Published: November 2022

Open Natural Ecosystems (ONEs), such as tropical grasslands, are among the most threatened habitats on Earth today. The long-term monitoring of ONEs is an important research domain that is essential for understanding anthropogenic impacts and facilitating conservation action. Using a simple day-listing method over a 13-year period, we studied species trends in a central Indian grassland-agriculture mosaic experiencing several land-use changes. Our results indicate that some grassland species (such as the Great Indian BustardArdeotis nigriceps) show steep declines during the study period, while other generalist species (such as the Indian PeafowlPavo cristatus) show an increasing trend. Daily listing also reveals distinct seasonal patterns, and we discuss the Great Indian Bustard and Western Marsh HarrierCircus aeruginosusas examples. Our study highlights the utility of consistent checklist surveys to monitor population trends of bird communities within a changing landscape.
Programmed death-ligand 1 expression in human cancer three-dimensional cell culture models
Authors: Hudson K , Cross NA , Jordan-Mahy N , Leyland R
Published: November 2022

Programmed death-ligand 1 (PD-L1) expression is a survival mechanism employed by tumours to mediate immune evasion and tumour progression. PD-1/PD-L1-targeted therapies have revolutionised the cancer therapy landscape due to their ability to promote durable anti-tumour immune responses in select patients with advanced cancers. However, some patients are unresponsive, hyper-progressive or develop resistance. Better characterisation of the 3D architecture of solid tumours by utilising 3D cell culture could provide an environment that more closely recapitulatesin vivohuman tumours for investigating tumour-intrinsic PD-L1 signalling and immunotherapy responses. Here we investigated whether PD-L1 expression by human breast, prostate and colorectal cancer cell lines altered in 3D cell culture models compared to their 2D monolayer counterparts. We found that PD-L1 expression changed in 3D-cultured cancer cells when compared to 2D-cultured cells. Additionally, the expression of immunological markers, PD-1, PD-L2, CD44, DR4, DR5, Fas, and HLA-ABC were assessed in 3D cell culture and compared to their expression in 2D. These markers were also altered in 3D compared to 2D-cultured cells, highlighting the importance of utilising 3D models which may better able the investigation of tumour-intrinsic PD-L1 signalling, responses to PD-1/PD-L1-targeted therapy, and combination therapies.
Quantitative trait and transcriptome analysis of genetic complexity underpinning cardiac interatrial septation in mice using an advanced intercross line
Authors: Marjaneh Mahdi Moradi , Kirk Edwin P. , Patrick Ralph , Alankerage Dimuthu , Humphreys David T. , Del Monte-Nieto Gonzalo , Cornejo-Paramo Paola , Janbandhu Vaibhao , Doan Tram B. , Dunwoodie Sally L. , Wong Emily S. , Moran Chris , Martin Ian C.A. , Thomson Peter C. , Harvey Richard P.
Published: November 2022

Unlike single-gene mutations leading to Mendelian conditions, common human diseases are likely emergent phenomena arising from multilayer, multiscale and highly interconnected interactions. Atrial and ventricular septal defects are the most common forms of cardiac congenital anomalies in humans. Atrial septal defects (ASD) show an open communication between left and right atria postnatally, potentially resulting in serious hemodynamic consequences if untreated. A milder form of atrial septal defect, patentforamen ovale(PFO), exists in about one quarter of the human population, strongly associated with ischaemic stroke and migraine. The anatomic liabilities and genetic and molecular basis of atrial septal defects remain unclear. Here, we advance our previous analysis of atrial septal variation through quantitative trait locus (QTL) mapping of an advanced intercross line (AIL) established between the inbred QSi5 and 129T2/SvEms mouse strains, that show extremes of septal phenotypes. Analysis resolved 37 unique septal QTL with high overlap between QTL for distinct septal traits. Whole genome sequencing of parental strains identified high confidence candidate deleterious variants, including in known human congenital heart disease genes, whereas transcriptome analysis of developing septa revealed networks involving ribosome, nucleosome, mitochondrial and extracellular matrix biosynthesis underlying septal variation. Analysis of variant architecture across different gene features, including enhancers and promoters, provided evidence for involvement of non-coding as well as protein coding variants. Our study provides the first high resolution picture of genetic complexity and network liability underlying common congenital heart disease, with relevance to human ASD and PFO.
Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter
Authors: Bull Freya , Tavaddod Sharareh , Bommer Nick , Perry Meghan , Brackley Chris A. , Allen Rosalind J.
Published: November 2022

Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter, that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals, and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.
Sphere-sequencing unveils local tissue microenvironments at single cell resolution
Authors: Handler Kristina , Bach Karsten , Borrelli Costanza , Ficht Xenia , Acar Ilhan E. , Moor Andreas E.
Published: November 2022

The spatial organization of cells within tissues is tightly linked to their biological function. Yet, methods to probe the entire transcriptome of multiple native tissue microenvironments at single cell resolution are lacking. Here, we introduce spheresequencing, a method that enables the transcriptomic characterization of single cells within spatially distinct tissue niches. Sphere-sequencing of the mouse metastatic liver revealed previously uncharacterized zonated genes and ligand-receptor interactions enriched in different hepatic microenvironments and the metastatic niche.
Spike-and-wave discharges of absence seizures in a sleep waves-constrained corticothalamic model
Authors: Dervinis Martynas , Crunelli Vincenzo
Published: November 2022

Aims

Recurrent network activity in corticothalamic circuits generates physiological and pathological EEG waves. Many computer models have simulated spike-and-wave discharges (SWDs), the EEG hallmark of absence seizures (ASs). However, these models either provided detailed simulated activity only in a selected territory (i.e. cortical or thalamic) or did not test whether their corticothalamic networks could reproduce the physiological activities that are generated by these circuits.

Methods

Using a biophysical large-scale corticothalamic model that reproduces the full extent of EEG sleep waves, including sleep spindles, delta and slow (<0.1 Hz) waves, here we investigated how single abnormalities in voltage- or transmitter-gated channels in the neocortex or thalamus lead to SWDs.

Results

We found that a selective increase in the tonic γ-aminobutyric acid type A receptor (GABA-A) inhibition of first order thalamocortical (TC) neurons or a selective decrease in cortical phasic GABA-A inhibition are sufficient to generate ∼4 Hz SWDs (as in humans) that invariably start in neocortical territories. Decreasing the leak conductance of higher order TC neurons leads to ∼7 Hz SWDs (as in rodent models) while maintaining sleep spindles at 7-14 Hz.

Conclusion

By challenging key features of current mechanistic views, this simulated ictal corticothalamic activity provides novel understanding of ASs and makes key testable predictions.
ThePlasmodium falciparumapicoplast cysteine desulfurase provides sulfur for both iron sulfur cluster assembly and tRNA modification
Authors: Swift Russell P. , Elahi Rubayet , Rajaram Krithika , Liu Hans B. , Prigge Sean T.
Published: November 2022

Iron sulfur clusters (FeS) are ancient and ubiquitous protein cofactors that play fundamental roles in many aspects of cell biology. These cofactors cannot be scavenged or trafficked within a cell and thus must be synthesized in any subcellular compartment where they are required. We examined the FeS synthesis proteins found in the relict plastid organelle, called the apicoplast, of the human malaria parasitePlasmodium falciparum.Using a chemical bypass method, we deleted four of the FeS pathway proteins involved in sulfur acquisition and cluster assembly and demonstrated that they are all essential for parasite survival. However, the effect that these deletions had on the apicoplast organelle differed. Deletion of the cysteine desulfurase SufS led to disruption of the apicoplast organelle and loss of the organellar genome, whereas the other deletions did not affect organelle maintenance. Ultimately, we discovered that the requirement of SufS for organelle maintenance is not driven by its role in FeS biosynthesis, but rather, by its function in generating sulfur for use by MnmA, a tRNA modifying enzyme that we localized to the apicoplast. By complementing the activity of the parasite MnmA and SufS with a bacterial MnmA and its cognate cysteine desulfurase, we showed that the parasite SufS provides sulfur for both FeS biosynthesis and tRNA modification in the apicoplast. The dual role of parasite SufS is likely to be found in other plastid-containing organisms and highlights the central role of this enzyme in plastid biology.
Automated community ecology using deep learning: a case study of planktonic foraminifera
Authors: Hsiang Allison Y. , Hull Pincelli M.
Published: November 2022

