bluuebunny/crossref_metadata_2025 huggingface dataset:
Concurrent Benign Iodine-Avid Thymic and Liver Cysts Mimicking Metastatic Disease on 131I Whole-Body Scintigraphy
Authors: Kamarulzaman Kamalia , Mohd Rohani Mohd Fazrin , Mat Nawi Norazlina , Amir Hassan Siti Zarina
Published: February 2024

A 57-year-old woman received radioiodine therapy post total thyroidectomy for pT3aNxMx follicular thyroid carcinoma. Posttherapy 131I whole-body scan showed 131I concentration in the chest, mediastinum, and left upper thigh with stimulated thyroglobulin (Tg) of 89 μg/L. Subsequent radioiodine therapies showed persistent 131I accumulation in the anterior mediastinal soft tissue lesions and a hypodense segment VII liver lesion visualized on SPECT/CT, suggestive of iodine-avid metastatic disease despite the undetectable serum Tg (<1.0 μg/L) with no Tg antibody interference. Biopsy of the liver lesion revealed liver cyst, and consequent removal of the mediastinal lesions showed benign thymic cysts.
Misleading FDG Uptake in Oncology Assessment
Authors: Moreau Aurélie , Mognetti Thomas , Kryza David
Published: February 2024

Here, we report the case of a 35-year-old woman who performed PET/CT 18F-FDG as an initial workup for HER2+ right breast invasive ductal carcinoma. Examination revealed multifocal breast involvement with homolateral lymph node involvement. Contralateral axillary adenopathy and diffuse splenic and osteomedullary hypermetabolism were also observed, suggesting associated lymphoma in the absence of a recent COVID-19 vaccination. Cytopuncture was discussed and finally postponed after the patient was found to have recently received a pneumococcal vaccination.
Clinical Efficacy of Modified Nonmesh Sacral Colpopexy for Pelvic Organ Prolapse
Authors: Zhao Jinchai , Liu Yibin , Cui Lili , Sun Xianghang , Meng Li , Zhao Yi , Zhou Xiaoyuan , Huang Xianghua
Published: February 2024

Importance

As an increasing number of mesh-related complications have been reported, the availability of nonmesh alternatives becomes crucial for situations where mesh is not desired or unavailable. A new modified procedure of nonmesh laparoscopic sacral colpopexy (LSC) was performed in our department, which used a nonabsorbable polyester suture (Ethibond) combined with uterosacral ligament suspension.

Objective

The aim of this study was to evaluate the clinical efficacy of the modified procedure in comparison with traditional LSC in patients with pelvic organ prolapse.

Methods

This retrospective study assessed the treatment outcomes of 60 patients who were underwent LSC with or without mesh from January 2017 to April 2019. Patients were divided into 2 groups based on the presence or absence of mesh during the operation: mesh group (n = 34) and nonmesh group (n = 26). General data, perioperative indexes, postoperative complications, and recurrence rates were comparatively analyzed between 2 groups.

Results

In perioperative indexes, the nonmesh group exhibited shorter operation time (P < 0.001) and less intraoperative blood loss compared with the mesh group (P = 0.004). There was no significant difference in postoperative indwelling urinary catheter duration (P = 0.425) and hospitalization time (P = 0.827) between the 2 groups. In postoperative complications, the incidence of postoperative complications showed no significant difference between the 2 groups (P > 0.05). No occurrences of mesh exposure and erosion were observed in the mesh group during at least a 2-year follow-up period. In postoperative recurrence, none of the patients in either group experienced prolapse recurrence.

Conclusions

In comparison with the traditional LSC with mesh, the modified laparoscopic nonmesh sacral colpopexy presents advantages of reduced surgical trauma, less pain, and lower cost. However, a long-term and large sample study is required for evaluating the surgery’s long-term efficacy.
Vesicovaginal Fistula Repair Simulation Model and Hierarchical Task Analysis
Authors: Kent Laura M. , Vinas Emily K. , Rieger Mary M. , Caldwell Lauren , White Amanda B. , High Rachel A.
Published: February 2024

Importance

There is a need for surgeons skilled in vesicovaginal fistula (VVF) repair, yet training opportunities are limited.

Objectives

This study aimed to create a low-fidelity simulation model for transvaginal VVF repair, identify essential steps of VVF repair, and evaluate the model's ability to replicate essential steps.

Study Design

First, a low-fidelity VVF repair simulation model was designed and built by the authors. Next, a hierarchical task analysis was performed by urogynecologic surgeons with expertise in VVF repair. Each expert submitted an outline of tasks required to perform VVF repair. To control for bias, an education specialist de-identified, reviewed, and collated the submitted outlines. The education specialist then led a focus group, and through a modified Delphi process, the experts reached consensus on the essential steps. A separate group of urogynecologic surgeons then tested the model and completed an anonymous questionnaire assessing how well the model replicated the essential steps. Descriptive analyses were performed.

Results

Five experts submitted an outline of steps for transvaginal VVF repair, and 4 experts participated in a focus group to reach consensus on the essential steps. Nine urogynecologic surgeons, with a median of 10 years in practice (interquartile range, 7–12 years), tested the model and completed the postsimulation questionnaire. Most testers thought that tasks involving identification and closure of the fistula were replicated by the model. Testers thought that tasks involving cystoscopy or bladder filling were not replicated by the model.

