bluuebunny/crossref_metadata_2025 huggingface dataset:
Establishing Primary and Stable Cell Lines from Frozen Wing Biopsies for Cellular, Physiological, and Genetic Studies in Bats
Authors: Deng Fengyan , Morales-Sosa Pedro , Bernal-Rivera Andrea , Wang Yan , Tsuchiya Dai , Javier Jose Emmanuel , Rohner Nicolas , Zhao Chongbei , Camacho Jasmin
Published: March 2024

Bats stand out among mammalian species for their exceptional traits, including the capacity to navigate through flight and echolocation, conserve energy through torpor/hibernation, harbor a multitude of viruses, exhibit resistance to disease, survive harsh environmental conditions, and demonstrate exceptional longevity compared to other mammals of similar size.In vivostudies of bats can be challenging for several reasons such as ability to locate and capture them in their natural environments, limited accessibility, low sample size, environmental variation, long lifespans, slow reproductive rates, zoonotic disease risks, species protection, and ethical concerns. Thus, establishing alternative laboratory models is crucial for investigating the diverse physiological adaptations observed in bats. Obtaining quality cells from tissues is a critical first step for successful primary cell derivation. However, it is often impractical to collect fresh tissue and process the samples immediately for cell culture due to the resources required for isolating and expanding cells. As a result, frozen tissue is typically the starting resource for bat primary cell derivation. Yet, cells in frozen tissue are usually damaged and represent low integrity and viability. As a result, isolating primary cells from frozen tissues poses a significant challenge. Herein, we present a successfully developed protocol for isolating primary dermal fibroblasts from frozen bat wing biopsies. This protocol marks a significant milestone, as this the first protocol specially focused on fibroblasts isolation from bat frozen tissue. We also describe methods for primary cell characterization, genetic manipulation of primary cells through lentivirus transduction, and the development of stable cell lines.

Basic Protocol 1:Bat wing biopsy collection and preservation

Support Protocol 1:Blood collection from bat-venipuncture

Basic Protocol 2:Isolation of primary fibroblasts from adult bat frozen wing biopsy

Support Protocol 2:Maintenance of primary fibroblasts

Support Protocol 3:Cell banking and thawing of primary fibroblasts

Support Protocol 4:Growth curve and doubling time

Support Protocol 5:Lentiviral transduction of bat primary fibroblasts

Basic Protocol 3:Bat stable fibroblasts cell lines development

Support Protocol 6:Bat fibroblasts validation by immunofluorescence staining

Support Protocol 7:Chromosome counting
Sediment-associated processes drive spatial variation in ecosystem respiration in the Yakima River basin
Authors: Kaufman Matthew , Garayburu-Caruso Vanessa A. , Forbes Brieanne , Lin Xinming , Hall Robert O. , Fulton Stephanie , Renteria Lupita , Fang Yilin , Son Kyongho , Stegen James C.
Published: March 2024

Areas where groundwater and surface water mix (i.e., hyporheic zones, HZ) contribute substantially to stream ecosystem respiration (ERtot). We rely on reactive transport models to understand HZ respiration at large scales; however, model outputs have not been evaluated with field estimates of ERtot. Here we evaluate the degree to which spatial variation in model-predicted HZ respiration can explain spatial variation in field-estimated ERtot across 32 sites in the Yakima River basin (YRB). We find that predicted HZ respiration did not explain spatial variation in ERtot. We hypothesize that ERtot is influenced by processes that integrate contributions from sediments, such as benthic algae, submerged macrophytes, and shallow HZ. Our results indicate that sediment-associated processes hydrologically connected to the active channel are primary drivers of spatial variation in ERtot in the YRB. We encourage conceptual and physical models of stream ERtot to integrate shallow hyporheic exchange with sediment-associated primary production.
mm2-gb: GPU Accelerated Minimap2 for Long Read DNA Mapping
Authors: Dong Juechu , Liu Xueshen , Sadasivan Harisankar , Sitaraman Sriranjani , Narayanasamy Satish
Published: March 2024

Long-read DNA sequencing is becoming increasingly popular for genetic diagnostics. Minimap2 is the state-of-the-art long-read aligner. However, Minimap2’s chaining step is slow on the CPU and takes 40-68% of the time especially for long DNA reads. Prior works in accelerating Minimap2 either lose mapping accuracy, are closed source (and not updated) or deliver inconsistent speedups for longer reads. We introducemm2-gbwhich accelerates the chaining step of Minimap2 on GPU without compromising mapping accuracy. In addition to intra- and inter-read parallelism exploited by prior works,mm2-gbexploits finer levels of parallelism by breaking down high latency large workloads into smaller independent segments that can be run in parallel and leverages several strategies for better workload balancing including split-kernels and prioritized scheduling of segments based on sorted size. We show thatmm2-gbon an AMD Instinct™ MI210 GPU achieves 2.57-5.33x performance improvement on long nanopore reads (10kb-100kb), and up to 1.87x performance gain on super long reads (100kb-300kb) compared to SIMD accelerated mm2-fast.mm2-gbis open-sourced and available athttps://github.com/Minimap2onGPU/mm2-gb.
Genome-wide analysis of mRNA decay in Arabidopsis shoot and root reveals the importance of co-translational mRNA decay in the general mRNA turnover
Authors: Marie-Christine Carpentier , Anne-Elodie Receveur , Alexandre Boubegtitene , Adrien Cadoudal , Cécile Bousquet-Antonelli , Rémy Merret
Published: March 2024

