bluuebunny/crossref_metadata_2025 huggingface dataset:
Spectrum of somatic mutational features of colorectal tumors in ancestrally diverse populations
Authors: Matejcic Marco , Teer Jamie K. , Hoehn Hannah J. , Diaz Diana B. , Shankar Kritika , Gong Jun , Nguyen Nathalie T. , Lorona Nicole , Coppola Domenico , Fulmer Clifton , Saglam Ozlen , Jiang Kun , Cress Douglas , Muñoz-Antonia Teresita , Flores Idhaliz , Gordian Edna , Oliveras Torres José A. , Felder Seth I. , Sanchez Julian A. , Fleming Jason , Siegel Erin M. , Freedman Jennifer A. , Dutil Julie , Stern Mariana C. , Fridley Brooke L. , Figueiredo Jane C. , Schmit Stephanie L.
Published: March 2024

Ancestrally diverse and admixed populations, including the Hispanic/Latino/a/x/e community, are underrepresented in cancer genetic and genomic studies. Leveraging the Latino Colorectal Cancer Consortium, we analyzed whole exome sequencing data on tumor/normal pairs from 718 individuals with colorectal cancer (128 Latino, 469 non-Latino) to map somatic mutational features by ethnicity and genetic ancestry.

Global proportions of African, East Asian, European, and Native American ancestries were estimated using ADMIXTURE. Associations between global genetic ancestry and somatic mutational features across genes were examined using logistic regression.

TP53,APC, andKRASwere the most recurrently mutated genes. Compared to non-Latino individuals, tumors from Latino individuals had fewerKRAS(OR=0.64, 95%CI=0.41-0.97, p=0.037) andPIK3CAmutations (OR=0.55, 95%CI=0.31-0.98, p=0.043). Genetic ancestry was associated with presence of somatic mutations in 39 genes (FDR-adjusted LRT p<0.05). Among these genes, a 10% increase in African ancestry was associated with significantly higher odds of mutation inKNCN(OR=1.34, 95%CI=1.09–1.66, p=5.74×10-3) andTMEM184B(OR=1.53, 95%CI=1.10–2.12, p=0.011). Among RMGs, we found evidence of association between genetic ancestry and mutation status inCDC27(LRT p=0.0084) and betweenSMAD2mutation status and AFR ancestry (OR=1.14, 95%CI=1.00-1.30, p=0.046). Ancestry was not associated with tumor mutational burden. Individuals with above-average Native American ancestry had a lower frequency of microsatellite instable (MSI-H) vs microsatellite stable tumors (OR=0.45, 95%CI=0.21-0.99, p=0.048).

Our findings provide new knowledge about the relationship between ancestral haplotypes and somatic mutational profiles that may be useful in developing precision medicine approaches and provide additional insight into genomic contributions to cancer disparities.

Significance

Our data in ancestrally diverse populations adds essential information to characterize mutational features in the colorectal cancer genome. These results will help enhance equity in the development of precision medicine strategies.
Neural mechanisms of disease pathology and cognition in young-onset Alzheimer’s Disease variants
Authors: Sacu Seda , Slattery Catherine F. , Friston Karl J. , Paterson Ross W. , Foulkes Alexander J.M. , Yong Keir , Crutch Sebastian , Schott Jonathan M. , Razi Adeel
Published: March 2024

Late-onset Alzheimer’s disease is consistently associated with alterations in the default-mode network (DMN)—a large-scale brain network associated with self-related processing and memory. However, the functional organization of DMN is far less clear in young-onset Alzheimer’s disease (YOAD). We assessed resting-state DMN effective connectivity in two common YOAD variants (i.e., amnestic variant (n = 26) and posterior cortical atrophy (n = 13) and healthy participants (n=24) to identify disease- and variant-specific connectivity differences using spectral dynamic causal modelling. Patients with the amnestic variant showed increased connectivity from prefrontal cortex to posterior DMN nodes relative to healthy controls, whereas patients with posterior cortical atrophy exhibited decreased posterior DMN connectivity. Right hippocampus connectivity differentiated the two patient groups. Furthermore, disease-related connectivity alterations were also predictive of group membership and cognitive performance. These findings suggest that resting-state DMN effective connectivity provides a new understanding of neural mechanisms underlying the disease pathology and cognition in YOAD.
metaGWASmanager: A toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia
Authors: Rodriguez-Hernandez Zulema , Gorski Mathias , Plaza Maria Tellez , Schlosser Pascal , Wuttke Matthias
Published: March 2024

This paper introduces the metaGWASmanager, which streamlines genome-wide association studies within large-scale meta-analysis consortia. It is a toolbox for both the central consortium analysis group and participating studies to generate homogeneous phenotypes, minimize variance from inconsistent methodologies, ensure high-quality association results, and implement time-efficient quality control workflows. The toolbox features a plug-in-based approach for customization.

Results

The metaGWASmanager toolbox has been successfully deployed in both the CKDGen and MetalGWAS Initiative consortia across hundreds of participating studies, demonstrating its effectiveness in improving the efficiency of GWAS analysis by automating routine tasks and ensuring the value and reliability of association results, thus, ultimately promoting scientific discovery.