The development of deep learning methods using convolutional neural networks (CNNs) has revolutionised the field of computer vision in recent years. The automation of taxonomic identification using CNNs leads naturally to the use of such technology for rapidly generating large organismal datasets in order to study the evolutionary and ecological dynamics of biological communities across time and space. While CNNs have been used to train machine learning classifiers that can identify organisms to the species level for several groups, this vision of automated community ecology has yet to be thoroughly tested or fulfilled. Here, we present a case study of automated community ecology using a large dataset of Atlantic planktonic foraminifera for which the generation of species labels and morphometric measurements was completely automated. We compare standard community diversity metrics between the fully automated dataset and a “traditional” dataset with human-identified specimens. We show that there is high congruence between the results, and that machine classifications help avoid biases that can result in the inference of misleading biodiversity patterns. Our study demonstrates the viability and potential of fully automated community ecology and sets the stage for a new era of ecological and evolutionary inquiry driven by artificial intelligence.
Landscape heterogeneity and soil biota are central to multi-taxa diversity for landscape restoration
Authors: Montoya-Sánchez Vannesa , Kreft Holger , Arimond Isabelle , Ballauff Johannes , Berkelmann Dirk , Brambach Fabian , Daniel Rolf , Grass Ingo , Hines Jes , Hölscher Dirk , Irawan Bambang , Krause Alena , Polle Andrea , Potapov Anton , Sachsenmaier Lena , Scheu Stefan , Sundawati Leti , Tscharntke Teja , Zemp Delphine Clara , Guerrero-Ramírez Nathaly R.
Published: November 2022

How to enhance biodiversity in monoculture-dominated landscapes is a key sustainability question that requires considering the spatial organization of ecological communities (beta diversity). Here, we experimentally tested if increasing landscape heterogeneity – through tree islands – is a suitable landscape restoration strategy when aiming to enhance multi-taxa diversity. We found that multi-taxa diversity resulted from islands fostering unique species (turnover: between 0.18 - 0.73) rather than species losses and gains (nestedness: between 0.03 - 0.34), suggesting that tree islands enhance diversity at the landscape scale. Through partial correlation networks, we revealed that landscape heterogeneity is associated with multi-taxa diversity (strength = 0.84). Soil biota were also central to the overall community by connecting beta diversity patterns across taxa. Our results show that increasing landscape heterogeneity enhances multi-taxa diversity in monoculture-dominant landscapes. Furthermore, we highlight that strategies aiming to enhance multi-taxa diversity should consider that spatial distributions of above- and below-ground communities are associated.
In vivoCharacterization of the Critical Interaction between the RNA Exosome and the Essential RNA Helicase Mtr4 inSaccharomyces cerevisiae
Authors: Sterrett Maria C. , Farchi Daniela , Strassler Sarah E. , Boise Lawrence H. , Fasken Milo B. , Corbett Anita H.
Published: November 2022

The RNA exosome is a conserved molecular machine that processes/degrades numerous coding and non-coding RNAs. The 10-subunit complex is composed of three S1/KH cap subunits (human EXOSC2/3/1; yeast Rrp4/40/Csl4), a lower ring of six PH-like subunits (human EXOSC4/7/8/9/5/6; (yeast Rrp41/42/43/45/46/Mtr3), and a singular 3’-5’ exo/endonuclease DIS3/Rrp44. Recently, several disease-linked missense mutations have been identified in genes encoding the structural cap and core subunits of the RNA exosome. In this study, we characterize a rare multiple myeloma patient missense mutation that was identified in the cap subunit geneEXOSC2. This missense mutation results in a single amino acid substitution, p.Met40Thr, in a highly conserved domain of EXOSC2. Structural studies suggest this Met40 residue makes direct contact with the essential RNA helicase, MTR4, and may help stabilize the critical interaction between the RNA exosome complex and this cofactor. To assess this interactionin vivo, we utilized theSaccharomyces cerevisiaesystem and modeled theEXOSC2patient mutation into the orthologous yeast geneRRP4, generating the variantrrp4 M68T. Therrp4 M68Tcells have accumulation of certain RNA exosome target RNAs and show sensitivity to drugs that impact RNA processing. Additionally, we identified robust negative genetic interactions therrp4 M68Tvariant and RNA exosome cofactor mutants, particularlymtr4mutant variants. This study suggests that theEXOC2mutation identified in a multiple myeloma patient may impact the function of the RNA exosome and provides anin vivoassessment of a critical interface between the RNA exosome and Mtr4.
A multivariate regressor of patterned dopamine release predicts relapse to cocaine
Authors: Luján Miguel Á. , Young-Morrison Reana , Engi Sheila A. , Oliver Brandon L. , Zhang Lan-Yuan , Wenzel Jennifer M. , Li Yulong , Zlebnik Natalie E. , Cheer Joseph F.
Published: November 2022

