bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of adolescent high-fat diet and psychosocial stress on neuroendocrine stress responses and binge eating behavior in adult male Lewis rats
Authors: Sierra Julio , Simon Timothy B. , Hilal Darine Abu , Torres Yaria Arroyo , Santana José M. Santiago , Figueroa Johnny D.
Published: November 2024

Childhood obesity is a multifactorial disease affecting more than 160 million adolescents worldwide. Adolescent exposure to obesogenic environments, characterized by access to high-fat diets and stress, precipitates maladaptive eating habits in adulthood such as binge eating. Evidence suggests a strong association between Western-like high-saturated-fat (WD) food consumption and dysregulated hormone fluctuations. However, few studies have explored the long-term impact of adolescent WD and psychosocial stress on brain and behavior. This longitudinal study aimed to investigate the impact of adolescent exposure to an obesogenic diet on stress resiliency and increased susceptibility for binge-like eating behaviors. Adolescent male Lewis rats were given WD (41% fat; n=40) or control diet (CD, 16% fat; n=38) for 4 weeks before undergoing a stress paradigm of predator exposure and social instability (CDE, WDE, CDU, WDU; n=16/group). Subjects were provided intermittent WD access (24 h/week) to evaluate binge eating–like behavior in adulthood. Fecal corticosterone and testosterone were measured at four timepoints throughout adolescence and adulthood. WD rats exhibited increased body weight (p = 0.0217) and elevated testosterone in mid-adolescence (p=0.0312) and blunted stress-induced corticosterone response in mid-late adolescence (CDE:WDE, p=0.028). Adolescent hormone levels were negatively correlated with bingeing and explained the variability between adult rats expressing hyperphagic and hypophagic behaviors. These results demonstrate that exposure to WD in adolescence disrupts hormone fluctuations and stress responsivity, with effects persisting into adulthood. This underscores the importance of addressing obesogenic environments early to mitigate their lasting impact on hormone regulation and stress responsiveness.
Long-Read Sequencing Reveals Increased Isoform Diversity in Key Transcription Factor Effectors of Intercellular Signalling at the Invertebrate-Vertebrate Transition
Authors: Torres-Aquila Nuria P. , Salonna Marika , Shimeld Sebastian , Hoppler Stefan , Ferrier David E.K.
Published: November 2024

Several intercellular signalling pathways (namely wingless - Wnt, Hedgehog - Hh, and Bone Morphogenetic Protein - BMP) are used repeatedly in animals throughout development and evolution, and are also frequent targets for disease-associated disruptions. We have previously shown that the major transcriptional effectors of β-catenin-dependent Wnt signalling, the TCF/LEF proteins, in contrast to other pathway components, have a higher gene number and isoform diversity in vertebrates versus invertebrates, but this increased diversity has only been poorly quantified. Considering that isoform diversity correlates with organism complexity, any increase in major signalling effectors is likely to have made a significant contribution to vertebrate evolution. Usingde novolong-read transcriptomes, we compared isoform number per gene for the chordatesCiona intestinalis, Lampetra planeriandXenopus tropicalis, thus encompassing the invertebrate sister group to vertebrates, as well as a cyclostome and a gnathostome vertebrate. Our results implicate an increase in isoform diversity of the transcription factors of major intercellular signalling pathways as having a disproportionate role in the evolutionary origin and diversification of vertebrates.
Automated plasmid design for marker-free genome editing in budding yeast
Authors: Stojković Lazar , Gligorovski Vojislav , Geramimanesh Mahsa , Labagnara Marco , Rahi Sahand Jamal
Published: November 2024

The ease of genome editing has contributed to the popularity of budding yeast as a model organism. However, the palette of selectable markers is in principle limited as most can only be used once. Some markers such asURA3andTRP1can be recycled through counterselection. This permits seamless genome modification with pop-in/pop-out (PIPO), in which a DNA construct first integrates in the genome and, subsequently, homologous regions recombine and excise undesired sequences. Popular approaches for creating such constructs use oligonucleotides and polymerase chain reaction (PCR). The drawbacks are that long oligonucleotides are unstable, can form secondary structures that interfere with PCR, cannot be regenerated in a typical biological laboratory, and are only widely available for lengths less than about 120, which limits the homology and efficiency that can be attained. With the rapid reduction in price, synthesizing custom DNA sequences in specific plasmid backbones has become an appealing alternative. For designing plasmids for seamless PIPO gene tagging or deletion, there are a number of factors to consider. To create only the shortest DNA sequences necessary, avoid errors in manual design, specify the amount of homology desired, and customize restriction sites, we created the computational tool PIPOline. Using it, we tested the ratios of homology that improve pop-out efficiency when targeting the genesHTB2orWHI5. We supply optimal PIPO plasmid sequences for tagging or deleting almost all S288C budding yeast open reading frames (ORFs). Finally, we demonstrate how the histone variant Htb2 marked with a red fluorescent protein can be used as a cell-cycle stage marker, alternative to superfolder GFP (sfGPF), reducing light toxicity. We expect PIPOline to streamline genome editing in budding yeast.
Mechanisms driving epigenetic and transcriptional responses of microglia in a neurodegenerative lysosomal storage disorder model
Authors: Balak Christopher D. , Schlachetzki Johannes C.M. , Lana Addison J. , West Elizabeth , Hong Christine , DuGal Jordan , Zhou Yi , Li Benjamin , Saisan Payam , Spann Nathanael J. , Sarsani Vishal , Pasillas Martina P. , O’Brien Sydney , Gordts Philip , Stevens Beth , Kamme Fredrik , Glass Christopher K.
Published: November 2024