Availability

GitHub:https://github.com/genepi-freiburg/metaGWASmanager

Contact

pschlos3@jhu.edu,matthias.wuttke@uniklinik-freiburg.de
Cervical collagen network porosity assessed by SHG endomicroscopy distinguishes preterm and normal pregnancy – a pilot study
Authors: Liang Wenxuan , Liu Yuehan , Guan Honghua , Sakulsaengprapha Vorada , Luby-Phelps Katherine , Mahendroo Mala , Li Xingde
Published: March 2024

Structured Abstract

Background

Preterm birth (PTB) is a global public health issue affecting millions of newborns every year. Orchestrated remodeling of the cervix is essential for normal pregnancy and birth, while PTB is closely related with premature cervical ripening and loss of cervical mechanical strength. The structure and organization of fibrillar collagen in the extracellular matrix are of vital importance to the biomechanical properties of the cervix. Second harmonic generation (SHG) microscopy has proved capable of revealing the progressive changes in cervical collagen morphology over the course of pregnancy. To translate this promising imaging technology to clinical practice, a flexible SHG endomicroscope has long been envisaged for label-free, non-invasive visualization of cervical collagen architecture and for assessment of PTB risk.

Objective

To evaluate the potential of our newly-developed SHG endomicroscope for imaging-based differentiation of cervical collagen architecture between normal pregnant mice and RU486/mifepristone-induced PTB mouse models.

Study Design

We undertook endomicroscopy SHG imaging of cervical collagen on two types ofex vivosamples: 1) frozen cervical tissue sections (∼50 µm thick) and 2) resected intact cervices, and performed SHG-image-based quantitative collagen morphology analysis to distinguish RU486 mouse models from normal pregnant mice.

Results

Endomicroscopic SHG images of cervical tissue sections from mifepristone-treated mouse models exhibit statistically larger collagen fiber diameter, increased pore size, and reduced pore numbers than those of normal pregnant mice. Similar changes are also observed on SHG images of subepithelial collagen fibers acquired from intact cervices by the endomicroscope.

Conclusion

The experiment results demonstrated that SHG endomicroscopy along with quantitative image analysis holds promising potential for clinical assessment of cervical collagen remodeling and preterm birth risk.
Inactive Parp2 causes Tp53-dependent lethal anemia by blocking replication-associated nick ligation in erythroblasts
Authors: Lin Xiaohui , Gupta Dipika , Vaitsiankova Alina , Bhandari Seema Khattri , Leung Kay Sze Karina , Menolfi Demis , Lee Brian J. , Russell Helen R. , Gershik Steven , Gu Wei , McKinnon Peter J. , Dantzer Françoise , Rothenberg Eli , Tomkinson Alan E. , Zha Shan
Published: March 2024

PARP1&2 enzymatic inhibitors (PARPi) are promising cancer treatments. But recently, their use has been hindered by unexplained severe anemia and treatment-related leukemia. In addition to enzymatic inhibition, PARPi also trap PARP1&2 at DNA lesions. Here, we report that unlikeParp2-/-mice, which develop normally, mice expressing catalytically-inactive Parp2 (E534A,Parp2EA/EA) succumb toTp53-andChk2-dependent erythropoietic failurein utero, mirroringLig1-/-mice. While DNA damage mainly activates PARP1, we demonstrate that DNA replication activates PARP2 robustly. PARP2 is selectively recruited and activated by 5’-phosphorylated nicks (5’p-nicks) between Okazaki fragments, typically resolved by Lig1. Inactive PARP2, but not its active form or absence, impedes Lig1- and Lig3-mediated ligation, causing dose-dependent replication fork collapse, particularly harmful to erythroblasts with ultra-fast forks. This PARylation-dependent structural function of PARP2 at 5’p-nicks explains the detrimental effects of PARP2 inhibition on erythropoiesis, revealing the mechanism behind the PARPi-induced anemia and leukemia, especially those with TP53/CHK2 loss.

Significance

This work shows that the hematological toxicities associated with PARP inhibitors stem not from impaired PARP1 or PARP2 enzymatic activity but rather from the presence of inactive PARP2 protein. Mechanistically, these toxicities reflect a unique role of PARP2 at 5’-phosphorylated DNA nicks during DNA replication in erythroblasts.
Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer
Authors: Montgomery Julia M , Lemkul Justin A
Published: March 2024

The cell membrane functions as a semi-permeable barrier that governs the transport of materials into and out of cells. The bilayer features a distinct dielectric gradient due to the amphiphilic nature of its lipid components. This gradient influences various aspects of small molecule permeation and the folding and functioning of membrane proteins. Here, we employ polarizable molecular dynamics simulations to elucidate the impact of the electronic environment on the permeation process. We simulated eight distinct amino acid sidechain analogs within a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer using the Drude polarizable force field (FF). Our approach including both unbiased and umbrella sampling simulations. By using a polarizable FF, we sought to investigate explicit dipole responses in relation to local electric fields along the membrane normal. We evaluate molecular dipole moments, which exhibit variation based on their localization within the membrane, and compare the outcomes with analogous simulations using the nonpolarizable CHARMM36 FF. This comparative analysis aims to discern characteristic differences in the free energy surfaces of permeation for the various amino acid analogs. Our results provide the first systematic quantification of the impact of employing an explicitly polarizable FF in this context compared to the fixed-charge convention inherent to nonpolarizable FFs, which may not fully capture the influence of the membrane dielectric gradient.
Unexpected transformations during pyrroloiminoquinone biosynthesis
Authors: Figueroa Josseline Ramos , Zhu Lingyang , van der Donk Wilfred A.
Published: March 2024

