bluuebunny/crossref_metadata_2025 huggingface dataset:
Practical application of digital therapeutics in people with mood disorders
Authors: Orsolini Laura , Longo Giulio , Volpe Umberto
Published: November 2023

Digital therapeutics (DTx) offer evidence-based digitally-delivered high quality standards applications and/or softwares in the prevention, management and treatment of several medical conditions, including mood disorders. Nowadays, there are only three DTx officially approved by the Food and Drug Administration for mental conditions and there are still very few DTx developed in the context of mood disorders. The current comprehensive overview aims at providing a summary of currently published studies on DTx clinical applications in major depressive disorder (MDD), depressive symptomatology and bipolar disorder (BD), by using PubMed/MEDLINE and Scopus databases. Fifteen studies have been selected (10 on DTx in depressive symptomatology and/or MDD; 4 on BD; 1 on MDD and BD). Literature on DTx in mood disorders is still lacking, being mostly constituted by feasibility and acceptability rather than efficacy/effectiveness outcomes, particularly in BD. More studies focused on MDD compared to BD. Most DTx on MDD have been developed based on cognitive behaviour therapy interventions while on BD are based on psychoeducation. All studies assessing symptom severity improvement pre- vs. postinterventions demonstrated a significant postintervention improvement. Therefore, despite the preliminary encouraging results of studies here retrieved, their methodology is still too heterogeneous to allow comparisons and the generalizability of their findings. Further studies are warranted, in more larger samples involving multiple sites, including measures of both specific symptom effects as well as acceptability, feasibility and effectiveness in the real-world settings.
Isolation and expansion of pure and functional γδ T cells
Authors: Verkerk T. , Pappot A. T. , Jorritsma T. , King L.A. , Spaapen R. M. , van Ham S. M.
Published: November 2023

γδ T cells are important components of the immune system due to their ability to elicit a fast and strong response against infected and transformed cells. Because they can specifically and effectively kill target cells in an MHC independent fashion, there is great interest to utilize these cells in anti-tumor therapies where antigen presentation may be hampered. Since only a small fraction of T cells in the blood or tumor tissue are γδ T cells, they require extensive expansion to allow for fundamental, preclinical andex vivoresearch. Although expansion protocols can be successful, most are based on depletion of other cell types rather than γδ T cell specific isolation, resulting in unpredictable purity of the isolated fraction. Moreover, the primary focus only lies with expansion of Vδ2+T cells, while Vδ1+T cells likewise have anti-tumor potential. Here, we investigated whether γδ T cells directly isolated from blood could be efficiently expanded while maintaining function. γδ T cell subsets were isolated using MACS separation, followed by FACS sorting, yielding >99% pure γδ T cells. Isolated Vδ1+and Vδ2+T cells could effectively expand immediately after isolation or upon freeze/thawing and reached expansion ratios between 200 to 2000-fold starting from varying numbers using cytokine supported feeder stimulations. After expansion, potential effector functions of γδ T cells were demonstrated by IFN-γ, TNF-α and granzyme B production upon PMA/ionomycin stimulation and effective killing capacity of multiple tumor cell lines was confirmed in killing assays.

In conclusion, pure γδ T cells can productively be expanded while maintaining their anti-tumor effector functions against tumor cells. Moreover, γδ T cells could be expanded from low starting numbers suggesting that this protocol may even allow for expansion of cells extracted from tumor biopsies.
Methylome-wide association studies of traumatic injury identifies differential DNA methylation of synaptic plasticity and GABAergic-signalling
Authors: Brown Jodie P. , Marshall Sally , Walker Rosie M. , Campbell Archie , Hayward Caroline , McIntosh Andrew M. , Evans Kathryn L. , Thomson Pippa A.
Published: November 2023

Traumatic physical injury is often associated with psychological trauma and is a risk factor for major depressive disorder (MDD). In Generation Scotland traumatic injury was significantly associated with recurrent major depression (OR = 2.10, 95% CI 1.33-3.33,PLJ=LJ0.0016). and schizotypal symptoms, particularly disorganised thought (βLJ=LJ0.111, 95% CI 0.049-0.177,PLJ=LJ0.0004). We performed methylome-wide analyses of traumatic injury in individuals with MDD and controls separately to investigate the link between traumatic injury and MDD. Nominally significant differences in differential DNA methylation between MDD and control groups were identified at 40 003 CpG sites (p < 0.05). Individuals with recurrent MDD showed significantly higher levels of DNA methylation associated with traumatic injury at CpG sites at the first exon and lower levels at exon boundaries, this was significant different to the association pattern at these sites in controls (mean difference in M-value = 0.0083,P= 21.1×10-10, and -0.0125,P= 2.1×10-174, respectively). Analyses at the level of CpG site, genes and gene ontologies implicated dysregulation of processes related to synaptic plasticity, including dendrite development, excitatory synapse and GABAergic signalling (normalised enrichment values > 2, FDR q-values < 0.01). Enrichment analyses for regional brain-expression in the recurrent MDD group highlight the limbic lobe and supraoptic nuclei (recurrent MDD FWER = 0.028 and 0.034, respectively). These results suggest that traumatic injury is associated with patterns of DNA methylation differentially in individuals with MDD compared to controls, highlighting the need for novel analysis approaches.
Photosymbiosis reduces the environmental stress response under a heat challenge in a facultatively symbiotic coral
Authors: Wuitchik DM , Aichelman HE , Atherton KF , Brown CM , Chen X , DiRoberts L , Pelose GE , Tramonte CA , Davies SW
Published: November 2023

