bluuebunny/crossref_metadata_2025 huggingface dataset:
Stepwise design of pseudosymmetric protein hetero-oligomers
Authors: Kibler Ryan D. , Lee Sangmin , Kennedy Madison A. , Wicky Basile I. M. , Lai Stella M. , Kostelic Marius M. , Li Xinting , Chow Cameron M. , Carter Lauren , Wysocki Vicki H. , Stoddard Barry L. , Baker David
Published: April 2023

Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteinsde novowould provide new routes to controlling cell signaling and designing complex protein materials. However, thede novodesign of protein hetero-oligomers with three or more distinct chains with nearly identical structures is a challenging problem because it requires the accurate design of multiple protein-protein interfaces simultaneously. Here, we describe a divide-and-conquer approach that breaks the multiple-interface design challenge into a set of more tractable symmetric single-interface redesign problems, followed by structural recombination of the validated homo-oligomers into pseudosymmetric hetero-oligomers. Starting fromde novodesigned circular homo-oligomers composed of 9 or 24 tandemly repeated units, we redesigned the inter-subunit interfaces to generate 15 new homo-oligomers and recombined them to make 17 new hetero-oligomers, including ABC heterotrimers, A2B2 heterotetramers, and A3B3 and A2B2C2 heterohexamers which assemble with high structural specificity. The symmetric homo-oligomers and pseudosymmetric hetero-oligomers generated for each system share a common backbone, and hence are ideal building blocks for generating and functionalizing larger symmetric assemblies.

Significance Statement

Protein oligomers composed of multiple unique subunits are versatile building blocks for creating functional materials and controlling biological processes. However, designing robust hetero-oligomers with distinct subunits and precise structural symmetry remains a major challenge. Here, we present a general strategy for designing such complexes by breaking down the problem into simpler steps by first symmetrically re-designing the interfaces of homo-oligomeric proteins, and then recombining validated variants to form pseudosymmetric hetero-oligomers. Using this method, we generated 17 hetero-oligomers with up to three unique subunits that assemble with high specificity. Our approach can be extended to create a wide range of pseudosymmetric assemblies for manipulating cellular signaling and as building blocks for advanced protein materials. These pseudosymmeteric heterotrimers have already enabled the construction of a set of massive nanocages, including a T=4 icosahedral nanocage with a 70 nm diameter and 240 subunits.1
Targeting MCL1-driven anti-apoptotic pathways to overcome hypomethylating agent resistance inRAS-mutated chronic myelomonocytic leukemia
Authors: Montalban-Bravo Guillermo , Ma Feiyang , Thongon Natthakan , Yang Hui , Gomez Irene Ganan- , Rodriguez-Sevilla Juanjo Jose , Adema Vera , Wildeman Bethany , Lockyer Pamela , Kim Yi June , Tanaka Tomoyuki , Darbaniyan Faezeh , Pancholy Shivam , Zhang Geoffrey , Al-Atrash Gheath , Dwyer Karen , Takahashi Koichi , Garcia-Manero Guillermo , Kantarjian Hagop , Colla Simona
Published: April 2023

RASpathway mutations, which are present in 30% of patients with chronic myelomonocytic leukemia (CMML) at diagnosis, confer a high risk of resistance to and progression after hypomethylating agent (HMA) therapy, the current standard of care for the disease. Using single-cell, multi-omics technologies, we sought to dissect the biological mechanisms underlying the initiation and progression ofRASpathway–mutated CMML. We found thatRASpathway mutations induced the transcriptional reprogramming of hematopoietic stem and progenitor cells (HSPCs), which underwent proliferation and monocytic differentiation in response to cell-intrinsic and -extrinsic inflammatory signaling that also impaired immune cells’ functions. HSPCs expanded at disease progression and relied on the NF-KB pathway effector MCL1 to maintain their survival, which explains why patients withRASpathway– mutated CMML do not benefit from BCL2 inhibitors such as venetoclax. Our study has implications for developing therapies to improve the survival of patients withRASpathway– mutated CMML.
L-Ascorbic acid restrictsVibrio choleraesurvival in various growth conditions
Authors: Sen Himanshu , Kaur Manpreet , Raychaudhuri Saumya
Published: April 2023

Cholera, a deadly diarrheal disease, continues to ravage various parts of the world. It is caused byVibrio cholerae, an important member of the gamma-proteobacteria. Based on certain genetic and phenotypic tests, the organism is classified into two major biotypes, namely classical and El Tor. The El Tor and its variants are majorly responsible for the ongoing seventh pandemic across the globe. Previously, we have shown that cross feeding of glucose metabolic acidic by products of gut commensal can severely affect viability of the biotypes. In this work, we examined the effect of L-ascorbic acid on the survival ofVibrio choleraestrains belonging to both biotypes and different serotypes. We observed that L-ascorbic acid is effective in restricting the growth of all strains under various conditions including strains adapted with acid stress.
Evaluating proteomics imputation methods with improved criteria
Authors: Harris Lincoln , Fondrie William E. , Oh Sewoong , Noble William S.
Published: April 2023