Until recently, the general 5’-3’ mRNA decay was placed in the cytosol after the mRNA was released from ribosomes. However, the discovery of an additional 5’ to 3’ pathway, the Co-Translational mRNA Decay (CTRD), changed this paradigm. Up to date, defining the real contribution of CTRD in the general mRNA turnover has been hardly possible as the enzyme involved in this pathway is also involved in cytosolic decay. Here we overcame this obstacle and created an Arabidopsis line specifically impaired for CTRD called XRN4ΔCTRD. Through a genome-wide analysis of mRNA decay rate in shoot and root, we tested the importance of CTRD in mRNA turnover. First, we observed that mRNAs tend to be more stable in root than in shoot. Next, using XRN4ΔCTRD line, we demonstrated that CTRD is a major determinant in mRNA turnover. In shoot, the absence of CTRD leads to the stabilization of thousands of transcripts while in root its absence is highly compensated resulting in faster decay rates. We demonstrated that this faster decay rate is partially due to the XRN4-dependent cytosolic decay. Finally, we correlated this organ-specific effect with XRN4ΔCTRD line phenotypes revealing a crucial role of CTRD in mRNA homeostasis and proper organ development.
Development of a tightly regulated copper-inducible transient gene expression system inNicotiana benthamianaincorporating suicide exon and Cre recombinase
Authors: Chiang Bing-Jen , Lin Kuan-Yu , Chen Yi-Feng , Huang Ching-Yi , Goh Foong-Jing , Huang Lo-Ting , Chen Li-Hung , Wu Chih-Hang
Published: March 2024

Chemical-inducible gene expression systems have been frequently used to regulate gene expression for functional genomics in various plant species. However, a convenient chemical-inducible system that can tightly regulate transgene expression inNicotiana benthamianais still missing. In this study, we developed a tightly regulated copper-inducible system that can be used to regulate transgene expression and perform cell death assays inN. benthamiana. We tested several chemical-inducible systems usingAgrobacterium-mediated transient expression and found that the copper-inducible system showed the least concerns of leakiness issues. Using the MoClo-based synthetic biology approach, we optimized the design of the copper-inducible system and incorporated the use of the suicide exon HyP5SM/OsL5 and Cre/LoxP as additional regulatory elements to enhance the tightness of the regulation. This new design allowed us to tightly control the hypersensitive cell death induced by several tested NLRs and their matching AVRs, and it can also be easily applied to regulate the expression of other transgenes in transient expression assays. Our findings provide new approaches for both fundamental and translational studies in plant functional genomics.
Decomposed frontal corticostriatal ensemble activity changes across trials, revealing distinct features relevant to outcome-based decision making
Authors: Handa Takashi , Fukai Tomoki , Kurikawa Tomoki
Published: March 2024

The frontal cortex-striatum circuit plays a pivotal role in adaptive goal-directed behaviours. However, the mediation of decision-related signals through cross-regional transmission between the medial frontal cortex and the striatum by neuronal ensembles remains unclear. We analysed neuronal ensemble activity obtained through simultaneous multiunit recordings in the secondary motor cortex (M2) and dorsal striatum (DS) while the rats performed an outcome-based choice task. Tensor component analysis (TCA), an unsupervised dimensionality reduction approach at the single-trial level, was adopted for concatenated ensembles of M2 and DS neurons. We identified distinct three spatiotemporal neural dynamics (TCA components) at the single-trial level specific to task-relevant variables. Choice-position selective neural dynamics was correlated with the trial-to-trial fluctuation of behavioural variables. This analytical approach unveiled choice-pattern selective neural dynamics distinguishing whether the incoming choice was a repetition or switch from the previous choice. Other neural dynamics was selective to outcome. Choice-pattern selective within-trial activity increased before response choice, whereas outcome selective within-trial activity increased following response. These results suggest that the concatenated ensembles of M2 and DS process distinct features of decision-related signals at various points in time. The M2 and DS may collaboratively monitor action outcomes and determine the subsequent choice, whether to repeat or switch, for coordinated action selection.
Kilohertz volumetric imaging of in-vivo dynamics using squeezed light field microscopy
Authors: Wang Zhaoqiang , Zhao Ruixuan , Wagenaar Daniel A , Espino Diego , Sheintuch Liron , Benshlomo Ohr , Kang Wenjun , Lee Calvin , Schmidt William , Pammar Aryan , Zhu Enbo , Wang Jing , Wong Gerard C. L. , Liang Rongguang , Golshani Peyman , Hsiai Tzung , Gao Liang
Published: March 2024

Volumetric functional imaging of transient cellular signaling and motion dynamics poses a significant challenge to current microscopy techniques, primarily due to limitations in hardware bandwidth and the restricted photon budget within short exposure times. In response to this challenge, we present squeezed light field microscopy (SLIM), a computational imaging method that enables rapid detection of high-resolution three-dimensional (3D) light signals using only a single, low-format camera sensor area. SLIM pushes the boundaries of 3D optical microscopy, achieving over one thousand volumes per second across a large field of view of 550 μm in diameter and 300 μm in depth with a spatial resolution of 3.6 μm laterally and 6 μm axially. Using SLIM, we demonstrated blood cell velocimetry across the embryonic zebrafish brain and in a free-moving tail exhibiting high-frequency swinging motion. The millisecond temporal resolution also enables accurate voltage imaging of neural membrane potentials in the leech ganglion, and in the hippocampus of behaving mice. These results collectively establish SLIM as a versatile and robust imaging tool for high-speed microscopy applications.
Exploring the impact of sequence context on errors in SNP genotype calling with Whole Genome Sequencing data using AI-based autoencoder approach
Authors: Kotlarz Krzysztof , Mielczarek Magda , Biecek Przemysław , Guldbrandtsen Bernt , Szyda Joanna
Published: March 2024

