bluuebunny/crossref_metadata_2025 huggingface dataset:
Reported transgenerational responses toPseudomonas aeruginosainC. elegansare not robust
Authors: Gainey D. Patrick , Shubin Andrey V. , Hunter Craig P.
Published: June 2024

Here we report our attempt to replicate reports of transgenerational epigenetic inheritance inCaenorhabditis elegans. Published results from multiple laboratories show thatC. elegansadults and their F1 embryos exposed to the pathogenPseudomonas aeruginosashow pathogen aversion behavior and a pathogen exposure-dependent increase indaf-7/TGFβreporter gene expression. However, results from one group show persistence of the aversion behavior and elevateddaf-7expression in the F2, F3, and F4 generations. In contrast, we failed to consistently detect either the pathogen avoidance response or elevateddaf-7expression beyond the F1 generation. We did confirm that the dsRNA transport proteins SID-1 and SID-2 are required for the intergenerational (F1) inheritance of pathogen avoidance, but not for the F1 inheritance of elevateddaf-7expression. Furthermore, our reanalysis of RNA seq data provides additional evidence that this intergenerational inherited PA14 response may be mediated by small RNAs. The experimental methods are well-described, the source materials are readily available, including samples from the reporting laboratory, and we explored a variety of environmental conditions likely to account for lab-to-lab variability. None of these adjustments altered our results. We conclude that this example of transgenerational inheritance lacks robustness, confirm that the intergenerational avoidance response, but not the elevateddaf-7p::gfpexpression in F1 progeny, requiressid-1andsid-2, and identify candidate siRNAs and target genes that may mediate this intergenerational response.
The small non-coding RNAVaultrc5is dispensable to mouse development
Authors: Prajapat Mahendra , Sala Laura , Vidigal Joana A.
Published: June 2024

Vault RNAs (vRNAs) are evolutionarily conserved small non-coding RNAs transcribed by RNA polymerase lll. Initially described as components of the vault particle, they have since also been described as noncanonical miRNA precursors and as riboregulators of autophagy. As central molecules in these processes, vRNAs have been attributed numerous biological roles including regulation of cell proliferation and survival, response to viral infections, drug resistance, and animal development. Yet, their impact to mammalian physiology remains largely unexplored. To study vault RNAsin vivo,we generated a mouse line with a conditionalVaultrc5loss of function allele. BecauseVaultrc5is the sole murine vRNA, this allele enables the characterization of the physiological requirements of this conserved class of small regulatory RNAs in mammals. Using this strain, we show that mice constitutively null forVaultrc5are viable and histologically normal but have a slight reduction in platelet counts pointing to a potential role for vRNAs in hematopoiesis. This work paves the way for furtherin vivocharacterizations of this abundant but mysterious RNA molecule. Specifically, it enables the study of the biological consequences of constitutive or lineage-specificVaultrc5deletion and of the physiological requirements for an intactVaultrc5during normal hematopoiesis or in response to cellular stresses such as oncogene expression, viral infection, or drug treatment.
CRISPRi-based screen of Autism Spectrum Disorder risk genes in microglia uncovers roles ofADNPin microglia endocytosis and synaptic pruning
Authors: Teter Olivia M , McQuade Amanda , Hagan Venus , Liang Weiwei , Dräger Nina M , Sattler Sydney M , Holmes Brandon B , Castillo Vincent Cele , Papakis Vasileios , Leng Kun , Boggess Steven , Nowakowski Tomasz J , Wells James , Kampmann Martin
Published: June 2024

Autism Spectrum Disorders (ASD) are a set of neurodevelopmental disorders with complex biology. The identification of ASD risk genes from exome-wide association studies and de novo variation analyses has enabled mechanistic investigations into how ASD-risk genes alter development. Most functional genomics studies have focused on the role of these genes in neurons and neural progenitor cells. However, roles for ASD risk genes in other cell types are largely uncharacterized. There is evidence from postmortem tissue that microglia, the resident immune cells of the brain, appear activated in ASD. Here, we used CRISPRi-based functional genomics to systematically assess the impact of ASD risk gene knockdown on microglia activation and phagocytosis. We developed an iPSC-derived microglia-neuron coculture system and high-throughput flow cytometry readout for synaptic pruning to enable parallel CRISPRi-based screening of phagocytosis of beads, synaptosomes, and synaptic pruning. Our screen identifiedADNP, a high-confidence ASD risk genes, as a modifier of microglial synaptic pruning. We found that microglia with ADNP loss have altered endocytic trafficking, remodeled proteomes, and increased motility in coculture.
A machine learning framework for extracting information from biological pathway images in the literature
Authors: Kwon Mun Su , Lee Junkyu , Kim Hyun Uk
Published: June 2024