Lysosomal dysfunction is causally linked to neurodegeneration in many lysosomal storage disorders (LSDs) and is associated with various age-related neurodegenerative diseases1,2, but there is limited understanding of the mechanisms by which altered lysosomal function leads to changes in gene expression that drive pathogenic cellular phenotypes. To investigate this question, we performed systematic imaging, transcriptomic, and epigenetic studies of major brain cell types inSgshnull (KO) mice, a preclinical mouse model for Sanfilippo syndrome (Mucopolysaccharidosis Type IIIA, MPS-IIIA)3,4. MPS-IIIA is a neurodegenerative LSD caused by homozygous loss-of-function (LoF) mutations inSGSHwhich results in severe early-onset developmental, behavioral, and neurocognitive impairment5–15. Electron microscopy, immunohistochemistry, and single-nucleus RNA-sequencing analysis revealed microglia as the cell type exhibiting the most dramatic phenotypic alterations inSgshKO mice. Further temporal analysis of microglia gene expression showed dysregulation of genes associated with lysosomal function and immune signaling pathways beginning early in the course of the disease.Sgshdeficiency similarly resulted in increases in open chromatin and histone acetylation at thousands of putative microglia-specific enhancers associated with upregulated genes but had much less impact on the epigenetic landscapes of neurons or oligodendrocytes. We provide evidence for dominant and context-dependent roles of members of the MITF/TFE family as major drivers of microglia-specific epigenetic and transcriptional changes resulting from lysosomal stress that are dependent on collaborative interactions with PU.1/ETS and C/EBP transcription factors. Lastly, we show that features of the transcriptomic and epigenetic alterations observed in murineSgshdeficiency are also observed in microglia derived from mouse models of age-related neurodegeneration and in human Alzheimer’s disease patients, revealing common and disease-specific transcriptional mechanisms associated with disease-associated microglia phenotypes.
Multi-stage-mixing to control the supramolecular structure of lipid nanoparticles, thereby creating a core-then-shell arrangement that improves performance by orders of magnitude
Authors: Nong Jia , Gong Xijing , Dang Quang Minh , Tiwari Sachchidanand , Patel Manthan , Wu Jichuan , Hanna Andrew , Park Wook-Jin , Atochina-Vasserman Elena N. , Huang Hui-Ting , Marcos-Contreras Oscar A. , Morris-Blanco Kahlilia C. , Miner Jonathan J. , Weissman Drew , Muzykantov Vladimir R. , Gupta Kushol , Issadore David , Myerson Jacob W. , Wang Zhicheng , Brenner Jacob S.
Published: November 2024

As they became the dominant gene therapy platform, lipid nanoparticles (LNPs) experienced nearly all their innovation in varying the structure of individual molecules in LNPs. This ignored control of the spatial arrangement of molecules, which is suboptimal because supramolecular structure determines function in biology. To control LNPs’ supramolecular structure, we introduce multi-stage-mixing (MSM) to successively add different molecules to LNPs. We first utilize MSM to create a core-then-shell (CTS) synthesis. CTS-LNPs display a clear core-shell structure, vastly lower frequency of LNPs containing no detectable mRNA, and improved mRNA-LNP expression. With DNA-loaded LNPs, which for decades lagged behind mRNA-LNPs due to low expression, CTS improved DNA-LNPs’ protein expression by 2-3 orders of magnitude, bringing it within range of mRNA-LNPs. These results show that supramolecular arrangement is critical to LNP performance and can be controlled by mixing methodology. Further, MSM/CTS have finally made DNA-LNPs into a practical platform for long-term gene expression.
Low-frequency Cortical Activity Reflects Context-dependent Parsing of Word Sequences
Authors: Chen Honghua , Ye Tianyi , Zhang Minhui , Ding Nai
Published: November 2024

During speech listening, it has been hypothesized that the brain builds representations of large linguistic structures such as sentences, which are captured by neural activity tracking the rhythm of these structures. Nevertheless, it has been concerned that the brain may only encode words, and neural activity tracking structures may be confounded by neural activity tracking the predictability or syntactic properties of individual words. Here, to disentangle the neural responses to sentences and words, we design word sequences that are parsed into different sentences in different contexts. By analyzing neural activity recorded by magnetoencephalography, we find that low-frequency neural activity strongly depends on the context – The difference between MEG responses to the same word sequence in two contexts yields a low-frequency signal, most strongly generated in the superior temporal gyrus, which precisely tracks sentences. The predictability and syntactic properties of words can partly explain the neural response in each context but cannot explain the difference between contexts. In summary, low-frequency neural activity encodes sentences and can reliably reflect how the same word sequence is parsed in different contexts.
A NovelC. elegansModel for Tau Spreading Reveals Genes Critical for Endolysosomal Integrity and Seeded Tau Aggregation
Authors: Sandhof Carl Alexander , Martin Nicole , Tittelmeier Jessica , Schlueter Annabelle , Pezzali Martina , Schoendorf David C. , Lange Timo , Reinhardt Peter , Ried Janina S. , Liang Siwen , Uzunoglu Gamze , Gasparini Laura , Jahn Thomas R. , Ehrnhoefer Dagmar E. , Nussbaum-Krammer Carmen
Published: November 2024

The spreading of Tau pathology is closely associated with the progression of neurodegeneration and cognitive decline in Alzheimer’s disease and other tauopathies. A key event in this process is the rupture of endolysosomal vesicles following the intercellular transfer of Tau aggregates, releasing the transferred Tau species into the cytosol where they can promote the aggregation of endogenous Tau. However, understanding of the cellular pathways involved in this process remains limited.

