bluuebunny/crossref_metadata_2025 huggingface dataset:
Benzimidazolium quaternary ammonium salts: synthesis, single crystal and Hirshfeld surface exploration supported by theoretical analysis
Authors: Jamil Sajid , Gondal Humaira Yasmeen , Ali Akbar , Hussain Ajaz , Akram Nadia , Nisar Muhammad , Tahir Muhammad Nawaz , Ashfaq Muhammad , Raza Abdul Rauf , Muhammad Shabbir , Cheema Zain M. , Mustafai Aleena , Sameeh Manal Y.
Published: February 2024

Owing to the broad applications of quaternary ammonium salts (QAS), we present the synthesis of benzimidazolium-based analogues with variation in the alkyl and alkoxy group at N-1 and N-3 positions. All the compounds were characterized by spectroscopic techniques and found stable to air and moisture both in the solid and solution state. Moreover, molecular structures were established through single-crystal X-ray diffraction studies. The crystal packing of the compounds was stabilized by numerous intermolecular interactions explored by Hirshfeld surface analysis. The enrichment ratio was calculated for the pairs of chemical species to acquire the highest propensity to form contacts. Void analysis was carried out to check the mechanical response of the compounds. Furthermore, theoretical investigations were also performed to explore the optoelectronic properties of compounds. Natural population analysis (NPA) has been conducted to evaluate the distribution of charges on the synthesized compounds, whereas high band gaps of the synthesized compounds by frontier molecular orbital (FMO) analysis indicated their stability. Nonlinear optical (NLO) analysis revealed that the synthesized QAS demonstrates significantly improved NLO behaviour than the standard urea.
Fossil-calibrated phylogenies of Southern cave wētā show dispersal and extinction confound biogeographic signal
Authors: Dowle Eddy J. , Trewick Steven A. , Morgan-Richards Mary
Published: February 2024

The biota of continents and islands are commonly considered to have a source–sink relationship, but small islands can harbour distinctive taxa. The distribution of four monotypic genera of Orthoptera on young subantarctic islands indicates a role for long-distance dispersal and extinction. Phylogenetic relationships were inferred from whole mtDNA genomes and nuclear sequences (45S cassette; four histones). We used a fossil and one palaeogeographic event to calibrate molecular clock analysis. We confirm that neither the Australian nor Aotearoa-New Zealand Rhaphidophoridae faunas are monophyletic. The radiation of Macropathinae may have begun in the late Jurassic, but trans-oceanic dispersal is required to explain the current distribution of some lineages within this subfamily. Dating the most recent common ancestor of seven island endemic species with their nearest mainland relative suggests that each existed long before their island home was available. Time estimates from our fossil-calibrated molecular clock analysis suggest several lineages have not been detected on mainland New Zealand, Australia, or elsewhere most probably due to their extinction, providing evidence that patterns of extinction, which are not consistently linked to range size or lineage age, confound biogeographic signal.
One-pot domino syntheses of 3-alkyl-3-
N
-substituted aminobenzofuran-2(3
H
)-ones based on alkali-promoted Michael addition and lactonization
Authors: Chu Xiao-Hui , Gao Na , Wang Wei , Zheng Zhong , Wang Jin-Jun
Published: February 2024

In this paper, a novel cascade reaction of caesium carbonate-promoted Michael addition and lactonization for the one-pot synthesis of 3-alkyl-3-
N
-substituted aminobenzofuran-2(3
H
)-one derivatives has been established based on the screening of the alkaline reagents and optimization of reaction conditions, in which the
N
-substituted (
ortho
-hydroxy)aryl glycine esters were used as the Michael donors to react with different
α
, β-unsaturated carbonyl compounds. In the case of using the asymmetric starting material, the epimers could be successfully separated by conventional chromatography. In addition, plausible mechanisms were suggested and the absolute configuration of the epimer was analysed. All the chemical structures of unreported benzofuran-2(3
H
)-one derivatives were characterized by
1
H nuclear magnetic resonance (NMR),
13
C NMR, IR and high-resolution mass spectrometry (HRMS).
Dormancy break, sprouting and later tuber reproduction in response to different tuber sizes of tiger nut (Cyperus esculentusL.)
Authors: Liu Binshuo , Li Hanbo , Chen Wei , Wang Ying , Chen Yubo , Wei Xiaowei
Published: February 2024

Dormancy release pattern, sprout growth and later reproduction were studied among various tuber sizes ofCyperus esculentusto determine effective methods to release dormancy and further to select suitable tuber size of this species in production. The results showed that medium tubers performed better during sprouting than large and small tubers under all pre-sprouting treatments. Pre-sprouting treatments at 25°C, 35°C, RT (room temperature) and −2°C were effective in relieving dormancy in medium tubers. Tiller number from medium tubers were significantly higher under 25°C, RT and 45°C than under 35°C and −2°C. Shoot and root mass from medium tubers were significantly higher under the 25°C, 35°C and RT than under other treatments. Tiller and tuber numbers both decreased with decreasing tuber size, as did tuber yield after three months of growth. Furthermore, leftover mass decreased with decreasing tuber mass and remained unchanged at sprouting and maturity periods. A significantly negative allometric correlation was found between plant mass and tuber mass from small tubers. However, a significantly positive allometric correlation was found between tuber size and tuber number from large tubers. In conclusion, medium tubers had a competitive advantage in sprouting, growth and reproduction.
Complete integrability and equilibrium thermodynamics of biaxial nematic systems with discrete orientational degrees of freedom
Authors: De Matteis Giovanni , Giglio Francesco , Moro Antonio
Published: February 2024