There have been significant advances in literature mining, allowing for the extraction of target information from the literature. However, biological literature often includes biological pathway images that are difficult to extract in an easily editable format. To address this challenge, this study aims to develop a machine learning framework called the “Extraction of Biological Pathway Information” (EBPI). The framework automates the search for relevant publications, extracts biological pathway information from images within the literature, including genes, enzymes, and metabolites, and generates the output in a tabular format. For this, this framework determines the direction of biochemical reactions, and detects and classifies texts within biological pathway images. Performance of EBPI was evaluated by comparing the extracted pathway information with manually curated pathway maps. EBPI will be useful for extracting biological pathway information from the literature in a high-throughput manner, and can be used for pathway studies, including metabolic engineering.
Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions
Authors: Volz Sara , Malone Jadyn R. , Guseman Alex J. , Gronenborn Angela M. , Marqusee Susan
Published: June 2024

Human γD-crystallin, a monomeric protein abundant in the eye lens nucleus, must remain stably folded for an individual’s entire lifetime to avoid aggregation and protein deposition-associated cataract formation. γD-crystallin contains two homologous domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), which interact via a hydrophobic interface. A number of familial mutations in the gamma crystallin gene are linked to congenital early-onset cataract, most of which result in amino acid changes in the NTD. Several of these, such as V75D and W42R, are known to populate intermediates that, under partially denaturing conditions, possess a natively folded CTD and a completely unfolded NTD, with studies on W42R showing further evidence for a minor population of an intermediate under native conditions. We employed hydrogen-deuterium exchange mass spectrometry (HDX-MS) to probe the structural and energetic features of variants of γD-crystallin under both native and partially denaturing conditions. For V75D and W42R, we identify a species under native conditions that retains partial structure in the NTD and is structurally and energetically distinct from the intermediate populated under partially denaturing conditions. Residues at the NTD-CTD interface play crucial roles in stabilizing this intermediate, and disruption of interface contacts either by amino acid substitution or partial denaturation permits direct observation of two intermediates at the same time. The newly identified intermediate exposes hydrophobic amino acids that are buried in both the folded full-length protein and in the protein’s stable isolated domains. Such non-native exposure of a hydrophobic patch may play an important role in cataract formation.

Significance Statement

Human γD-crystallin, which plays a structural role in the eye lens, is a long-lived protein that must remain folded for an individual’s entire lifetime to avoid aggregation and protein deposition - associated cataract formation. By using hydrogen-deuterium exchange mass spectrometry, we demonstrate that two cataract-associated variants of γD-crystallin populate an intermediate with partial structure along the interface between its two domains under native conditions. In these intermediates, hydrophobic amino acids that are normally buried in the N-terminal domain’s native folded structure become exposed, possibly leading to aggregation and cataract formation. Our findings illustrate the importance of studying a protein’s energy landscapes under conditions that are close to physiological.
Self-growth suppression inBradyrhizobium diazoefficiensis caused by a diffusible antagonist
Authors: Sandhu Armaan Kaur , Fischer Brady R. , Subramanian Senthil , Hoppe Adam D. , Brözel Volker S.
Published: June 2024

Microbes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed inBradyrhizobium diazoefficiensUSDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of otherBradyrhizobiumstrains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but have reduced respiratory activity, ATP levels and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments.Bradyrhizobium’sutilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.
Enhanced Treatment Efficiency of Holmium:YAG Laser Lithotripsy by Using PEDOT:PSS Nanofluid
Authors: Fan Qingsong , Chen Junqin , Anees Faisal , Dominguez Judith , Chen Ting-Hsuan , Payne Christine , Zhong Pei , Hsu Po-Chun
Published: June 2024

Holmium: yttrium-aluminum-garnet (Ho:YAG) laser lithotripsy has been considered the gold standard for treating urinary stones, a disease with increasing prevalence in the US in recent years. While various efforts have been made to enhance the stone ablation efficiency of Ho:YAG laser, these have primarily focused on adjusting laser source settings such as pulse energy and frequency. In this study, we introduced a novel strategy to improve the ablation efficiency of the Ho:YAG laser by incorporating nanoparticles into the fluid surrounding the stone with strong near-infrared light absorption. Experimental results of stone damage revealed an 82% increase in photothermal ablation efficiency when using a “dusting” mode of laser lithotripsy in 0.03 wt.% PEDOT:PSS solution in direct contact. The enhanced NIR absorbance of the fluid was found to promote vapor tunnel formation, facilitating increased laser energy transmission to the stone surface, and to enhance stone absorbance due to trapped fluid inside, leading to greater laser energy absorption for photothermal ablation. Furthermore, cytotoxicity tests on PEDOT:PSS solution demonstrated minimal toxicity when carefully controlling concentration and application duration. This modification of fluid absorbance for efficiency improvement presents a versatile approach compatible with previously reported laser setting modulation methods, showcasing significant potential for enhancing Ho:YAG laser lithotripsy.
Biomolecular Condensation of Trypsin Prevents Autolysis and Promotes Ca2+-Mediated Activation of Esterase Activity
Authors: Patel Chinmaya Kumar , Mukherjee Tushar Kanti
Published: June 2024