In this study, we investigated cellular pathways that prevent endolysosomal vesicle rupture. We established a newC. elegansmodel of Tau spreading by introducing an mCherry-labelled, disease-associated aggregation-prone fragment of human Tau (F3ΔK281::mCh) into the six touch receptor neurons. F3ΔK281::mCh transgenic animals exhibited significant neurotoxicity and mechanosensory deficits due to the accumulation of this Tau fragment. In addition, its intercellular transmission compromised the endolysosomal system in receiving hypodermal cells. Using this model, we conducted an unbiased genome-wide RNAi screen and identified 59 genes critical for maintaining endolysosomal integrity. GO-term analysis revealed an enrichment of genes related to the ESCRT complex, the ubiquitin-proteasome system, mRNA splicing, and fatty acid metabolism. Silencing of selected conserved genes exacerbated seeded Tau aggregation in a human induced pluripotent stem cell (hiPSC)-derived cortical neuron model and triggered endolysosomal rupture in HEK293T cells, confirming the crucial role of endolysosomal damage in seeded Tau aggregation.

Overall, this study discovered novel cellular pathways that safeguard endolysosomal integrity. These findings may guide the development of therapeutics that improve endolysosomal integrity to halt the progression of Tau pathology.
Individual brain activity patterns during task are predicted by distinct resting-state networks that may reflect local neurobiological features
Authors: Scholz Robert , Benn R. Austin , Shevchenko Victoria , Klatzmann Ulysse , Wei Wei , Alberti Francesco , Chiou Rocco , Zhang Xi-Han , Leech Robert , Smallwood Jonathan , Margulies Daniel S.
Published: November 2024

Understanding how individual cortical features shape functional brain organization offers a promising framework for examining the principles of cognitive specialization in the human brain. This study explores the relationship between various cortical characteristics—i.e resting-state functional connectivity, structural connectivity, microstructure, morphology, and geometry—and the layout of task-specific functional activations. We employ linear models to predict the functional layout of the cortex at the individual level from each of these feature modalities. Our findings demonstrate that resting-state component loadings predict individual task activations, consistently across hemispheres and independent datasets. Whereas the first few components provide a common space for functional activations across tasks, predictive higher-order component loadings demonstrated task-specificity. Cortical microstructure/morphology was notably predictive of activation strength in the occipital cortex, highlighting its relevance for cortical functional specialization. By relating resting state components to a set of reference maps of cortical organization, we identify associations that suggest possible neurobiological underpinnings of specific cognitive functions. The remaining feature modalities were only predictive of group-level functional activations. These results advance our understanding of how distinct cortical features may contribute to functional specialization, guiding future inquiry into the organization of cognitive functions on the cortex.
Sex differences in auditory function of the desert locust
Authors: Tom Austin T , Christian Thomas L , Ben Warren
Published: November 2024

Age-related auditory decline manifests across the animal kingdom, from humans and mice to zebrafish and insects. Sex differences in auditory decline are established for humans, but there is now evidence in mice and even zebrafish. Here, we found sex differences in auditory decline in an insect, the Desert Locust and investigated its biological basis. We profiled gene expression in a dedicated auditory organ, Müller’s organ to understand the genetic underpinning of sex differences and measured sound-evoked transduction currents and electrophysiological properties of auditory neurons to quantify auditory decline. We analysed gene expression in Müller’s organ of young locusts where sex differences were absent and in older, noise-exposed locusts where sex differences were maximal. The largest differences in gene expression between the sexes was between young and stressed (aged and noise-exposed) auditory organs. We found sex-specific genes and gene ontology terms for juvenile hormone (JH) and sex-specific estrogen-related steroids. We hypothesise that sex differences in auditory decline are due to differences in hormones which then affect metabolic processes in and mitochondria.

Highlights

Female Desert Locusts have less auditory decline than males.

Female’s auditory organs maintain better metabolism under stressed conditions.

Sex differences in gene expression are maximal during aging and noise-exposure.

Sex differences are minimal between the sexes for young and stressed auditory organs.
Mind Your Spectra: Points to be Aware of when Validating the Identification of Isobaric Histone Peptidoforms
Authors: Hijazi Hassan M. , Manessier Julie , Brugière Sabine , Ravnsborg Tina , Courçon Marie , Brulé Baptiste , Merienne Karine , Jensen Ole N , Hesse Anne-Marie , Bruley Christophe , Pflieger Delphine
Published: November 2024