The symbiosis between corals of the order Scleractinia and dinoflagellates of the family Symbiodiniaceae is sensitive to environmental stress. The oxidative bleaching hypothesis posits that extreme temperatures lead to accumulation of photobiont-derived reactive oxygen species ROS, which exacerbates the coral environmental stress response (ESR). To understand how photosymbiosis modulates coral ESRs, these responses must be explored in hosts in and out of symbiosis. We leveraged the facultatively symbiotic coralAstrangia poculata, which offers an opportunity to uncouple the ESR across its two symbiotic states (symbiotic, aposymbiotic). Colonies of both symbiotic states were exposed to three temperature treatments for 15 days: i) control (static 18°C), ii) heat challenge (increasing from 18 to 32°C), and iii) cold challenge (decreasing from 18 to 6°C) after which host gene expression was profiled. Cold challenged corals elicited widespread differential expression, however, there were no differences between symbiotic states. In contrast, symbiotic colonies exhibited greater gene expression plasticity under heat challenge, including enrichment of cell cycle pathways involved in controlling photobiont growth. Counter to the oxidative bleaching hypothesis, this plasticity did not include signatures of stress, and rather a dampened ESR under heat challenge was observed, suggesting that photobionts reduce the host’s ESR under elevated temperatures inA. poculata.
Phenological and epidemiological impacts of climate change on peach production
Authors: Vanalli Chiara , Radici Andrea , Casagrandi Renato , Gatto Marino , Bevacqua Daniele
Published: November 2023

Agricultural food security is threatened by climate change impacts, which can distress crop growth and favor the spread of infectious diseases. Here, we examined the synergism of the two potentially most disruptive causes of future yield failure in peach production: the effects of global climate change on fruit growth and on the spread of fungal diseases. Coupling a phenological and epidemiological model across the French continental territory, we provided projections of yield losses for four peach cultivars (early, mid-early, mid-late, and late) in the XXI century under different climate change scenarios. Global warming is expected to impair fruit phenology with blooming failure events in the south-western part of the country. This will be less extreme under the more moderate emission scenario, even though sporadic blooming failures will still occur. In contrast, future warmer and drier conditions will decrease brown rot-induced yield loss in the historical locations devoted to peach cultivation. To adapt to these changes, the benefits of shifting peach production sites to new suitable areas are evaluated. Thanks to this strategy, the peach national yield could still be fulfilled even under the most extreme climate change scenario. Comprehensive mathematical frameworks, that concomitantly consider the climatic effects on the plant hosts and on their pathogens, are required to provide reliable future predictions of crop yields and to inform control and adaptation strategies to guarantee food security under global warming.
Regenerative Signatures in Bronchioalveolar Lavage of Acute Respiratory Distress Syndrome
Authors: Zhao Runzhen , Hadisurya Marco , Ndetan Harrison , Xi Nan Miles , Adduri Sitaramaraju , Konduru Nagarjun Venkata , Samten Buka , Tao W. Andy , Singh Karan P , Ji Hong-Long
Published: November 2023

Background

In patients with severe acute respiratory distress syndrome (ARDS) associated with sepsis, lung recovery is considerably delayed, and mortality is much high. More insight into the process of lung regeneration in ARDS patients is needed. Exosomes are important cargos for intercellular communication by serving as autocrine and/or paracrine. Cutting-edge exomics (exosomal proteomics) makes it possible to study the mechanisms of re-alveolarization in ARDS lungs.

Aims

This study aimed to identify potential regenerative niches by characterizing differentially expressed proteins in the exosomes of bronchioalveolar lavage (BAL) in ARDS patients.

Methods

We purified exosomes from BAL samples collected from ARDS patients by NIH-supported ALTA and SPIROMICS trials. The abundance of exosomal proteins/peptides was quantified using liquid chromatography-mass spectrometry (LC-MS). Differentially expressed exosomal proteins between healthy controls and ARDS patients were profiled for functional annotations, cell origins, signaling pathways, networks, and clinical correlations.

Results

Our results show that more exosomal proteins were identified in the lungs of late-stage ARDS patients. Immune cells and lung epithelial stem cells were major contributors to BAL exosomes in addition to those from other organs. We enriched a wide range of functions, stem cell signals, growth factors, and immune niches in both mild and severe patients. The differentially expressed proteins that we identified were associated with key clinical variables. The severity-associated differences in protein-protein interaction, RNA crosstalk, and epigenetic network were observed between mild and severe groups. Moreover, alveolar type 2 epithelial cells could serve as both exosome donors and recipients via autocrine and paracrine mechanisms.