Drug addiction is characterized by a sustained vulnerability to relapse even after long periods of abstinence. A deeper understanding of the brain systems underlying this state could inform therapeutic strategies with novel prognostic biomarkers aimed at preventing renewed drug seeking. Most drugs of abuse, in particular psychostimulants such as cocaine, lead to long-lasting mesolimbic dopamine system adaptations, that ultimately facilitate drug seeking following exposure to drug-paired cues. This “dopaminergic hypothesis” of relapse has been previously addressed, but technical limitations in measuringin vivodopamine release have precluded the assessment of its sufficiency without introducing pharmacological, electrical, or optogenetic confounds. Using a dopamine receptor-based fluorescent sensor in freely moving mice, we show that long-lasting dopamine recordings in the nucleus accumbens (NAc), throughout the animal’s entire history of cocaine self-administration, are strong predictors of relapse as well as the time it takes an animal to extinguish its drug seeking behavior. Moreover, we reveal previously unseen sex-specific trajectories of cocaine-related phasic dopamine responses from acquisition to relapse. We show that males exhibit higher-amplitude phasic dopamine responses, a trait accompanied by a greater resistance to extinguish their cocaine seeking, compared to females. Furthermore, we show that a semi-parametric model of the transition to extinction – using only multivariate patterns of dopamine release and sex as covariates – faithfully recapitulates male-specific vulnerability to persistent cocaine seeking. In conclusion, we present a predictive model of reinstatement behavior that uses information exclusively conveyed by NAc phasic dopamine responses, thus confirming, and actuating the sufficiency of the dopaminergic hypothesis of relapse.
A Biophysical Basis for Learning and Transmitting Sensory Predictions
Authors: Muller Salomon Z. , Abbott LF , Sawtell Nathaniel B.
Published: November 2022

Homeostatic (anti-Hebbian) forms of synaptic are effective at eliminating “prediction errors” that signal the differences between predicted and actual sensory input. However, such mechanisms appear to preclude the possibility of transmitting the resulting predictions to downstream circuits, severely limiting their utility. Using modeling and recordings from the electrosensory lobe of mormyrid fish, we reveal interactions between axonal and dendritic spikes that support both the learningandtransmission of predictions. We find that sensory input modulates the rate of dendritic spikes by adjusting the amplitude of backpropagating axonal action potentials. Homeostatic plasticity counteracts these effects through changes in the underlying membrane potential, allowing the dendritic spike rate to be restored to equilibrium while simultaneously transmitting predictions through modulation of the axonal spike rate. These results reveal how two types of spikes dramatically enhance the computational power of single neurons in support of an ethologically relevant multi-layer computation.
A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell therapy applications
Authors: Palianina Darya , Di Roberto Raphaël B. , Castellanos-Rueda Rocío , Schlatter Fabrice , Reddy Sai T. , Khanna Nina
Published: November 2022

Adoptive cell therapy of donor-derived, antigen-specific T cells expressing native T cell receptors (TCRs) is a powerful strategy to fight viral infections in immunocompromised patients. Determining the fate of T cells following patient infusion hinges on the ability to track themin vivo. While this is possible by genetic labeling of parent cells, the applicability of this approach has been limited by the non-specificity of the edited T cells.

Here, we devised a method for CRISPR-targeted genome integration of a barcoded gene into Epstein-Barr virus-antigen-stimulated T cells and demonstrated its use for exclusively identifying expanded virus-specific cell lineages. Our method facilitated the enrichment of antigen-specific T cells, which then mediated improved cytotoxicity against EBV-transformed target cells. Single-cell and deep sequencing for lineage tracing revealed the expansion profile of specific T cell clones and their corresponding gene expression signature. This method has the potential to enhance the traceability and the monitoring capabilities during immunotherapeutic T cell regimens.
A representative Performance Assessment of Maximum Likelihood based Phylogenetic Inference Tools
Authors: Höhler Dimitri , Haag Julia , Kozlov Alexey M. , Stamatakis Alexandros
Published: November 2022