Mass spectrometry (MS) has become a central technique to identify and quantify post-translational modifications (PTMs), overcoming limitations of antibody-based methods. Histones get dynamically modified by diverse chemical groups, particularly on their numerous lysine residues, to fine-tune all DNA-templated processes. Reliable identification of histone PTMs remains challenging and still requires manual data curation. This study focused on the Lys27-Arg40 stretch of histone H3, considered four sequence variants, an increasing number of lysine PTMs and artifacts coming from histone sample processing, which resulted in many peptides with the same atomic composition. Our analysis revealed the value of low-mass b1 and cyclic immonium fragment ions to validate identification of the distinct peptidoforms. We examined how MS/MS spectra are transformed by common software tools during the conversion of RAW files into peak lists, and highlighted how some parameters may erase the informative low-mass fragments. We established the fragmentation profiles and retention times for forty H3 K27-R40 variant×PTM combinations, including the mouse-specific variants H3mm7 and H3mm13, and targeted their detection in histone samples extracted from mouse testis and brain via a scheduled parallel reaction monitoring (PRM) analysis. The transcripts of these two mousespecific variants were reported to be highly abundant in these tissues and the corresponding proteins may seem to be identified by data-dependent analyses. However, we only detected very low levels of the unmodified form of H3mm7 and found no trace of H3mm13 by PRM. Our work contributes to reliably deciphering the histone code shaped by distinct sequence variants and numerous combinations of PTMs.
Manipulation of Host Cholesterol by SARS-CoV-2
Authors: Doyle Aliza , Goodson Baley A. , Kolaczkowski Oralia M. , Liu Rui , Jia Jingyue , Wang Hu , Han Xianlin , Ye Chunyan , Bradfute Steven B. , Kell Alison M. , Rosas Lemus Monica , Pu Jing
Published: November 2024

SARS-CoV-2 infection is associated with alterations in host lipid metabolism, including disruptions in cholesterol homeostasis. However, the specific mechanisms by which viral proteins influence cholesterol remain incompletely understood. Here, we report that SARS-CoV-2 infection induces cholesterol sequestration within lysosomes, with the viral protein ORF3a identified as the primary driver of this effect. Mechanistically, we found that ORF3a interacts directly with the HOPS complex subunit VPS39 through a hydrophobic interface formed by residues W193 and Y184. A W193A mutation in ORF3a significantly rescues cholesterol egress and corrects the mislocalization of the lysosomal cholesterol transporter NPC2, which is caused by defective trafficking of the trans-Golgi network (TGN) sorting receptor, the cation-independent mannose-6-phosphate receptor (CI-MPR). We further observed a marked reduction in bis(monoacylglycero)phosphate (BMP), a lipid essential for lysosomal cholesterol egress, in both SARS-CoV-2-infected cells and ORF3a-expressing cells, suggesting BMP reduction as an additional mechanism of SARS-CoV-2-caused cholesterol sequestration. Inhibition of lysosomal cholesterol egress using the compound U18666A significantly decreased SARS-CoV-2 infection, highlighting a potential viral strategy of manipulating lysosomal cholesterol to modulate host cell susceptibility. Our findings reveal that SARS-CoV-2 ORF3a disrupts cellular cholesterol transport by altering lysosomal protein trafficking and BMP levels, providing new insights into virus-host interactions that contribute to lipid dysregulation in infected cells.
Food environment components influencing consumption trends of neglected and underutilized species in northern Benin
Authors: Bankole Bissola Malikath , Amoussa Hounkpatin Waliou , Bodjrenou Sam , Bodecker Julia , Julen Lynn , Chadare Flora Josiane , Termote Celine
Published: November 2024

Malnutrition is a global problem driven by food systems that impact climate and biodiversity. Neglected and underutilized species (NUS) could improve diets, but what drives their choices and consumption, particularly in low and middle-income countries, is poorly documented. This study investigated the influences of the personal food environment on the consumption of NUS in three communities in the department of Atacora in northern Benin. Following a purposive sampling strategy, 24 semi-structured interviews were conducted with local and 18 with professional experts. 12 group discussions with villagers from six villages in the three communes complemented and deepened the information gathered, focusing on both barriers and factors for enhancing consumption. The data collected was translated and transcribed into French and analyzed using qualitative content analysis with Atlas.ti software. Among the investigated plant parts, an upward trend was found forMoringa oleiferaleaves andVigna radiataseeds, a downward trend forAdansonia digitatapulps, and a varied trend forOcimum gratissimumleaves andAdansonia digitatakernels and leaves. Drivers for changes in consumption were found in all four dimensions of the food environment. Among the plant parts with the main increasing trend in consumption, various aspects of desirability, above all increased food and nutrition knowledge and skills, led to a positive consumption trend. The downward trend has most often been attributed to declining accessibility, but several aspects have also made these plant parts less affordable and less desirable (taboos for example). The strong variation in dimensions’ influence on plant parts with variable trends reflects their non-unanimous changes. Research and policies should address the factors influencing the consumption of these foods. Making neglected species more accessible, affordable, and desirable can enhance food security and environmental sustainability.
Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells
Authors: Dickmann Johanna E. M. , Martin Marjolaine , Lionnet Claire , Nemec-Venza Zoe , Hamant Olivier
Published: November 2024