Quantitative measurements produced by tandem mass spectrometry proteomics experiments typically contain a large proportion of missing values. This missingness hinders reproducibility, reduces statistical power, and makes it difficult to compare across samples or experiments. Although many methods exist for imputing missing values in proteomics data, in practice, the most commonly used methods are among the worst performing. Furthermore, previous benchmarking studies have focused on relatively simple measurements of error, such as the mean-squared error between the imputed and the held-out observed values. Here we evaluate the performance of a set of commonly used imputation methods using three practical, “downstream-centric” criteria, which measure the ability of imputation methods to reconstruct differentially expressed peptides, identify new quantitative peptides, and improve peptide lower limit of quantification. Our evaluation spans several experiment types and acquisition strategies, including datadependent and data-independent acquisition. We find that imputation does not necessarily improve the ability to identify differentially expressed peptides, but that it can identify new quantitative peptides and improve peptide lower limit of quantification. We find that MissForest is generally the best performing method per our downstream-centric criteria. We also argue that exisiting imputation methods do not properly account for the variance of peptide quantifications and highlight the need for methods that do.
Doxorubicin inhibits phosphatidylserine decarboxylase and confers broad-spectrum antifungal activity
Authors: Zhou Yaru , Zhao Juan , Yang Lei , Bi Ruiqing , Qin Ziting , Sun Peng , Li Renjian , Zhao Mengfei , Wang Yin , Chen Guang , Wan Hu , Zheng Lu , Chen Xiao-Lin , Wang Guanghui , Li Qiang , Li Guotian
Published: April 2023

As phospholipids of cell membranes, phosphatidylethanolamine (PE) and phosphatidylserine (PS) play crucial roles in glycerophospholipid metabolism. Broadly, some phospholipid biosynthesis enzymes serve as potential fungicide targets. Therefore, revealing the functions and mechanism of PE biosynthesis in plant pathogens would provide potential targets for crop disease control.

We performed analyses including phenotypic characterizations, lipidomics, enzyme activity, site-directed mutagenesis, and chemical inhibition assays to study the function of PS decarboxylase-encoding geneMoPSD2in rice blast fungusMagnaporthe oryzae.

TheMopsd2mutant was defective in development, lipid metabolism and plant infection. The PS level increased while PE decreased inMopsd2, consistent with the enzyme activity. Furthermore, chemical doxorubicin inhibited the enzyme activity of MoPsd2 and showed antifungal activity against ten phytopathogenic fungi includingM. oryzaeand reduced disease severity of two crop diseases in the field. Three predicted doxorubicin-interacting residues are important for MoPsd2 functions.

Our study demonstrates that MoPsd2 is involved inde novoPE biosynthesis and contributes to the development and plant infection ofM. oryzaeand that doxorubicin shows broad-spectrum antifungal activity as a fungicide candidate. The study also implicates that bacteriumStreptomyces peucetius, which biosynthesizes doxorubicin, could be potentially used as an eco-friendly biocontrol agent.
Deep origin of the long root tuft: the oldest stalk-bearing sponge from the Cambrian Stage 3 black shale of South China
Authors: Yun Hao , Janussen Dorte , Zhang Xingliang , Reitner Joachim
Published: April 2023

In virtue of remarkable tolerance on hypoxia and adaptive specialization in morphology, diverse hexactinellid sponges were prosperous in an early Cambrian living condition that characterized by dysoxic to anoxic bottom waters documented by black shales. New fossils from the black shale of Niutitang Formation (basal Stage 3 of Cambrian) in Hunan Province of China, reveal for the first time an articulated body of the spongeHyalosinica archaicaMehl & Reitner in Steineret al., 1993, which possesses an ovoid main body and an impressive long stalk. The specular skeleton includes large diactines that are generally organized as fan-shaped clusters, a few small stauractines and hexactines, and twisted bundles of long monaxons that form the stalk/root tuft. This hexactinellid sponge represents the oldest extinct taxon that took advantage of a long stalk to elevate the main body above the sediment surface and thus to adapt to the oxygen-deficient sea-bottom environment. The long root tuft linksHyalosinicato a series of fossil and recent sponge taxa and proves a deep origin of the stalk-bearing morphology, indicating a likely parallel evolution within the Hexactinellida in response to special environmental pressures. Furthermore, the overall skeletal organization indicates thatHyalosinica, as well as related early “rossellimorphs”, are basal stem group representatives of Hexactinellida and probably branched before the extinct Reticulosa and before the two extant hexactinellid subclasses.
MOViDA: Multi-Omics Visible Drug Activity Prediction with a Biologically Informed Neural Network Model
Authors: Ferraro Luigi , Scala Giovanni , Cerulo Luigi , Carosati Emanuele , Ceccarelli Michele
Published: April 2023