A critical step in the analysis of WGS data is variant calling. Despite its importance, variant calling is prone to errors. Our study investigated the association between incorrect SNP and variant quality metrics and nucleotide context. In our study, incorrect SNPs were defined in twenty Holstein-Friesian cows by comparing their SNPs genotypes identified by whole genome sequencing with the IlluminaNovaSeq6000 and the EuroGMD50K genotyping microarray. The data set was divided into the correct set of SNPs (666,333 SNPs) and the incorrect set of SNPs (4,557 SNPs). The training data set consisted of only the correct SNPs, while the test data set contained a balanced mix of all the incorrectly and correctly called SNPs. An autoencoder was constructed to identify systematically incorrect SNPs that were marked as outliers by a one-class support vector machine and isolation forest algorithms. The results showed that 59.53% (±0.39%) of the incorrect SNPs had systematic patterns, with the remainder being random errors. The frequent occurrence of the CGC trimer was due to mislabeling a call for C. Incorrect T instead A call was associated with the presence of T in the neighboring downstream position. These errors may arise due to the fluorescence patterns of nucleotide labelling.
EXPLORING THE DISTRIBUTION OF SINGLE NUCLEOTIDE POLYMORPHISMS ACROSS HUMAN EXONS AND INTRONS
Authors: Fraszczak Magdalena , Liu Jakub , Mielczarek Magda , Dobosz Paula , Szyda Joanna
Published: March 2024

Among all types of mutations, single nucleotide polymorphisms are the most common type of genomic variation. In our study, we explore the counts of single nucleotide polymorphisms in particular exons and introns of the human genome based on the data set of 1,222 individuals of Polish origin that comprises 41,836,187 polymorphisms. In particular, chromosomes 1 and 22 were considered as representatives of two markedly different DNA molecules, since HSA01 represents the longest and HSA22 is one of the shortest chromosomes. The results demonstrate that outer (first, last) exons as well as the first introns harbour significantly more SNPs than other genic regions. The observed differences in counts reflect the distinct functional roles of those genomic units.
Puberty Blocker and Aging Impact on Testicular Cell States and Function
Authors: Murugesh Varshini , Ritting Megan , Salem Salem , Aalam Syed Mohammed Musheer , Garcia Joaquin , Chattha Asma J , Zhao Yulian , Knapp David JHF , Kalthur Guruprasad , Granberg Candace F , Kannan Nagarajan
Published: March 2024

Spermatogonial stem cell (SSC) acquisition of meiotogenetic state during puberty to produce genetically diverse gametes is blocked by drugs collectively referred as ‘puberty blocker’ (PB). Investigating the impact of PB on juvenile SSC state and function is challenging due to limited tissue access and clinical data. Herein, we report largest clinically annotated juvenile testicular biorepository with all children with gender dysphoria on chronic PB treatment highlighting shift in pediatric patient demography in US. At the tissue level, we report mild-to-severe sex gland atrophy in PB treated children. We developed most extensive integrated single-cell RNA dataset to date (>100K single cells; 25 patients), merging both public and novel (52 month PB-treated) datasets, alongside innovative computational approach tailed for germ cells and evaluated the impact of PB and aging on SSC. We report novel constitutional ranges for each testicular cell type across the entire age spectrum, distinct effects of treatments on prepubertal vs adult SSC, presence of spermatogenic epithelial cells exhibiting post-meiotic-state, irrespective of age, puberty status, or PB treatment. Further, we defined distinct effects of PB and aging on testicular cell lineage composition, and SSC meiotogenetic state and function. Using single cell data from prepubertal and young adult, we were able to accurately predict sexual maturity based both on overall cell type proportions, as well as on gene expression patterns within each major cell type. Applying these models to a PB-treated patient that they appeared pre-pubertal across the entire tissue. This combined with the noted gland atrophy and abnormalities from the histology data raise a potential concern regarding the complete ’reversibility’ and reproductive fitness of SSC. The biorepository, data, and research approach presented in this study provide unique opportunity to explore the impact of PB on testicular reproductive health.
Heterogeneity in slow synaptic transmission diversifies Purkinje cell timing
Authors: Thomas Riya Elizabeth , Mudlaff Franziska , Schweers Kyra , Farmer W. Todd , Suvrathan Aparna
Published: March 2024