In contrast to animal cells with their contractile cortical cytoskeleton, plant cells are encased in walls and are usually thought to behave like stiff, pressurized vessels. When digesting the cell wall, plant protoplasts form spherical shapes, further consolidating this model. Here we challenge this apparent opposition between animal and plant cells. We show that plant protoplasts can form protrusions. More precisely, using plasma membrane markers, we reveal that 27 ± 1% of the protoplasts show dot-like protrusions and 16 ± 7% of protoplasts show long (typically 1-20 μm, up to 200 μm) protrusions that we name “filopods”. We demonstrate that this behavior is independent of the plant species, the membrane marker or the osmolyte. Protrusions can host large and long structures, such as microtubule bundles, which in turn can impact the mechanical behavior of the protrusions. We find that filopods can formde novowhen increasing osmolarity, that they most likely move passively, and that they can attach to artificial surfaces. Altogether, these observations show that forming and retaining protrusions is not exclusive to animal cells. This calls for revisiting the dynamics and probing ability of the plant cell cortex in different osmotic and mechanical environments.
Pin4 Links Post-transcriptional and Transcriptional Responses to Glucose Starvation in Yeast
Authors: Ristová Michaela , Bexley Katherine , Shchepachev Vadim , Cook Atlanta G. , Tollervey David
Published: November 2024

Adaptation to environmental change is essential in all organisms, with RNA-binding proteins (RBPs) playing critical roles in rapid cellular responses. We analyzed the largely uncharacterized yeast RBP Pin4, and its involvement in adaptation to glucose depletion. A UV crosslinking technique to identify protein-RNA interactions (reCRAC) revealed that in glucose conditions Pin4 selectively binds a specific motif in 3’ UTRs of mRNAs involved in glycolysis, amino acid, and mitochondrial metabolism. Following glucose withdrawal, Pin4-RNA binding was greatly reduced, with residual binding favoring transcripts associated with protein translation. Cells lacking Pin4 were greatly impaired in recovery from nutrient starvation and hypersensitive to oxidative stress, consistent with the mRNA targets. RNAseq and reporter assays indicated that loss of Pin4 caused increased target mRNA abundance. In wildtype yeast, glucose depletion induces “diauxic shift”, with massive changes in transcription patterns. Very unexpectedly, this response was almost entirely abolished in cells lacking Pin4, or carrying a point mutation in its RNA-recognition motif. We conclude that Pin4 contributes to energy homeostasis by regulating post-transcriptional and transcriptional responses, and postulate that this key stress response pathway is riboregulated.
Early seedling development in dark conditions is directly controlled by plastids through the GUN1-dependent plastid retrograde pathway
Authors: Sajib Salek Ahmed , Bykowski Michał , Barreto Pedro , Mauve Caroline , Delannoy Etienne , Blanchet Sophie , Chamas Rim , Schwarzländer Markus , Kowalewska Łucja , Gakière Bertrand , Merendino Livia
Published: November 2024

In dark growth conditions, seedlings develop specific features such as an elongated hypocotyl, a tightly folded apical hook, and non-green cotyledons. This dark-specific process, known as skotomorphogenesis, relies primarily on mitochondria and eventually etioplasts for energy. Our previous research shows that skotomorphogenesis is reprogrammed in response to mitochondrial and plastidial dysfunction. Even though the direct link between mitochondria and skotomorphogenesis was described, the impact of plastid dysfunction on early development could not be separated from mitochondrial stress.

In this study, we aim to determine the direct connection between plastid functionality and skotomorphogenic response. In this situation, we analyze the phenotypic, molecular, and metabolic effects of treating etiolated seedlings using lincomycin and spectinomycin, which target plastid translation. Our results with the lincomycin treatment highlight the direct role of plastids in the control of early development, even in dark growth conditions, in the absence of any photosynthetic activity, and without the involvement of mitochondrial intermediates. Additionally, our findings suggest that GUN1 plays a regulatory role in regulating nuclear gene expression in response to plastid translation inhibition. Thanks to our study, we can now build a more precise model proposing a straight link between the reprogramming of early development and the dysfunction of plastids in dark-growth conditions.

Significance statement

In underground germination conditions, seedlings follow a dark-specific development program, called skotomorphogenesis, that is required for their efficient emergence from the soil. Our study demonstrates that plastids play a crucial role in controlling skotomorphogenesis, even in the absence of photosynthetic activity and without affecting mitochondrial function, and therefore we propose that regulation of etioplast functions might contribute to the adaptation of seedling development to constraining environmental conditions.
The Arabidopsis Class I formin AtFH5 contributes to seedling resistance to salt stress
Authors: Kollárová Eva , Forero Anežka Baquero , Yildiz Ali Burak , Kočová Helena , Žárský Viktor , Cvrčková Fatima
Published: November 2024

The family of formins, evolutionarily conserved multidomain proteins engaged in the control of actin and microtubule cytoskeleton organization, exhibits considerable diversity in plants. Angiosperms have two formin clades consisting of multiple paralogs, Class I and Class II, the former being often transmembrane proteins located at the plasmalemma or endomembranes. According to available transcriptome data, theArabidopsis thalianaClass I transmembrane formin AtFH5 (At5g54650) exhibits a distinct pattern of transcript abundance in various seedling root tissues with massive increase of transcript level upon salinity stress. To examine a possible role of AtFH5 in NaCl stress response, we generated transgenic plants expressing green fluorescent protein (GFP)-tagged AtFH5 under its native promoter and characterized its tissue and intracellular localization under standard culture conditions and under NaCl stress. While we confirmed the induction of AtFH5 expression by salt treatment, the distribution of tagged protein, with maxima in the border-like cells of the root cap, in the phloem and at lateral root emergence sites, did not reflect previously reported transcript abundance, suggesting posttranscriptional regulation of gene expression. Subcellular localization studies employing also membrane trafficking inhibitors suggested that AtFH5 protein level may be modulated by endocytosis and autophagy. Notably, loss-of-functionatfh5mutants exhibited increased sensitivity to NaCl stress, indicating that AtFH5 contributes to the development of seedling salt tolerance. These findings highlight the functional importance of AtFH5 in abiotic stress responses.
Transient upregulation of procaspase-3 during oligodendrocyte fate decisions
Authors: Kamen Yasmine , Chapman Timothy W. , Piedra Enrique T. , Ciolkowski Matthew E. , Hill Robert A.
Published: November 2024