Drug discovery is a challenging task, characterized by a protracted period of time between initial development and market release, with a high rate of attrition at each stage. Computational virtual screening, powered by machine learning algorithms, has emerged as a promising approach for predicting therapeutic efficacy. However, the complex relationships between features learned by these algorithms can be challenging to decipher. We have devised a neural network model for the prediction of drug sensitivity, which employs a biologically-informed visible neural network (VNN), enabling a greater level of interpretability. The trained model can be scrutinized to investigate the biological pathways that play a fundamental role in prediction, as well as the chemical properties of drugs that influence sensitivity. The model leverages multi-omics data obtained from diverse tumor tissue sources and molecular descriptors that encode drug properties. We have extended the model to predict drug synergy, resulting in favorable outcomes while retaining interpretability. Given the often imbalanced nature of publicly available drug screening datasets, our model demonstrates superior performance compared to state-of-the-art visible machine learning algorithms.
DEVELOPMENTAL ULTRASTRUTCTURE MICROSCOPY IN DRUG DISCOVERY FROM DIOSCOREA SPECIES
Authors: Odimegwu Joy Ifunanya , Sangwan Neelam Singh , Chanotiya C. S. , Steve Ogbonnia , Abiodun Odukoya Olukemi
Published: April 2023

Tubers of wild Dioscorea species (yam) are used as low-cost materials for the synthesis of steroids; cortisone and progesterone using the Marker Degradation chemical route. Decoctions from yam leaves and tubers are also used in ethnomedicine for regulating female fertility and alleviating painful periods and menopausal symptoms. It is now known that yam tuber extracts reduce and inhibit the proliferative action of breast cancer cells and reverse cardiovascular diseases.

Due to current urgent needs and global interest in plants’ biodiversity advancement and drug discovery importance:Dioscorea compositaandDioscorea floribundashoots were studied with Scanning Electron Microscopy (SEM) to detect anatomical types of trichomes compared to essential oil production as integrated into the ontogeny of the studied shoots and hydro-distilled oils from the same organs were characterized with Gas Chromatography/Mass Spectrometry (GC/MS).

The SEM study revealed the presence of oil glands, the capitate type on the epidermal layers of parts studied which GC/MS analysis further revealed the components of the oils on the leaves to be Farnesene, Citronellyl acetate, Terpinene, Elemol, Nerolidol, Farnesol and Valerenyl acetate. This is the first time these phytoconstituents are reported in the species. In this light, microscopical methods supported by chromatography contribute to the rapid identification of novel lead compounds contributing to important drug discovery.
Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon
Authors: Deng Pujuan , Tan Shun-Qing , Yang Qi-Yu , Zhu Han-Zhou , Sun Lei , Bao Zhangbin , Lin Yi , Zhang Qiangfeng Cliff , Wang Jia , Liu Jun-Jie Gogo
Published: April 2023

Retroelements are the widespread jumping elements considered as major drivers for genome evolution, which can also be repurposed as gene-editing tools. Here, we determined the cryo-EM structures of eukaryotic R2 retrotransposon with ribosomal DNA target and regulatory RNAs. Combined with biochemical and sequencing analysis, we revealed two essential DNA regions, Drr and Dcr, required for R2 recognition and cleavage. The association of 3’ regulatory RNA with R2 protein accelerates the first-strand cleavage, blocks the second-strand cleavage, and initiates the reverse transcription starting from the polyA tail. Removing 3’ regulatory RNA by reverse transcription allows the association of 5’ regulatory RNA and initiates the second-strand cleavage. Our work explained the DNA recognition and supervised sequential retrotransposition mechanisms by R2 machinery, providing novel insights into the retrotransposon and application reprogramming.
scSPARKL: Apache Spark based parallel analytical framework for the downstream analysis of scRNA-seq data
Authors: Adil Asif , Bhattacharya Namrata , Asger Mohammed
Published: April 2023

As the field of single-cell genomics continues to develop, the generation of large-scale scRNA-seq datasets has become more prevalent. While these datasets offer tremendous potential for shedding light on the complex biology of individual cells, the sheer volume of data presents significant challenges for management and analysis. To address these challenges, a new discipline, known as “big single-cell data science,” has emerged. Within this field, a variety of computational tools have been developed to facilitate the processing and interpretation of scRNA-seq data. In this paper, we present a novel parallel analytical framework, scSPARKL, that leverages the power of Apache Spark to enable the efficient analysis of single-cell transcriptomic data. Our methodology incorporates six key operations for dealing with single-cell Big Data, including data reshaping, data preprocessing, cell/gene filtering, data normalization, dimensionality reduction, and clustering. By utilizing Spark’s unlimited scalability, fault tolerance, and parallelism, scSPARKL enables researchers to rapidly and accurately analyze scRNA-seq datasets of any size. We demonstrate the utility of our framework through a series of experiments on simulated and real-world scRNA-seq data. Overall, our results suggest that scSPARKL represents a powerful and flexible tool for the analysis of single-cell transcriptomic data, with broad applications across the fields of biology and medicine.
The BTB-ZF geneBm-mamoregulates pigmentation in silkworm caterpillars
Authors: Wu Songyuan , Tong Xiaoling , Peng Chenxing , Luo Jiangwen , Zhang Chenghao , Lu Kunpeng , Li Chunlin , Ding Xin , Duan Xiaohui , Lu Yaru , Hu Hai , Tan Duan , Dai Fangyin
Published: April 2023