The cerebellum plays an important role in diverse brain functions, ranging from motor learning to cognition. Recent studies have suggested that molecular and cellular heterogeneity within cerebellar lobules contributes to functional differences across the cerebellum. However, the specific relationship between molecular and cellular heterogeneity and diverse functional outputs of different regions of the cerebellum remains unclear. Here, we describe a previously unappreciated form of synaptic heterogeneity at parallel fiber synapses to Purkinje cells. In contrast to uniform fast synaptic transmission, we found that the properties of slow synaptic transmission varied by up to three-fold across different lobules of the mouse cerebellum, resulting in surprising heterogeneity. Depending on the location of a Purkinje cell, the time of peak of slow synaptic currents varied by hundreds of milliseconds. The duration and decay-time of these currents also spanned hundreds of milliseconds, based on lobule. We found that, as a consequence of the heterogeneous synaptic dynamics, the same brief stimulus was transformed into prolonged firing patterns over a range of timescales that depended on Purkinje cell location
Aging impacts basic auditory and timing processes
Authors: Criscuolo Antonio , Schwartze Michael , Bonetti Leonardo , Kotz Sonja A.
Published: March 2024

Deterioration in the peripheral and central auditory systems is common in older adults and often leads to hearing and speech comprehension difficulties. Even when hearing remains intact, electrophysiological data of older adults frequently exhibit altered neural responses along the auditory pathway, reflected in variability in phase alignment of neural activity to speech sound onsets. However, it remains unclear whether these challenges in speech processing in aging stem from more fundamental deficits in auditory and timing processes. Here, we investigatedifandhowaging individuals encoded temporal regularities in isochronous auditory sequences presented at 1.5Hz, andifthey employed adaptive mechanisms of neural phase alignment in anticipation of next sound onsets. We recorded EEG in older and young individuals listening to simple isochronous tone sequences. We show that aging individuals displayed increased amplitudes and variability in time-locked responses to sounds, an increased 1/F slope, but reduced phase-coherence in the delta and theta frequency-bands. These observations suggest a lack of repetition-suppression and inhibition when processing repeated and predictable sounds in a sequence and altered mechanisms of continuous phase-alignment to expected sound onsets in aging. Given that deteriorations in these basic timing capacities may affect other higher-order cognitive processes (e.g., attention, perception, and action), these results underscore the need for future research examining the link between basic timing abilities and general cognition across the lifespan.

Highligths

Aging individuals (HO) show increased cortical excitability as compared to younger adults (HY);

HO’s neural responses to fully predictable isochronous tones were larger and more variable than HY;

HO showed reduced phase coherence in delta- and theta-band oscillations during listening to auditory sequence;

Altogether, these results show altered sensory and timing processes in aging.
Root surface treatment for delayed replantation of avulsed teeth in animal models: a systematic review
Authors: Huaman Stephanie Díaz , Vilela Marina Moscardini , Nelson-Filho Paulo , De Rossi Andiara , de Queiroz Alexandra Mussolino , Paula-Silva Francisco Wanderley Garcia
Published: March 2024

The aim of this study was to perform a systematic review of thein vivoeffectiveness of different types of root surface treatment materials used in delayed replanted teeth following tooth avulsion in animal models. A systematic review was conducted according to the PRISMA statement. Two reviewers performed a database search for studies published between January 1966 and April 2019 which were indexed in the PubMed, Scopus, and Bireme databases. Studies performedin vivo, in animal models with an avulsion/delayed replantation design (≥ 20 min of extra oral dry time) that evaluated the use of different materials for root surface treatment were included. The assessment for risk of bias was performed following recommendations included in Cochrane handbook for systematic reviews of interventions. We found 21 types of materials used for root surface treatment alone and 29 materials used with associations. Stannous fluoride, sodium fluoride, citric acid, doxycycline, Emdogain, alendronate, minocycline, Odanacatib, MFR buffer, recombinant human bone morphogenetic protein, gallium nitrate, acidulated phosphate fluoride, vitamin C, propolis, zoledronic acid, diode laser, indomethacin, fibrin sealant, adipose-tissue derived stem cells treatment and basic fibroblast growth gel. After Grading of Recommendations Assessment, Development, and Evaluation, four studies were scored as low quality of evidence, fifteen studies with moderate quality and six with high quality of evidence. Meta-analysis was not performed due to heterogeneity among studies and materials used for root surface treatment and therefore it was not possible to ascertain which material or protocol present better efficacy when used as root surface treatment material.
Patient-derived response estimates from zero-passage organoids of luminal breast cancer
Authors: Przanowska Roza , Labban Najwa , Przanowski Piotr , Hawes Russell , Atkins Kristen , Showalter Shayna , Janes Kevin
Published: March 2024