The evaluation of phylogenetic inference tools is commonly conducted on simulated and empirical sequence data alignments. An open question is how representative these alignments are with respect to those, commonly analyzed by users. Based upon the RAxMLGrove database, it is now possible to simulate DNA sequences based on more than 70, 000 representative RAxML and RAxML-NG tree inferences on empirical datasets conducted on the RAxML web servers. This allows to assess the phylogenetic tree inference accuracy of various inference tools based on realistic and representative simulated DNA alignments. We simulated 20, 000 MSAs based on representative datasets (in terms of signal strength) from RAxMLGrove, and used 5, 000 datasets from the TreeBASE database, to assess the inference accuracy of FastTree2, IQ-TREE2, and RAxML-NG. We find that on quantifiably difficult-to-analyze MSAs all of the analysed tools perform poorly, such that the quicker FastTree2, can constitute a viable alternative to infer trees. We also find, that there are substantial differences between accuracy results on simulated and empirical data, despite the fact that a substantial effort was undertaken to simulate sequences under as realistic as possible settings.

Contact

Dimitri Höhler,dimitri.hoehler@h-its.org
ALaSCA: a computational platform for quantifying the effect of proteins using Pearlian causal inference, with an example application in Alzheimer’s disease
Authors: Truter Nina , Jansen van Rensburg Zuné , Oudrhiri Radouane , Van Niekerk David D. , Loos Ben , Singh Raminderpal , Louw Carla
Published: November 2022

Introduction

An urgent need to delay the onset of aging-associated diseases has arisen due to increasing human lifespan. A dramatic surge in the number of identified potential molecular targets that could promote successful aging, has led to the challenge of prioritizing these targets for further research and drug development. In our previous work, we prioritized genes associated with aging processes based on their similarity to known aging-related genes and dysfunction marker genes inC. elegans. The goal of this study was to demonstrate the ability of our computational platform to identify molecular drivers of neuronal aging using specialized causal inference techniques. S6K was highly ranked in the previous study and here the nearby neighbors in its protein interaction network were selected to explore ALaSCA’s (Adaptable Large-Scale Causal Analysis) ability to identify possible drivers of Alzheimer’s disease.

Methods

Utilizing head and brain proteome data, two of ALaSCA’s capabilities were used to understand how protein changes over the lifespan ofDrosophila melanogasteraffect a feature of neuronal aging, namely climbing ability:

Pearson correlation analysis was used to assess the relationship between the changes in abundance of specific proteins associated (through protein-protein interactions) with S6K and climbing ability.

Pearlian causal inference, required to achieve formal causal analysis, was used to determine which pathway, associated with proteins linked to S6K, has the largest effect on climbing ability and therefore to what degree these specific proteins are driving neuronal aging.

Results and discussion

Based on the correlation results, the proteins associated withfz, a gene encoding for the fz family of receptors that are involved in Wnt signaling, display an increase in abundance as climbing ability declines over time. When viewed together with thefzproteins’ strong negative causal value, it seems that their increased abundance over the lifespan ofDrosophilais an important driver of the observed decrease in climbing ability. Additionally, expression of the genes FZD1 and FZD7 (fzorthologs) is altered in the hippocampus early on in Alzheimer’s disease human samples and in an amyloid precursor protein mouse model.

Conclusion

We have demonstrated the potential of the ALaSCA platform to identify and provide evidence behind molecular mechanisms. This capability enables identification of possible drivers of Alzheimer’s disease - as the human orthologs of the proteins identified here, through its Pearlian causal inference capability, have been linked to Alzheimer’s disease progression.
Druggable Growth Dependencies and Tumor Evolution Analysis in Patient-Derived Organoids of Neuroendocrine Cancer
Authors: Dayton Talya L. , Alcala Nicolas , Moonen Laura , den Hartigh Lisanne , Mangiante Lise , Lap Lisa , Dost Antonella F. M. , Beumer Joep , Levy Sonja , van Leeuwaarde Rachel S. , Hackeng Wenzel M. , Samsom Kris , Voegele Catherine , Sexton-Oates Alexandra , Begthel Harry , Korving Jeroen , Hillen Lisa , Brosens Lodewijk A. A. , Lantuejoul Sylvie , Jaksani Sridevi , Kok Niels F.M. , Hartemink Koen J. , Klomp Houke M. , Rinkes Inne H.M. Borel , Dingemans Anne-Marie , Valk Gerlof D. , Vriens Menno R. , Buikhuisen Wieneke , van den Berg José , Tesselaar Margot , Derks Jules , Speel Ernst Jan , Foll Matthieu , Fernández-Cuesta Lynnette , Clevers Hans
Published: November 2022