The presence of Ca2+ions is known to facilitates the biocatalytic activity of trypsin-like serine proteases via structural stabilization against thermal denaturation and autolysis. Herein, we report a new and hidden regulatory role of Ca2+in the catalytic pathways of trypsin and α-chymotrypsin under physiological conditions. We discovered that macromolecular crowding promotes spontaneous homotypic condensation of native trypsin via liquid-liquid phase separation to yield membraneless condensates/droplets in a broad range of concentrations, pH, and temperature. These condensates are stabilized by multivalent hydrophobic interactions between short patches of hydrophobic residues. Importantly, no liquid-to-solid-like phase transition has been observed over a period of 14 days, indicating the structural intrigrity of phase-separated trypsin within the droplets. Structural insights revealed minimal conformational perturbation of trypsin upon phase separation. Interestingly, we found that Ca2+binding in the calcium binding loop reversibly regulates the biomolecular condensation of trypsin and α-chymotrypsin. While Ca2+-bound trypsin are ineffective to undergo LLPS to form condensate, its removal facilitates condensation under similar experimental conditions. More importantly, we show that biomolecular condensation effectively prevents autolysis of trypsin at physiological conditions and preserve its native-like esterase activity over a period of 14 days, whereas free trypsin loses 86% of its initial activity. In addition, it has been found that phase-separated trypsin responds to Ca2+-dependent activation of its esterase activity even after 14 days of storage while free trypsin failed to do so. Our findings indicate that biomolecular condensates of trypsin and trypsin-like serine proteases act as storage media to prevent autolysis and premature activation, and at the same time preserve their native-like active conformations. The present study highlights an important physiological aspect of biomolecular condensates of trypsin-like serine proteases by which cells can spatio-temporally regulate their biocatalytic efficacy via Ca2+-signalling.
Anaesthesia and delirium: a Mendelian randomization study
Authors: Li YanHui , Sun Yingwei , Zhou Chuanyang , Tan Lei
Published: June 2024

Background

Delirium is a frequent complication in hospitalized older adults post-surgery associated with adverse outcomes. Although anaesthesia is traditionally linked to increased delirium risk, the causal relationship remains uncertain.

Methods

We conducted Mendelian randomization (MR) analyses using genome-wide association studies (GWAS) summary statistics to explore the causal effects of different anaesthesia types (general, regional, and local) on delirium risk. We employed the weighted median, MR-Egger, and MR-PRESSO methods for estimation and conducted sensitivity analyses to address pleiotropy and heterogeneity.

Results

Genetically determined anaesthesia types showed no significant causal effect on delirium risk. Sensitivity analyses confirmed the robustness of these findings, with no evidence of horizontal pleiotropy or significant heterogeneity.

Conclusions

Mendelian randomization provides strong evidence against a causal link between genetically determined anaesthesia and increased delirium risk.
Knockdown of PAK1IP1 can induce CASP-3-dependent pyroptosis to inhibit the progression of hepatocellular carcinoma
Authors: Lu Xiaoliang , Chen Jie , Lu Zefa , Zang Hong
Published: June 2024

Background

Hepatocellular carcinoma (HCC), is a prevalent and fatal malignancy originating from hepatic cells with a consistently rising incidence in recent decades. In this study, we aim to identify potential prognostic biomarkers and reveal new mechanism in HCC.

Methods

HCC-related datasets (GSE45267 and GSE49515) and TCGA information were downloaded for DEGs, and the common DEGs were WGCNA, protein-protein interaction network (PPI), risk model, expression, survival and prognostic nomogram to determine the key gene related to HCC. Further, the key gene was analyzed by clinical feature analysis, immunoassay and cell experiments to investigate its exact role in HCC.

Results

Based on the above comprehensive analysis, we targeted the key gene PAK1-interacting protein 1(PAK1IP1) with a good prognostic value in HCC. PAK1IP1 was remarkably increased in tumor samples than normal samples, which might be related to immune cell infiltration in liver cancer. It was up-regulated in HCC cells, and its knockdown could suppress HCC proliferation and migration. Besides, ELISA and flow cytometry showed that PAK1IP1 could regulate Lipopolysaccharide (LPS)-induced pyroptosis of HCC cells. Knocking down PAK1IP1 could induce CASP-3-dependent pyroptosis in HCC cells to suppress the development of HCC.

Conclusion

To sum up, PAK1IP1 was identified as a promising prognostic biomarker, and knockdown of PAK1IP1 can induce CASP-3-dependent pyroptosis to suppress HCC development, which sheds new light on HCC tumorigenesis.
Mechanosensory representation of wing deformations
Authors: Yarger Alexandra M. , Maeda Masateru , Siwanowicz Igor , Kajiyama Haruhiro , Walker Simon M. , Bomphrey Richard J. , Lin Huai-Ti
Published: June 2024

Efficient representation of structural deformations is crucial for monitoring the instantaneous state of biological structures. Insects’ ability to encode wing deformations during flight demonstrates a general morphological computing principle applicable across sensory systems in nature as well as engineered systems. To characterize how relevant features are encoded, we measured and modelled displacement and strain across dragonfly wing surfaces in tethered and free flight. Functional interpretations were supported by neuroanatomical maps, and ablation and perturbation experiments. We find that signal redundancy is reduced by non-random sensor distributions and that morphology limits the stimulus space such that sensory systems can monitor natural states with few sensors. Deviations from the natural states are detected by a flexible population of additional sensors with many distinguishable activation patterns.
Testing the reality gap with kilobots performing two ant-inspired foraging behaviours
Authors: Ellis Niamh , Caravaggio Alexander , Kelly Jonathan , Young Ian , Manfredini Fabio , Giannaccini Maria Elena
Published: June 2024