We study a discrete version of a biaxial nematic liquid crystal model with external fields via an approach based on the solution of differential identities for the partition function. In the thermodynamic limit, we derive the free energy of the model and the associated closed set of equations of state involving four order parameters, proving the integrability and exact solvability of the model. The equations of state are specified via a suitable representation of the orientational order parameters, which imply two-order parameter reductions in the absence of external fields. A detailed exact analysis of the equations of state reveal a rich phase diagram where isotropic versus uniaxial versus biaxial phase transitions are explicitly described, including the existence of triple and tricritical points. Results on the discrete models are qualitatively consistent with their continuum analogue. This observation suggests that, in more general settings, discrete models may be used to capture and describe phenomena that also occur in the continuum for which exact equations of state in closed form are not available.
Growth and morphogenesis of an everted tubular biological tissue
Authors: Liu Congshan , Du Yangkun , Li Kecheng , Han Zilong , Lü Chaofeng
Published: February 2024

Eversion, a ubiquitous phenomenon in living organisms, significantly contributes to the growth and morphogenesis of soft biological tissues and organs. In this study, we examine the role of elasticity and geometry in the morphogenesis of everted tubular biological tissues, both theoretically and experimentally. Our findings demonstrate that the morphogenesis of an everted tubular tissue is primarily influenced by its elasticity and geometry. Through linear stability analysis, we show that an everted bilayer tubular tissue, with isotropic differential growth, can generate a circumferential or two-dimensional pattern, but fails to produce an axial pattern, which distinguishes it from a bilayer tubular tissue without eversion. Furthermore, as the modulus ratio and layer thicknesses increase, the surface instability pattern transitions from a two-dimensional pattern to a circumferential pattern. Notably, when the modulus ratio or layer thickness reaches sufficiently high values, spontaneous instabilities emerge on the inner surface of the everted bilayer tubular tissues pre-growth. To investigate the morphological instability of everted bilayer tubes, we perform a series of quantificational finite-element simulations and swelling experiments. The results of both numerical simulations and experimental observations align well with our theoretical analysis. This study not only enhances our comprehension of everted tubular tissue morphogenesis but also offers valuable insights for biomedical engineering and growth self-assembly applications.
Enhanced electrophysiological responses to explicitly predicted and pre-imagined inputs, with confirmation from online decoding with neuro-feedback
Authors: Arnold Derek H. , Electricity Felicity , Saurels Blake W.
Published: February 2024

Neural responses to sensory inputs can scale with the likelihood of encountering the input. This is consistent with the predictive coding framework, in that the human brain is expected to be less responsive to predicted inputs. Typically, however, prediction is not explicitly measured. It is inferred from the probability of encountering an event. When an input is explicitly predicted, responses to predicted inputs can be enhanced. Here, we ask if this effect can be ascribed to a generic priming effect, from pre-cogitating about one of two possible inputs. Consistent with this, we find that P300s (a relatively late event-related potential measured with electroencephalography) are greater for explicitly predicted audio and visual inputs, and that this effect cannot be distinguished from a priming effect from pre-imagining audio or visual presentations. Evidence indicates that participants engaged in pre-imagining presentations, as we were able to decode online what type of presentation (audio or visual) they were imagining with a high success rate (approx. 73%), and we encouraged compliance with neuro-feedback regarding this success rate. Our data confirm that human cortex can be more responsive to inputs that have been subject to pre-cogitation—including explicit predictions. This highlights that while anticipatory processes can reduce responding to likely inputs, they can also enhance responding to explicitly predicted inputs.
Significant differences in the caecal bacterial microbiota of red and grey squirrels in Britain
Authors: Hall Lucy , Nichols Christopher , Martelli Francesca , Leng Joy , Shuttleworth Craig , La Ragione Roberto
Published: February 2024

Introduction. Red squirrel populations have declined in the UK since the introduction of the grey squirrel, due to resource competition and grey squirrels carrying a squirrelpox virus that is fatal to red squirrels.

Hypothesis/Gap Statement. It is not known if the gut microbiota of the two species is similar and if this could impact the survival of red squirrels.

Aim. The aim of this study was to profile the caecal microbiota of red and grey squirrels obtained opportunistically from a conservation programme in North Wales.

Methodology. Bacterial DNA was extracted from ten red and ten grey squirrels and sent for 16S rRNA sequencing. Three samples from red squirrels returned less than 5000 reads, and so were not carried forward for further analyses.

Results. Samples taken from the caeca of red squirrels had significantly lower bacterial diversity and a higher percentage of Bacilli bacteria when compared to samples from grey squirrels. When the abundance of bacterial groups across all levels of phylogenetic classifications was compared between the two groups of squirrels, grey squirrels had a higher abundance of bacteria belonging to the families S24-7, RF39 and Rikenellaceae. Escherichia coli with resistance to amoxicillin/clavulanic acid was identified in all samples. Cefotaxime resistance was identified in two samples from grey squirrels along with sulfamethoxazole/trimethoprim in one of these samples.