The color pattern of insects is one of the most diverse adaptive evolutionary phenotypes. However, the molecular regulation of this color pattern is not fully understood. In this study, we found that the transcription factor Bm-mamo is responsible forblack dilute(bd) allele mutations in the silkworm. Bm-mamo belongs to the BTB zinc finger family and is orthologous to mamo inDrosophila melanogaster. This gene has a conserved function in gamete production inDrosophilaand silkworms and has evolved a pleiotropic function in the regulation of color patterns in caterpillars. Using RNAi and clustered regularly interspaced short palindromic repeats (CRISPR) technology, we showed that Bm-mamo is a repressor or has dark melanin patterns in the larval epidermis. Using in vitro binding assays and gene expression profiling in wild-type and mutant larvae, we also showed thatBm-mamolikely regulates the expression of related pigment synthesis and cuticular protein genes in a coordinated manner to mediate its role in color pattern formation. This mechanism is consistent with the dual role of this transcription factor in regulating both the structure and shape of the cuticle and the pigments that are embedded within it. This study provides new insight into the regulation of color patterns as well as into the construction of more complex epidermis features in some insects.
Extensive genetic variation of leaf specialized metabolites in sessile oak (Quercus petraea) populations
Authors: Coq--Etchegaray Domitille , Bernillon Stéphane , Le-Provost Grégoire , Kremer Antoine , Ducousso Alexis , Lalanne Céline , Bonne Fabrice , Moing Annick , Plomion Christophe , Brachi Benjamin
Published: April 2023

Specialized or secondary metabolites play a key role in plant resistance against abiotic stresses and defences against bioaggressors. For example, in sessile oaksQuercus petraea, phenolics contribute to reduce herbivore damage and improve drought resistance. Here, we explored the natural variation of specialized metabolites in nine European provenances of sessile oaks and aimed to detect its underlying genetic bases. We sampled mature leaves from high and low branches on 225 sessile oak trees located in a common garden and used untargeted metabolomics to characterise the variation of 217 specialized metabolites. In addition, we used whole genome low-depth sequencing to genotype individuals for 1.4M genetic markers. We found that leaf specialized metabolites displayed extensive within-provenance variation, but very little differentiation between provenances. In addition, a genome-wide association study allowed detecting significant associations for 42% of these metabolites. Hence, our results suggest that genetic variation for most leaf specialized metabolites is unlikely to be locally adaptive, however lack of differentiation among populations suggests selection acts locally to maintain diversity at loci associated with leaf specialized metabolites variation.
The origin of a mountain biota: hyper-aridity shaped reptile diversity in an Arabian biodiversity hotspot
Authors: Burriel-Carranza Bernat , Tejero-Cicuéndez Héctor , Carné Albert , Riaño Gabriel , Talavera Adrián , Saadi Saleh Al , Els Johannes , Šmíd Jiří , Tamar Karin , Tarroso Pedro , Carranza Salvador
Published: April 2023

Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These include from broad biogeographic patterns, to population dynamics and adaptations to these environments. However, significant challenges remain in integrating these large-scale and fine-scale findings to develop a comprehensive understanding of mountain biodiversity. One significant challenge is the lack of genomic data, particularly in historically understudied arid regions where reptiles are a particularly diverse vertebrate group. We generatedde novogenome-wide SNP data for more than 600 specimens and integrated state-of-the-art biogeographic analyses at the community, species and population level. We, thus, provide for the first time, a holistic integration of how a whole endemic reptile community has originated, diversified and dispersed through a mountain range. Our results show that reptiles independently colonized the Hajar Mountains of eastern Arabia 11 times. After colonization, species delimitation methods suggest high levels of within-mountain diversification, supporting up to 49 putative species. This diversity is strongly structured following local topography, with the highest peaks acting as a broad barrier to gene flow among the entire community. Surprisingly, orogenic events do not seem to rise as key drivers of the biogeographic history of reptiles in this system. However, paleoclimate seems to have had a major role in this community assemblage. We observe an increase of vicariant events from Late Pliocene onwards, coinciding with an unstable climatic period of rapid shifts between hyper-arid to semiarid conditions that led to the ongoing desertification of Arabia. We conclude that paleoclimate, and particularly extreme aridification, acted as a main driver of diversification in arid mountain systems which is tangled with the generation of highly adapted endemicity. Our study provides a valuable contribution to understanding the evolution of mountain biodiversity and the role of environmental factors in shaping the distribution and diversity of reptiles in arid regions.
Reversal learning of visual cues in Heliconiini butterflies
Authors: Young Fletcher J. , Melo-Flórez Lina , McMillan W. Owen , Montgomery Stephen H.
Published: April 2023