Pyrroloiminoquinone containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP and tRNA dependent manner catalyzed by a PEptide Amino-acyl tRNA ligase (PEARL). The indole of the Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes that show that the proposed pathway is incorrect and that Nature’s route towards pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, the amino groups in pyrroloiminoquinones are derived from three different sources, glycine, asparagine, and leucine, all introduced in a tRNA dependent manner. We also show that an FAD-dependent putative glycine oxidase is required for the process that incorporates the nitrogens from glycine and leucine, and that a quinone reductase is required for the incorporation of the asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes such as the glutamyl-tRNA dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
Comparison of telephone and in-person interview modalities: duration, richness, and costs in the context of exploring determinants of equitable access to community health services in Meru, Kenya
Authors: Allen Luke N , Karanja Sarah , Tlhakanelo John , Macleod David , Tlhajoane Malebogo , Bastawrous Andrew
Published: March 2024

Background

Our research team is conducting phenomenological interviews in Kenya with people who have not been able to access community eye health services, aiming to explore the barriers and ideas for potential service modifications. We conducted an embedded study that compared in-person and telephone interview modalities in terms of time requirements, costs, and data richness.

Methods

A team of six interviewers conducted 31 in-person interviews and 31 telephone interviews using the same recruitment strategy, topic guide, and analytic matrix for each interview. We compared the mean duration; mean number of themes reported by each participant; total number of themes reported; interviewer rating of perceived richness; interviewer rating of perceived ease of building rapport; number of days taken by the team to complete all interviews; and all costs associated with conducting the interviews in each modality.

Findings

In-person interviews were 44% more expensive and took 60% longer to complete than our telephone interviews (requiring 5 days and 3 days respectively). The average in-person interview lasted 110 seconds longer than the average telephone interview (p=0.05) and generated more words and themes. However, the full set of interviews from both approaches identified similar numbers of barriers (p=0.14) and the same number of solutions (p=0.03). Interviewers universally felt that the in-person approach was associated with better rapport and higher quality data (p=0.01). Triangulation of themes revealed good agreement, with 88% of all solutions occurring in both sets, and no areas of thematic dissonance.

Discussion

The in-person approach required more time and financial resources, but generated more words and themes per person, and was perceived to afford richer data by interviewers. However, this additional richness did not translate into a greater number of themes that our team can act upon to improve services.
Dietary and Lifestyle Factors of Brain Iron Accumulation and Parkinson’s Disease Risk
Authors: Ahern Jonathan , Boyle Mary ET , Thompson Wesley K. , Fan Chun Chieh , Loughnan Robert
Published: March 2024

Purpose

Iron is an essential nutrient which can only be absorbed through an individual’s diet. Excess iron accumulates in organs throughout the body including the brain. Iron dysregulation in the brain is commonly associated with neurodegenerative diseases like Alzheimer’s disease and Parkinson’s Disease (PD). Our previous research has shown that a pattern of iron accumulation in motor regions of the brain related to a genetic iron-storage disorder called hemochromatosis is associated with an increased risk of PD. To understand how diet and lifestyle factors relate to this brain endophenotype and risk of PD we analyzed the relationship between these measures, estimates of nutrient intake, and diet and lifestyle preference using data from UK Biobank.

Methods

Using distinct imaging and non-imaging samples (20,477 to 28,388 and 132,023 to 150,603 participants, respectively), we performed linear and logistic regression analyses using estimated dietary nutrient intake and food preferences to predict a) brain iron accumulation score (derived from T2-Weighted Magnetic Resonance Imaging) and b) PD risk. In addition, we performed a factor analysis of diet and lifestyle preferences to investigate if latent lifestyle factors explained significant associations. Finally, we performed an instrumental variable regression of our results related to iron accumulation and PD risk to identify if there were common dietary and lifestyle factors that were jointly associated with differences in brain iron accumulation and PD risk.

Results

We found multiple highly significant associations with measures of brain iron accumulation and preferences for alcohol (factor 7: t=4.02, pFDR=0.0003), exercise (factor 11: t=-4.31, pFDR=0.0001), and high-sugar foods (factor 2: t=-3.73, pFDR=0.0007). Preference for alcohol (factor 7: t=-5.83, pFDR<1×10-8), exercise (factor 11: t=-7.66, pFDR<1×10-13), and high sugar foods (factor 2: t=6.03, pFDR<1×10-8) were also associated with PD risk. Instrumental variable regression of individual preferences revealed a significant relationship in which dietary preferences associated with higher brain iron levels also appeared to be linked to a lower risk for PD (p=0.004). A similar relationship was observed for estimates of nutrient intake (p=0.0006). Voxel-wise analysis of i) high-sugar and ii) alcohol factors confirmed T2-weighted signal differences consistent with iron accumulation patterns in motor regions of the brain including the cerebellum and basal ganglia.