Conclusions

We developed a novel, low-fidelity transvaginal VVF repair simulation model that consistently replicated tasks involving identification and closure of the fistula.
Source Localization of Normal Variants Seen on EEG
Authors: Rahman Shareena , Burch Michael , Parikh Prachi , Zafar Muhammad
Published: February 2024

Purpose:

The EEG is an essential neurological diagnostic tool. EEG abnormalities can guide diagnosis and management of epilepsy. There are also distinctive EEG waveforms that are seen in healthy individuals. It is critical not to misinterpret these as abnormal. To emphasize the importance of these waveforms, we analyzed different normal variants via the source localization technology.

Methods:

This is a retrospective analysis of EEGs performed at the Duke University Hospital between June 2014 and Dec 2019. We selected samples of vertex waves, Mu, lambda, POSTS, wickets, and sleep spindles for analysis. EEG were imported to Curry 8 (Compumedics) to calculate the dipole and current density. The averaged head model from the Montreal Neurological Institute database was used for reconstruction.

Results:

Thirty-four patient EEG samples were selected including five vertex, six Mu, four wicket, seven lambda, five POSTS, and seven spindles. Results from source localization showed that vertex waves are localized in the frontocentral area, whereas spindles in the deep midline central region. Mu were identified in the ipsilateral somatosensory cortex. Lambda and POSTS, on the other hand, had maximum results over the bilateral occipital region and wickets in the ipsilateral temporal lobe.

Conclusions:

Our results confirm and expand previous hypotheses. This allows us to speculate on the origin of these normal EEG variants. Although this study is limited by small sample size, lack of high-density EEG, and patient-specific MRI, our analysis provides an easily replicable three-dimensional visualization of these waveforms.
HIV combined with skin infection of Nocardia brasiliensis: A rare case report
Authors: XING YUN , Li Shilu
Published: February 2024

Introduction. The HIV virus can attack and gradually damage the human immune system, causing the host to be unprotected when infected. Nocardia is a type of opportunistic pathogenic bacteria that can easily cause infections in patients with chronic wasting diseases, immune dysfunction, and the use of immunosuppressants. Nocardia can invade various tissues and parts of the body, causing corresponding clinical symptoms. There are few reports of HIV patients being infected with Brazilian Nocardia.
 
Case presentation. This article reports a case of an HIV patient with concurrent infection with Brazilian Nocardia. A patient with HIV developed a lump on the surface of their left skin without any obvious cause. Due to improper disinfection and treatment methods, the condition worsened, and they subsequently sought medical attention at our hospital. A series of laboratory related tests are conducted clinically based on the patient's medical history, symptoms, and signs. Based on the test results, a reasonable treatment plan was adopted clinically, ultimately achieving satisfactory treatment outcomes for patients.
 
Conclusion . HIV patients are prone to various types of infections, even rare bacteria, as their immune function decreases. With the popularity of new identification methods such as mass spectrometry, laboratories should pay attention to traditional staining methods and use microscopes to detect pathogens.
A simple, robust, broadly applicable insertion mutagenesis method to create random fluorescent protein – target protein fusions
Authors: Pike Andrew , Pietryski Cassandra , Deighan Padraig , Kuehner Jason , Lau Derek , Seshan Anupama , March Paul E.
Published: February 2024

A simple broadly applicable method was developed using anin vitrotransposition reaction followed by transformation intoEscherichia coliand screening plates for fluorescent colonies. The transposition reaction catalyzes the random insertion of a fluorescent protein open reading frame into a target gene on a plasmid. The transposition reaction is employed directly in anE. colitransformation with no further procedures. Plating at high colony density yields fluorescent colonies. Plasmids purified from fluorescent colonies contain random, in-frame fusion proteins into the target gene. The plate screen also results in expressed, stable proteins. A large library of chimeric proteins was produced that was useful for downstream research. The effect of using different fluorescent proteins was investigated as well as the dependence of linker sequence between the target and fluorescent protein open reading frames. The utility and simplicity of the method was demonstrated by the fact that it has been employed in an undergraduate biology laboratory class without failure over dozens of class sections. This suggests that the method will be useful in high impact research at small liberal arts colleges with limited resources. However, in frame fusion proteins were obtained from eight different targets suggesting that the method is broadly applicable in any research setting.

This report describes a simple screen to obtain random insertions of fluorescent proteins into a target protein of interest. The screen results in a useful library of mutated and functional tagged proteins that can be employed to investigate protein biochemical activity, protein structure, protein function and protein cellular localization. The screen is robust, generally applicable, and has been employed in an undergraduate laboratory class. It is also useful for studies in advanced research-intensive projects carried out in institutions of all types.