Conclusion. Clear differences between the caecal microbiota of the two species of squirrel were identified, which could potentially impact their overall health and ability to compete for resources.
Microenvironment Shapes Small Cell Lung Cancer Neuroendocrine States and Presents Therapeutic Opportunities
Authors: Desai Parth , Takahashi Nobuyuki , Kumar Rajesh , Nichols Samantha , Malin Justin , Hunt Allison , Schultz Christopher , Cao Yingying , Tillo Desiree , Nousome Darryl , Chauhan Lakshya , Sciuto Linda , Jordan Kimberly , Rajapakse Vinodh , Tandon Mayank , Lissa Delphine , Zhang Yang , Kumar Suresh , Pongor Lorinc , Singh Abhay , Schroder Brett , Sharma Ajit Kumar , Chang Tiangen , Vilimas Rasa , Pinkiert Danielle , Graham Chante , Butcher Donna , Warner Andrew , Sebastian Robin , Mahon Mimi , Baker Karen , Cheng Jennifer , Berger Ann , Lake Ross , Abel Melissa , Krishnamurthy Manan , Chrisafis George , Fitzgerald Peter , Nirula Micheal , Goyal Shubhank , Atkinson Devon , Bateman Nicholas W. , Abulez Tamara , Nair Govind , Apolo Andrea , Guha Udayan , Karim Baktiar , Meskini Rajaa El , Ohler Zoe Weaver , Jolly Mohit Kumar , Schaffer Alejandro , Ruppin Eytan , Kleiner David , Miettinen Markku , Brown G Tom , Hewitt Stephen , Conrads Thomas , Thomas Anish
Published: February 2024

Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the tumor microenvironment (TME) exhibits substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAF) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Together, our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLCs adaptable nature, opening possibilities for re-programming the intercellular communications that shape SCLC tumor states.
The effect of constitutive root isoprene emission on root phenotype and physiology under control and salt stress conditions
Authors: Bellucci Manuel , Mostofa Mohammad Golam , Weraduwage Sarathi M. , Xu Yuan , Abdelrahman Mostafa , De Gara Laura , Loreto Francesco , Sharkey Thomas D.
Published: February 2024

ABSTRACT

Isoprene, a volatile hydrocarbon, is typically emitted from the leaves and other aboveground plant organs; isoprene emission from roots is not well studied. Given its well-known function in plant growth and defense aboveground, isoprene may also be involved in shaping root physiology to resist belowground stress. We used isoprene-emitting transgenic lines (IE) and a non-emitting empty vector and/or wild type lines (NE) ofArabidopsisto elucidate the roles of isoprene in root physiology and salt stress resistance. We assessed root phenotype and metabolic changes, hormone biosynthesis and signaling, and stress-responses under normal and saline conditions of IE and NE lines. We also analyzed the root transcriptome in the presence or absence of salt stress. IE lines emitted isoprene from roots, which was associated with higher primary root growth, root biomass, and root/shoot biomass ratio under both control and salt stress conditions. Transcriptome data indicated that isoprene altered the expression of key genes involved in hormone metabolism and plant responses to stress factors. Our findings reveal that root constitutive isoprene emission sustains root growth also under salinity by regulating and/or priming hormone biosynthesis and signaling mechanisms, amino acids biosynthesis, and expression of key genes relevant to salt stress defense.
A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures
Authors: Škrbić Tatjana , Giacometti Achille , Hoang Trinh X. , Maritan Amos , Banavar Jayanth R.
Published: February 2024

Linear chain molecules play a central role in polymer physics with innumerable industrial applications. They are also ubiquitous constituents of living cells. Here we highlight the similarities and differences between two distinct ways of viewing a linear chain. We do this, on the one hand, through the lens of simulations for a standard polymer chain of tethered spheres at low and high temperatures and, on the other hand, through published experimental data on an important class of biopolymers, proteins. We present detailed analyses of their local and non-local structures as well as the maps of their closest contacts. We seek to reconcile the startlingly different behaviors of the two types of chains based on symmetry considerations.
GX-I7(rhIL-7-hyFc, efineptakin alfa), a long-acting IL-7, safely and effectively increased peripheral CD8+and CD4+T cells and TILs in patients with solid tumors
Authors: Kim Gun Min , Kim Sojeong , Lee Myung Ah , Byun Mi-Sun , Choi Donghoon , Yang Se Hwan , Woo Jung Won , Sung Young Chul , Shin Eui-Cheol , Park Su-Hyung , Kim Tae Won , Sohn Joohyuk
Published: February 2024

Purpose

GX-I7 (rhIL-7-hyFc, efineptakin alfa) is a hybrid Fc-fused long-acting recombinant human interleukin-7 (IL-7) developed by Genexine, Inc. with the aim of correcting T-cell deficiency, thereby strengthening the immune response to fight against cancer. This Phase 1b trial (NCT03478995) was designed to assess the safety, tolerability, pharmacokinetics (PK), and pharmacodynamics (PD) of GX-I7 in patients with locally advanced or metastatic solid tumors.

Methods

This study consisted of two phases: dose-escalation and expansion. Eight dose groups were administered GX-I7 intramuscularly at doses ranging from 60 to 1700 μg/kg every three or six weeks.