Conclusion

Dietary and lifestyle factors and preferences, especially those related to carbohydrates, alcohol, and exercise, are related to detectable differences in brain iron accumulation and alterations in risk of PD, suggesting a potential avenue for lifestyle interventions that could influence risk.

Graphical Abstract
TheGPAT4/6/8clade functions in Arabidopsis root suberization non-redundantly with theGPAT5/7clade required for suberin lamellae
Authors: Gully Kay , Berhin Alice , De Bellis Damien , Herrfurth Cornelia , Feussner Ivo , Nawrath Christiane
Published: March 2024

Lipid polymers such as cutin and suberin strengthen the diffusion barrier properties of the cell wall in specific cell types and are essential for water relations, mineral nutrition, and stress protection in plants. Land plant–specific glycerol-3-phosphate acyltransferases (GPATs) of different clades are central players in cutin and suberin monomer biosynthesis. Here, we show that theGPAT4/6/8clade inArabidopsis thaliana, which is known to mediate cutin formation, is also required for developmentally regulated root suberization, in addition to the established roles ofGPAT5/7in suberization. TheGPAT5/7clade is mainly required for abscisic acid–regulated suberization. In addition, theGPAT5/7clade is crucial for the formation of the typical lamellated suberin ultrastructure observed by transmission electron microscopy, as distinct amorphous globular polyester structures were deposited in the apoplast of thegpat5 gpat7double mutant, in contrast to the thinner but still lamellated suberin deposition in thegpat4 gpat6 gpat8triple mutant. The intrinsic phosphatase activity of GPAT4, GPAT6, and GPAT8, which leads to monoacylglycerol biosynthesis, may be important for suberin biosynthesis. GPAT5/7 lack an active phosphatase domain. Notably,gpat5 gpat7phenotypes were partially reverted by treatment with a phosphatase inhibitor or the expression of phosphatase-dead variants ofGPAT4/6/8.Thus, GPATs that lack an active phosphatase domain, which are predicted to synthetize lysophosphatidic acids, might be crucial for the formation of the lamellated structure of suberin. GPATs with active and non-active phosphatase domains appear to have non-redundant functions and must cooperate to achieve the efficient biosynthesis of correctly structured suberin.

Significance statement

The establishment of proper lamellated suberin in roots plays essential roles in regulating mineral nutrition and water relations in plants. The basis for the macromolecular arrangement determining the ultrastructure and properties of suberin lamellae is unknown. Here, we report that both theGPAT4/6/8andGPAT5/7clades of glycerol-3-phosphate acyltransferases (GPATs) contribute to suberin formation in Arabidopsis roots. In addition, we reveal that theGPAT5/7clade is required for the formation of the lamellated suberin ultrastructure. Several lines of evidence suggest that the loss of phosphatase activity in GPATs might have played a crucial role in the formation of suberin lamellae during evolution.
Joint contribution of adaptation and neuronal population recruitment to response level in visual area MT: a computational model
Authors: Cravo Maria Inês , Bernardes Rui , Castelo-Branco Miguel
Published: March 2024

Adaptation is a form of short-term plasticity triggered by prolonged exposure to a stimulus, often resulting in altered perceptual sensitivity to stimulus features through a reduction in neuronal firing rates. Experimental studies have explored adaptation to bistable stimuli, specifically a stimulus comprising inward-moving plaids that can be perceived as either a grating moving coherently downward or two plaids moving incoherently through each other. Functional magnetic resonance imaging (fMRI) recordings have shown higher activity during incoherent perception and lower activity during coherent stimulus perception. There are two potential explanations for the underlying neural mechanisms: a weaker coherent stimulus response may result from stronger adaptation to coherent versus incoherent motion, or a stronger incoherent stimulus response could stem from the involvement of more neural populations to represent motion in more directions. Here, we employ a computational model of visual neurons with and without firing rate adaptation to test these hypotheses. By simulating the mean activity of a network of thirty-two columnar populations of visual area MT, each tuned to one direction of motion, we investigate the impact of firing rate adaptation on the blood-oxygen-level-dependent (BOLD) signal generated by the network in response to coherent and incoherent stimuli. Our results replicate the experimental curves both during and after stimulus presentation only when the model includes adaptation, highlighting the importance of this mechanism. However, our findings reveal that the response to incoherent motion is larger than the response to coherent motion for a wide variety of stimulus parameters and adaptation regimes, suggesting that the observed reduced response to coherent stimuli is most likely due to the activation of smaller neuronal populations, in alignment with the second hypothesis. Hence, adaptation and differential neuronal recruitment work together to give rise to the observed hemodynamic responses. This computational work sheds light on experimental results and enriches our understanding of the mechanisms involved in neural adaptation, particularly in the context of heterogeneous neuronal populations.
Structures of transcription-translation coupling complexes at each stage of the translation cycle
Authors: Zhang Jing , Lu Guoliang , Zhou Wei , Yang Mingxia , Li Li , Shao Huihui , Zhou Xiaogen , Chen Changbin , Ebright Richard H. , Gao Yue , Lin Jinzhong , Wang Chengyuan
Published: March 2024