Oligodendrocytes are generated throughout life and in neurodegenerative conditions from brain resident oligodendrocyte precursor cells (OPCs). The transition from OPC to oligodendrocyte involves a complex cascade of molecular and morphological states that position the cell to make a fate decision to integrate as a myelinating oligodendrocyte or die through apoptosis. Oligodendrocyte maturation impacts the cell death mechanisms that occur in degenerative conditions, but it is unclear if and how the cell death machinery changes as OPCs transition into oligodendrocytes. Here, we discovered that differentiating oligodendrocytes transiently upregulate the zymogen procaspase-3, equipping these cells to make a survival decision during differentiation. Pharmacological inhibition of caspase-3 decreases oligodendrocyte density, indicating that procaspase-3 upregulation promotes differentiation. Moreover, using procaspase-3 as a marker, we show that oligodendrocyte differentiation continues in the aging cortex and white matter. Taken together, our data establish procaspase-3 as a differentiating oligodendrocyte marker and provide insight into the underlying mechanisms occurring during the decision to integrate or die.
Modeling Complex Animal Behavior with Latent State Inverse Reinforcement Learning
Authors: Jha Aditi , Geadah Victor , Pillow Jonathan W.
Published: November 2024

Understanding complex animal behavior is crucial for linking brain computation to observed actions. While recent research has shifted towards modeling behavior as a dynamic process, few approaches exist for modeling long-term, naturalistic behaviors such as navigation. We introduce discrete Dynamical Inverse Reinforcement Learning (dDIRL), a latent state-dependent paradigm for modeling complex animal behavior over extended periods. dDIRL models animal behavior as being driven by internal state-specific rewards, with Markovian transitions between the distinct internal states. Using expectation-maximization, we infer reward functions corresponding to each internal states and the transition probabilities between them, from observed behavior. We applied dDIRL to water-starved mice navigating a labyrinth, analyzing each animal individually. Our results reveal three distinct internal states sufficient to describe behavior, including a consistent water-seeking state occupied for less than half the time. We also identified two clusters of animals with different exploration patterns in the labyrinth. dDIRL offers a nuanced understanding of how internal states and their associated rewards shape observed behavior in complex environments, paving the way for deeper insights into the neural basis of naturalistic behavior.
Structural basis of augment taurine uptake by taurine transporter alleviating cellular senescence
Authors: Zhang Heng , Cui Nana , Ma Xiong , Xu H. Eric
Published: November 2024

Taurine, a sulfur-containing amino acid, is critical for diverse physiological processes including liver function, cardiovascular health, and neurological development. Its deficiency has been linked to liver damage, cardiomyopathy, retinal degeneration, and accelerated aging. Despite its importance in metabolic regulation and disease prevention, the structural basis for taurine’s cellular uptake and its potential therapeutic applications have remained elusive. Here, we present high-resolution cryo-electron microscopy structures of the human taurine transporter (TauT) in multiple conformational states, revealing key insights into the taurine transport mechanism. We identify five distinct taurine-binding sites, elucidating a continuous pathway for taurine translocation across the cell membrane. Notably, we discover a novel gating mechanism involving a conserved salt bridge, which when disrupted, significantly enhances taurine uptake. Leveraging these structural insights, we demonstrate that augmented taurine uptake via TauT alleviates stress-induced senescence in biliary epithelial cells, potentially through the upregulation of the stress-responsive gene ATF3. Our findings not only advance the understanding of neurotransmitter transport but also unveil TauT as a promising therapeutic target for age-related liver diseases and other senescence-associated disorders. This work bridges structural biology with physiological function, offering new avenues for developing interventions to combat cellular aging and taurine-deficiency related diseases.
Genome-wide analysis of heart failure yields insights into disease heterogeneity and enables prognostic prediction in the Japanese population
Authors: Enzan Nobuyuki , Miyazawa Kazuo , Koyama Satoshi , Kurosawa Ryo , Ieki Hirotaka , Yoshida Hiroki , Takechi Fumie , Fukuyama Masashi , Osako Ryosuke , Tomizuka Kohei , Liu Xiaoxi , Ozaki Kouichi , Onouchi Yoshihiro ,   BioBank Japan Project, Matsuda Koichi , Momozawa Yukihide , Aburatani Hiroyuki , Kamatani Yoichiro , Yamaguchi Takanori , Hiroshi Akazawa , Node Koichi , Ellinor Patrick T. , Levin Michael G. , Damrauer Scott M. , Voight Benjamin F. , Joseph Jacob , Sun Yan V. , Terao Chikashi , Ninomiya Toshiharu , Komuro Issei , Ito Kaoru
Published: November 2024