Results

All regimens were safe and well tolerated, with the most frequently reported adverse drug reactions being injection site reactions, which were manageable with or without pharmacological intervention. GX-I7 demonstrated dose-dependent increases in the maximum serum concentration (Cmax) and area under the curve up to the last measurable concentration (AUClast). In addition, a dose-dependent increase in circulating CD8+/CD4+T cells was observed. In five patients who consented for biopsy, a statistically significant increase in tumor-infiltrating CD8+/CD4+T cell lymphocytes after GX-I7 treatment was observed.

Conclusion

These findings support the use of GX-I7 as a safe and effective T cell-amplifying agent capable of correcting T cell deficiencies. GX-I7 is expected to result in better clinical outcomes when used in combination with other anti-cancer agents by creating a better environment for immune checkpoint inhibitors and anti-cancer treatments to fight cancer.
The lateral habenula is required for maternal behavior in the mouse dam
Authors: Benedict Jessie , Cudmore Robert H. , Oden Diarra , Spruell Aleah , Linden David J.
Published: February 2024

Mammalian parenting is an unusually demanding commitment. How did evolution co-opt the reward system to ensure parental care? Previous work has implicated the lateral habenula (LHb), an epithalamic nucleus, as a potential intersection of parenting behavior and reward. Here, we examine the role of the LHb in the maternal behavior of naturally parturient mouse dams. We show that kainic acid lesions of the LHb induced a severe maternal neglect phenotype in dams towards their biological pups. Next, we demonstrate that through chronic chemogenetic inactivation of the LHb using DREADDs impaired acquisition and performance of various maternal behaviors, such as pup retrieval and nesting. We present a random intercepts model suggesting LHb-inactivation prevents the acquisition of the novel pup retrieval maternal behavior and decreases nest building performance, an already-established behavior, in primiparous mouse dams. Lastly, we examine the spatial histology of kainic-acid treated dams with a random intercepts model, which suggests that the role of LHb in maternal behavior may be preferentially localized at the posterior aspect of this structure. Together, these findings serve to establish the LHb as required for maternal behavior in the mouse dam, thereby complementing previous findings implicating the LHb in parental behavior using pup-sensitized virgin female mice.

Significance Statement

Work conducted using rats in the 1990s suggested an important role for the LHb in maternal behavior, but this area of research has since lain dormant. In the interim, the LHb has been garnering attention as a hub for punishment signaling. Recently, interest in the LHb’s role in maternal behavior was renewed, with an important paper examining LHb function during pup-directed behaviors in pup-sensitized virgin female mice. But it is unknown how closely pup-directed behaviors in sensitized virgin females may mimic maternal behavior in natural mouse mothers. This work demonstrates the importance of the LHb in the regulation of natural maternal behavior in the mouse.
Biological management, rather than chemical management, promotes the interaction between plants and their microbiome
Authors: Zhao Tianci , Jia Xiu , Liu Xipeng , Nepal Jyotsna , Attard Eléonore , Guyoneaud Rémy , Treder Krzysztof , Pawłowska Anna , Michałowska Dorota , Berg Gabriele , Stocker Franz , Cernava Tomislav , Elzenga J. Theo M. , Salles Joana Falcão
Published: February 2024

In the face of climate change, developing sustainable agricultural practices to reduce the use of synthetic herbicides and pesticides is crucial. However, breeding for higher yields can lead to the decoupling of plant roots and beneficial rhizosphere microbes. In this study, we aim to identify potato cultivars with functional traits facilitating efficient interactions with the rhizosphere microbiome under various agricultural treatments in the field. With the results of profiling microbial communities with amplicon sequencing data of bacteria (16S rRNA gene fragments) and fungi (ITS2 region), a piecewise structural equation model was developed. This model explains the trade-off effects of agricultural management and potato cultivars on plant growth by affecting the rhizosphere microbiome. Furthermore, we highlight that plant cultivar and the rhizosphere microbiome together determine plant below-ground growth under biological management. In contrast, both components are found to be uncoupled under chemical and control management. Our study reveals the importance of considering microbiomes in the breeding process to achieve the goals of sustainable agriculture.
Infer metabolic velocities from moment differences of molecular weight distributions
Authors: Tuobang Li
Published: February 2024

Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a challenge in inferring metabolic balance changes over time or after different treatments. Isotopic labeling experiment is the standard method to infer metabolic flux, which is currently defined as the flow of a single metabolite through a given pathway over time. However, there is still no way to accurately infer the metabolic balance changes after different treatments in an experiment. This study introduces a different concept: molecular weight distribution, which is the empirical distribution of the molecular weights of all metabolites of interest. By estimating the differences of the location and scale estimates of these distributions, it becomes possible to quantitatively infer the metabolic balance changes even without requiring knowledge of the exact chemical structures of these compounds and their related pathways. This research article provides a mathematical framing for a classic biological concept.
Intrinsic diving reflex induces potent antioxidative response by activation of NRF2 signaling
Authors: Powell Keren , Wadolowski Steven , Tambo Willians , Strohl Joshua J. , Kim Daniel , Turpin Justin , Al-Abed Yousef , Brines Michael , Huerta Patricio T. , Li Chunyan
Published: February 2024

Aims

This study aims to elucidate the underlying mechanisms of diving reflex, a powerful endogenous mechanism supporting underwater mammalian survival. Antioxidative responses, observed in marine mammals, may be contributing factors. Using a multi-organ approach, this study assesses whether acute and chronic diving reflex activate nuclear factor-erythroid-2-related factor 2 (NRF2) signaling pathways, which regulate cellular antioxidant responses.