Background Primary luminal breast cancer cells lose their identity rapidly in standard tissue culture, which is problematic for testing hormone interventions and molecular pathways specific to the luminal subtype. Breast cancer organoids are thought to retain tumor characteristics better, but long-term viability of luminal-subtype cases is a persistent challenge. Our goal was to adapt short-term organoids of luminal breast cancer for parallel testing of genetic and pharmacologic perturbations. Methods We freshly isolated patient-derived cells from luminal tumor scrapes, miniaturized the organoid format into 5 microliter replicates for increased throughput, and set an endpoint of 14 days to minimize drift. Therapeutic hormone targeting was mimicked in these zero-passage organoids by withdrawing beta-estradiol and adding 4-hydroxytamoxifen. We also examined sulforaphane as an electrophilic stress and commercial neutraceutical with reported anti-cancer properties. Downstream mechanisms were tested genetically by lentiviral transduction of two complementary sgRNAs and Cas9 stabilization for the first week of organoid culture. Transcriptional changes were measured by RT-qPCR or RNA sequencing, and organoid phenotypes were quantified by serial brightfield imaging, digital image segmentation, and regression modeling of cellular doubling times. Results We achieved >50% success in initiating luminal breast cancer organoids from tumor scrapes and maintaining them to the 14-day zero-passage endpoint. Success was mostly independent of clinical parameters, supporting general applicability of the approach. Abundance of ESR1 and PGR in zero-passage organoids consistently remained within the range of patient variability at the endpoint. However, responsiveness to hormone withdrawal and blockade was highly variable among luminal breast cancer cases tested. Combining sulforaphane with knockout of NQO1 (a phase II antioxidant response gene and downstream effector of sulforaphane) also yielded a breadth of organoid growth phenotypes, including growth inhibition with sulforaphane, growth promotion with NQO1 knockout, and growth antagonism when combined. Conclusions Zero-passage organoids are a rapid and scalable way to interrogate properties of luminal breast cancer cells from patient-derived material. This includes testing drug mechanisms of action in different clinical cohorts. A future goal is to relate inter-patient variability of zero-passage organoids to long-term outcomes.
Fast volumetric fluorescence lifetime imaging of multicellular systems using single-objective light-sheet microscopy
Authors: Dunsing-Eichenauer Valentin , Hummert Johan , Chardès Claire , Schönau Thomas , Guignard Léo , Galland Rémi , Grenci Gianluca , Tillmann Max , Koberling Felix , Nock Corinna , Sibarita Jean-Baptiste , Viasnoff Virgile , Antolovic Ivan Michel , Erdmann Rainer , Lenne Pierre-François
Published: March 2024

Fluorescence lifetime imaging (FLIM) is widely used for functional and multiplexed bioimaging, but is limited in speed, volumetric sampling of multicellular specimen, and live cell compatibility. To overcome these limitations, we have combined single objective light-sheet microscopy with pulsed excitation and time-resolved detection on a SPAD array detector. We report excellent quantitative agreement with confocal FLIM at 10-100-fold shorter acquisition times, down to 100 ms per image. We demonstrate lifetime-based multiplexing in 3D and time-lapse FLIM of mechanosensitive tension probes on living embryonic organoids, providing a powerful tool for functional imaging of dynamic multicellular systems.
Theta-Gamma Phase-Amplitude Coupling Supports Working Memory Performance in the Human Hippocampus
Authors: Salimpour Yousef , Anderson William S.
Published: March 2024

Phase-amplitude coupling (PAC) occurs in the human hippocampus during working memory and supports the contribution of the hippocampus in the maintenance of multiple items. Additionally, PAC has the potential to reveal the neural mechanisms underlying multi-item maintenance in the hippocampus by providing a putative architecture for multi-item representation. Theta and gamma range rhythms are prominent neuronal oscillations in the hippocampus. Studies on the role of theta frequency oscillation in local field potentials in human memory have shown mixed evidence for successful remembering. The role of gamma oscillatory activity in contributing to memory retrieval is not yet fully understood. They also interact with each other in the form of PAC during memory performance. This study aims to investigate the neurophysiological function of theta-gamma PAC in the human hippocampus during a multi-item working memory task and characterize its association with performance. Theta-gamma cross-coupling investigation in the electrocorticographic signals was performed from the hippocampus recording of ten epilepsy patients while they were engaged with the working memory task. The results show strong correlations between PAC levels and the subjects memory performance, but no correlation with theta and gamma power individually, specifically in the retrieval phase of a working memory task. These observations demonstrate the possible role of PAC in memory-related operations, suggesting a PAC-based neural mechanism for working memory in the hippocampus.

Significance Statement

The findings from this study elucidate the crucial role of phase-amplitude coupling in the human hippocampus during working memory tasks, specifically in the maintenance of multiple items. By analyzing electrocorticographic recordings from epilepsy patients engaged in a working memory task, our research unveils a direct correlation between PAC levels and memory performance during the retrieval phase, which is not observed when analyzing theta and gamma oscillations individually. These findings suggest a theta-gamma coupling based mechanism within the hippocampus that facilitates working memory, offering new insights into the complex neural processes underlying memory encoding and retrieval. This advancement in understanding the neural architecture of memory not only contributes to the foundational knowledge of cognitive neuroscience but also opens avenues for developing targeted interventions for enhancing memory performance with translational application in treating memory-related neurological disorders.
Enhancing amino acid productivity and profile in black soldier fly larvae through NAT transporter suppression in the excretion system
Authors: Liu Chia-Ming , Uehara Takuya , Shimoda Masami
Published: March 2024

Larvae of the black soldier fly (Hermetia illucens, BSFL) are rich in valuable nutrients and offer a promising alternative protein source for animal feeds. Nonetheless, there is a pressing need to improve both the productivity and quality of BSFL proteins to ensure their viability, facilitating the industrial production. To fulfil the needs of different animals, it is necessary to adjust the profile of essential amino acids (AAs) in BSFL. Insects excrete surplus nutrients to maintain homeostasis; AAs are excreted by nutrient AA transporters (NATs) in the Malpighian tubules. We aimed to modify the composition of essential AAs by silencing the NAT in Malpighian tubules of BSFL (HiNATt). Silencing HiNATt resulted in a 56.2% decrease in body weight but a 77.3% increase in the total AA content. Notably, the contents of some valuable essential AAs were strongly increased (histidine, 156.8%; valine, 98.1%). These results suggest that inhibiting the function of HiNATt could modify the composition of accumulated AAs. This finding opens a new avenue for producing of BSFL with increased nutritional value as an alternative protein source.
Higher amplitudes of visual networks are associated with trait-but not state-depression
Authors: Zhang Wei , Dutt Rosie , Lew Daphne , Barch Deanna M. , Bijsterbosch Janine
Published: March 2024

Despite depression being a leading cause of global disability, neuroimaging studies have struggled to identify replicable neural correlates of depression or explain limited variance. This challenge may, in part, stem from the intertwined state (current symptoms; variable) and trait (general propensity; stable) experiences of depression.