Graphical Abstract
Potential role of microRNAs in regulating transcriptional profile, and sculpting development and metabolism in cavefish
Authors: Biswas Tathagata , Hassan Huzaifa , Rohner Nicolas
Published: February 2024

Astyanax mexicanus, a species with both surface-dwelling and multiple cave-dwelling populations, offers a unique opportunity to study repeated adaptation to dark and resource-scarce environments. While previous work has identified large-scale changes in gene expression between morphs even under identical laboratory conditions, the regulatory basis of these expression differences remains largely unexplored. In this study, we focus on microRNAs (miRNAs) as key regulators of gene expression to understand cavefish adaptation nuances. Our analysis identified 683 miRNAs, which not only surpasses the number documented in related species but also provides the first comprehensive catalog of miRNAs for this species. We identified a unique subset of differentially expressed miRNAs common to all studied cave-dwelling populations, potentially orchestrating the nuanced gene expression patterns required for survival in the challenging cave milieu. Gene Ontology analysis of the predicted miRNA targets revealed involvement in developmental and metabolic pathways that are pivotal for thriving in nutrient-limited environments, such as the regulation of neuromast migration. Moreover, our study provides evidence for miRNA influence on circadian rhythm and oxidative stress response, both essential adaptations for the cave-dwelling lifestyle. The comprehensive miRNA catalog generated will guide future investigations into the intricate world of miRNA-mediated evolution of complex traits.
Perceptual and cognitive effects of focal tDCS of auditory cortex in tinnitus
Authors: Leaver Amber M.
Published: February 2024

OBJECTIVES

Noninvasive brain stimulation continues to grow as an effective, low-risk way of improving the symptoms of brain conditions. Transcranial direct current stimulation (tDCS) is particularly well-tolerated, with benefits including low cost and potential portability. Nevertheless, continued study of perceptual and cognitive side effects is warranted, given the complexity of functional brain organization. This paper describes the results of a brief battery of tablet-based tasks used in a recent pilot study of auditory-cortex tDCS in people with chronic tinnitus.

METHODS

Volunteers with chronic tinnitus (n=20) completed two hearing tasks (pure-tone thresholds, Words In Noise) and two cognitive tasks (Flanker, Dimension Change Card Sort) from the NIH Toolbox. Volunteers were randomized to active or sham 4×1 Ag/AgCl tDCS of auditory cortex, and tasks were completed immediately before and after the first tDCS session, and after the fifth/final tDCS session. Statistics included linear mixed-effects models for change in task performance over time.

RESULTS

Before tDCS, performance on both auditory tasks was highly correlated with clinical audiometry, supporting the external validity of these measures (r2>0.89 for all). Although overall auditory task performance did not change after active or sham tDCS, detection of right-ear Words in Noise stimuli modestly improved after five active tDCS sessions (t(34)=-2.07, p=0.05). On cognitive tasks, reaction times were quicker after sham tDCS, reflecting expected practice effects (e.g., t(88)=3.22, p=0.002 after 5 sessions on Flanker task). However, reaction times did not improve over repeated sessions in the active group, suggesting that tDCS interfered with learning these practice effects.

CONCLUSIONS

Repeated sessions of auditory-cortex tDCS does not appear to adversely affect hearing or cognition, but may modestly improve hearing in noisy environments and interfere with some types of motor learning. Low-burden cognitive/perceptual test batteries could be a powerful way to identify adverse effects and new treatment targets in brain stimulation research.
Calcium-driven In Silico Inactivation of a Human Olfactory Receptor
Authors: Pirona Lorenza , Ballabio Federico , Alfonso-Prieto Mercedes , Capelli Riccardo
Published: February 2024

Conformational changes as well as molecular determinants related to the activation and inactivation of olfactory receptors are still poorly understood due to the intrinsic difficulties in the structural determination of this GPCR family. Here, we perform, for the first time, thein silicoinactivation of the human olfactory receptor OR51E2, highlighting the possible role of calcium in this receptor state transition. Using molecular dynamics simulations, we show that a divalent ion in the ion binding site, coordinated by two acidic residues at positions 2.50 and 3.39 conserved across most ORs, stabilizes the receptor in its inactive state. In contrast, protonation of the same two acidic residues is not sufficient to drive inactivation within theµs timescale of our simulations. Our findings suggest a novel molecular mechanism for OR inactivation, potentially guiding experimental validation and offering insights into the possible broader role of divalent ions in GPCR signaling.
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
Authors: Hu Kaixin , Meyer Fernando , Deng Zhi-Luo , Asgari Ehsaneddin , Kuo Tzu-Hao , Münch Philipp C. , McHardy Alice C.
Published: February 2024

The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored for this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno, and Aytan-Aktug), an ML baseline, and the rule-based ResFinder by training and testing each of them across 78 species–antibiotic datasets, using a rigorous benchmarking workflow that integrates three evaluation approaches, each paired with three distinct sample splitting methods. Our analysis revealed considerable variation in the performance across techniques and datasets. Whereas ML methods generally excelled for closely related strains, ResFinder excelled for handling divergent genomes. Overall, Kover most frequently ranked top among the ML approaches, followed by PhenotypeSeeker and Seq2Geno2Pheno. AMR phenotypes for antibiotic classes such as macrolides and sulfonamides were predicted with the highest accuracies. The quality of predictions varied substantially across species–antibiotic combinations, particularly for beta-lactams; across species, resistance phenotyping of the beta-lactams compound, aztreonam, amox-clav, cefoxitin, ceftazidime, and piperacillin/tazobactam, alongside tetracyclines demonstrated more variable performance than the other benchmarked antibiotics. By organism,C. jejuniandE. faeciumphenotypes were more robustly predicted than those ofEscherichia coli,Staphylococcus aureus,Salmonella enterica,Neisseria gonorrhoeae,Klebsiella pneumoniae,Pseudomonas aeruginosa,Acinetobacter baumannii,Streptococcus pneumoniae, and Mycobacterium tuberculosis. In addition, our study provides software recommendations for each species–antibiotic combination. It furthermore highlights the need for optimization for robust clinical applications, particularly for strains that diverge substantially from those used for training.
Revision of splicing variants in theDMDgene
Authors: Davydenko Kseniya , Filatova Alexandra , Skoblov Mikhail
Published: February 2024