Methods

Male Sprague-Dawley rats (n=38) underwent either a single diving session to elicit acute diving reflex, or daily diving sessions for 4-weeks to produce chronic diving reflex. NRF2 (total, nuclear, phosphorylated), NRF2-downstream genes, and malondialdehyde were assessed via Western blot, immunofluorescence, RT-PCR, and ELISA in brain, lung, kidney, and serum.

Results

Diving reflex increased nuclear NRF2, phosphorylated NRF2, and antioxidative gene expression, in an organ-specific and exposure time-specific manner. Comparing organs, the brain had the highest increase of phosphorylated NRF2 expression, while kidney had the highest degree of nuclear NRF2 expression. Comparing acute and chronic sessions, phosphorylated NRF2 increased the most with chronic diving reflex, but acute diving reflex had the highest antioxidative gene expression. Notably, calcitonin gene-related peptide appears to mediate diving reflex’ effects on NRF2 activation.

Conclusions

Acute and chronic diving reflex activate potent NRF2 signaling in the brain and peripheral organs. Interestingly, acute diving reflex induces higher expression of downstream antioxidative genes compared to chronic diving reflex. This result contradicts previous assumptions requiring chronic exposure to diving for induction of antioxidative effects and implies that the diving reflex has a strong translational potential during preconditioning and postconditioning therapies.

Key Points

Diving reflex activates potent NRF2 signaling via multiple mechanisms, including phosphorylation, nuclear translocation, and KEAP1 downregulation with both acute and chronic exposure.

Diving reflex activates NRF2 via differential pathways in the brain and other organs; phosphorylated NRF2 increases more in the brain, while nuclear NRF2 increases more in the peripheral organs.

Acute diving reflex exposure induces a more pronounced antioxidative effect than chronic diving reflex exposure, indicating that the antioxidative response activated by diving reflex is not dependent upon chronic adaptive responses and supports diving reflex as both a preconditioning and postconditioning treatment.
iSCORE-PD: an isogenic stem cell collection to research Parkinson’s Disease
Authors: Busquets Oriol , Li Hanqin , Syed Khaja Mohieddin , Jerez Pilar Alvarez , Dunnack Jesse , Bu Riana Lo , Verma Yogendra , Pangilinan Gabriella R. , Martin Annika , Straub Jannes , Du YuXin , Simon Vivien M. , Poser Steven , Bush Zipporiah , Diaz Jessica , Sahagun Atehsa , Gao Jianpu , Hernandez Dena G. , Levine Kristin S. , Booth Ezgi O. , Bateup Helen S. , Rio Donald C. , Hockemeyer Dirk , Blauwendraat Cornelis , Soldner Frank
Published: February 2024

Parkinson’s disease (PD) is a neurodegenerative disorder caused by complex genetic and environmental factors. Genome-edited human pluripotent stem cells (hPSCs) offer the uniique potential to advance our understanding of PD etiology by providing disease-relevant cell-types carrying patient mutations along with isogenic control cells. To facilitate this experimental approach, we generated a collection of 55 cell lines genetically engineered to harbor mutations in genes associated with monogenic PD (SNCAA53T,SNCAA30P,PRKNEx3del,PINK1Q129X,DJ1/PARK7Ex1-5del,LRRK2G2019S,ATP13A2FS,FBXO7R498X/FS,DNAJC6c.801 A>G+FS,SYNJ1R258Q/FS,VPS13CA444P,VPS13CW395C,GBA1IVS2+1). All mutations were generated in a fully characterized and sequenced female human embryonic stem cell (hESC) line (WIBR3; NIH approval number NIHhESC-10-0079) using CRISPR/Cas9 or prime editing-based approaches. We implemented rigorous quality controls, including high density genotyping to detect structural variants and confirm the genomic integrity of each cell line. This systematic approach ensures the high quality of our stem cell collection, highlights differences between conventional CRISPR/Cas9 and prime editing and provides a roadmap for how to generate gene-edited hPSCs collections at scale in an academic setting. We expect that our isogenic stem cell collection will become an accessible platform for the study of PD, which can be used by investigators to understand the molecular pathophysiology of PD in a human cellular setting.
Urinary Metabolomic Profile is Minimally Impacted by Common Storage Conditions and Additives
Authors: Weldon Kelly C. , Panitchpakdi Morgan , Caraballo-Rodríguez Andrés Mauricio , Wolfe Alan J. , Dorrestein Pieter C. , Brubaker Linda , Burnett Lindsey A.
Published: February 2024

Metabolomics reflects the molecular communications within a biological system. Urine can be obtained non-invasively and is rich in metabolites that are potential biomarkers for human health and disease. The optimal urine storage conditions for metabolomic analysis are unknown. We measured the impact of common storage conditions and the presence of a DNA-stabilizer, AssayAssure® (Thermo Scientific), on metabolite content of voided human urine. Urinary metabolite composition was not altered across storage conditions. Although addition of AssayAssure® significantly alters metabolic profile by adduct addition, this does not preclude the identification of parent metabolites or overshadow biological differences. These data suggest biobanked urine stored in any of the tested conditions for metabolomic studies may be considered for metabolomic analysis.
The transition state for coupled folding and binding of a disordered DNA binding domain resembles the unbound state
Authors: Kuravsky Mikhail , Kelly Conor , Redfield Christina , Shammas Sarah L
Published: February 2024