Robotics looks to nature for inspiration to perform effectively in unstructured environments and can be used as a platform to test biological hypotheses. Social animals often share information about food source locations: one example is tandem running in ants, where a leader guides a naive recruit to a known profitable food site. This is extremely advantageous as it allows the sharing of important information among colony members, but it also has costs, such as waiting time inside the nest when no leaders are around, and a reduced walking speed for the tandem couple compared to individual ants. Whether and when these costs outweigh the benefits is not well understood as it is challenging to observe complex social behaviours in nature. We developed two kilobot-based approaches to compare tandem running and lone scout foraging, where an ant searches for food without any previous knowledge of its location: one approach based on real-life experiments and one on computer simulations. We investigated the role that the size of the search arena played in the effectiveness of foraging. Tandem pairs were faster for all three arena sizes; however, this result was reversed in the simulations. These results highlight the inconsistencies between simulation and real-life kilobot experiments, previously reported for other systems and known as reality gap. Further testing is needed to inform on whether robotic applications should utilise agents with the same roles and capabilities for search, detection and repair-type tasks as simulations, or whether instead the two approaches should be treated separately.
stVCR: Reconstructing spatio-temporal dynamics of cell development using optimal transport
Authors: Peng Qiangwei , Zhou Peijie , Li Tiejun
Published: June 2024

Time-series spatial transcriptome data with single-cell resolution provide an opportunity to study cell differentiation, growth and migration in physical space over time. Due to the destructive nature of sequencing, simultaneous reconstruction of cell differentiation, growth and migration trajectories remains challenging, especially migration in physical space, as the coordinates obtained at different temporal snapshots are not in the same coordinate system. To realize this potential, we developed stVCR, which is an optimal transport algorithm with dynamical form, unbalanced setting and invariance to rigid body transformations. stVCR extends the previous algorithm, which only reconstructs differentiation trajectories and population growth, to end-to-end simultaneously reconstruct cell differentiation, growth, migration in physical space and align spatial coordinates of multiple snapshots. In addition, stVCR allows the study of the interaction between gene expression and spatial migration and the effect of gene expression and spatial migration on growth. We verified the effectiveness of stVCR on simulated data and axolotl brain regeneration data.
Consciousness in Non-REM-parasomnia episodes
Authors: Siclari Francesca
Published: June 2024

Sleepwalking and related parasomnias are thought to result from incomplete awakenings out of Non rapid eye movement (Non-REM) sleep. Non-REM parasomnia behaviors have been described as unconscious and automatic, or related to vivid, dream-like conscious experiences. Similarly, some observations have suggested that patients are unresponsive during episodes, while others that they can interact with their surroundings. To better grasp and characterize the full spectrum of consciousness and environmental disconnection associated with behavioral episodes, 35 adult patients with Non-REM sleep parasomnias were interviewed in-depth about their experiences. The level of consciousness during parasomnia episodes was reported to be variable both within and between individuals, ranging from minimal or absent consciousness and largely automatic behaviors (frequently/always present in 36% of patients) to preserved conscious experiences characterized by delusional thinking of varying degrees of specificity (65%), often about impending danger, variably formed, uni- or multisensory hallucinations (53%), impaired insight (77%), negative emotions (75%) and variable, but often pronounced amnesia (30%). Patients described their experiences as a dream scene during which they felt awake (‘awake dreaming’). Surroundings were either realistically perceived, misinterpreted (in the form of perceptual illusions or misidentifications of people) or entirely hallucinated as a function of the prevailing delusion. These observations suggest that the level of consciousness and sensory disconnection in Non-REM parasomnias is variable and graded. In their full-fledged expression, Non-REM parasomnia experiences feature several core features of dreams. They therefore represent a valuable model for the study of consciousness, sleep-related sensory disconnection and dreaming.
Integrating diverse statistical methods to analyse stage-discriminatory cell interactions in colorectal neoplasia
Authors: Bull Joshua A. , Mulholland Eoghan J. , Moore Joshua W. , Bosque Jesús J. , Stolz Bernadette J. , Boen Joseph , Eggington Holly R. , Belnoue-Davis Hayley L. , Jones Helen , Gatenbee Chandler D. , Anderson Alexander R. A. , Easton Alistair , Todd Peter , Cunningham Christopher , Taylor Stephen , Byrne Helen M. , Leedham Simon
Published: June 2024

Spatial biology has the potential to unlock information about the disrupted cellular ecosystems that define human disease. Quantitative analysis of spatially-resolved cell interactions allows mapping of tissue self-organisation and assessment of why cells interact differently in physiological and pathological contexts. However, the complexity of mammalian tissues, that occur across a spectrum of length scales, presents significant challenges for spatial analysis, increasing the gap between our capacity to generate and biologically interpret these datasets. Here, we have adapted a range of mathematical tools to develop a suite of spatial descriptors, and deployed them to determine how cell interactions change as colorectal cancer progresses from benign precursors. We demonstrate that combining mathematical analyses permits insightful examination of tissue organisational structures and identifies variable cell-interaction pathways that underpin disease progression. Mathematical tool triangulation can cross-corroborate spatial biology findings, facilitating development of analysis pipelines that are robust to individual method limitations.
A CRISPR homing screen finds a chloroquine resistance transporter-like protein of thePlasmodiumoocyst essential for mosquito transmission of malaria
Authors: Balakrishnan Arjun , Hunziker Mirjam , Tiwary Puja , Pandey Vikash , Drew David , Billker Oliver
Published: June 2024