The mushroom bodies, an integrative region of the insect brain involved in learning and memory, have undergone volumetric increase in several independent lineages includes bees and ants, cockroaches and some beetles. However, the selective pressures driving these expansion events are not fully understood. One promising system for investigating this question is the Neotropical butterfly genusHeliconius, which exhibits markedly enlarged mushroom bodies compared with other members of the Heliconiini tribe. Notably, this neural elaboration co-occurs with the evolution of trapline foraging behaviour and an improved capacity for learning complex visual cues and long-term memory. Here, we further investigate the behavioural consequences of this brain expansion by testing reversal learning ability, a commonly used measure of cognition and behavioural flexibility in both vertebrates and invertebrates, across threeHeliconiusand three closely-related Heliconiini species. We trained butterflies to associate a food reward with either purple or yellow flowers, before training them with the reversed associations, and then reversing the cues again. All six successfully learned the reversed cues, and, contrary to our expectations, we found no evidence thatHeliconiusperformed better than the other Heliconiini species. These results are surprising, given previous evidence linking the mushroom bodies to reversal learning in other insects, and the enhanced performance ofHeliconiusin other cognitive tests. This serves as a reminder that the functional consequences of brain expansion can be multifaceted, and do not necessarily result in an overall increase in general cognitive ability, but rather enhanced performance in specific, ecologically-relevant tasks.
Gut barrier defects, increased intestinal innate immune response, and enhanced lipid catabolism drive lethality inN-glycanase 1 deficientDrosophila
Authors: Pandey Ashutosh , Galeone Antonio , Han Seung Yeop , Story Benjamin A , Consonni Gaia , Mueller William F , Steinmetz Lars M , Vaccari Thomas , Jafar-Nejad Hamed
Published: April 2023

Intestinal barrier dysfunction leads to inflammation and associated metabolic changes. However, the relative impact of infectious versus non-infectious mechanisms on animal health in the context of barrier dysfunction is not well understood. Here, we establish that loss ofDrosophila N-glycanase 1 (Pngl) leads to gut barrier defects, which cause starvation and increased JNK activity. These defects result in Foxo overactivation, which induces a hyperactive innate immune response and lipid catabolism, thereby contributing to lethality associated with loss ofPngl. Notably, germ-free rearing ofPnglmutants did not rescue lethality. In contrast, raisingPnglmutants on isocaloric, fat-rich diets improved animal survival in a dosage-dependent manner. Our data indicate that Pngl functions inDrosophilalarvae to establish the gut barrier, and that the immune and metabolic consequences of loss ofPnglare primarily mediated through non-infectious mechanisms.
Repurposing the Memory-promoting Meclofenoxate Hydrochloride as a Treatment for Parkinson‘s Disease through Integrative Multi-omics analysis
Authors: Zhang Huasong , Fan Cong , Li Ling , Liu Feiyi , Li Shaoying , Ma Linyun , Yang Yuanhao , Cooper David N. , Yang Yuedong , Hu Ronggui , Zhao Huiying
Published: April 2023

Parkinson‘s disease (PD) is a devastating neurodegenerative disorder with growing prevalence worldwide and, as yet, no effective treatment. Drug repurposing promises to be invaluable for the identification of novel therapeutics for the treatment of PD due to the associated shortened drug development time, fewer safety concerns, and reduced costs. Here, we compiled gene expression data from 1,231 healthy human brains and 357 PD patients across ethnicities, brain regions, Braak stages, and disease status. By integrating them with multiple-source PD-associated genomic data, we found a conserved PD-associated gene co-expression module, and its alignment with the CMAP database successfully identified 15 drug candidates. Among these, we selected meclofenoxate hydrochloride (MH) and sodium phenylbutyrate (SP) for experimental validation because they are capable of passing through the blood brain barrier. In primary neurons, MH was found to prevent the neuronal death and synaptic damage associated with PD and to reverse the abnormal mitochondrial metabolism caused by PD. In hippocampal tissues, MH and SP were found to prevent the destruction of mitochondria, to reduce lipid peroxidation and to protect dopamine synthesis by PET-CT examination, malondialdehyde (MAD) testing and glutathione (GSH) testing, and immunohistochemical tests. Finally, MH was found to have the ability to improve gait behavior, and reduce anhedonic and depressive-like behaviors that are characteristics of PD mice. Taken together, our findings support the contention that MH may have the potential to ameliorate PD by improving mitochondrial metabolism and brain function.
Predictive power of non-identifiable models
Authors: Grabowski Frederic , Nałęcz-Jawecki Paweł , Lipniacki Tomasz
Published: April 2023