Background

Pathogenic variants in the dystrophin (DMD) gene lead to X-linked recessive Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Nucleotide variants that affect splicing are a known cause of hereditary diseases. However, their representation in the public genomic variation databases is limited due to the low accuracy of their interpretation, especially if they are located within exons. The analysis of splicing variants in theDMDgene is essential both for understanding the underlying molecular mechanisms of the dystrophinopathies’ pathogenesis and selecting suitable therapies for patients.

Results

Using deepin silicomutagenesis of the entireDMDgene sequence and subsequent SpliceAI splicing predictions, we identified 7,948DMDsingle nucleotide variants that could potentially affect splicing, 863 of them were located in exons. Next, we analyzed over 1,300 disease-associatedDMDSNVs previously reported in the literature (373 exonic and 956 intronic) and intersected them with SpliceAI predictions. We predicted that ∼95% of the intronic and ∼10% of the exonic reported variants could actually affect splicing. Interestingly, the majority (75%) of patient-derived intronic variants were located in the AG-GT terminal dinucleotides of the introns, while these positions accounted for only 13% of all intronic variants predictedin silico. Of the 97 potentially spliceogenic exonic variants previously reported in patients with dystrophinopathy, we selected 38 for experimental validation. For this, we developed and tested a minigene expression system encompassing 27DMDexons. The results showed that 35 (19 missense, 9 synonymous, and 7 nonsense) of the 38DMDexonic variants tested actually disrupted splicing. We compared the observed consequences of splicing changes between variants leading to severe Duchenne and milder Becker muscular dystrophy and showed a significant difference in their distribution. This finding provides extended insights into relations between molecular consequences of splicing variants and the clinical features.

Conclusions

Our comprehensive bioinformatics analysis, combined with experimental validation, improves the interpretation of splicing variants in theDMDgene. The new insights into the molecular mechanisms of pathogenicity of exonic single nucleotide variants contribute to a better understanding of the clinical features observed in patients with Duchenne and Becker muscular dystrophy.
Mechanically Tunable, Compostable, Healable and Scalable Engineered Living Materials
Authors: Manjula-Basavanna Avinash , Duraj-Thatte Anna M. , Joshi Neel S.
Published: February 2024

Novel design strategies are essential to realize the full potential of Engineered Living Materials (ELMs), including their biodegradability, manufacturability, sustainability, and ability to tailor functional properties. Toward these goals, we presentMechanicallyEngineered Living Material withCompostability,Healability, andScalability (MECHS) – a material that integrates these features in the form of a stretchable plastic that is simultaneously flushable, compostable, and exhibits the characteristics of paper. This plastic/paper-like material is produced directly from cultured bacterial biomass (40%) producing engineered curli protein nanofibers in scalable quantities (0.5-1 g L-1). The elongation at break (1-160%) and Young’s modulus (6-450 MPa) of MECHS was tuned to more than two orders of magnitude. By genetically encoded covalent crosslinking of curli nanofibers, we increase the Young’s modulus by two times. MECHS biodegrades completely in 15-75 days, while its mechanical properties are comparable to petrochemical plastics and thus may find use as compostable materials for primary packaging.
Depth-dependent scaling of axial distances in light microscopy
Authors: Loginov S.V. , Boltje D.B. , Hensgens M.N.F. , Hoogenboom J.P. , van der Wee E.B.
Published: February 2024

In volume fluorescence microscopy, refractive index matching is essential to minimize aberrations. There are however, common imaging scenarios, where a refractive index mismatch (RIM) between immersion and sample medium cannot be avoided. This RIM leads to an axial deformation in the acquired image data. Over the years, different axial scaling factors have been proposed to correct for this deformation. While some reports have suggested adepth-dependentaxial deformation, so far none of the scaling theories has accounted for a depth-dependent, non-linear scaling. Here, we derive an analytical theory based on determining the leading constructive interference band in the objective lens pupil under RIM. We then use this to calculate a depth-dependent re-scaling factor as a function of the numerical aperture (NA), the refractive indicesn1andn2, and the wavelengthλ. We compare our theoretical results with wave-optics calculations and experimental results obtained using a novel measurement scheme for different values of NA and RIM. As a benchmark, we recorded multiple datasets in different RIM conditions, and corrected these using our depth-dependent axial scaling theory. Finally, we present an online web applet that visualizes the depth-dependent axial re-scaling for specific optical setups. In addition, we provide software which will help microscopists to correctly re-scale the axial dimension in their imaging data when working under RIM.
Manipulation of the Nuclear Envelope-Associated Protein SLAP During Mammalian Brain Development Affects Cortical Lamination and Exploratory Behavior
Authors: Mestres Ivan , Atabay Azra , Escolano Joan-Carles , Arndt Solveig , Schmidtke Klara , Einsiedel Maximilian , Patsonis Melina , Castro Lizbeth Airais Bolanos , Yun Maximina , Bernhardt Nadine , Taubenberger Anna , Calegari Federico
Published: February 2024