The basic zippers (bZIPs) are one of two large eukaryotic families of transcription factors whose DNA binding domains are disordered in isolation but fold into stable α-helices upon target DNA binding. Here we systematically disrupt pre-existing helical propensity within the DNA binding region of the homodimeric bZIP domain of cAMP-response element binding protein (CREB) using Ala-Gly scanning and examine the impact on target binding kinetics. We find that the secondary structure of the transition state strongly resembles that of the unbound state. The closest residue to the dimerisation domain that has been examined is largely folded within both unbound and transition states; dimerisation apparently propagates additional helical propensity into the basic region. The results are consistent with electrostatically-enhanced DNA binding, followed by rapid folding from the folded zipper outwards. Interestingly, despite taking the exact experimental approach suggested for testing it, we find no evidence for disorder-mediated rate enhancement predicted by fly-casting theory.
Bifidobacterium longumsubsp. longumBG-L47 boosts growth and activity ofLimosilactobacillus reuteriDSM 17938 and its extracellular membrane vesicles
Authors: Lundberg Ludwig Ermann , Mishra Punya Pallabi , Liu Peidi , Forsberg Manuel Mata , Sverremark-Ekström Eva , Grompone Gianfranco , Håkansson Sebastian , Linninge Caroline , Roos Stefan
Published: February 2024

The aim was to identify aBifidobacteriumstrain that improved the performance ofLimosilactobacillus reuteriDSM 17938. Initial tests showed thatBifidobacterium longumsubsp.longumstrains boosted the growth of DSM 17938 duringin vivo-like conditions. Further characterization revealed that one of the strains, BG-L47, had better bile and acid tolerance compared to BG-L48, as well as mucus adhesion compared to both BG-L48 and the control strain BB536. BG-L47 also had the capacity to metabolize a broad range of carbohydrates and sugar alcohols. Mapping of glycoside hydrolase (GH) genes of BG-L47 and BB536 revealed many GHs associated with plant-fiber utilization. However, BG-L47 had a broader phenotypic fiber utilization capacity. In addition,B. longumsubsp.longumcells boosted the bioactivity of extracellular membrane vesicles (MV) produced byL. reuteriDSM 17938 during cocultivation. Secreted 5’ nucleotidase (5’NT), an enzyme that converts AMP into the signal molecule adenosine, was increased in MV boosted by BG-L47. The MV exerted an improved antagonistic effect on the pain receptor TRPV1 and increased the expression of the immune development markers IL-6 and IL-1ß in a PBMC model. Finally, the safety of BG-L47 was evaluated both by genome safety assessment and in a human safety study. Microbiota analysis showed that the treatment did not induce significant changes in the composition. In conclusion,B. longumsubsp.longumBG-L47 has favorable physiological properties, can boost thein vitroactivity ofL. reuteriDSM 17938, and is safe for consumption, making it a candidate for further evaluation in probiotic studies.

Importance

By using probiotics that contain a combination of strains with synergistic properties, the likelihood of achieving beneficial interactions with the host can increase. In this study, we first performed a broad screening ofBifidobacterium longumsubsp.longumstrains in terms of synergistic potential and physiological properties. We identified a superior strain, BG-L47, with favorable characteristics and potential to boost the activity of the known probiotic strainLimosilactobacillus reuteriDSM 17938. Further, we demonstrated that BG-L47 is safe for consumption in a human randomized clinical study and by performing a genome safety assessment. This work illustrates that bacteria-bacteria interactions differ at the strain level and further provides a strategy for finding and selecting companion strains of probiotics.
Tumor-localized interleukin-2 and interleukin-12 combine with radiation therapy to safely potentiate regression of advanced malignant melanoma in pet dogs
Authors: Stinson Jordan A. , Barbosa Matheus Moreno P. , Sheen Allison , Momin Noor , Fink Elizabeth , Hampel Jordan , Selting Kimberly , Kamerer Rebecca , Bailey Keith L. , Wittrup K. Dane , Fan Timothy M.
Published: February 2024

The clinical use of interleukin-2 and -12 cytokines against cancer is limited by their narrow therapeutic windows due to on-target, off-tumor activation of immune cells when delivered systemically. Engineering IL-2 and IL-12 to bind to extracellular matrix collagen allows these cytokines to be retained within tumors after intralesional injection, overcoming these clinical safety challenges. While this approach has potentiated responses in syngeneic mouse tumors without toxicity, the complex tumor-immune interactions in human cancers are difficult to recapitulate in mouse models of cancer. This has driven an increased role for comparative oncology clinical trials in companion (pet) dogs with spontaneous cancers that feature analogous tumor and immune biology to human cancers. Here, we report the results from a dose-escalation clinical trial of intratumoral collagen-binding IL-2 and IL-12 cytokines in pet dogs with malignant melanoma, observing encouraging local and regional responses to therapy that may suggest human clinical benefit with this approach.
Trim66’s paternal deficiency causes intrauterine overgrowth
Authors: Mielnicka Monika , Tabaro Francesco , Sureka Rahul , Acurzio Basilia , Paoletti Renata , Scavizzi Ferdinando , Raspa Marcello , Crevenna Alvaro H. , Lapouge Karine , Remans Kim , Boulard Matthieu
Published: February 2024