Bacterial transcription and translation are frequently linked through a transcribing RNA polymerase following the leading ribosome, a process termed transcription-translation coupling (TTC). Three distinct TTC structures, the “collided expressome” (TTC-A), the “coupled expressome” (TTC-B) and the “long-range coupled expressome” (TTC-LC) have been reported, but the biological significance of all complexes is still subject to uncertainty. Furthermore, all of the ribosomes in the structures are determined in a static state. The underlying translation dynamics within these TTCs remain elusive. Here, we reconstitute the complete active transcription-translation system, using antibiotics and a series of different lengths of mRNAs to trap intermediate coupling states, and determine Cryo-EM structures showing the snapshots for the dynamic reaction trajectory. The results show five states of TTC-B representing the whole stages of the translation elongation cycle. TTC-B is compatible with ribosome conformational changes during translation elongation and coordinates transcription elongation with translation elongation. The results show two distinct TTC-A in translational pre-translocation and translocation intermediate states in which the RNAP becomes unstable as the translation progresses. The results further show that TTC-A is the crucial state where the ribosomes could exert mechanical force on RNAP, leading to the potential transition between TTC-A and TTC-B within mRNA spacer ranging from 7 to 9 codons and suggesting a ribosome-dependent transcription termination within mRNA spacer shorter than 7 codons. The results further show TTC-LC is also compatible with ribosome conformational changes during translation elongation cycle but with less stability compared with TTC-B and shows the potential transition with TTC-B within mRNA spacer of 13 codons. Our results provide a comprehensive blueprint detailing the dynamic interplay of transcription-translation coupling.
Unveiling shared genetic regulators for plant architectural and biomass yield traits in sorghum
Authors: Singh Anuradha , Newton Linsey A , Schnable James C , Thompson Addie M.
Published: March 2024

Sorghum is emerging as an ideal genetic model for designing high-biomass bioenergy crops. Biomass yield, a complex trait influenced by various plant architectural features, is typically regulated by numerous genes. This study aims to dissect the genetic mechanisms underlying fourteen plant architectural and ten biomass yield traits in a sorghum association panel (SAP) across two growing seasons. We identified 321 associated loci via genome-wide association studies involving 234,264 single nucleotide polymorphisms (SNPs). These loci encompass both genes with a priori links to biomass traits, such as maturity, dwarfing (Dw), leafbladeless1, cryptochrome, and several loci not previously linked to roles in determining these traits. We identified 22 pleiotropic loci associated with variation in multiple phenotypes. Three of these loci, located on chromosomes 3 (S03_15463061), 6 (S06_42790178; Dw2), and 9 (S09_57005346; Dw1), exert significant and consistent effects on multiple traits. Additionally, we identified three genomic hotspots on chromosomes 6, 7, and 9, containing multiple SNPs associated with variation in plant architecture and biomass yield traits. Positive correlations were observed among linked SNPs close to or within the same genomic regions. Thirteen haplotypes were identified from these positively correlated SNPs on chr 6, with haplotypes 8 and 11 emerging as optimal combinations, exhibiting pronounced effects on the traits. Lastly, network analysis revealed that loci associated with flowering, plant heights, leaf characteristics, plant number, and tiller number per plant were highly interconnected with other genetic loci linked to plant architecture and biomass yield traits. The pyramiding of favorable alleles related to these traits holds promise for enhancing the future development of bioenergy sorghum crops.
Escherichia coli grown in cost-effective conical tubes produces more plasmid DNA
Authors: Marquez Mayra , Chen Qian , Cachaco Silvia , Sui Hongyan , Imamichi Tomozumi
Published: March 2024

Before the COVID-19 pandemic, we grew plasmid-transformedEscherichia coliin Falcon round-bottom-polypropylene tubes (F-Round-PP) and isolated plasmid using a Miniprep kit. When obtaining sufficient quantities of F-Round-PP became problematic during the pandemic and the inflation, we grew them using any available tubes. Notably, we observed that plasmid yield from cells grown in a cost-effective Oxford conical-polypropylene tubes (O-Conical-PP) was higher than that from F-Round-PP. We assessed the impact using O-Conical-PP and other conical brand tubes. As a result, the plasmid yield from O-Conical-PP (the list price is nearly 1/3 of F-Round-PP) was 1.5-fold higher than other PP tubes (p<0.001). We propose that researchers may need to re-assess the effectiveness of their laboratory supplies to optimize the budget during this inflationary period.
Biophysical metabolic modeling of complex bacterial colony morphology
Authors: Dukovski Ilija , Golden Lauren , Zhang Jing , Osborne Melisa , Segrè Daniel , Korolev Kirill S.
Published: March 2024

Microbial colony growth is shaped by the physics of biomass propagation and nutrient diffusion, and by the metabolic reactions that organisms activate as a function of the surrounding environment. While microbial colonies have been explored using minimal models of growth and motility, full integration of biomass propagation and metabolism is still lacking. Here, building upon our framework for Computation of Microbial Ecosystems in Time and Space (COMETS), we combine dynamic flux balance modeling of metabolism with collective biomass propagation and demographic fluctuations to provide nuanced simulations ofE. colicolonies. Simulations produced realistic colony morphology, consistent with our experiments. They characterize the transition between smooth and furcated colonies and the decay of genetic diversity. Furthermore, we demonstrate that under certain conditions, biomass can accumulate along “metabolic rings” that are reminiscent of coffee-stain rings, but have a completely different origin. Our approach is a key step towards predictive microbial ecosystems modeling.
Enhanced Data Pre-processing for the Identification of Alzheimer’s Disease-Associated SNPs
Authors: Alves Juliana F , Costa Eduardo , Xavier Alencar , Brito Luiz , Cerri Ricardo
Published: March 2024