Conclusions

This study identifies novel exosomal proteins associated with diverse functions, signaling pathways, and cell origins in ARDS lavage samples. These differentiated proteins may serve as regenerative niches for re-alveolarization in injured lungs.
Can non-invasive brain stimulation modulate peak alpha frequency in the human brain? A systematic review and meta-analysis
Authors: Millard S.K. , Speis D.B. , Skippen P. , Chiang A.K.I. , Chang W.J. , Lin A.J. , Furman A.J. , Mazaheri A. , Seminowicz D.A. , Schabrun S.M.
Published: November 2023

Peak alpha frequency, the dominant oscillatory frequency within the alpha range (8–12 Hz), is associated with cognitive function and several neurological conditions, including chronic pain. Manipulating PAF could offer valuable insight into the relationship between PAF and various functions and conditions and provide new treatment avenues. This systematic review aimed to comprehensively synthesise effects of non-invasive brain stimulation (NIBS) on PAF speed. Relevant studies assessing PAF pre- and post-NIBS in healthy adults were identified through systematic searches of electronic databases (Embase, PubMed, PsychINFO, Scopus, The Cochrane Library) and trial registers. The Cochrane risk-of-bias tool was employed for assessing study quality. Quantitative analysis was conducted through pairwise meta-analysis when possible; otherwise, qualitative synthesis was performed. The review protocol was registered with PROSPERO (CRD42020190512) and the Open Science Framework (https://osf.io/2yaxz/). Eleven NIBS studies were included, all with a low risk-of-bias, comprising seven transcranial alternating current stimulation (tACS), three repetitive transcranial magnetic stimulation (rTMS), and one transcranial direct current stimulation (tDCS) study. Meta-analysis of active tACS conditions (eight conditions from five studies) revealed no significant effects on PAF (mean difference [MD] = -0.12, 95% CI = -0.32 to 0.08, p = 0.24). Qualitative synthesis provided no evidence that tDCS altered PAF and moderate evidence for transient increases in PAF with 10 Hz rTMS. There is limited evidence that NIBS can modulate PAF, and existing evidence does not demonstrate robust effects. Further studies employing standardised stimulation protocols are necessary to determine the potential of NIBS to modulate PAF.
Quality Matters: Deep Learning-Based Analysis of Protein-Ligand Interactions with Focus on Avoiding Bias
Authors: Sellner Manuel S. , Lill Markus A. , Smieško Martin
Published: November 2023

The efficient and accurate prediction of protein-ligand binding affinities is an extremely appealing yet still unresolved goal in computational pharmacy. In recent years, many scientists have taken advantage of the remarkable progress of deep learning and applied it to address this issue. Despite all the advances in this field, there is increasing evidence that the typically applied validation of these methods is not suitable for medicinal chemistry applications. This work assesses the importance of dataset quality and proper dataset splitting techniques demonstrated on the example of the PDBbind dataset. We also introduce a new tool for the analysis of protein-ligand complexes, called po-sco. Po-sco allows the extraction of interaction information with much higher detail and comprehensibility than the tools available to date. We trained a transformer-based deep learning model to generate protein-ligand interaction fingerprints that can be utilized for downstream predictions, such as binding affinity. When using po-sco, this model generated predictions that were superior to those based on commonly used PLIP and ProLIF tools. We also demonstrate that the quality of the dataset is more important than the number of data points and that suboptimal dataset splitting can lead to a significant overestimation of model performance.
“A Man Never Cries”: A Mixed-Methods Analysis of Gender Differences in Depression and Alcohol Use in Moshi, Tanzania
Authors: Pauley Alena , Buono Mia , Metcalf Madeline , West Kirstin , Rent Sharla , Nkenguye William , Sawe Yvonne , Mikindo Mariana , Kilasara Joseph , Boshe Judith , Knettel Brandon A. , Mmbaga Blandina T. , Staton Catherine A.
Published: November 2023

Background

Unhealthy alcohol use negatively impacts many components of health and wellness, including mental health conditions like major depressive disorder (MDD). Globally, gender differences are common for both alcohol use behaviors and MDD, but these differences have not been studied within Moshi, Tanzania. To provide more effective and culturally appropriate mental health treatments, gender nuances around these conditions must be known. As such, this study aims to explore gender differences in MDD, alcohol use, and other aspects of mental well-being among patients at Kilimanjaro Christian Medical Center (KCMC) in Moshi.

Methods

Six hundred and seventy-six patients presenting for care at the KCMC Emergency Department (ED) and Reproductive Health Centre (RHC) were enrolled in this mixed-methods study between October 2021 and May 2022. Patients were selected through systematic random sampling and completed quantitative surveys including the Alcohol Use Disorder Identification Test (AUDIT) and the Patient Health Questionnaire 9 (PHQ-9). Nineteen patients were purposively chosen from the study population to participate in in-depth interviews (IDIs) exploring topics related to alcohol use, gender, and depression. Descriptive frequencies, univariate log-binomial regressions, and a linear regression model were used to analyze quantitative data, all of which were analyzed in RStudio. A grounded theory approach was used to analyze all IDIs in NVivo.

Results

Average [SD] PHQ-9 scores were 7.22 [5.07] for ED women, 4.91 [4.11] for RHC women, and 3.75 [4.38] among ED men. Similarly, ED women held the highest prevalence of MDD (25%) as compared to RHC women (11%) and ED men (7.9%) (p<0.001). Depressive symptoms were associated with higher AUDIT scores only for ED men (R2 = 0.11, p<0.001). Our qualitative analysis showed that while present for women, social support networks were notably absent for men in Moshi, the lack of which was seen to play a role in alcohol use. For men, alcohol was described as a coping mechanism for stress.