The tripartite motif-containing protein 66 (TRIM66, also known as TIF1-delta) is a PHD-Bromo containing protein primarily expressed in post-meiotic male germ cells known as spermatids. Biophysical assays showed that TRIM66 PHD-Bromo domain binds to H3 N-terminus only when lysine 4 is unmethylated. We addressed TRIM66’s role in reproduction by loss-of-function genetics in the mouse. Males homozygous forTrim66-nullmutations produced functional spermatozoa. Round spermatids lacking TRIM66 upregulated a network of genes involved in histone acetylation and H3K4 methylation. Profiling of H3K4me3 patterns in the sperm produced byTrim66-null mutant showed minor alterations below statistical significance. Unexpectedly,Trim66-null males, but not females, sired pups overweight at birth, hence revealing thatTrim66mutations cause a paternal effect phenotype.
Mechanism Study on the Effect of Kidney Tonifying and Liver Soothing Methods on Mouse Oocyte Quality by Regulating OSFs and Smads Pathways
Authors: Zhang Ruijuan , Jia Rui , Bai Jing , Du Huilan , Yang Liyun
Published: February 2024

Objective: To observe the effects of kidney tonifying and liver soothing methods on the secretion of factor BMP-6, related receptors ALK-2/6, and downstream Smads pathway Smad1/5/844 in oocytes, and to explore the targeted mechanisms of their effects on mouse oocyte quality; Method: Healthy female mice aged 6-7 weeks were randomly divided into 6 groups, namely high and low dose kidney tonifying groups; High – and low-dose liver soothing groups; Control group and normal group. The high-dose and low-dose groups of tonifying the kidney were given oral solution of tonifying the kidney and regulating the meridian at 5.4g/ml and 2.7g/ml, respectively. The high-dose and low-dose groups of soothing the liver were given suspension of Xiaoyao Pill at 0.6g/ml and 0.3g/ml, respectively. The control group and normal group were given distilled water by gavage. Immunohistochemistry and Western blot were used to detect the expression of BMP-6, ALK-2/6, and Smad1/5/8/4 proteins in oocytes, while PCR was used to detect the mRNA expression of these indicators in oocytes; Result: Both methods can increase the expression of BMP-6 in oocytes of mice in the treatment group, activate ALK-2/6, and phosphorylate Smad1/5/8 to bind with Smad4, initiating signal transduction; The high-dose group of kidney tonifying is superior to other groups in regulating BMP-6, ALK-2/6, and Smad1/5/4. Conclusion: Kidney tonifying and liver soothing methods can regulate BMP-6 and its Smads pathway through different mechanisms to improve mouse oocyte quality.
Differential Impact of Biomechanical Constraints on Control Signal Dimensionality for Gravity Support Versus Propulsion
Authors: Korol AS , Gritsenko V
Published: February 2024

Neural control of movement has to overcome the problem of redundancy in the multidimensional musculoskeletal system. The problem can be solved by reducing the dimensionality of the control space of motor commands, i.e., through muscle synergies or motor primitives. Evidence for this solution exists, multiple studies have obtained muscle synergies using decomposition methods. These synergies vary across different workspaces and are present in both dominant and non-dominant limbs. Here we explore the dimensionality of control space by examining muscle activity patterns across reaching movements in different directions starting from different postures performed bilaterally by healthy individuals. We further explore the effect of biomechanical constraints on the dimensionality of control space. We are building on top of prior work showing that muscle activity profiles can be explained by applied moments about the limb joints that reflect the biomechanical constraints. These muscle torques derived from motion capture represent the combined actions of muscle contractions that are under the control of the nervous system. Here we test the generalizability of the relationship between muscle torques and muscle activity profiles across different starting positions and between limbs. We also test a hypothesis that the dimensionality of control space is shaped by biomechanical constraints. We used principal component analysis to evaluate the contribution of individual muscles to producing muscle torques across different workspaces and in both dominant and non-dominant limbs. Results generalize and support the hypothesis. We show that the muscle torques that support the limb against gravity are produced by more consistent combinations of muscle co-contraction than those that produce propulsion. This effect was the strongest in the non-dominant arm moving in the lateral workspace on one side of the body.
SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition
Authors: Zhang Qianyi E , Lindenberger Jared , Parsons Ruth , Thakur Bhishem , Parks Rob , Park Chan Soo , Huang Xiao , Sammour Salam , Janowska Katarzyna , Spence Taylor N , Edwards Robert J. , Martin Mitchell , Williams Wilton B , Gobeil Sophie , Montefiori David C , Korber Bette , Saunders Kevin O'Neil , Haynes Barton F , Haynes Barton F. , Henderson Rory , Acharya Priyamvada
Published: February 2024