Here we report the first characterization of the effects resulting from the manipulation of Soluble-Lamin Associated Protein (SLAP) expression during mammalian brain development. We found that SLAP localizes to the nuclear envelope and when overexpressed causes changes in nuclear morphology and lengthening of mitosis. SLAP overexpression in apical progenitors of the developing mouse brain altered asymmetric cell division, neurogenic commitment and neuronal migration ultimately resulting in unbalance in the proportion of upper, relative to deeper, neuronal layers. Several of these effects were also recapitulated upon Cas9-mediated knock-down. Ultimately, SLAP overexpression during development resulted in a reduction in subcortical projections of young mice and, notably, reduced their exploratory behavior. Our study shows the potential relevance of the previously uncharacterized nuclear envelope protein SLAP in neurodevelopmental disorders.
Distributional shifts change the biodiversity–ecosystem stability relationship under climate change
Authors: Kanamori Yuki , Nishijima Shota , Misawa Ryo , Seto Takashi , Narimatsu Yoji
Published: February 2024

Distributional shifts under climate change are increasingly recognized as a biotic change worldwide. However, the effects of distributional shifts on ecosystem variability through changes in biodiversity remain to be clariﬁed. In this study, to elucidate the impact of population-level distributional shifts under climate change on community structure and ecosystem function through ecological hierarchy, we investigated the temporal changes in alpha and beta diversity, the contribution of individual species to the observed changes in biodiversity, and the changes in the relationship between biodiversity and ecosystem variability, using over 25 years of data on about 700 species. We found that ecosystem variability was largely stabilized by beta diversity, especially in the present period (2012 to 2021), because beta diversity increased due to the invasion of species that were distributed mainly in tropic and subtropic areas. Despite the effect of beta diversity, ecosystem variability increased in the present period. This increase in ecosystem variability was caused by the spatially synchronized temporal variation in sea-bottom temperature, which resulted in synchronized temporal variation in species abundance among local communities, as well as the increased impact of alpha variability on ecosystem variability. These results indicate that the impact of alpha diversity on ecosystem variability is more changeable than the impact of beta diversity on ecosystem variability under climate change, suggesting the importance of focusing on changes in alpha diversity resulting from local colonization from other habitats and local extinction in existing habitats.
The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition
Authors: Kavaklıoğlu Gülnihal , Podhornik Alexandra , Vcelkova Terezia , Marjanovic Jelena , Beck Mirjam A. , Phan-Canh Trinh , Mair Theresia , Miccolo Claudia , Drino Aleksej , Doni Mirko , Egger Gerda , Chiocca Susanna , Modic Miha , Seiser Christian
Published: February 2024

Repression of retrotransposition is crucial for the successful fitness of a mammalian organism. The domesticated transposon protein L1TD1, derived from LINE-1 (L1) ORF1p, is an RNA-binding protein that is expressed only in some cancers and early embryogenesis. In human embryonic stem cells, it is found to be essential for maintaining pluripotency. In cancer, L1TD1 expression is highly correlative with malignancy progression and as such considered a potential prognostic factor for tumors. However, its molecular role in cancer remains largely unknown. Our findings reveal that DNA hypomethylation induces the expression of L1TD1 in HAP1 human tumor cells. L1TD1 depletion significantly modulates both the proteome and transcriptome and thereby reduces cell viability. Notably, L1TD1 associates with L1 transcripts and interacts with L1 ORF1p protein, thereby facilitating L1 retrotransposition. Our data suggest that L1TD1 collaborates with its ancestral L1 ORF1p as an RNA chaperone, ensuring the efficient retrotransposition of L1 retrotransposons, rather than directly impacting the abundance of L1TD1 targets. In this way, L1TD1 might have an important role not only during early development but also in tumorigenesis.
Global Release of Translational Repression AcrossPlasmodium’sHost-to-Vector Transmission Event
Authors: Rios Kelly T. , McGee James P. , Sebastian Aswathy , Moritz Robert L. , Feric Marina , Absalon Sabrina , Swearingen Kristian E. , Lindner Scott E.
Published: February 2024

Malaria parasites must be able to respond quickly to changes in their environment, including during their transmission between mammalian hosts and mosquito vectors. Therefore, before transmission, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. This essential regulatory control requires the orthologues of DDX6 (DOZI), LSM14a (CITH), and ALBA proteins to form a translationally repressive complex in female gametocytes that associates with many of the affected mRNAs. However, while the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. Moreover, the changes in spatial arrangement and composition of the DOZI/CITH/ALBA complex that contribute to translational control are also not known.