Conclusion

Intersectionality of gender, alcohol use, and depression is influenced by sociocultural and behavioral norms in Moshi. As such, multi-layered, gender-differentiated programming should be considered for the treatment of substance use and mental health conditions in this region.
Olfaction foraging in visually oriented tropical arboreal antsOecophylla smaragdina: Implications for insect predation studies using artificial sentinel prey
Authors: Yan Lin , Kagame Samuel Paul , Liu Yang , Mizuno Takafumi , Nakamura Akihiro
Published: November 2023

Predation is the key to understanding trophic interactions. Because of the brief and cryptic nature of predatory behavior, sentinel prey has been widely adopted as an indirect way to identify predators and understand trophic interactions. However, sentinel prey presents only static visual cues, potentially biasing toward visually oriented predators whilst ignoring those that require other sensory cues to forage. Despite this, the effectiveness of sentinel prey has rarely been tested. Here, we focused on the weaver ant,Oecophylla smaragdina, a keystone predator widespread in the Asian and Australian tropics. As this species has large eyes and is known to visually navigate in their arboreal habitats, we hypothesized that they rely on visual cues to forage and that their predatory behavior will be captured by caterpillar-shaped sentinel prey. Ants were collected as colonies, and preference trials on baits were conducted using combinations of olfactory and static visual cues including the caterpillar shape. Surprisingly,O. smaragdinashowed little or no preference for baits in the absence of olfactory cues and did not differentiate the shapes of baits regardless of the presence of olfactory cues. Our results indicate thatO. smaragdinais likely to make predatory decisions based primarily on olfactory cues, while visual cues might be used for other behaviors. Furthermore,O. smaragdinais likely to be left out by the predation studies using sentinel prey models which is particularly alarming considering the dominant role of this species in the trophic interactions of tropical rainforests. Our study demonstrates that morphological characteristics, arboreal habitats, and visually oriented behavior do not necessarily suggest the use of static visual cues for predatory decisions. We suggest that sentinel prey models should not be used alone when the dominant predators are unlikely to use visual cues to make predatory decisions.
Simultaneous single-cell calcium imaging of neuronal population activity and brain-wide BOLD fMRI
Authors: Ubaghs Rik L.E.M. , Boehringer Roman , Marks Markus , Hesse Helke K. , Yanik Mehmet Fatih , Zerbi Valerio , Grewe Benjamin F.
Published: November 2023

Blood Oxygen Level-Dependent (BOLD) functional Magnetic Resonance Imaging (fMRI) allows for non-invasive, indirect recordings of neural activity across the whole brain in both humans and animals. However, the relationship between the local neural population activity and the vascular activity is not completely understood. To investigate this relationship, we present a novel MRI compatible single-photon microscope capable of measuring cellular resolution Ca2+activity of genetically defined neurons during whole-brain BOLD fMRI in awake behaving mice. Using this combined imaging approach, we found a difference in activity patterns between cells which was dependent on their location with respect to the vasculature. Notably, neurons near the vasculature showed pronounced negative activity during contralateral whisker movements at 3 Hz. In a second proof of concept experiment, we demonstrate the potential of recording both local neural activities, like those in the barrel field (SSp-bfd), and BOLD fMRI readings from interlinked brain regions. In sum, the presented technological advancement paves the way for studies examining the interplay between local brain circuits and overarching brain functions. In addition, the new approach enhances our understanding of the vascular BOLD fMRI signal, providing insights into the determinants of local neurovascular functions and the brain’s organizational framework across various scales.
Unravelling the metastasis-preventing effect of miR-200cin vitroandin vivo
Authors: Köhler Bianca , Brieger Emily , Brandstätter Tom , Hörterer Elisa , Wilk Ulrich , Pöhmerer Jana , Jötten Anna , Paulitschke Philipp , Broedersz Chase P , Zahler Stefan , Rädler Joachim O , Wagner Ernst , Roidl Andreas
Published: November 2023

Advanced breast cancer as well as insufficient treatment can lead to the dissemination of malignant cells from the primary tumor to distant organs. Recent research has shown that miR-200c can hamper certain steps of the invasion-metastasis cascade. However, it is still unclear, whether sole miR-200c expression is sufficient to prevent breast cancer cells from metastasis formation. Hence, we performed a xenograft mouse experiment with inducible miR-200c expression in MDA-MB 231 cells. Theex vivoanalysis of metastatic sites in a multitude of organs including lung, liver, brain, and spleen has revealed a dramatically reduced metastatic burden of mice with miR-200c expressing tumors. A fundamental prerequisite for metastasis formation is the motility of cancer cells and, therefore, their migration. Consequently, we analyzed the effect of miR-200c on collective and single cell migrationin vitro, utilizing MDA-MB 231 and MCF7 cell systems with genetically modified miR-200c expression. Analysis of collective cell migration has resulted in confluence dependent motility of cells with altered miR-200c expression. Additionally, scratch assays have shown enhanced predisposition of miR-200c negative cells to leave cell clusters. The in-between stage of collective and single cell migration was validated using transwell assays, which have displayed reduced migration of miR-200c positive cells. Finally, to measure migration on single cell level, a novel assay on dumbbell shaped micropatterns was performed, which revealed that miR-200c critically determines confined cell motility. All of these results demonstrate that exclusive expression of miR-200c impedes metastasis formationin vivoand migrationin vitroand highlight miR-200c as metastatic suppressor in breast cancer.
Dorsal Motor Vagal Neurons Can Elicit Bradycardia and Reduce Anxiety-Like Behavior
Authors: Strain Misty M. , Conley Nicholas J. , Kauffman Lily S. , Espinoza Liliana , Fedorchak Stephanie , Martinez Patricia Castro , Crook Maisie E. , Jalil Maira , Hodes Georgia E. , Abbott Stephen B. G. , Güler Ali D. , Campbell John N. , Boychuk Carie R.
Published: November 2023