Resolving practical nonidentifiability of computational models typically requires either additional data or non-algorithmic model reduction, which frequently results in models containing parameters lacking direct interpretation. Here, instead of reducing models, we explore an alternative, Bayesian approach, and quantify predictive power of non-identifiable models. Considering an example biochemical signalling cascade model as well as its mechanical analog, we demonstrate that by measuring a single variable in response to a properly chosen stimulation protocol, the dimensionality of the parameter space is reduced, which allows for prediction of its trajectory in response to different stimulation protocols even if all model parameters remain unidentified. Successive measurements of remaining variables further constrain model parameters and enable more predictions. We analyse potential pitfalls of the proposed approach that can arise when the investigated model is oversimplified, incorrect, or when the training protocol is inadequate. The main advantage of the suggested iterative approach is that the predictive power of the model can be assessed and practically utilised at each step.
Allele pairing at Sun1-enriched domains at the nuclear periphery viaT1A3tandem DNA repeats
Authors: Balasooriya Gayan I. , Spector David L.
Published: April 2023

Spatiotemporal gene regulation is fundamental to the biology of diploid cells. Therefore, effective communication between two alleles and their geometry in the nucleus is important. However, the mechanism that fine-tunes the expression from each of the two alleles of an autosome is enigmatic. Establishing an allele-specific gene expression visualization system in living cells, we show that alleles of biallelically expressedCthandTtc4genes are paired prior to acquiring monoallelic expression. We found that active alleles of monoallelic genes are preferentially localized at Sun1-enriched domains at the nuclear periphery. These peripherally localized active DNA loci are enriched with adenine-thymidine-rich tandem repeats that interact with Hnrnpd and reside in a Hi-C-defined A compartment within the B compartment. Our results demonstrate the biological significance ofT1A3tandem repeat sequences in genome organization and how the regulation of gene expression, at the level of individual alleles, relates to their spatial arrangement.
Late gene therapy limits the restoration of retinal function in a mouse model of retinitis pigmentosa
Authors: Scalabrino Miranda L. , Thapa Mishek , Wang Tian , Sampath Alapakkam P. , Chen Jeannie , Field Greg D.
Published: April 2023

Retinitis pigmentosa is an inherited photoreceptor degeneration that begins with rod loss followed by cone loss and eventual blindness. Gene therapies are being developed, but it is unknown how retinal function depends on the time of intervention. To uncover this dependence, we utilized a mouse model of retinitis pigmentosa capable of artificial genetic rescue. This model enables a benchmark of best-case gene therapy by removing the variables that complicate the ability to answer this vital question. Complete genetic rescue was performed at 25%, 50%, and 70% rod loss (early, mid and late, respectively). Early and mid treatment restored retinal function to near wild-type levels, specifically the sensitivity and signal fidelity of retinal ganglion cells (RGCs), the ‘output’ neurons of the retina. However, some anatomical defects persisted. Late treatment retinas exhibited continued, albeit slowed, loss of sensitivity and signal fidelity among RGCs, as well as persistent gliosis. We conclude that gene replacement therapies delivered after 50% rod loss are unlikely to restore visual function to normal. This is critical information for administering gene therapies to rescue vision.
Determinants of cytoplasmic microtubule depolymerization during ciliogenesis inChlamydomonas reinhardtii
Authors: Dougherty Larissa L , Avasthi Prachee
Published: April 2023

At the core of cilia are microtubules which are important for establishing length and assisting ciliary assembly and disassembly; however, another role for microtubule regulation on ciliogenesis lies outside of the cilium. The microtubule cytoskeleton is a highly dynamic structure which polymerizes and depolymerizes rapidly to assist in cellular processes. These processes have been studied across various organisms with chemical as well as genetic perturbations. However, these have generated conflicting data in terms of the role of cytoplasmic microtubules (CytoMTs) and free tubulin dynamics during ciliogenesis. Here we look at the relationship between ciliogenesis and cytoplasmic microtubule dynamics inChlamydomonas reinhardtiiusing chemical and mechanical perturbations. We find that not only can stabilized CytoMTs allow for normal ciliary assembly, but high calcium concentrations and low pH-induced deciliation cause CytoMTs to depolymerize separately from ciliary shedding. In addition, we find that ciliary shedding through mechanical shearing, cilia regenerate earlier despite intact CytoMTs. Our data suggests that cytoplasmic microtubules are not a sink for a limiting pool of cytoplasmic tubulin inChlamydomonas, depolymerization that occurs following deciliation is a consequence rather than a requirement for ciliogenesis, and intact CytoMTs in the cytoplasm and the proximal cilium support more efficient ciliary assembly.
Evolution of neuronal cell classes and types in the vertebrate retina
Authors: Hahn Joshua , Monavarfeshani Aboozar , Qiao Mu , Kao Allison , Kölsch Yvonne , Kumar Ayush , Kunze Vincent P , Rasys Ashley M. , Richardson Rose , Baier Herwig , Lucas Robert J. , Li Wei , Meister Markus , Trachtenberg Joshua T. , Yan Wenjun , Peng Yi-Rong , Sanes Joshua R. , Shekhar Karthik
Published: April 2023