Alzheimer’s Disease (AD) is a complex neurodegenerative disorder that has gained significant attention in scientific research, particularly since the Human Genome Project. Based on twin studies that utilize the resemblance of Alzheimer’s disease risk between pairs of twins, it has been found that the overall heritability of the disease is estimated at 0.58. When shared environmental factors are taken into account, the maximum heritability reaches 0.79. This suggests that approximately 58-79% of the susceptibility to late-onset Alzheimer’s disease can be attributed to genetic factors [4]. In 2022, it is estimated that AD will affect over 50 million people worldwide, and its economic burden exceeds a trillion US dollars per year. One promising approach is Genome-Wide Association Studies (GWAS), which allow the identification of genetic variants associated with AD susceptibility. Of particular interest are Single Nucleotide Polymorphisms (SNPs), which represent variations in a single nucleotide base in the DNA sequence. In this study, we investigated the association between SNPs and AD susceptibility by applying various quality control (QC) parameters during data pre-processing and rank the SNP associations through mixed linear models-based GWAS implemented in BLUPF90. Our findings indicate that the identified SNPs are located in regions already associated with Alzheimer’s Disease, including non-coding regions. We also investigated the impact of incorporating demographic data into our models. However, the results indicated that the inclusion of such data did not yield any benefits for the model. This study highlights the importance of GWAS in identifying potential genetic risk factors for AD and underscores the need for further research to gain a better understanding of the complex genetic mechanisms underlying this debilitating disease.
Creating an Early Diagnostic Method for Glaucoma Using Convolutional Neural Networks
Authors: Alqarni Areej A. , Al Harbi Sanad H. , Subhan Irshad A.
Published: March 2024

According to the World Health Organization, glaucoma is a leading cause of blindness, accounting for over 12% of global blindness as it affects one in every 100 people. In fact, 79.6 million people worldwide live with blindness caused by glaucoma. This is because the current method for diagnosing glaucoma is by examining retinal fundus images. However, it is considerably difficult to distinguish the lesions’ features solely through manual observations by ophthalmologists, especially in the early phases. This study introduces a novel glaucoma detection method using attention-enhanced convolutional neural networks, achieving 98.9% accuracy and a swift 30-second detection time, vastly surpassing traditional diagnostic methods. The attention mechanism is utilized to learn pixel-wise features for accurate prediction. Several attention strategies have been developed to guide the networks in learning the important features and factors that affect localization accuracy. The algorithms were trained for glaucoma detection using Python 2.7, TensorFlow, Py Torch, and Keras Machine Learning-Based Applications. The methods were evaluated on Drishti-GS and RIM-ONE datasets with 361 training and 225 test sets, consisting of 344 healthy and 242 glaucomatous images. The proposed algorithms can achieve impressive results that show an increase in overall diagnostic efficiency, as the algorithm displays a 30-second detection time with 98.9% accuracy compared to the 72.3% accuracy of traditional testing methods. Finally, this algorithm has been implemented as a webpage, allowing patients to test for glaucoma. This webpage offers various services such as: connecting the patient to the nearest care setup; offering scientific articles regarding glaucoma; and a video game that supports eye-treatment yogic exercises to strengthen vision and focus. This early diagnostic method has the near future potential to decrease the percentage of irreversible vision loss due to glaucoma by 42.79% (the percentage was calculated using the mean absolute error function), which could prevent glaucoma from remaining the leading cause of blindness worldwide. Our glaucoma diagnostic webpage can be found at:Glaucoma Detector(glaucomadiagnosis.com)
Association between fruit and vegetable consumption and chronic diseases among food pantry users
Authors: Chen Jiacheng , Hosler Akiko S. , O’Grady Thomas J. , Romeiko Xiaobo X.
Published: March 2024

Introduction

Fruit and vegetable (FV) consumption can be a protective factor for chronic diseases, but few studies have investigated FV’s impact on health in the context of food/nutrition assistance system.

Methods

We used three health survey data collected in Upstate New York communities to construct a predictive model of food pantry use. The model was applied to a Northeastern US regional subset of SMART Behavioral Risk Factor Surveillance System (BRFSS) data to identify potential food pantry users. The associations between FV intake and diabetes, hypertension, and BMI were examined through multivariable logistic regression and linear regression analyses with food pantry use as a potential effect modifier.

Results

The analysis dataset had 5,257 respondents, and 634 individuals were estimated as food pantry users. Consumption of vegetables was associated with decreased odds of hypertension and a lower BMI regardless of food pantry use. Consumption of fruits was associated with decreased odds of diabetes regardless of food pantry use. The association between fruit consumption and BMI was modified by food pantry use. Among food pantry users, consumption of fruits was associated with a greater BMI, while among food pantry non-users, it was associated with a lower BMI.