Therefore, we have conducted the first quantitative, comparative transcriptomics and DIA-MS proteomics ofPlasmodiumparasites across the host-to-vector transmission event to document the global release of translational repression. Using female gametocytes and zygotes ofP. yoelii, we found that nearly 200 transcripts are released for translation soon after fertilization, including those with essential functions for the zygote. However, we also observed that some transcripts remain repressed beyond this point. In addition, we have used TurboID-based proximity proteomics to interrogate the spatial and compositional changes in the DOZI/CITH/ALBA complex across this transmission event. Consistent with recent models of translational control, proteins that associate with either the 5’ or 3’ end of mRNAs are in close proximity to one another during translational repression in female gametocytes and then dissociate upon release of repression in zygotes. This observation is cross-validated for several protein colocalizations in female gametocytes via ultrastructure expansion microscopy and structured illumination microscopy. Moreover, DOZI exchanges its interaction from NOT1-G in female gametocytes to the canonical NOT1 in zygotes, providing a model for a trigger for the release of mRNAs from DOZI. Finally, unenriched phosphoproteomics revealed the modification of key translational control proteins in the zygote. Together, these data provide a model for the essential translational control mechanisms used by malaria parasites to promote their efficient transmission from their mammalian host to their mosquito vector.
Topology-informed regulatory element collections coordinate cell identity gene expression programs
Authors: Lv Jie , Maher Kelsey A. , Veluchamy Alaguraj , Kim Yuna , Dong Li , Ju Bensheng , Valentine Virginia , Valentine Marc , Burden Steven , Easton John , Pounds Stanley B. , Abraham Brian J
Published: February 2024

Cis-regulatory elements (CREs) contact target genes to regulate their transcription, but CRE interactions are complex and predicting their function is challenging. Contemporary approaches to predict CRE targets generally assume one-to-one associations and linear genomic proximity. These methods fail to account for long-range CRE contacts caused by folding of the genome, for circumstances in which a single CRE regulates multiple genes, or, conversely, when a single gene is regulated by multiple CREs. To address these challenges and investigate three-dimensional (3D) CRE communities, we developed BOUQUET, an integrative, graph-theory-based approach that uses multiple aspects of genome topology to probe communities of CREs, their bound apparatus, and their target genes. Using this approach, we uncover communities of CREs that are undetectable by existing unbiased methods, such as those with interactions that span insulating loop boundaries, and regulatory communities that comprise clustered promoter elements. A subset of these communities, which we term “3D super-enhancer CRE communities” (3DSE CRE communities), accrues exceptional amounts of regulatory apparatus at cell identity-defining genes and evolves the super-enhancer concept. In imaging assays, we observe co-localization and co-expression of in-community genes within puncta of transcriptional co-factors, consistent with microcompartment biology. Genome-wide, pairs of genes within the same 3D CRE community are co-expressed in single cells, and pairs of CREs are co-accessible, suggesting both chromatin activity and transcription within a topologically defined community is coordinated. Our model more accurately reflects the complexity of CRE interaction networks, underscores the need for approaches that incorporate spatial organization in the study of enhancer biology, and provides a framework for the reinterpretation of SEs, their condensates, and their target genes through the lens of 3D chromatin structure.
Tbx1 haploinsufficiency causes brain metabolic and behavioral anomalies in adult mice which are corrected by vitamin B12 treatment
Authors: Caterino Marianna , Paris Debora , Torromino Giulia , Costanzo Michele , Flore Gemma , Tramice Annabella , Golini Elisabetta , Mandillo Silvia , Cavezza Diletta , Angelini Claudia , Ruoppolo Margherita , Motta Andrea , Leonibus Elvira De , Baldini Antonio , Illingworth Elizabeth , Lania Gabriella
Published: February 2024

Introduction

The brain-related phenotypes observed in 22q11.2 deletion syndrome (22q11.2DS) are highly variable and their origin is poorly understood. Changes in brain metabolism may cause or contribute to the phenotypes, given that many of the deleted genes (approx. 10%) are implicated in metabolic processes, but this is currently unknown. It is clearly important to address this knowledge gap, but in humans, the primary material required for studying brain metabolism is inaccessible. For this reason, we sought to address the issue using two mouse models of 22q11.2DS.

Methods

We used three independent approaches to investigate brain metabolism in young adult mice, namely, mass spectrometry, nuclear magnetic resonance spectroscopy and transcriptomics. We selected to study primarilyTbx1single gene mutants because it is the primary candidate disease gene. We then confirmed key findings in the multi-gene deletion mutantDf1/+.