Cardiovagal neurons (CVNs) innervate cardiac ganglia through the vagus nerve to control cardiac function. Although the cardioinhibitory role of CVNs in nucleus ambiguus (CVNNA) is well established, the nature and functionality of CVNs in dorsal motor nucleus of the vagus (CVNDMV) is less clear. We therefore aimed to characterize CVNDMVanatomically, physiologically, and functionally. Optogenetically activating cholinergic DMV neurons resulted in robust bradycardia through peripheral muscarinic (parasympathetic) and nicotinic (ganglionic) acetylcholine receptors, but not beta-1-adrenergic (sympathetic) receptors. Retrograde tracing from the cardiac fat pad labeled CVNNAand CVNDMVthrough the vagus nerve. Using whole cell patch clamp, CVNDMVdemonstrated greater hyperexcitability and spontaneous action potential firingex vivodespite similar resting membrane potentials, compared to CVNNA. Chemogenetically activating DMV also caused significant bradycardia with a correlated reduction in anxiety-like behavior. Thus, DMV contains uniquely hyperexcitable CVNs capable of cardioinhibition and robust anxiolysis.
Gray matter volume in women with the BRCA mutation with and without ovarian removal
Authors: Witt Suzanne T , Brown Alana , Gravelsins Laura , Engström Maria , Classon Elisabet , Lykke Nina , Lundqvist Elisabeth Åvall , Theordorsson Elvar , Ernerudh Jan , Kjölhede Preben , Einstein Gillian
Published: November 2023

Objective

Ovarian removal prior to spontaneous/natural menopause (SM) is associated with increased risk of late life dementias including Alzheimer’s disease. This increased risk may be related to the sudden and early loss of endogenous estradiol. Women with breast cancer gene mutations (BRCAm) are counselled to undergo oophorectomy prior to SM to significantly reduce their risk of developing breast, ovarian, and cervical cancers. There is limited evidence of the neurological effects of ovarian removal prior to the age of SM and this is in women without the BRCAm showing cortical thinning in medial temporal lobe structures. A second study in women with BRCAm and BSO noted changes in cognition.

Methods

The present study looked at whole-brain changes in gray matter volume using high-resolution, quantitative MRI in women with BRCAm and intact ovaries (BRCA-preBSO) and after surgery with (BSO+ERT) and without (BSO) post-surgical estradiol hormone replacement therapy compared with agematched women (AMC) with their ovaries.

Results

The BRCA-preBSO and BSO groups showed significant gray matter loss in left medial temporal and frontal lobe structures. BSO+ERT exhibited few areas of gray matter reductions compared to AMC. Novel to this study, we also observed that all three BRCAm groups exhibited gray matter increases compared with AMC, suggesting continued plasticity.

Conclusions

The present study provides evidence, through gray matter volume reductions, to support both the possibility that the BRCAm, alone, and early life BSO may play a role in increasing the risk for late-life dementia. At least for BRCAm with BSO, post-surgical ERT seems to ameliorate gray matter losses.
Telomerase reverse transcriptase induces targetable alterations in glutathione and nucleotide biosynthesis in glioblastomas
Authors: Udutha Suresh , Taglang Céline , Batsios Georgios , Gillespie Anne Marie , Tran Meryssa , Ronen Sabrina M , ten Hoeve Johanna , Graeber Thomas G , Viswanath Pavithra
Published: November 2023

Telomerase reverse transcriptase (TERT) is essential for glioblastoma (GBM) proliferation. Delineating metabolic vulnerabilities induced by TERT can lead to novel GBM therapies. We previously showed that TERT upregulates glutathione (GSH) pool size in GBMs. Here, we show that TERT acts via the FOXO1 transcription factor to upregulate expression of the catalytic subunit of glutamate-cysteine ligase (GCLC), the rate-limiting enzyme ofde novoGSH synthesis. Inhibiting GCLC using siRNA or buthionine sulfoximine (BSO) reduces synthesis of13C-GSH from [U-13C]-glutamine and inhibits clonogenicity. However, GCLC inhibition does not induce cell death, an effect that is associated with elevated [U-13C]-glutamine metabolism to glutamate and pyrimidine nucleotide biosynthesis. Mechanistically, GCLC inhibition activates MYC and leads to compensatory upregulation of two key glutamine-utilizing enzymes i.e., glutaminase (GLS), which generates glutamate from glutamine, and CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, dihydroorotatase), the enzyme that converts glutamine to the pyrimidine nucleotide precursor dihydroorotate. We then examined the therapeutic potential of inhibiting GLS and CAD in combination with GCLC. 6-diazo-5-oxy-L-norleucin (DON) is a potent inhibitor of glutamine-utilizing enzymes including GLS and CAD. The combination of BSO and DON suppresses GSH and pyrimidine nucleotide biosynthesis and is synergistically lethal in GBM cells. Importantly,in vivostable isotope tracing indicates that combined treatment with JHU-083 (a brain-penetrant prodrug of DON) and BSO abrogates synthesis of GSH and pyrimidine nucleotides from [U-13C]-glutamine and induces tumor shrinkage in mice bearing intracranial GBM xenografts. Collectively, our studies exploit a mechanistic understanding of TERT biology to identify synthetically lethal metabolic vulnerabilities in GBMs.