To understand the genetic basis of heart failure (HF) in the Japanese population, we performed genome-wide association studies (GWASs) comprising 16,251 all-cause HF cases, 4,254 HF with reduced ejection fraction cases, 7,154 HF with preserved ejection fraction cases, and 11,122 non-ischemic HF cases among 213,828 individuals and identified five novel loci. A subsequent cross-ancestry meta-analysis and multi-trait analysis of the GWAS data identified 19 novel loci in total. Among these susceptibility loci, a common non-coding variant inTTN(rs1484116) was associated with reduced cardiac function and worse long-term mortality. We leveraged the HF meta-GWASs along with cardiac function-related GWASs to develop a polygenic risk score (PRS) for HF. The PRS successfully identified early-onset HF and those with an increased risk of long-term HF mortality. Our results shed light on the shared and distinct genetic basis of HF between Japanese and European populations and improve the clinical value of HF genetics.
Prevalence and associated factors of advanced HIV disease among ART-naïve and ART-experienced people with HIV at AHF-supported sites in Zambia
Authors: Chewe Webster , Chanda Chitalu , Hamooya Benson M. , Siame Lukundo , Mfune Ruth Lindizyani , Kayembe Mazinga , Mpoyi Eric , Dube Nduduzo
Published: November 2024

Background

Individuals with advanced HIV disease (AHD) have a heightened risk of mortality despite access to antiretroviral therapy (ART). Sub-Saharan Africa (SSA) has a disproportionate burden of AHD-associated deaths. However, there is limited country-specific data on AHD’s burden and associated risk factors to help design targeted interventions. Therefore, this study determined the prevalence and factors associated with AHD among ART-naïve and ART-experienced adults with HIV at five AIDS Healthcare Foundation (AHF)-supported facilities in Zambia.

Methodology

We conducted a cross-sectional study among 231 ART-naïve and ART-experienced people living with HIV (PLHIV) and collected demographic and clinical data using a structured questionnaire. The primary outcome was AHD, defined as a CD4 count less than 200 cells/µL using the VISITECT® CD4 point-of-care test. Multivariable logistic regression was used to assess factors associated with AHD.

Results

Among the study participants, 59.7% were female, and 54% were aged 19–35 years. Most participants were ART-naïve (79.2%), with 85.3% classified in WHO clinical stage 1. The prevalence of AHD was 47.6% (110/231), significantly higher among ART-naïve participants [51.9% (95/183)] compared to ART-experienced participants [31.2% (15/48), p=0.011]. ART-naïve participants aged 19–35 years exhibited a notably higher prevalence of AHD (51.6%) compared to those aged 13-18, 36-45, and >45 years (5.3%, 34.7%, and 8.4%, respectively) and had significantly higher baseline viral load values (25,000 copies/mL vs. 9,690 copies/mL, p=0.037). Additionally, among ART-naïve participants, a significantly higher proportion of individuals in WHO stages 2, 3, and 4 had AHD compared to those without AHD. Across all participants, the factors significantly associated with AHD included anemia (adjusted odds ratio [aOR] 3.03, 95% confidence interval [CI]: 1.15–7.97) and being from the New Masala Clinic health facility (aOR 3.79, 95% CI: 1.17–12.30)

Conclusion

Advanced HIV disease was prevalent, particularly among ART-naïve individuals, and it was significantly associated with anemia and health facility location. There is a need for formulation of interventions, especially among ART-naïve PLHIV who are anemic. Additionally, studies to integrate point-of-care diagnostics such as the VISITECT® CD4 test into routine HIV care be conducted in resource-limited settings are warranted for early detection of AHD.
Characterizing Behavioral Dynamics in Bipolar Disorder with Computational Ethology
Authors: Zhang Zhanqi , Chou Chi K. , Rosberg Holden , Perry William , Young Jared W , Minassian Arpi , Mishne Gal , Aoi Mikio
Published: November 2024

New technologies for the quantification of behavior have revolutionized animal studies in social, cognitive, and pharmacological neurosciences. However, comparable studies in understanding human behavior, especially in psychiatry, are lacking. In this study, we utilized data-driven machine learning to analyze natural, spontaneous open-field human behaviors from people with euthymic bipolar disorder (BD) and non-BD participants. Our computational paradigm identified representations of distinct sets of actions (motifs) that capture the physical activities of both groups of participants. We propose novel measures for quantifying dynamics, variability, and stereotypy in BD behaviors. These fine-grained behavioral features reflect patterns of cognitive functions of BD and better predict BD compared with traditional ethological and psychiatric measures and action recognition approaches. This research represents a significant computational advancement in human ethology, enabling the quantification of complex behaviors in real-world conditions and opening new avenues for characterizing neuropsychiatric conditions from behavior.
Koolen-de Vries Syndrome causal geneKANSL1is required for motile ciliogenesis
Authors: Schmidt James D. , Terala Ananya , McCluskey Kate E. , Wang Belinda , Pfalzer Anna C. , Willsey Helen Rankin
Published: November 2024