Here, we sought to disentangle state from trait experiences of depression by leveraging a longitudinal cohort and stratifying individuals into four groups: those in remission (‘trait depression group’), those with large longitudinal severity changes in depression symptomatology (‘state depression group’), and their respective matched control groups (total analytic n=1,030). We hypothesized that spatial network organization would be linked to trait depression due to its temporal stability, whereas functional connectivity between networks would be more sensitive to state-dependent depression symptoms due to its capacity to fluctuate.

We identified 15 large-scale probabilistic functional networks from resting-state fMRI data and performed group comparisons on the amplitude, connectivity, and spatial overlap between these networks, using matched control participants as reference. Our findings revealed higher amplitude in visual networks for the trait depression group at the time of remission, in contrast to controls. This observation may suggest altered visual processing in individuals predisposed to developing depression over time. No significant group differences were observed in any other network measures for the trait-control comparison, nor in any measures for the state-control comparison. These results underscore the overlooked contribution of visual networks to the psychopathology of depression and provide evidence for distinct neural correlates between state and trait experiences of depression.
Sexual dimorphism in the dorsal spot number and yellow surface in fire salamandersSalamandra salamandra ssp terrestrisLinnaeus, 1758 (Caudata: Salamandridae)
Authors: Bozon Martin , Marteau Basile
Published: March 2024

Sexual selection among amphibians is mainly based on size and colour dimorphism. Those criteria are less studied in salamanders. Only morphometric and yellow surface differences between males and females are known. We studied aSalamandra salamandra terrestrispopulation and observed significant differences in spots number and yellow surface area between males and females. Females have on average more spots and are blacker than males on their back.
Bisphosphonates synergistically enhance the antifungal activity of azoles in dermatophytes and other pathogenic molds
Authors: Kane Aidan , Rothwell Joanna G. , Guttentag Annabel , Hainsworth Steven , Carter Dee
Published: March 2024

Superficial infections of the skin, hair and nails by fungal dermatophytes are the most prevalent of human mycoses, and many infections are refractory to treatment. As current treatment options are limited, recent research has explored drug synergy with azoles for dermatophytoses. Bisphosphonates, which are approved to treat osteoporosis, can synergistically enhance the activity of azoles in diverse yeast pathogens but their activity has not been explored in dermatophytes or other molds. Market bisphosphonates risedronate, alendronate and zoledronate (ZOL) were evaluated for antifungal efficacy and synergy with three azole antifungals: fluconazole (FLC), itraconazole (ITR), and ketoconazole (KET). ZOL was the most active bisphosphonate tested, displaying moderate activity against nine dermatophyte species (MIC range 64–256 µg/mL), and was synergistic with KET in 88.9% of these species. ZOL was also able to synergistically improve the anti-biofilm activity of KET and combining KET and ZOL prevented the development of antifungal resistance. Rescue assays inTrichophyton rubrumrevealed that the inhibitory effects of ZOL alone and in combination with KET were due to the inhibition of squalene synthesis. Fluorescence microscopy using membrane- and ROS-sensitive probes demonstrated that ZOL and KET:ZOL compromised membrane structure and induced oxidative stress. Antifungal activity and synergy between bisphosphonates and azoles were also observed in other clinically relevant molds, including species ofAspergillusandMucor. These findings indicate that repurposing bisphosphonates as antifungals is a promising strategy for revitalising certain azoles as topical antifungals, and that this combination could be fast-tracked for investigation in clinical trials.

Importance

Fungal infections of the skin hair and nails, generally grouped together as “tineas” are the most prevalent infectious disease globally. These infections, caused by fungal species known as dermatophytes, are generally superficial, but can in some cases become aggressive. They are also notoriously difficult to resolve, with few effective treatments and rising levels of drug resistance. Here we report a potential new treatment that combines azole antifungals with bisphosphonates. Bisphosphonates are approved for the treatment of low bone density diseases, and in fungi they inhibit the biosynthesis of the cell membrane, which is also the target of azoles. Combinations were synergistic across the dermatophyte species and prevented the development of resistance. We extended the study to molds that cause invasive disease, finding synergy in some problematic species. We suggest bisphosphonates could be repurposed as synergents for tinea treatment, and that this combination could be fast-tracked for use in clinical therapy.
Integrating Chromosome Conformation and DNA Repair in a Computational Framework to Assess Cell Radiosensitivity
Authors: Andriotty Matthew , Wang C.-K. Chris , Kapadia Anuj , McCord Rachel , Agasthya Greeshma
Published: March 2024

Objective

The arrangement of chromosomes in the cell nucleus has implications for cell radiosensitivity. The development of new tools to utilize Hi-C chromosome conformation data in nanoscale radiation track structure simulations allows forin silicoinvestigation of this phenomenon. We have developed a framework employing Hi-C-based cell nucleus models in Monte Carlo radiation simulations, in conjunction with mechanistic models of DNA repair, to predict not only the initial radiation-induced DNA damage, but also the repair outcomes resulting from this damage, allowing us to investigate the role chromosome conformation plays in the biological outcome of radiation exposure.