SIGNIFICANCE

Usingin vivostable isotope tracing, metabolomics, and loss-of-function studies, we demonstrate that TERT expression is associated with metabolic alterations that can be synergistically targeted for therapy in glioblastomas.
The neurons that drive infradian sleep-wake and mania-like behavioral rhythms
Authors: Markam Pratap S. , Bourguignon Clément , Zhu Lei , Darvas Martin , Sabatini Paul V. , Kokoeva Maia V. , Giros Bruno , Storch Kai-Florian
Published: November 2023

Infradian mood and sleep-wake rhythms with periods of 48 hr and beyond have been observed in bipolar disorder (BD) subjects that even persist in time isolation, indicating an endogenous origin. Here we show that mice exposed to methamphetamine (Meth) in drinking water develop infradian locomotor rhythms with periods of 48 hr and beyond which extend to sleep length and mania-like behaviors in support of a model for cycling in BD. This cycling capacity is abrogated upon genetic disruption of DA production in DA neurons of the ventral tegmental area (VTA) or ablation of nucleus accumbens (NAc) projecting, dopamine (DA) neurons. Chemogenetic activation of NAc-projecting DA neurons leads to locomotor period lengthening in clock deficient mice, while cytosolic calcium in DA processes of the NAc was found fluctuating synchronously with locomotor behavior. Together, our findings argue that BD cycling relies on infradian rhythm generation that depends on NAc-projecting DA neurons.
Utilizing the Scale-Invariant Feature Transform Algorithm to Align Distance Matrices Facilitates Systematic Protein Structure Comparison
Authors: Guo Zhengyang , Wang Yang , Ou Guangshuo
Published: November 2023

Protein structure comparison is pivotal for deriving homological relationships, elucidating protein functions, and understanding evolutionary developments. The burgeoning field ofin-silicoprotein structure prediction now yields billions of models with near-experimental accuracy, necessitating sophisticated tools for discerning structural similarities among proteins, particularly when sequence similarity is limited. Here, we have developed the ADAMS pipeline, which synergizes the distance matrix alignment method with the scale-invariant feature transform (SIFT) algorithm, streamlining protein structure comparison on a proteomic scale. Utilizing a computer vision-centric strategy for contrasting disparate distance matrices, ADAMS adeptly alleviates challenges associated with proteins characterized by a high degree of structural flexibility. Our findings indicate that ADAMS achieves a level of performance and accuracy on par with Foldseek, while maintaining similar speed. Crucially, ADAMS overcomes certain limitations of Foldseek in handling structurally flexible proteins, establishing it as an efficacious tool for in-depth protein structure analysis with heightened accuracy.
Remodelling of skeletal muscle myosin metabolic states in hibernating mammals
Authors: Lewis Christopher T. A. , Melhedegaard Elise G. , Ognjanovic Marija M. , Olsen Mathilde S. , Laitila Jenni , Seaborne Robert A. E. , Grønset Magnus Nørregaard , Zhang Chengxin , Iwamoto Hiroyuki , Hessel Anthony L. , Kuehn Michel N. , Merino Carla , Amigó Nuria , Fröbert Ole , Giroud Sylvain , Staples James F. , Goropashnaya Anna V. , Fedorov Vadim B. , Barnes Brian M. , Tøien Øivind , Drew Kelly L. , Sprenger Ryan J. , Ochala Julien
Published: November 2023

Hibernation is a period of metabolic suppression utilized by many small and large mammal species to survive during winter periods. As the underlying cellular and molecular mechanisms remain incompletely understood, our study aimed to determine whether skeletal muscle myosin and its metabolic efficiency undergo alterations during hibernation to optimize energy utilization. We isolated muscle fibers from small hibernators,Ictidomys tridecemlineatusandEliomys quercinusand larger hibernators,Ursus arctosandUrsus americanus. We then conducted loaded Mant-ATP chase experiments alongside X-ray diffraction to measure resting myosin dynamics and its ATP demand. In parallel, we performed multiple proteomics analyses. Our results showed a preservation of myosin structure inU. arctosandU. americanusduring hibernation, whilst inI. tridecemlineatusandE. quercinus, changes in myosin metabolic states during torpor unexpectedly led to higher levels in energy expenditure of type II, fast-twitch muscle fibers at ambient lab temperatures (20°C). Upon repeating loaded Mant-ATP chase experiments at 8°C (near the body temperature of torpid animals), we found that myosin ATP consumption in type II muscle fibers was reduced by 77-107% during torpor compared to active periods. Additionally, we observed Myh2 hyper-phosphorylation during torpor inI. tridecemilineatus, which was predicted to stabilize the myosin molecule. This may act as a potential molecular mechanism mitigating myosin-associated increases in skeletal muscle energy expenditure during periods of torpor in response to cold exposure. Altogether, we demonstrate that resting myosin is altered in hibernating mammals, contributing to significant changes to the ATP consumption of skeletal muscle. Additionally, we observe that it is further altered in response to cold exposure and highlight myosin as a potentially contributor to skeletal muscle non-shivering thermogenesis.
Elucidating Partial Folding State of Bovine Pancreatic Trypsin Inhibitor by a Combined Study of Molecular Dynamics Simulations, Information Theory, Molecular Graph Theory, and Machine Learning
Authors: Kamberaj Hiqmet
Published: November 2023