Koolen-de Vries Syndrome (KdVS), characterized by hypersociability, intellectual disability, and seizures, is caused by pathogenic variants in the geneKANSL1, which encodes a chromatin regulator in the NSL complex that also directly functions in mitotic spindle microtubule stability. Here we explored whether KANSL1 functions at the cilium, a microtubule-rich organelle critical for brain development, neuronal excitability, and sensory integration. Leveraging theXenopusmodel, we found that Kansl1 is highly expressed in developing ciliated tissues and localizes within motile cilia. Moreover,Kansl1depletion caused ciliogenesis defects that could be partially rescued by humanKANSL1. Based on these findings, we explored the prevalence of cilia-related clinical features including structural heart defects, hypogonadism, and structural respiratory defects among 99 individuals with KdVS, ages 1 month to 37 years old. To directly test if KdVS causes ciliary dysfunction in humans, we measured the well-established ciliary functional biomarker, nasal nitric oxide, in 11 affected individuals and observed a significant decrease when compared to unaffected family members. Together, this work establishes a ciliary contribution ofKANSL1mutations to KdVS. This work adds to a growing literature highlighting the relevance of the cilium to neurodevelopmental disorders, particularly to those impacting sociability. Going forward, KANSL1 provides a unique opportunity to study a monogenic mechanism of hypersociability that may be useful in elaborating the molecular underpinnings of social behavior.
RhoA Allosterically Activates Phospholipase Cε via its EF Hands
Authors: Ohri Vaani , Samassekou Kadidia , Muralidharan Kaushik , Garland-Kuntz Elisabeth E. , Fisher Isaac J. , Hogan William C. , Davis Bailey M. , Lyon Angeline M.
Published: November 2024

Phospholipase Cε (PLCε) cleaves phosphatidylinositol lipids to increase intracellular Ca2+and activate protein kinase C (PKC) in response to stimulation of cell surface receptors. PLCε is activated via direct binding of small GTPases at the cytoplasmic leaflets of cellular membranes. In the cardiovascular system, the RhoA GTPase regulates PLCε to initiate a cardioprotective pathway, but the underlying molecular mechanism is not known. We present here the cryo-electron microscopy (cryo-EM) reconstruction of RhoA bound to PLCε. The G protein binds a unique insertion in the PLCε EF hands. Deletion of or mutations to this PLCε insertion decrease RhoA-dependent activation without impacting regulation by other G proteins. Together, our data support a model wherein RhoA binding to PLCε allosterically activates the lipase and increases its interactions with the membrane, resulting in maximum activity and cardiomyocyte survival.
Variable Cerebral Blood Flow Responsiveness to Acute Hypoxic Hypoxia
Authors: Johnson Hannah R , Wang Max C , Stickland Rachael C , Chen Yufen , Parrish Todd B , Sorond Farzaneh A , Bright Molly G
Published: November 2024

Cerebrovascular reactivity (CVR) to changes in blood carbon dioxide and oxygen levels is a robust indicator of vascular health. Although CVR is typically assessed with hypercapnia, the interplay between carbon dioxide and oxygen, and their ultimate roles in dictating vascular tone, can vary with pathology. Methods to characterize vasoreactivity to oxygen changes, particularly hypoxia, would provide important complementary information to established hypercapnia techniques. However, existing methods to study hypoxic CVR, typically with arterial spin labeling (ASL) MRI, demonstrate high variability and paradoxical responses. To understand whether these responses are real or due to methodological confounds of ASL, we used phase-contrast MRI to quantify whole-brain blood flow in 21 participants during baseline, hypoxic, and hypercapnic respiratory states in three scan sessions. Hypoxic CVR reliability was poor-to-moderate (ICC=0.42 for CVR relative to PETO2changes, ICC=0.56 relative to SpO2changes) and was less reliable than hypercapnic CVR (ICC=0.67). Without the uncertainty from ASL-related confounds, we still observed paradoxical responses at each timepoint. Concurrent changes in blood carbon dioxide levels did not account for paradoxical responses. Hypoxic CVR and hypercapnic CVR shared approximately 40% of variance across the dataset, indicating that the two effects may indeed reflect distinct, complementary elements of vascular regulation.
LATE MERISTEM IDENTITY2 regulates cuticle formation on the seed surface and influences seed longevity
Authors: Oshima Yoshimi , Narumi Takako , Kaneko Yasuko , Ishikawa Toshiki , Kawai-Yamada Maki , Ohme-Takagi Masaru , Mitsuda Nobutaka
Published: November 2024

The seed coat protects the embryo from severe external environment. Like the aerial plant parts, the exterior surface of the seed coat is surrounded by a cuticle consisting of lipid polyesters and wax. However, the protective role of the cuticle in mature seeds has not been characterized. We herein study the transcriptional regulation of cuticle formation on the seed surface, which influences seed longevity. A chimeric repressor ofArabidopsis thalianaR2R3 MYB transcription factor geneLATE MERISTEM IDENTITY2(LMI2)and aTorenia fournieriortholog (TfMYBML3) was expressed inA. thalianaandT. fournieri, respectively. These lines andA. thaliana LMI2T-DNA insertion lines were analyzed for cuticle deficiencies.A. thaliana LMI2mutants and chimeric repressor lines exhibited a similar cuticle deficiency in immature seeds. Transmission electron microscopy observations, polyester composition analyses, and gene expression investigations revealed thatLMI2plays an essential role in cuticle development in the seed coat epidermis by regulating cutin biosynthesis. Thelmi2-2mutant exhibited shorter seed longevity than the wild-type controls in an accelerated aging test. These results indicate that LMI2 is a key regulator of cuticle formation in the seed coat, and is important for maintaining seed longevity.

Significance statement

Cuticle is well known to have multiple important roles for surviving in the terrestrial environment, but their specific role on the seed coat and transcriptional regulation have not yet been elucidated. Here we show thatLATE MERISTEM IDENTITY 2, encoding a transcription factor regulating floral meristem transition, is required for seed cuticle formation and maintaining seed longevity, providing evidence for a link between surface cuticle and seed longevity.