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.
Genomic language model predicts protein co-regulation and function
Authors: Hwang Yunha , Cornman Andre L. , Kellogg Elizabeth H. , Ovchinnikov Sergey , Girguis Peter R.
Published: April 2023

Deciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-function paradigm from massive protein sequence datasets. However, to date, limited attempts have been made in extending this continuum to include higher order genomic context information. Evolutionary processes dictate the specificity of genomic contexts in which a gene is found across phylogenetic distances, and these emergent genomic patterns can be leveraged to uncover functional relationships between gene products. Here, we trained a genomic language model (gLM) on millions of metagenomic scaffolds to learn the latent functional and regulatory relationships between genes. gLM learns contextualized protein embeddings that capture the genomic context as well as the protein sequence itself, and encode biologically meaningful and functionally relevant information (e.g. enzymatic function, taxonomy). Our analysis of the attention patterns demonstrates that gLM is learning co-regulated functional modules (i.e. operons). Our findings illustrate that gLM’s unsupervised deep learning of the metagenomic corpus is an effective and promising approach to encode functional semantics and regulatory syntax of genes in their genomic contexts and uncover complex relationships between genes in a genomic region.
Pancreatic loss of Mig6 alters murine endocrine cell fate and protects functional beta cell mass in an STZ-induced model of diabetes
Authors: Bauer Brandon M. , Irimia Jose M. , Bloom-Saldana Elizabeth , Jeong Jae-Wook , Fueger Patrick T.
Published: April 2023

Background

Maintaining functional beta cell mass (BCM) to meet glycemic demands is essential to preventing or reversing the progression of diabetes. Yet the mechanisms that establish and regulate endocrine cell fate are incompletely understood. We sought to determine the impact of deletion of mitogen-inducible gene 6 (Mig6), a negative feedback inhibitor of epidermal growth factor receptor (EGFR) signaling, on mouse endocrine cell fate. The extent to which loss of Mig6 might protect against loss of functional BCM in a multiple very low dose (MVLD) STZ-induced model of diabetes was also determined.

Methods

Ten-week-old male mice with whole pancreas (Pdx1:Cre, PKO) and beta cell-specific (Ins1:Cre, BKO) knockout of Mig6 were used alongside control (CON) littermates. Mice were given MVLD STZ (35 mg/kg for five days) to damage beta cells and induce hyperglycemia. In vivo fasting blood glucose and glucose tolerance were used to assess beta cell function. Histological analyses of isolated pancreata were utilized to assess islet morphology and beta cell mass. We also identified histological markers of beta cell replication, dedifferentiation, and death. Isolated islets were used to reveal mRNA and protein markers of beta cell fate and function.

Results

PKO mice had significantly increased alpha cell mass with no detectable changes to beta or delta cells. The increase in alpha cells alone did not impact glucose tolerance, BCM, or beta cell function. Following STZ treatment, PKO mice had 18±8% higher BCM than CON littermates and improved glucose tolerance. Interestingly, beta cell-specific loss of Mig6 was insufficient for protection, and BKO mice had no discernable differences compared to CON mice. The increase in BCM in PKO mice was the result of decreased beta cell loss and increased beta cell replication. Finally, STZ-treated PKO mice had more Ins+/Gcg+ bi-hormonal cells compared to controls suggesting alpha to beta cell trans differentiation.

Conclusions

Mig6 exerted differential effects on alpha and beta cell fate. Pancreatic loss of Mig6 reduced beta cell loss and promoted beta cell growth following STZ. Thus, suppression of Mig6 may provide relief of diabetes.
A correlative study of the genomic underpinning of virulence traits and drug tolerance ofCandida auris
Authors: Yang Bo , Vaisvil Benjamin , Schmitt Daniel , Collins Joseph , Young Eric , Kapatral Vinayak , Rao Reeta
Published: April 2023