Using a notably large amount of data in investigating physical and chemical phenomena demands new statistical and computational approaches; besides, the cross-validations require well-established theoretical frameworks. This study aims to validate the statistical efficiency of alternative definitions for the information-theoretic measures, such as transfer entropy, using the so-called (α, q)-framework. The primary goal is to find measurements of high-order correlations that preserve information-theoretic properties of information transfer between the components of a dynamical system (such as a protein) due to local operations. Besides, this study aims to decode the information contained in the amino acid sequence establishing a three-dimensional protein structure by comparing the amino acids physical-chemical properties with their ranked role in the protein interaction network topology using new graph-theoretic measures based on the constructed digraph models of (α, q) information transfer within a heat flow kernel embedding framework. Moreover, this study aims to use the Deep Graph Convolution Neural Networks for classifying the role of each amino acid in a protein trained upon short equilibrium structure fluctuations at sub-nanosecond time scales.

In particular, this study examines the influence of disulphide bridges on the three-dimensional structure of the Bovine Pancreatic Trypsin Inhibitor wild type and mutated analogue protein.
Automated Model Refinement Using Perturbation-Observation Pairs
Authors: Park Kyu Hyong , Rozum Jordan C. , Albert Réka
Published: November 2023

Network-based dynamic modeling is useful for studying the responses of complex biomolecular systems to environmental changes and internal perturbations. In modeling signal transduction and other regulatory networks, it is common to integrate evidence from perturbation (e.g. gene knockout) - observation pairs, where the perturbed and observed variables may be distant in the network. For a model to capture these non-local effects, its construction, validation, and refinement necessarily involve trial and error, constrained by domain knowledge.

We propose and implement a genetic algorithm-based workflow to streamline model refinement. This workflow applies to any biological system for which an interaction network and enough perturbation experiments exist. We implement our workflow for Boolean networks, which are a popular and successful tool for modeling biological systems. The algorithm we introduce adjusts the functions of the model to enhance agreement with a corpus of curated experimental results and leverages existing mechanistic knowledge to automatically limit the search space to biologically plausible models. To account for the interdependence of experimental results, we develop a hierarchical scoring technique for assessing model performance. Our implementation is available as the open-source Python libraryboolmore.

We demonstrateboolmore’s effectiveness in a published plant signaling model that exemplifies the challenges of manual model construction and refinement. This model describes how plant stomata close in response to the drought hormone abscisic acid. After several hours of automatic refinement on a personal computer, the fittest models recapture and surpass the accuracy gain achieved over two years of manual revision. The refined models yield new, testable predictions, such as explanations for the role of reactive oxygen species in drought response. By automating the laborious task of model validation and refinement, this workflow is a step towards fast, fully automated, and reliable model construction.
RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
Authors: Bernard Clément , Postic Guillaume , Ghannay Sahar , Tahi Fariza
Published: November 2023

RNA is a complex macromolecule that plays central roles in the cell. While it is well-known that its structure is directly related to its functions, understanding and predicting RNA structures is challenging. Assessing the real or predictive quality of a structure is also at stake with the complex 3D possible conformations of RNAs. Metrics have been developed to measure model quality while scoring functions aim at assigning quality to guide the discrimination of structures without a known and solved reference. Throughout the years, many metrics and scoring functions have been developed, and no unique assessment is used nowadays. Each developed assessment method has its specificity and might be complementary to understanding structure quality. Therefore, to evaluate RNA 3D structure predictions, it would be important to calculate different metrics and/or scoring functions. For this purpose, we developed RNAdvisor, a comprehensive automated software that integrates and enhances the accessibility of existing metrics and scoring functions. In this paper, we present our RNAdvisor tool, as well as state-of-the-art existing metrics, scoring functions and a set of benchmarks we conducted for evaluating them. Source code is freely available on the EvryRNA platform:https://evryrna.ibisc.univ-evry.fr.
A large-scale assessment of sequence database search tools for homology-based protein function prediction
Authors: Zhang Chengxin , Freddolino P. Lydia
Published: November 2023

Sequence database searches followed by homology-based function transfer form one of the oldest and most popular approaches for predicting protein functions, such as Gene Ontology (GO) terms. Although sequence search tools are the basis of homology-based protein function prediction, previous studies have scarcely explored how to select the optimal sequence search tools and configure their parameters to achieve the best function prediction. In this paper, we evaluate the effect of using different options from among popular search tools, as well as the impacts of search parameters, on protein function prediction. When predicting GO terms on a large benchmark dataset, we found that BLASTp and MMseqs2 consistently exceed the performance of other tools, including DIAMOND - one of the most popular tools for function prediction - under default search parameters. However, with the correct parameter settings, DIAMOND can perform comparably to BLASTp and MMseqs2 in function prediction. This study emphasizes the critical role of search parameter settings in homology-based function transfer.
Small dams driveAnophelesabundance during the dry season in a high malaria burden area of Malawi
Authors: Zembere Kennedy , Jones Christopher M , Mthawanji Rhosheen , Nkolokosa Clinton , Kamwezi Richard , Kalonde Patrick Ken , Stanton Michelle C
Published: November 2023

This study explores the influence of small dams on the exposure to malaria vectors during the dry season in Kasungu district, Malawi, an area recently identified as high priority for malaria interventions by the National Malaria Control Programme. Small dam impoundments provide communities with a continuous supply of water for domestic and agricultural activities across sub-Saharan Africa and are considered vital to food security and climate change resilience. However, these permanent water bodies also create ideal breeding sites for mosquitoes in typically arid landscapes. The study focuses on a specific dam impoundment and its vicinity, aiming to assess its spatial and temporal influence on indoor vector densities.