Conclusion

The overall protective effects of increased FV consumption on chronic diseases suggest that increasing FV availability in food pantries may not only alleviate hunger but also improve health. Further research is needed to investigate the role of fruit including 100% fruit juice consumption and BMI among food pantry users.
Direct Ink Writing of Graphene Oxide Reinforced 13-93B1 Bioactive Glass Scaffolds for Bone Tissue Engineering Applications
Authors: Dixit Kartikeya , Vishwakarma Ashok , Kumar Hitendra , Kim Keekyoung , Sinha Niraj
Published: March 2024

Graphene-reinforced bioactive glass scaffolds have gained significant attention in the field of bone tissue engineering due to their unique combination of mechanical strength, bioactivity, and electrical conductivity. Additive manufacturing techniques, such as 3D printing, provide a versatile platform for fabricating these scaffolds with precise control over their architecture and composition. Consequently, in this work, we have fabricated graphene oxide (GO)-reinforced 13-93B1 bioactive glass scaffold using the direct ink writing technique. A Pluronic F-127- based ink was prepared for scaffold fabrication, and its rheological properties were assessed for shear thinning behaviour, structural support, and recovery. Further, the fabricated scaffolds were characterized using micro-computed tomography, scanning electron microscopy, and energy dispersive x-ray spectroscopy. Additionally, computational fluid dynamics simulations with Dulbecco’s modified eagle medium and blood were performed to evaluate the perfusion kinetics of the scaffolds. The inclusion of GO enhanced the compressive strength of the fabricated scaffolds by ∼225%. The morphological characterization based on micro-computed tomography showed that additively manufactured scaffolds have appropriate porosity, pore size, pore throat size, and interconnectivity. The live-dead assay results showed no cytotoxicity towards C2C12 mouse myoblast cells. Also, cell adhesion and cell viability results show better cell growth on the nanocomposite scaffolds. Overall, the fabricated scaffold is found suitable for bone tissue engineering applications.
The specific AMPK activator A-769662 ameliorates pathological phenotypes following mitochondrial DNA depletion
Authors: Carvalho Gustavo , Repolês Bruno , Nguyen Tran V.H. , Forslund Josefin M.E. , Ranjbarian Farahnaz , Mendes Isabela C. , Falabella Micol , Doimo Mara , Wanrooij Sjoerd , Pitceathly Robert D.S. , Hofer Anders , Wanrooij Paulina H.
Published: March 2024

AMP-activated protein kinase (AMPK) is a master regulator of cellular energy homeostasis that also plays a role in preserving mitochondrial function and integrity. Upon a disturbance in the cellular energy state that increases AMP levels, AMPK activity promotes a switch from anabolic to catabolic metabolism to restore energy homeostasis. However, it is currently unclear how severe of a mitochondrial dysfunction is required to trigger AMPK activation, and whether stimulation of AMPK using specific agonists can improve the cellular phenotype following mitochondrial dysfunction. Using a cell model of mitochondrial disease characterized by progressive mitochondrial DNA (mtDNA) depletion and deteriorating mitochondrial metabolism, we show that mitochondria-associated AMPK becomes activated early in the course of the advancing mitochondrial dysfunction, before any quantifiable decrease in the ATP/(AMP+ADP) ratio or respiratory chain activity. Moreover, stimulation of AMPK activity using the specific small-molecule agonist A-769662 alleviated the mitochondrial phenotypes caused by the mtDNA depletion and restored normal mitochondrial membrane potential. Notably, the agonist treatment was able to partially restore mtDNA levels in cells with severe mtDNA depletion, while it had no impact on mtDNA levels of control cells. The beneficial impact of the agonist was also observed in cells from patients suffering from mtDNA depletion. However, the positive effects of A-769662 in the two experimental cell models appeared to involve at least partially different mechanisms. These findings improve our understanding of the effects of specific small-molecule activators of AMPK on mitochondrial and cellular function, and suggest a potential utility for these compounds in disease states involving mtDNA depletion.
Early-life stress alters chromatin modifications in VTA to prime stress sensitivity
Authors: Geiger Luke T. , Balouek Julie-Anne , Farrelly Lorna A. , Chen Andy S. , Tang Megan , Bennett Shannon N. , Nestler Eric J. , Garcia Benjamin A. , Maze Ian , Peña Catherine Jensen
Published: March 2024

Early-life stress increases sensitivity to subsequent stress, which has been observed among humans, other animals, at the level of cellular activity, and at the level of gene expression. However, the molecular mechanisms underlying such long-lasting sensitivity are poorly understood. We tested the hypothesis that persistent changes in transcription and transcriptional potential were maintained at the level of the epigenome, through changes in chromatin. We used a combination of bottom-up mass spectrometry, viral-mediated epigenome-editing, behavioral quantification, and RNA-sequencing in a mouse model of early-life stress, focusing on the ventral tegmental area (VTA), a brain region critically implicated in motivation, reward learning, stress response, and mood and drug disorders. We find that early-life stress in mice alters histone dynamics in VTA and that a majority of these modifications are associated with an open chromatin state that would predict active, primed, or poised gene expression, including enriched histone-3 lysine-4 methylation and the H3K4 monomethylase Setd7. Mimicking ELS through over-expression of Setd7 and enrichment of H3K4me1 in VTA recapitulates ELS-induced behavioral and transcriptional hypersensitivity to future stress. These findings enrich our understanding of the epigenetic mechanisms linking early-life environmental experiences to long-term alterations in stress reactivity within the brain’s reward circuitry, with implications for understanding and potentially treating mood and anxiety disorders in humans.
Identification of a new family of peptidoglycan transpeptidases reveals atypical crosslinking is essential for viability inClostridioides difficile
Authors: Bollinger Kevin W. , Müh Ute , Ocius Karl L. , Apostolos Alexis J. , Pires Marcos M. , Helm Richard F. , Popham David L. , Weiss David S. , Ellermeier Craig D.
Published: March 2024