Approach

In this study, we used this framework to generate cell nucleus models based on Hi-C data from fibroblast and lymphoblastoid cells and explore the effects of cell type-specific chromosome structure on radiation response. The models were used to simulate external beam irradiation including DNA damage and subsequent DNA repair. The kinetics of the simulated DNA repair were compared with previous results.

Main Results

We found that the fibroblast models resulted in a higher rate of inter-chromosome misrepair than the lymphoblastoid model, despite having similar amounts of initial DNA damage and total misrepairs for each irradiation scenario.

Significance

This framework represents a step forward in radiobiological modeling and simulation allowing for more realistic investigation of radiosensitivity in different types of cells.
Nuclear actin and DNA replication stress regulate the recruitment of human telomerase to telomeres
Authors: Harman Ashley , Kartawinata Melissa , Maroun Nohad M. , Nguyen Darren R. , Hughes William E. , Winardi Kevin , Cesare Anthony J. , Lamm Noa , Bryan Tracy M.
Published: March 2024

The recruitment of telomerase to telomeres is a tightly regulated process which is stimulated by replication stress and mediated by the DNA damage response regulatory kinase ATR. Here, we demonstrate that nuclear filamentous actin is important for telomerase recruitment under endogenous and replication stress conditions in immortal human cells. Inhibition of nuclear actin polymerization decreases the presence of telomerase at telomeres. This process is regulated by both ATR and mTOR kinases, and employs other regulators of actin structure and function, such as WASP, ARP2/3 and myosin. Nuclear filamentous actin serves as a site for telomerase recruitment, which is mediated by telomere tethering on actin fibres in response to replication stress, allowing telomerase to localize to telomeres containing stalled replication forks. Overall, these data demonstrate that, in human cells which express telomerase, telomeric replication stress triggers the recruitment of telomerase to telomeres via a nuclear actin network, enabling telomere length maintenance.
Liver regeneration by oval cells employing bistability of stemness-senescence, Hippo signaling, EMT-MET, and polyploidy circuit
Authors: Lazovska Marija , Salmina Kristine , Pjanova Dace , Gerashchenko Bogdan I. , Erenpreisa Jekaterina
Published: March 2024

Liver hepatocytes possess remarkable regenerative capabilities, yet severe damage may compromise this process. Liver progenitor (“oval”) cells exhibit the potential to differentiate into both hepatocytes and cholangiocytes, making them promising candidates for cell therapy. However, their mechanisms in liver regeneration are not clear. Here, on rat liver oval stem-like epithelial cells (WB-F344) a wound healing assay was performed. The scratched near-confluent monolayers (70% area removed) underwent the G1-arrest, bi-nucleation at 10-12 hours post-wounding, starting movement of epithelial to mesenchymal transition (EMT) cell portion into the wounded areas. Nanog nuclear upregulation, fragmentation, and transition as granules into cytoplasm and around, along with p16Ink4anuclear intrusion from the cytoplasm, loss of epithelial markers, and YAP1/Hippo activation were seen near the wound edge. The replicative stress and proliferation boost followed, documented at 24 hours. Proliferation concluded at 40-48 hours, accomplished by reconstitution of epithelial tissue, the disappearance of Nanog granulation and p16Ink4areturn to the cytoplasm, releasing excess. This investigation reveals novel regulatory facets in liver regeneration by oval cells. It accentuates the stemness-senescence bistable switch regulated by reciprocal nucleo-cytoplasmic transitions of opposite regulators, coordinated with Hippo-pathway switch, replicative stress, and boost, along with ploidy, EMT-MET and paracrine secretome circuits - enabling successfully resolving the massive injury.

Abstract Figure

Fig 1.

Graphical abstract.

Bistable nuclear-cytoplasmic switch between stemness and senescence regulators in the wound healing process by oval liver cells: (1-2) Priming phase: (1) at the wound edge, (2) in the wound; (3) Proliferative phase, wound closure. Nanog – green; p16INK4A – red, EMT cell - with blue nucleus.
BAX and BAK expression triggers multiple IRE1 signaling outputs under ER stress
Authors: Sepulveda Claudia , Milani Mateus , Morales Vania , Tamburinni Giovanni , Montes Nicolas , Hetz Claudio
Published: March 2024

Adaptation to endoplasmic reticulum (ER) stress depends on the activation of the unfolded protein response (UPR) stress sensor inositol-requiring enzyme 1 alpha (IRE1). IRE1 is a central ER stress sensors, that signals through the activation of its RNase domain to catalyze the splicing the mRNA encoding the transcription factor X-box binding protein 1 (XBP1), resulting on the expression of a stable and active transcription factor termed XBP1s. The kinetics and amplitude of IRE1 signaling are regulated by different posttranslational modifications and the physical interaction of different factors. Early studies demonstrated that the expression of the proapoptotic proteins BAX and BAX enhance UPR signaling. However, the possible effects on the RNase activity were not defined. Here we provide preliminary evidence indicating that BAX and BAK deficiency increases the in 10 folds the threshold of ER stress to induce XBP1 mRNA splicing, and the upregulation of its target genes. In addition, the degradation of RIDD substrates was strongly reduced in BAX and BAK null cells. BAX and BAK double deficiency also attenuated the levels of IRE1 phosphorylation under mild ER stress. These results reinforce previous findings indicating that proapoptotic BAX and BAK have alternative functions at the ER regulating the UPR.
Dorsolateral septum GLP-1R neurons regulate feeding via lateral hypothalamic projections
Authors: Lu Yi , Wang Le , Luo Fang , Savani Rohan , Rossi Mark A. , Pang Zhiping P.
Published: March 2024

Objective

Although glucagon-like peptide 1 (GLP-1) is known to regulate feeding, the central mechanisms contributing to this function remain enigmatic. Here, we aim to test the role of neurons expressing GLP-1 receptors (GLP-1R) in the dorsolateral septum (dLS; dLSGLP-1R) and their downstream projections on food intake and determine the relationship with feeding regulation.