Throughout May to August 2021, CDC light traps were used to measure indoor mosquito densities for two consecutive nights per month in three communities located at increasing distances from the dam (0km, ∼1km, ∼2km). Simultaneously, drone imagery was captured for each community, enabling the identification of additional standing water within approximately 400 meters of selected households. Larval sampling was carried out within the impoundment periphery and in additional water bodies identified in the drone imagery. Generalised linear mixed models (GLMMs) were employed to analyse the indoorAnophelesabundance data, estimating the effects of household structure (open/closed eaves), month, temperature, and water proximity on malaria vector exposure.

Throughout 685 trapping nights, a total of 1,256 mosquitoes were captured, with 33% (412) being femaleAnopheles. Among these, 91% were morphologically identified asAn. funestuss.l., and 5% asAn. gambiaes.l. Catches progressively declines in each consecutive trapping month as the environment became drier. This decline was much slower in Malangano, the community next to the dam, with abundance being notably higher in June and July. Further, the majority ofAn. gambiaes.l. were caught in May, with none identified in July and August.Anopheleslarvae were found both in the impoundment and other smaller water bodies such as irrigation wells in each survey month, however the presence of these smaller water bodies did not have a significant impact on adult female mosquito catches in the GLMM. The study concludes that proximity to the dam impoundment was the primary driver of differences between survey communities with the abundance in Chikhombwe (∼1km away) and Chiponde (∼2km away) being 0.35 (95% CI 0.19-0.66) and 0.28 (95% CI 0.16-0.47) lower than Malangano respectively after adjusting for other factors.

These findings underscore the importance of targeted interventions, such as larval source management or housing improvements, near small dams to mitigate malaria transmission risks during the dry season. Further research is needed to develop cost-effective strategies for vector control within and around these impoundments.
TLR8-Activating miR-146a-3p is an Intermediate Signal Contributing to Fetal Membrane Inflammation in Response to Bacterial LPS
Authors: Georges Hanah M. , Cassin Caterina , Tong Mancy , Abrahams Vikki M.
Published: November 2023

Preterm birth is the largest contributor to neonatal morbidity and is often associated with chorioamnionitis, defined as inflammation/infection of the fetal membranes (FMs). Chorioamnionitis is characterized by neutrophil infiltration of the FMs and is associated with elevated levels of the neutrophil chemoattractant, interleukin (IL)-8, and the proinflammatory cytokine, IL-1β. While FMs can respond to infections through innate immune sensors, such as Toll-like receptors (TLRs), the downstream mechanisms by which chorioamnionitis arises are not fully understood. A novel group of non-classical microRNAs (miR-21a, miR-29a, miR-146a-3p, Let-7b) function as endogenous danger signals by activating the ssRNA viral sensors TLR7 and TLR8. In this study, the pro-inflammatory roles of TLR7/TLR8-activating miRs were examined as mediators of FM inflammation in response to bacterial lipopolysaccharide (LPS) using anin vitrohuman FM explant system, anin vivomouse model of pregnancy, and human clinical samples. Following LPS exposure, miR-146a-3p was significantly increased in both human FM explants and in wildtype mouse FMs. Expression of miR-146a-3p was also significantly elevated in FMs from women with preterm birth and chorioamnionitis. FM IL-8 and inflammasome-mediated IL-1β production in response to LPS was dependent on miR-146a-3p and TLR8, downstream of TLR4 activation. In wildtype mice, LPS exposure increased FM IL-8 and IL-1β production and induced preterm birth. InTLR7−/−/TLR8−/−mice, LPS exposure was able to initiate, but not sustain preterm birth, and FM inflammation was reduced. Together, we demonstrate a novel signaling mechanism at the maternal-fetal interface in which TLR8-activating miR-146a-3p acts as an intermediate danger signal to drive FM inflammasome-dependent and -independent mechanisms of inflammation and thus, may play a role in chorioamnionitis and subsequent preterm birth.
Analyzing photoactivation with diffusion models to study transport in the Endoplasmic Reticulum network
Authors: Dora M. , Paquin-Lefebvre F. , Holcman D.
Published: November 2023

Photoactivation is a paradigm consisting in local molecular fluorescent activation by laser illumination in a chosen region (source) while measuring the concentration at a target region. Data-driven modeling is concern with the following questions: how from the measurement in these two regions, is it possible to infer the properties of molecular propagation? How is it possible to use such reponses to infer motions occurring in networks such as the endoplasmic reticulum? In this article, we present a data-driven analysis based on diffusion-transport models and numerical simulations to interpret the photoactivation dynamics and extract biophysical parameters. Finally we discuss modeling approaches to reconstruct local network properties from photoactivation transients.