Genetic screens with barcodedPlasmoGEM vectors have identified thousands ofPlasmodiumgene functions in haploid blood stages, gametocytes and liver stages. However, the formation of diploid cells by fertilisation has hindered the use of genetic screens to investigate vector-parasite interactions during the mosquito stages of the parasite. In this study, we developed a scalable genetic system that uses barcoded gene targeting vectors equipped with a CRISPR-mediated homing mechanism to generate homozygous loss-of-function mutants to reveal gene functions in the functionally diploid life cycle stages. In this system, a knockout vector additionally expressing a gRNA for its target is integrated into one of the parental alleles and directs Cas9 to the intact allele after fertilisation, leading to its disruption. We find that this homing strategy is 90% effective in the oocyst, resulting in the generation of homozygous genotypes. A pilot screen reveals that PBANKA_0916000 encodes a chloroquine resistance transporter-like protein, CRTL, essential for oocyst growth and sporogony. The data point to an unexpected importance for the transmission of malaria of the poorly understood digestive vacuole of the oocyst that contains hemozoin crystals. The new screening strategy provides a method to discover systematically and at scale the essential malaria transmission genes whose first essential functions are after fertilisation in the bloodmeal, enabling their potential as targets for transmission-blocking interventions to be assessed.
Predicting binding events in very flexible, allosteric, multi-domain proteins
Authors: Basciu Andrea , Athar Mohd , Kurt Han , Neville Christine , Malloci Giuliano , Muredda Fabrizio C. , Bosin Andrea , Ruggerone Paolo , Bonvin Alexandre M. J. J. , Vargiu Attilio V.
Published: June 2024

Knowledge of the structures formed by proteins and small molecules is key to understand the molecular principles of chemotherapy and for designing new and more effective drugs. During the early stage of a drug discovery program, it is customary to predict ligand-protein complexesin silico, particularly when screening large compound databases. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology to generate bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites by exploiting only information on the unbound structure and the putative binding sites. The protocol is validated on the paradigm enzyme adenylate kinase, for which we generated a significant fraction of bound-like structures. A fraction of these conformations, employed in ensemble-docking calculations, allowed to find native-like poses of substrates and inhibitors (binding to the active form of the enzyme), as well as catalytically incompetent analogs (binding the inactive form). Our protocol provides a general framework for the generation of bound-like conformations of challenging drug targets that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein’s activity. We foresee applications in virtual screening, in the prediction of the impact of amino acid mutations on structure and dynamics, and in protein engineering.
In situ, High-Resolution Quantification of CO2Uptake Rates via Automated Off-Gas Analysis Illuminates Carbon Uptake Dynamics in Cyanobacterial Cultures
Authors: Jones Christopher M. , Innes Sean , Holland Steven , Burch Tyson , Parrish Sydney , Nielsen David R.
Published: June 2024

Quantification of CO2fixation rates by cyanobacteria is vital to determining their potential as industrial strains in a circular bioeconomy. Currently, however, CO2fixation rates are most often determined through indirect and/or low-resolution methods, resulting in an incomplete picture of both dynamic behaviors and total carbon fixing potential. To address this, we developed a novel, low-cost system forin situoff-gas analysis which supports the automated acquisition of high-resolution and CO2uptake rates from cyanobacterial cultures. Carbon fixation data obtained via this system was independently verified by elemental analysis of cultivated biomass. UsingSynechococcus sp.PCC 7002 andSynechocystis sp.PCC 6803, we demonstrate that phototrophic CO2uptake rates accelerate linearly to a maximum before then decaying monotonically to cessation by stationary phase. Furthermore, consistent with the expected stoichiometry, we found that strong correlations exist between both the rates and total levels of cell growth and carbon fixation. This system simultaneously provides a high-resolution growth curve, accurate carbon fixation rates, as well as the total amount of carbon fixed in a cyanobacterial batch culture, thus illuminating the parameters with which cyanobacterial researchers can exploit use to realize their full potential in industrial applications.
Tissue resident memory CD8+ T cells are present but not critical for demyelination and neurodegeneration in a mouse model of multiple system atrophy
Authors: Corbin-Stein Nicole J. , Childers Gabrielle M. , Webster Jhodi M. , Zane Asta , Yang Ya-Ting , Ali Md Akkas , Sandoval Ivette M. , Manfredsson Fredric P. , Kordower Jeffrey H. , Tyrrell Daniel J. , Harms Ashley S.
Published: June 2024