A recombinant lineage of the SARS-CoV-2 Omicron variant, named XBB, appeared in late 2022 and evolved descendants that successively swept local and global populations. XBB lineage members were noted for their improved immune evasion and transmissibility. Here, we determine cryo-EM structures of XBB.1.5, XBB.1.16, EG.5 and EG.5.1 spike (S) ectodomains to reveal reinforced 3-RBD-down receptor inaccessible closed states mediated by interprotomer receptor binding domain (RBD) interactions previously observed in BA.1 and BA.2. Improved XBB.1.5 and XBB.1.16 RBD stability compensated for stability loss caused by early Omicron mutations, while the F456L substitution reduced EG.5 RBD stability. S1 subunit mutations had long-range impacts on conformation and epitope presentation in the S2 subunit. Our results reveal continued S protein evolution via simultaneous optimization of multiple parameters including stability, receptor binding and immune evasion, and the dramatic effects of relatively few residue substitutions in altering the S protein conformational landscape.
Natural Variation in Age-Related Dopamine Neuron Degeneration is Glutathione-Dependent and Linked to Life Span
Authors: Coleman Colin R. , Pallos Judit , Arreola-Bustos Alicia , Wang Lu , Raftery Daniel , Promislow Daniel E.L. , Martin Ian
Published: February 2024

Aging is the biggest risk factor for Parkinson’s disease (PD), suggesting that age-related changes in the brain promote dopamine neuron vulnerability. It is unclear, however, whether aging alone is sufficient to cause significant dopamine neuron loss and if so, how this intersects with PD-related neurodegeneration. Here, through examining a large collection of naturally varyingDrosophilastrains, we find a strong relationship between life span and age-related dopamine neuron loss. Naturally short-lived strains exhibit a loss of dopamine neurons but not generalized neurodegeneration, while long-lived strains retain dopamine neurons across age. Metabolomic profiling reveals lower glutathione levels in short-lived strains which is associated with elevated levels of reactive oxygen species (ROS), sensitivity to oxidative stress and vulnerability to silencing the familial PD geneparkin. Strikingly, boosting neuronal glutathione levels via glutamate-cysteine ligase (GCL) overexpression is sufficient to normalize ROS levels, extend life span and block dopamine neurons loss in short-lived backgrounds, demonstrating that glutathione deficiencies are central to neurodegenerative phenotypes associated with short longevity. These findings may be relevant to human PD pathogenesis, where glutathione depletion is frequently reported in idiopathic PD patient brain. Building on this evidence, we detect reduced levels of GCL catalytic and modulatory subunits in brain from PD patients harboring the LRRK2 G2019S mutation, implicating possible glutathione deficits in familial LRRK2-linked PD. Our study acrossDrosophilaand human PD systems suggests that glutathione plays an important role in the influence of aging on PD neurodegeneration.
Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture
Authors: Vanhooydonck Michiel , Verlee Maxim , Silva Marta Santana , Pottie Lore , Boel Annekatrien , Van Impe Matthias , De Saffel Hanna , Caboor Lisa , Tapaneeyaphan Piyanoot , Bonnin Anne , Segers Patrick , De Clercq Adelbert , Willaert Andy , Syx Delfien , Sips Patrick , Callewaert Bert
Published: February 2024

Thoracic aortic aneurysm and dissection (TAAD) associates with a high mortality rate. Despite the existence of different mouse models for TAAD, the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical aortic diameters as current pharmacological interventions are unable to stop disease progression.

In humans, loss of function (LOF) ofSMAD3andSMAD6impairs vascular homeostasis, increasing the risk for TAAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs ofsmad3andsmad6. At 10 days post fertilization, we found an increased diameter of the ventral aorta insmad3a−/−;smad3b−/−double knockout zebrafish, whilesmad6a−/−;smad6b−/−double knockout zebrafish have a reduced aortic diameter associated with early mortality. We discovered that asmad3a−/−;smad3b−/−;smad6a−/−;smad6b−/−quadruple knockout (qKO) zebrafish model is viable and survives to adulthood, although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta shows medial elastolysis, aortic dissections and ruptures at sites exposed to high biomechanical stress. RNA-sequencing of 5 days post fertilization qKO zebrafish indicates a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis, a previously unaddressed pathway in this pathology. We confirm that pharmacological modulation of tyrosinase, the enzyme responsible for the production of melanin, influences aortic morphology.

Overall, the qKO mutant, thus far the only known zebrafish model of thoracic aortic dissection and rupture, reveals novel SMAD3/6-dependent pathways that impact thoracic aortic homeostasis, in this way opening avenues for the development of novel treatments in TAAD.
Aging disrupts blood-brain and blood-spinal cord barrier homeostasis, but does not increase paracellular permeability
Authors: Cummins Mitchell J , Cresswell Ethan T , Smith Doug W
Published: February 2024

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Blood-CNS barriers protect the CNS from circulating immune cells and damaging molecules. It is thought barrier integrity becomes disrupted with aging, contributing to impaired CNS function. Using genome-wide and targeted molecular approaches, we found aging affected expression of predominantly immune invasion and pericyte-related genes in most CNS regions investigated, especially after middle age, with spinal cord being most impacted. We did not find significant perturbation of tight junction genes, nor were vascular density or pericyte coverage affected by aging. We evaluated barrier paracellular permeability using small molecular weight tracers, serum protein extravasation, CNS water content, and iron labelling measures. We found no evidence for age-related increased barrier permeability in any of these tests. We conclude that blood-brain (BBB) and blood-spinal cord barrier (BSCB) paracellular permeability does not increase with normal aging in mouse. Whilst expression changes were not associated with increased permeability, they may represent an age-related primed state whereby additional insults cause increased leakiness.