Results

We found thatTbx1mutants have alterations of specific brain metabolites, including methylmalonic acid, which is highly brain-toxic, as well as a more general metabolomic imbalance. We provide transcriptomic evidence of an interaction genotype-vB12 treatment, and behavioural evidence of a response to vB12 treatment, which rescued some of the behavioural anomaly observed inTbx1mutants. We conclude thatTbx1haploinsufficiency causes extensive brain metabolic anomalies, which are partially responsive to vB12 treatment. We suggest that alterations of glutamine-glutamate metabolism and fatty acid metabolism are key components of the metabolic phenotype in these mutants.
The role of NMDA receptors in memory and prediction in cultured neural networks
Authors: Lamberti Martina , van Putten Michel J.A.M. , Marzen Sarah , le Feber Joost
Published: February 2024

Memory has been extensively studied at the behavioural as well as the cellular level. Spike timing dependent plasticity (STDP) is associated with N-methyl-D-aspartate (NMDA) receptor activation and is widely accepted to be essential for long-term memory. However, experimental evidence remains sparse, probably due to the required complex combination of cellular and functional readouts. Recent work showed that in-vitro cortical networks memorize and predict inputs. The initial dependency of prediction on short-term memory decreased during the formation of long-term memory traces. Here, we stimulated in-vitro networks to investigate memory and prediction under control conditions, or under NMDA block. The NMDA anatagonist 2-amino-5-phosphonovaleric acid (APV) at a concentration that did not significantly reduce network excitability, but did impede long-term memory trace formation. In APV-treated cultures short-term memory of stimuli persisted, and they were still able to predict. In contrast to control cultures, prediction remained fully dependent on short-term memory. This confirms that NMDA receptor activation is essential for the formation of long-term memory traces and supports the notion that, as control cultures learn to memorize the stimulus, long-term memory starts to contribute to their predictive capability.
DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements
Authors: DaSilva Lucas Ferreira , Senan Simon , Patel Zain Munir , Reddy Aniketh Janardhan , Gabbita Sameer , Nussbaum Zach , Córdova César Miguel Valdez , Wenteler Aaron , Weber Noah , Tunjic Tin M. , Khan Talha Ahmad , Li Zelun , Smith Cameron , Bejan Matei , Louis Lithin Karmel , Cornejo Paola , Connell Will , Wong Emily S. , Meuleman Wouter , Pinello Luca
Published: February 2024

The challenge of systematically modifying and optimizing regulatory elements for precise gene expression control is central to modern genomics and synthetic biology. Advancements in generative AI have paved the way for designing synthetic sequences with the aim of safely and accurately modulating gene expression. We leverage diffusion models to design context-specific DNA regulatory sequences, which hold significant potential toward enabling novel therapeutic applications requiring precise modulation of gene expression. Our framework uses a cell type-specific diffusion model to generate synthetic 200 bp regulatory elements based on chromatin accessibility across different cell types. We evaluate the generated sequences based on key metrics to ensure they retain properties of endogenous sequences: transcription factor binding site composition, potential for cell type-specific chromatin accessibility, and capacity for sequences generated by DNA diffusion to activate gene expression in different cell contexts using state-of-the-art prediction models. Our results demonstrate the ability to robustly generate DNA sequences with cell type-specific regulatory potential. DNA-Diffusion paves the way for revolutionizing a regulatory modulation approach to mammalian synthetic biology and precision gene therapy.
Mice born preterm develop gait dystonia and reduced cortical parvalbumin immunoreactivity
Authors: Gemperli Kat , Folorunso Femi , Norin Benjamin , Joshua Rebecca , Hill Clayton , Rykowski Rachel , Galindo Rafael , Aravamuthan Bhooma R.
Published: February 2024

Preterm birth leading to cerebral palsy (CP) is the most common cause of childhood dystonia, a movement disorder that is debilitating and often treatment refractory. Dystonia has been typically associated with dysfunction of striatal cholinergic interneurons, but clinical imaging data suggests that cortical injury may best predict dystonia following preterm birth. Furthermore, abnormal sensorimotor cortex inhibition has been found in many studies of non-CP dystonias. To assess the potential for a cortical etiology of dystonia following preterm birth, we developed a new model of preterm birth in mice. Noting that term delivery in mice on a C57BL/6J background is embryonic day 19.1 (E19.1), we induced preterm birth at the limits of pup viability at embryonic day (E) 18.3, equivalent to human 22 weeks gestation. Mice born preterm demonstrate display clinically validated metrics of dystonia during gait (leg adduction amplitude and variability) and also demonstrate reduced parvalbumin immunoreactivity in the sensorimotor cortex, suggesting dysfunction of cortical parvalbumin-positive inhibitory interneurons. Notably, reduced parvalbumin immunoreactivity or changes in parvalbumin-positive neuronal number were not observed in the striatum. These data support the association between cortical dysfunction and dystonia following preterm birth. We propose that our mouse model of preterm birth can be used to study this association and potentially also study other sequelae of extreme prematurity.
Parallel evolution in mosquito vectors – a duplicated esterase locus is associated with resistance to pirimiphos-methyl inAn. gambiae
Authors: Nagi Sanjay C. , Lucas Eric R. , Egyir-Yawson Alexander , Essandoh John , Dadzie Samuel , Chabi Joseph , Djogbénou Luc S. , Medjigbodo Adandé A. , Edi Constant V. , Ketoh Guillaume K. , Koudou Benjamin G. , Ashraf Faisal , Clarkson Chris S. , Miles Alistair , Weetman David , Donnelly Martin J.
Published: February 2024