Multiple system atrophy (MSA) is rare, fast progressing, and fatal synucleinopathy with alpha-synuclein (α-syn) inclusions located within oligodendroglia called glial cytoplasmic inclusions (GCI). Along with GCI pathology there is severe demyelination, neurodegeneration, and neuroinflammation. In post-mortem tissue, there is significant infiltration of CD8+ T cells into the brain parenchyma, however their role in disease progression is unknown. To determine the role of CD8+ T cells, a modified AAV, Olig001-SYN, was used to selectively overexpress α-syn in oligodendrocytes modeling MSA in mice. Four weeks post transduction, we observed significant CD8+ T cell infiltration into the striatum of Olig001-SYN transduced mice recapitulating the CD8+ T cell infiltration observed in post-mortem tissue. To understand the role of CD8+ T cells, a CD8 knockout mice were transduced with Olig001-SYN. Six months post transduction into a mouse lacking CD8+ T cells, demyelination and neurodegeneration were unchanged. Four weeks post transduction, neuroinflammation and demyelination were enhanced in CD8 knockout mice compared to wild type controls. Applying unbiased spectral flow cytometry, CD103+, CD69+, CD44+, CXCR6+, CD8+ T cells were identified when α-syn was present in oligodendrocytes, suggesting the presence of tissue resident memory CD8+ T (Trm) cells during MSA disease progression. This study indicates that CD8+ T cells are not critical in driving MSA pathology but are needed to modulate the neuroinflammation and demyelination response.
Necessity and Impact of Specialization of Large Foundation Model for Medical Segmentation Tasks
Authors: Nguyen Eric , Liu Hengjie , Ruan Dan
Published: June 2024

Background

Large foundation models, such as the Segment Anything Model (SAM), have shown remarkable performance in image segmentation tasks. However, the optimal approach to achieve true utility of these models for domain-specific applications, such as medical image segmentation, remains an open question. Recent studies have released a medical version of the foundation model MedSAM by training on vast medical data, who promised SOTA medical segmentation. Independent community inspection and dissection is needed.

Purpose

This study assesses the performance of off-the-shelf medical foundation model MedSAM for the segmentation of anatomical structures in pelvic MR images. We also evaluate the dependency on prompting scheme and demonstrate the gain of further specialized fine-tuning.

Methods

MedSAM and its lightweight version LiteMedSAM were evaluated out-of-the-box on a public MR dataset consisting of 589 pelvic images split 80:20 for training and testing. An nnU-Net model was trained from scratch to serve as a benchmark and to provide bounding box prompts for MedSAM. MedSAM was evaluated using different quality bounding boxes, those derived from ground truth labels, those derived from nnU-Net, and those derived from the former two but with 5-pixel isometric expansion. Lastly, LiteMedSAM was refined on the training set and reevaluated on this task.

Results

Out-of-the-box MedSAM and LiteMedSAM both performed poorly across the structure set, especially for disjoint or non-convex structures. Varying prompt with different bounding box inputs had minimal effect. The mean Dice score and mean Hausdorff distances (in mm) for obturator internus using MedSAM and LiteMedSAM were {0.251 ± 0.110, 0.101 ± 0.079} and {34.142 ± 5.196, 33.688 ± 5.306}, respectively. Fine-tuning of LiteMedSAM led to significant performance gain, improving Dice score and Hausdorff distance for the obturator internus to 0.864 ± 0.123 and 5.022 ± 10.684, on par with nnU-Net with no significant difference in evaluation of most structures. All segmentation structures all benefited significantly from specialized refinement, at varying improvement margin.

Conclusion

Our study alludes to the potential of deep learning models like MedSAM and lite MedSAM for medical segmentation but also highlight the need for specialized refinement and adjudication: it is quite likely that off-the-shelf use of such large foundation models may be suboptimal, and specialized fine-tuning can significantly enhance segmentation accuracy.
Identification of cortical targets for modulating function supported by the human hippocampal network
Authors: Lee Hsin-Ju , Lin Fa-Hsuan
Published: June 2024

Background

Individualized transcranial magnetic stimulation (TMS) targeting using functional connectivity analysis of functional magnetic resonance imaging (fMRI) has been demonstrated to be advantageous in inducing neuroplasticity. However, how this approach can benefit modulating the episodic memory function supported by the hippocampal network remains elusive.

Objective

We use the resting-state fMRI data from a large cohort to reveal tentative TMS targets at cortical regions within the hippocampal network.

Methods

Functional MRI from 1,133 individuals in the Human Connectome Project was used to analyze the hippocampal network using seed-based functional connectivity.

Results

Using a weighted sum of time series at the cortex, we identified the average centroids of individualized targets at the medial prefrontal cortex (mPFC) and posterior parietal cortices (PPC) at (-10, 49, 7) and (-40, -67, 30) in the left hemisphere, respectively. The mPFC and PPC coordinate at the right hemispheres are (11, 51, 6) and (48, -59, 24) in the right hemisphere, respectively. These coordinates can be reliably identified (>90% of individuals).