Neuroendocrine neoplasms (NENs) comprise well-differentiated neuroendocrine tumors and poorly-differentiated carcinomas. Treatment options for patients with NENs are limited, in part due to lack of accurate models. To address this need we established the first patient-derived tumor organoids (PDTOs) from pulmonary neuroendocrine tumors and derived PDTOs from an understudied NEN subtype, large cell neuroendocrine carcinoma (LCNEC). PDTOs maintain the gene expression patterns, intra-tumoral heterogeneity, and evolutionary processes of parental tumors. Through drug sensitivity analyses, we uncover therapeutic sensitivities to an inhibitor of NAD salvage biosynthesis and to an inhibitor of BCL-2. Finally, we identify a dependency on EGF in pulmonary neuroendocrine tumor PDTOs. Consistent with these findings, analysis of an independent cohort showed that approximately 50% of pulmonary neuroendocrine tumors expressed EGFR. This study identifies a potentially actionable vulnerability for a subset of NENs, and further highlights the utility of these novel PDTO models for the study of NENs.

Graphical abstract

Highlights

PDTOs of pulmonary NETs and LCNEC were established

PDTOs recapitulate intra-tumoral heterogeneity and evolution of parental tumors

Drug assays reveal therapeutic vulnerabilities and biomarkers

Pulmonary NET PDTOs are dependent on EGF
Generation of Unfolded Outer Membrane Protein Ensembles Targeted by Hydrodynamic Properties
Authors: Devlin Taylor , Fleming Patrick J. , Loza Nicole , Fleming Karen G.
Published: November 2022

Outer membrane proteins (OMPs) must exist as an unfolded ensemble while interacting with a chaperone network in the periplasm of Gram-negative bacteria. Here, we developed a method to model unfolded OMP (uOMP) conformational ensembles using experimental properties of two well-studied OMPs. The overall size and shape of the unfolded ensembles in water were experimentally defined by measuring the sedimentation coefficient as a function of urea concentration. We used these data to model a full range of unfolded conformations by parameterizing a targeted coarse-grained simulation protocol. The ensemble members were further refined by short molecular dynamics simulations to reflect proper torsion angles. The final conformational ensembles reveal inherent differences in the unfolded states that necessitate further investigation. Building these uOMP ensembles advances the understanding of OMP biogenesis and produces essential information for interpreting structures of uOMP-chaperone complexes.
Nascent-Chain Interaction Networks and Their Effect on the Bacterial Ribosome
Authors: Masse Meranda M. , Guzman-Luna Valeria , Varela Angela E. , Hutchinson Rachel B. , Srivastava Aniruddha , Wei Wanting , Fuchs Andrew M , Cavagnero Silvia
Published: November 2022

In order to become bioactive, proteins need to be biosynthesized and protected from aggregation during translation. The ribosome and molecular chaperones contribute to both of these tasks. While it is known that some ribosomal proteins (r-proteins) interact with ribosome-bound nascent chains (RNCs), specific interaction networks and their role within the ribosomal machinery remain poorly characterized and understood. Here, we find that RNCs of variable sequence and length (beyond the 1stC-terminal reside) do not modify the apparent stability of the peptidyl-transferase center (PTC) and r-proteins. Thus, RNC/r-protein interaction networks close to the PTC have no effect on the apparent stability of ribosome-RNC complexes. Further, fluorescence anisotropy decay, chemical-crosslinking and Western blots show that RNCs of the foldable protein apoHmp1-140have an N-terminal compact region (63–94 residues) and interact specifically with r-protein L23 but not with L24 or L29, at the ribosomal-tunnel exit. Longer RNCs bear a similar compact region and interact either with L23 alone or with L23 and another unidentified r-protein, or with molecular chaperones. The apparent strength of RNC/r-protein interactions does not depend on RNC sequence. Taken together, our findings show that RNCs encoding foldable protein sequences establish an expanding specific interaction network as they get longer, including L23, another r-protein and chaperones. Interestingly, the ribosome alone (i.e., in the absence of chaperones) provides indiscriminate support to RNCs bearing up to ca. 190 residues, regardless of nascent-chain sequence and foldability. In all, this study highlights the unbiased features of the ribosome as a powerful nascent-protein interactor.