Methods

Using chemogenetic manipulations, we assessed how activation or inhibition of dLSGLP-1Rneurons affected food intake inGlp1r-ires-Cremice. Then, we used channelrhodopsin-assisted circuit mapping, chemogenetics, and electrophysiological recordings to identify and assess the role of the pathway from dLSGLP-1Rneurons to the lateral hypothalamic area (LHA) in regulating food intake.

Results

Chemogenetic inhibition of dLSGLP-1Rneurons increases food intake. LHA is a major downstream target of dLSGLP-1Rneurons. The dLSGLP-1R→LHA projections are GABAergic, and chemogenetic inhibition of this pathway also promotes food intake. While chemogenetic activation of dLSGLP-1R→LHA projections modestly decreases food intake, optogenetic stimulation of the dLSGLP-1R→LHA projection terminals in the LHA rapidly suppressed feeding behavior. Finally, we demonstrate that the GLP-1R agonist, Exendin 4 enhances dLSGLP-1R→LHA GABA release.

Conclusions

Together, these results demonstrate that dLS-GLP-1R neurons and the inhibitory pathway to LHA can regulate feeding behavior, which might serve as a potential therapeutic target for the treatment of eating disorders or obesity.

Highlights

Chemogenetic inhibition of dLSGLP-1Rneurons boosts food intake in mice

dLSGLP-1Rneuron activation does not alter feeding, likely by collateral inhibition

dLSGLP-1Rneurons project to LHA and release GABA

Activation of dLSGLP-1R→LHA axonal terminals suppresses food intake

GLP-1R agonism enhances dLSGLP-1R→LHA GABA release via a presynaptic mechanism
Chara canescenspart I: Oospore differentiation of parthenogenic and dioecious strains and salt-dependent oospore sizes
Authors: Holzhausen A. , Romanov R.E. , Schubert H.
Published: March 2024

Chara canescensLoisel. is one of two European species of the section Desvauxia R.D. Wood of the genusCharaL. Whereas most populations ofC. canescensreproduce parthenogenetically, a few sites with sexual reproducing populations are known. Studies of EuropeanC. canescensoospore morphology led to open questions about the taxonomic status. Here we investigated nearly 1000 oospores from 16 European populations originated from plant release, sediments, germination experiments and herbaria and two Asian populations resulting in a regional determination key for studied populations as well as important database implications regarding origin, oospore plant position and equipment used. The impact of salinisation on oospore morphology were tested by artificial salt levels. The longest but smallest oospores were formed at 3 PSU, whereas the widest at 0.1 PSU and the shortest at 5 PSU. Basal width and shape, on the other hand, seem to be only affected by higher salt contents. This study contributes the lacking oospore-information for both reproduction modes of European ofC. canescens– populations.
A qualitative meta-synthesis of service users’ and carers’ experiences of assessment and involuntary hospital admissions under mental health legislations: a five-year update
Authors: Bartl Gergely , Stuart Ruth , Ahmed Nafiso , Saunders Katherine , Loizou Sofia , Brady Grainne , Gray Hannah , Grundy Andrew , Jeynes Tamar , Nyikavaranda Patrick , Persaud Karen , Raad Ari , Foye Una , Simpson Alan , Johnson Sonia , Lloyd-Evans Brynmor
Published: March 2024

Background

Compulsory admissions occur in psychiatric hospitals around the world. They result in coercive and sometimes traumatic experiences for service users and carers. Legal and service reforms in various countries are intended to reduce rates of detention and improve service user experience. We aimed to inform policy and service delivery by providing an up-to-date synthesis of qualitative evidence on service users’ and carers’ experiences of assessment and detention under mental health legislation, updating previous reviews in which we searched for literature published up to 2018.

Methods

We searched five bibliographic databases for studies published between January 2018 and March 2023. We identified 24 additional studies reporting qualitative investigations of service users’ or carers’ experiences of assessment or detention under mental health legislation. A team including researchers with relevant personal experience analysed and synthesised data using a thematic synthesis approach.

Results

Findings suggest that views on compulsory admissions and assessment varied: many reports highlighted its often negative, traumatic impacts on emotional well-being and self-worth, with fewer accounts of it as an opportunity to access help and support, accompanied by feelings of relief. Experiences of racial discrimination, inequality of access, and dissatisfaction with support before and after hospital stay were more prominent than in our previous reviews.

Conclusions

Increasing service user and carer involvement in treatment decisions, provision of timely information at key stages of the admission process, training of key personnel, addressing the issue of discrimination, and investing in community alternatives of inpatient care may contribute to and lead to better overall treatment experiences.