Clostridioides difficile, the leading cause of antibiotic-associated diarrhea, relies primarily on 3-3 crosslinks created by L,D-transpeptidases (LDTs) to fortify its peptidoglycan (PG) cell wall. This is unusual, as in most bacteria the vast majority of PG crosslinks are 4-3 crosslinks, which are created by penicillin-binding proteins (PBPs). Here we report the unprecedented observation that 3-3 crosslinking is essential for viability inC. difficile. We also report the discovery of a new family of LDTs that use a VanW domain to catalyze 3-3 crosslinking rather than a YkuD domain as in all previously known LDTs. Bioinformatic analyses indicate VanW domain LDTs are less common than YkuD domain LDTs and are largely restricted to Gram-positive bacteria. Our findings suggest that LDTs might be exploited as targets for antibiotics that killC. difficilewithout disrupting the intestinal microbiota that is important for keepingC. difficilein check.
Identification of novel evolutionarily conserved genes and pathways in human and mouse musculoskeletal progenitors
Authors: Saravanan S , Devika A. S , Pranty Abida Islam , Shaji R. V , Bhushan Raghu , Adjaye James , Sudheer Smita
Published: March 2024

The axial skeletal system and skeletal muscles of the vertebrates arise from somites, the blocks of tissues flanking both sides of the neural tube. The progenitors of Somites, called the Presomitic Mesoderm (PSM) reside at the posterior end of a developing embryo. Most of our understanding about these two early developmental stages comes from the studies on chick and mouse, and in the recent past, there have been a few studies on human. Here, we have analysed and compared the RNA-sequencing data of PSM and somite tissues from Mouse and Human. The functional and pathway enrichment analysis identified the key Hub-genes that are evolutionarily conserved in the PSM and the somites of both the organisms that include 23 multifunctional genes likely to be associated with different developmental disorders in humans. Our analysis revealed that NOTCH, WNT, MAPK, BMP, Calcium, ErbB, cGMP-PKG, RAS and RAP1 signaling pathways are conserved in both human and mouse during the development of PSM and Somites. Furthermore, we validated the expression of representative conserved candidates in the hESCs-derived PSM and somite cells (NOG,BMP2,BMP7,BMP5,HES5andMEF2C). Taken together, our study identifies putative gene interactions and pathways that are conserved across the mouse and human genomes, which may potentially have crucial roles in human PSM and somite development.
Association of microglia loss with hippocampal network impairments as a turning point in the amyloid pathology progression
Authors: Pizzirusso Giusy , Preka Efthalia , Goikolea Julen , Aguilar-Ruiz Celia , Rodriguez Patricia Rodriguez , Cabrera Guillermo Vazquez , Laterza Simona , Leal Maria Latorre , Eroli Francesca , Blomgren Klas , Maioli Silvia , Nilsson Per , Fragkopoulou Adamantia , Fisahn André , Arroyo-García Luis Enrique
Published: March 2024

Alzheimer’s disease is a progressive neurological disorder causing memory loss and cognitive decline. The underlying causes of cognitive deterioration and neurodegeneration remain unclear, leading to a lack of effective strategies to prevent dementia. Recent evidence highlights the role of neuroinflammation, particularly involving microglia, in Alzheimer’s disease onset and progression. Characterizing the initial phase of Alzheimer’s disease can lead to the discovery of new biomarkers and therapeutic targets, facilitating timely interventions for effective treatments. We used theAppNL-G-Fknock-in mouse model, which resembles the amyloid pathology and neuroinflammatory characteristics of Alzheimer’s disease, to investigate the transition from a pre-plaque to an early plaque stage with a combined functional and molecular approach. Our experiments show a progressive decrease in the power of cognition-relevant hippocampal gamma oscillations during the early stage of amyloid pathology, together with a modification of fast-spiking interneuron intrinsic properties and postsynaptic input. Consistently, transcriptomic analyses revealed that these effects are accompanied by changes in synaptic function-associated pathways. Concurrently, homeostasis-and inflammatory-related microglia signature genes were downregulated. Moreover, we found a decrease in Iba1-positive microglia in the hippocampus that correlates with plaque aggregation and neuronal dysfunction. Collectively, these findings support the hypothesis that microglia play a protective role during the early stages of amyloid pathology by preventing plaque aggregation, supporting neuronal homeostasis, and overall preserving the oscillatory network’s functionality. These results suggest that the early loss of microglia could be a pivotal event in the progression of Alzheimer’s disease, potentially triggering plaque deposition, impairment of fast-spiking interneurons, and the breakdown of the oscillatory circuitry in the hippocampus.