Significance Statement

The presence of interactions between nascent chains bearing a foldable amino-acid sequence (with no signal or arrest tags) and specific ribosomal proteins has never been experimentally demonstrated, up to now. Here, we identify the ribosomal protein L23 as a specific nascent-chain interacting partner. We show that L23 establishes noncovalent contacts with nascent chains of the multi-domain foldable model protein apoHmp, which lacks signal/arrest sequences. Interactions with another ribosomal protein and with the trigger-factor and Hsp70 chaperones were also detected. Interestingly, ribosomal-protein/nascent-chain complexes have similar apparent stability, in the case of nascent chains of variable sequence and degree of foldability. These findings are significant because they advance our knowledge on ribosome-mediated nascent-protein interaction networks and suggest avenues to prevent undesirable aggregation.
Genomic Selection Pressure Discovery using Site-Frequency Spectrum & Reduced Local-Variability Statistics in Pakistani Dera-Din-Panah Goat
Authors: Saif Rashid , Mahmood Tania , Ejaz Aniqa , Zia Saeeda
Published: November 2022

Population geneticists have long sought to comprehend various selection traces present in the goat genome due to natural or human-driven selection and breeding practices. As a step forward to pinpoint the selection signals in the Pakistani Dera-Din-Panah (DDP) goat breed, whole-genome pooled-sequencing (n=12) was performed and 618,236,192 clean paired-end reads were mapped against ARS1 reference goat assembly. Five different selection signal statistics were applied here using four Site-Frequency Spectrum (SFS) methods (Tajima’s D (TD), Fay & Wu’s H (H), Zeng’s E (E),Pool – HMM) and one Reduced Local-Variability approach named pooled-heterozygosity (Hp). The under-selection regions were annotated with significant threshold values of –ZTD≥4.7, –ZH≥6, –ZE≥2.5, Pool-HMM≥12, and –ZHp≥5, which resulted in accumulative 364 candidate gene hits, while the highest signals were observed on Chr. 4, 6, 10, 12, 15, 16, 18, 20, 27 harborADAMTS6, CWC27genes associated with body-height,RELN, MYCBP2, FGF14, STIM1, CFAP74, GNB1, CALML6, TMEM52, FAM149A, NADK, MMP23B, OPN3with body-weight/meat production,FH, MFHAS1, KLKB1with milk production,RRM1, KMO, SPEF2, F11with fecundity rate/reproduction,ATP8B4with immunity,KIT, KMOwith pigmentation,ERI1with olfaction andRHOGwith wool production traits. Furthermore, we accentuate to highlight the putative windows that were captured commonly by any of the five statistical methods applied which harbor meat production, immunity and reproduction-associated genes validating the genotype-phenotype relationship of aforementioned traits private to this goat breed. Current insight into the genomic architecture of DDP goat provides a better understanding to improve its genetic potential and other vested traits of large body size and fiber production by updating the breeding strategies to boost the livestock-based agricultural economy of the country.
Excitatory amino acid transporter 1 supports adult hippocampal neural stem cell self-renewal
Authors: Rieskamp Joshua D. , Rosado-Burgos Ileanexis , Christofi Jacob E. , Ansar Eliza , Einstein Dalia , Walters Ashley E. , Valentini Valentina , Bruno John P. , Kirby Elizabeth D.
Published: November 2022

Within the adult mammalian dentate gyrus (DG) of the hippocampus, glutamate stimulates neural stem cell (NSC) self-renewing proliferation, providing a link between adult neurogenesis and local circuit activity. Here, we show that glutamate-induced self-renewal of adult DG NSCs requires glutamate transport via excitatory amino acid transporter 1 (EAAT1) to stimulate lipogenesis. Loss of EAAT1 prevented glutamate-induced self-renewing proliferation of NSCs in vitro and in vivo, with little role evident for canonical glutamate receptors. Transcriptomics and further pathway manipulation revealed that glutamate simulation of NSCs relied on EAAT1 transport-stimulated lipogenesis. Our findings demonstrate a critical, direct role for EAAT1 in stimulating NSCs to support neurogenesis in adulthood, thereby providing insights into a non-canonical mechanism by which NSCs sense and respond their niche.