Conclusion

Our results suggest candidate TMS target coordinates to modulate the hippocampal function.
Amplified DNA Heterogeneity Assessment with Oxford Nanopore Sequencing Applied to Cell Free Expression Templates
Authors: Hejazi Sepehr , Ahsan Afrin , Kashani Mohammad , Reuel Nigel F
Published: June 2024

In this work, Oxford Nanopore sequencing is tested as an accessible method for quantifying heterogeneity of amplified DNA. This method enables rapid quantification of deletions, insertions, and substitutions, the probability of each mutation error, and their locations in the replicated sequences. Amplification techniques tested were conventional polymerase chain reaction (PCR) with varying levels of polymerase fidelity (OneTaq, Phusion, and Q5) as well as rolling circle amplification (RCA) with Phi29 polymerase. Plasmid amplification using bacteria was also assessed. By analyzing the distribution of errors in a large set of sequences for each sample, we examined the heterogeneity and mode of errors in each sample. This analysis revealed that Q5 and Phusion polymerases exhibited the lowest error rates observed in the amplified DNA. As a secondary validation, we analyzed the emission spectra of sfGFP fluorescent proteins synthesized with amplified DNA using cell free expression. Error-prone polymerase chain reactions confirmed the dependency of reporter protein emission spectra peak broadness to DNA error rates. The presented nanopore sequencing methods serve as a roadmap to quantify the accuracy of other gene amplification techniques, as they are discovered, enabling more homogenous cell-free expression of desired proteins.
Effects of Tasks on Functional Brain Connectivity Derived from Inter-Individual Correlations: Insights from Regional Homogeneity of Functional MRI Data
Authors: Di Xin , Jain Pratik , Biswal Bharat B.
Published: June 2024

Research on brain functional connectivity often relies on intra-individual moment-to-moment correlations of functional brain activity, typically using techniques like functional MRI (fMRI). Inter-individual correlations are also employed on data from fMRI and positron emission tomography (PET). Many past studies have not specified tasks for participants, keeping them in an implicit “resting” condition. This lack of task specificity raises questions about how different tasks impact inter-individual correlation estimates. In our analysis of fMRI data from 100 unrelated participants, scanned during seven task conditions and in a resting state, we calculated Regional Homogeneity (ReHo) for each task as a regional measure of brain functions. We found that changes in ReHo due to different tasks were relatively small compared with the variations across brain regions. Cross-region variations of ReHo were highly correlated between different tasks. Similarly, whole-brain inter-individual correlation patterns were remarkably consistent across the tasks, showing correlations greater than 0.78. Changes in inter-individual correlations between tasks were primarily driven by connectivity in the visual, somatomotor, default mode network, and the interactions between them. The subtle yet statistically significant differences in functional connectivity may be linked to specific brain regions associated with the studied tasks. Future studies should consider task design when exploring inter-individual connectivity in specific brain systems.
Reactivation-dependent transfer of fear memory between contexts requires M1 muscarinic receptor stimulation in dorsal hippocampus
Authors: Abouelnaga Karim H. , Huff Andrew E. , Jardine Kristen H. , O’Neill Olivia S. , Winters Boyer D.
Published: June 2024

Background

Memory updating is essential for integrating new information into existing representations. However, this process could become maladaptive in conditions like post-traumatic stress disorder (PTSD), when fear memories generalize to neutral contexts. Previously, we have shown that contextual fear memory malleability in rats requires activation of M1 muscarinic acetylcholine receptors in the dorsal hippocampus. Here, we investigated the involvement of this mechanism in transfer of contextual fear memories to other contexts using a novel fear memory updating paradigm.

Methods

Following brief re-exposure to a previously fear conditioned context, male rats (n=8-10/group) were placed into a neutral context to evaluate the transfer of fear memory. We also infused the selective M1 receptor antagonist pirenzepine into the dorsal hippocampus prior to memory reactivation to try to block this effect.

Results

Results support the hypothesis that fear memory can be updated with novel contextual information, but only if rats are re-exposed to the originally trained context relatively recently prior to the neutral context; evidence for transfer was not seen if the fear memory reactivation was omitted or if it occurred 6h prior to neutral context exposure. The transferred fear persisted for four weeks, and the effect was blocked by M1 antagonism.

Conclusions

These findings strongly suggest that fear transfer requires reactivation and destabilization of the original fear memory. Specific parameters likely dictate similar generalization in disorders like PTSD. The novel preclinical model introduced here, and its implication of muscarinic receptors in this process, should inform therapeutic strategies in this area.
Cognitive ability in offspring conscripts and cardiovascular disease risk in extended family members: assessing the impact of modifiable risk factors on familial risk
Authors: Vinueza-Veloz María Fernanda , Jones Paul Remy , Råberg Kjøllesdal Marte Karoline , Thu Huong , Carslake David , Næss Øyvind
Published: June 2024

Background and aim

Previous studies have demonstrated an inverse association between cognitive ability (CA) and risk of cardiovascular diseases (CVD). This study aims to investigate the associations between CA in offspring and CVD mortality in relatives of the parental generation (i.e., parents, aunts/uncles (A/U), and A/U partners), and assess the role of modifiable risk factors on these associations.

Methods

This longitudinal study included nearly 3 million adults who were followed up from age 45 until death. Data for participants were obtained through the linkage of various Norwegian surveys and registries. Hazard ratios (HR) for CVD mortality among the parental generation in relation to offspring CA were estimated using Cox proportional hazard regression.