The primary control methods for the African malaria mosquito,Anopheles gambiae, are based on insecticidal interventions. Emerging resistance to these compounds is therefore of major concern to malaria control programmes. The organophosphate, pirimiphos-methyl, is a relatively new chemical in the vector control armoury but is now widely used in indoor residual spray campaigns. Whilst generally effective, phenotypic resistance has developed in some areas in malaria vectors. Here, we used a population genomic approach to identify novel mechanisms of resistance to pirimiphos-methyl inAnopheles gambiae s.lmosquitoes. In multiple populations, we found large and repeated signals of selection at a locus containing a cluster of detoxification enzymes, some of whose orthologs are known to confer resistance to organophosphates inCulex pipiens. Close examination revealed a pair of alpha-esterases,Coeae1fandCoeae2f, and a complex and diverse pattern of haplotypes under selection inAn. gambiae, An. coluzziiandAn. arabiensis. As inCx. pipiens, copy number variation seems to play a role in the evolution of insecticide resistance at this locus. We used diplotype clustering to examine whether these signals arise from parallel evolution or adaptive introgression. Using whole-genome sequenced phenotyped samples, we found that in West Africa, a copy number variant inAnopheles gambiaeis associated with resistance to pirimiphos-methyl. Overall, we demonstrate a striking example of contemporary parallel evolution which has important implications for malaria control programmes.
Towards understanding of allostery in MALT1: a possible role of interdomain motions as revealed by NMR and AlphaFold
Authors: Wallerstein Johan , Han Xiao , Levkovets Maria , Lesovoy Dmitry , Malmodin Daniel , Mirabello Claudio , Wallner Björn , Sun Renhua , Sandalova Tatyana , Agback Peter , Karlsson Göran , Achour Adnane , Agback Tatiana , Orekhov Vladislav
Published: February 2024

Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) has emerged as an attractive target for the development of modulatory compounds, particularly in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1(PCASP-Ig3)339–719has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained largely unexplored. We present here inaugural dynamic analyses of the apo MALT1(PCASP-Ig3)339–719form along with its mutated variant, E549A. This investigation harnessed an array of NMR relaxation techniques, including longitudinal and transverse15N auto-relaxation, heteronuclear NOE, transverse cross-correlated relaxation and NOE measurements between side-chain methyl groups. Our findings unequivocally confirm that MALT1(PCASP-Ig3)339–719exists solely as a monomer in solution, and demonstrate that the two domains display semi-independent movements in relation to each other. Our extensive dynamic study, covering a range of time scales, along with the assessment of diverse conformational populations for MALT1(PCASP-Ig3)339–719, by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, shed light at potential mechanisms underlying the allosteric regulation of this enzyme, and the specific importance of interdomain motions.
A Multimodal Characterization of Low-Dimensional Thalamocortical Structural Connectivity Patterns
Authors: John Alexandra , Hettwer Meike D. , Schaare H. Lina , Saberi Amin , Bayrak Şeyma , Wan Bin , Royer Jessica , Bernhardt Boris C. , Valk Sofie L.
Published: February 2024

The human thalamus is a bilateral and heterogeneous grey matter structure that plays a crucial role in coordinating whole-brain activity. Investigations of its complex structural and functional internal organization revealed to a certain degree overlapping parcellations, however, a consensus on thalamic subnuclei boundaries remains absent. Recent work suggests that thalamic organization might additionally reflect continuous axes transcending nuclear boundaries. In this study, we used a multimodal approach to uncover how low-dimensional axes that describe thalamic connectivity patterns to the cortex are related to internal thalamic microstructural features, functional connectivity, and structural covariance. We computed a thalamocortical structural connectome via probabilistic tractography on diffusion MRI and derived two main axes of thalamic organization. The principal thalamic gradient, extending from medial to lateral and differentiating between transmodal and unimodal nuclei, was related to intrathalamic myelin profiles, and patterns of functional connectivity, while the secondary axis showed correspondence to core-matrix cell type distributions. Lastly, exploring multimodal thalamocortical associations on a global scale, we observed that the medial-to- lateral gradient consistently differentiated limbic, frontoparietal, and default mode network nodes from dorsal and ventral attention networks across modalities. However, the link with sensory modalities varied. In sum, we show the coherence between lower dimensional patterns of thalamocortical structural connectivity and various modalities, shedding light on multiscale thalamic organization.
Transcriptome analysis of the tardigradeHypsibius exemplarisexposed to the DNA-damaging agent bleomycin
Authors: Yoshida Yuki , Hirayama Akiyoshi , Arakawa Kazuharu
Published: February 2024

Tardigrades are microscopic animals that are renowned for their capabilities of tolerating near-complete desiccation by entering an ametabolic state called anhydrobiosis. However, many species also show high tolerance against radiation in the active state as well, suggesting cross-tolerance via the anhydrobiosis mechanism. Previous studies utilized indirect DNA damaging agents to identify core components of the cross-tolerance machinery; however, it was difficult to distinguish whether transcriptomic changes were the result of DNA damage or residual oxidative stress. To this end, we performed transcriptome analysis on bleomycin-exposedHypsibius exemplaris. We observed induction of several tardigrade-specific gene families that may be the core components of the cross-tolerance mechanism. We also identified an enrichment of the tryptophan metabolism pathway, which metabolomic analysis suggested the engagement of this pathway in stress tolerance. These results provide several candidates for the core component of the cross-tolerance, as well as possible anhydrobiosis machinery.