Candida aurisis an opportunistic fungal pathogen with high mortality rates that presents a clear and present threat to public health. The risk ofC. aurisinfection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well-known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns ofC. auriscarbon metabolism, drug resistance, and macrophage interaction. We chose to study twoC. aurisisolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we found that B11220 was missing a 12.8 kb gene cluster encoding proteins related to alternative sugar utilization, possibly L-rhamnose. We show that B11221, which has the cluster, more readily assimilates and utilizes D-galactose and L-rhamnose. B11221 also exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both strains grown on glucose or galactose showed that genes associated with translation were upregulated in B11221, and the putative L-rhamnose gene cluster was upregulated when grown on D-galactose. These findings reinforce the growing evidence of a link between metabolism and tolerance. Since immune system evasion depends heavily on the cell surface, we characterized cell wall composition and macrophage evasion for the two strains. We found that B11221 has far less β-1,3-glucan exposure, a key determinant of immune system evasion, and resists phagocytosis by macrophages compared to B11220. In a transcriptomic analysis of both strains co-cultured with macrophages we found that B11221 upregulates genes associated with early stages of growth and transcription factors that regulate transport. These key differences in growth and membrane composition could explain the resistance to phagocytosis and increased stress tolerance in general of B11221, and indicates another connection between metabolism and immune system evasion. Taken together, these data show that membrane composition, metabolism, and transport all correlate with colonization, drug resistance, and immune system evasion inC. auris.
Ticks (Acari: Ixodida) on synanthropic small and medium-sized mammals in areas of the northeastern United States infested with the Asian longhorned tick,Haemaphysalis longicornis
Authors: Ferreira Francisco C. , González Julia , Milholland Matthew T. , Tung Grayson A. , Fonseca Dina M.
Published: April 2023

The northeastern United States is a hot spot for tick-borne diseases. Adding to an already complex vector landscape, in 2017 large populations of the invasiveHaemaphysalis longicornis, the Asian longhorned tick, were detected in New Jersey (NJ) and later found to be widespread from Connecticut to Georgia. In its native range in northeastern Asia,H. longicornisis considered an important vector of deadly pathogens to humans, companion animals, and livestock. To identify the primary hosts ofH. longicorniswe surveyed synanthropic small and medium-sized mammals in three different sites in suburban New Brunswick, NJ. Specifically, we collected approximately 9,000 tick specimens belonging to nine species from 11 different species of mammals sampled between May and September 2021. We found thatH. longicornisfeeds more frequently on rodents than previously thought, and that this invasive tick is likely exposed to important enzootic and zoonotic pathogens. Overall, we obtained detailed information about the seasonal dynamics and feeding patterns of six tick species common in the northeastern US,Haemaphysalis longicornis,Amblyomma americanum, Dermacentor variabilis, Ixodes scapularis, I. texanusandI. cookei. We found that unlikeI. scapularisthat feeds on mammals of all sizes,H. longicornisfeeds on hosts following the general pattern ofA. americanum, favoring larger species such as skunks, groundhogs, and raccoons. However, our survey revealed that unlikeA. americanum,H. longicornisreaches high densities on Virginia opossum. Overall, the newly invasiveH. longicorniswas the most abundant tick species both on multiple host species and in the environment, raising significant questions regarding its role in the epidemiology of tick-borne pathogens, especially those affecting livestock, companion animals and wildlife. In conclusion, our findings provide valuable insights into the tick species composition on mammal hosts in New Jersey and the ongoing national expansion ofH. longicornis.
Δ246p53 is a new p53 isoform that responds to DNA damage and regulates tumour growth
Authors: Parkar Shrutee N. , López-Iniesta Maria José , Ramalho Ana Catarina , Kimura Koto , Zhao Jingyuan , da Silva Rita Filipa , Romão Luísa , Candeias Marco M
Published: April 2023

p53is with little doubt one of the most powerful genes in our genome, as it makes growthvsarrest, repairvsreplacement, metabolismvsanabolism, lifevsdeath decisions in the cell. One wrong action and a healthy cell is lost or transforms into cancer. So it is not surprising thatp53is also one of the most tightly regulated and complex genes.p53alone encodes for more than 10 RNA variants and 15 different protein forms. Here we identify yet another p53 protein isoform of around 18 KDa that we named Δ246p53. Δ246p53 is translated from an alternative translation initiation site (TIS) in codon 246. TIS-246 is preceded by a strong Kozak sequence and seems to be conserved in vertebrates, from sea lamprey to humans. Δ246p53’s origin and expression in cells were confirmed by frameshift and start codon mutations as well as siRNA and an antisense oligo targeting TIS-246, which knocked-down Δ246p53 with little or no effect on full-length (FL) p53 protein levels. Δ246p53 was induced by DNA damage in several cell lines tested and triggered senescence and impaired tumour formation/growth in colony formation assays. Lastly, we show that Δ246p53 binds to FLp53 and affects the transactivation ofp21, a known senescence activator. Our results add a new piece to the centre of the p53 puzzle, a previously unreported inside regulator of p53, which in the future may help us better understand p53’s still mystifying role in senescence and ageing.
DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins
Authors: Kong Shuyao , Zhu Mingyuan , Scarpin M. Regina , Pan David , Jia Longfei , Martinez Ryan E. , Alamos Simon , Vadde Batthula Vijaya Lakshmi , Garcia Hernan G. , Qian Shu-Bing , Brunkard Jacob O. , Roeder Adrienne H. K.
Published: April 2023

Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutantdevelopment related myb-like1(drmy1), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show thatdrmy1has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.