Results

One standard deviation (SD) unit increase in CA was associated with a reduction in CVD mortality among mothers (HR: 0.77, 95%CI [0.74, 0.81]); fathers (0.83, [0.81, 0.86]); A/U (0.91, [0.87, 0.94]); and A/U partners (0.91, [0.89, 0.94]). Adjusting the models for CVD risk factors in the parental generation attenuated all associations (mothers-HR: 0.91, 95%CI [0.87, 0.96]; fathers: 0.93, [0.91, 0.96]; A/U: 0.99, [0.96, 1.03]; A/U partners: 0.98, [0.95, 1.01]).

Conclusions

We observed an inverse association between offspring CA and CVD and all-cause mortality in various familial relationships. Our findings suggest the existence of factors shared among relatives that explain familial risk to suffer lower CA and higher CVD mortality. A significant portion of the association between CA and CVD mortality in all familial relationships was explained by modifiable risk factors in relatives of the older generation.

Highlights

A lower cognitive ability might drive inequalities in cardiovascular disease (CVD).

Shared environments explain most of the association between cognitive ability and CVD.

The role of genetic factors in this relationship has probably been overestimated.
Prevalence of indications of alcohol and drug use among patients treated for injurious falls by Emergency Medical Services
Authors: Itzkowitz Nicole G. , Burford Kathryn G. , Crowe Remle P. , Wang Henry E. , Lo Alexander X. , Rundle Andrew G.
Published: June 2024

Objective

To describe the distribution of alcohol and drug involvement in injurious falls by location and subtype of fall.

Methods

Using the 2019 National Emergency Medical Services Information System (NEMSIS) dataset we identified 1,854,909 patients injured from falls requiring an Emergency Medical Services (EMS) response and determined the fall location (e.g. indoors or on street/sidewalk) and the EMS clinician’s notation of alcohol or drug involvement. We analyzed substance involvement by fall subtype, location of fall and patient demographics.

Results

Overall, for 7.4% of injurious falls there was a notation of substance use: 6.5% for alcohol alone, 0.6% for drugs and 0.3% for alcohol and drugs. 21.2% of falls that occurred on a street or sidewalk had a notation of substance use; alcohol use alone for 18.5% of falls, drugs alone for 1.7% of falls and alcohol and drugs for 0.9% of falls. Substance use prevalence was highest, at 30.3%, in the age group 21 to 64 years, for falls occurring on streets and sidewalks, without syncope or heat illness as contributing factors; alcohol use alone for 26.3%, drugs alone for 2.6%, and alcohol and drugs for 1.4%. Reported substance use involvement was more frequent for men compared to women for each location type.

Conclusions

Overall, 1-in-5 injurious falls on streets and sidewalks and requiring EMS attention involved substance use, and these numbers likely underestimate the true burden. As cities seek to expand nightlife districts, design strategies to protect pedestrians from falls should be enacted.
Estimated global and regional incidence and prevalence of herpes simplex virus infections and genital ulcer disease in 2020: Mathematical modeling analyses
Authors: Harfouche Manale , AlMukdad Sawsan , Alareeki Asalah , Osman Aisha M. M. , Gottlieb Sami L. , Rowley Jane , Abu-Raddad Laith J. , Looker Katharine J.
Published: June 2024

Background

Genital herpes simplex virus (HSV) type 1 and 2 infections are lifelong and can cause symptomatic genital ulcer disease (GUD). HSV-2 almost always causes sexually transmitted genital infection, while HSV-1 mainly causes oral infection but can be sexually transmitted to cause genital infection. This study estimated genital infection with both HSV types and associated GUD globally in 2020, breaking down the data by World Health Organization (WHO) region and sex for females and males.

Methods

A calibrated mathematical model was employed to generate estimates for the incidence and prevalence of HSV-2 infection, genital HSV-1 infection, and GUD caused by both HSV types. Estimates for non-genital infections caused by HSV-1 were also generated. Model input was derived from a comprehensive systematic review and meta-analyses of HSV prevalence data for all WHO regions.

Results

Globally in 2020 there were 25.6 million (95% uncertainty interval (UI): 23.1-29.4 million) people aged 15 to 49 years with new HSV-2 infections and 519.5 million (95% UI: 464.3-611.3 million), or 13.3% (95% UI: 11.9-15.6%), with existing (prevalent) HSV-2 infections. In addition, there were 16.8 million (95% UI: 10.6-22.4 million) people aged 15-49 years with new genital HSV-1 infections and 376.2 million (95% UI: 235.6-483.5 million), or 10.2% (95% UI: 6.4-13.1%), with prevalent genital HSV-1 infections. The estimated number of people aged 15 to 49 years with at least one episode of HSV-attributable genital ulcer disease in 2020 was 187.9 million (95% UI: 116.0-291.8 million) for HSV-2 and 16.7 million (95% UI: 9.3-25.2 million) for HSV-1, totaling 204.6 million (95% UI: 132.3-306.5).

Conclusion

Genital HSV infections have a high incidence and prevalence worldwide, contributing to a significant GUD disease burden. New prevention and treatment measures, such as prophylactic and therapeutic HSV vaccines, are critically needed to control HSV infections and reduce the associated disease burden.