bluuebunny/crossref_metadata_2025 huggingface dataset:
Decay estimates for the time-fractional evolution equations with time-dependent coefficients
Authors: Smadiyeva Asselya G. , Torebek Berikbol T.
Published: August 2023

In this paper, the initial-boundary value problems for the time-fractional degenerate evolution equations are considered. Firstly, in the linear case, we obtain the optimal rates of decay estimates of the solutions. The decay estimates are also established for the time-fractional evolution equations with nonlinear operators such as: p-Laplacian, the porous medium operator, degenerate operator, mean curvature operator and Kirchhoff operator. At the end, some applications of the obtained results are given to derive the decay estimates of global solutions for the time-fractional Fisher-KPP-type equation and the time-fractional porous medium equation with the nonlinear source.
Impact of inoculum density of Fusarium oxysporum f. sp. zingiberi on symptomatic appearances and yield of ginger (Zingiber officinale Roscoe)

Authors: Matthews Andrea , Muthukumar Sharan Pradeep Thiruvazhuthi , Hamill Sharon , Aitken Elizabeth A. B. , Chen Andrew
Published: August 2023

Ginger (Zingiber officinale Roscoe) is an important horticultural crop valued for its medicinal and culinary properties. Fusarium yellows, caused by the ascomycete fungus Fusarium oxysporum f. sp. zingiberi (Foz) is a devastating soil borne disease of ginger. It has curtailed ginger production in Australia and around the world leading to significant economic losses. An integrated approach is required to manage soil-borne diseases such as those caused by Foz. However, little is known about the influence of Foz inoculum on disease severity. This study aimed to establish a minimum threshold level of spores per gram of soil required for plant infection and to develop and evaluate a pot inoculation method for suitability in screening large number of plants in a controlled environment. To achieve this, the dominant Australian ginger cultivar ‘Canton’ was inoculated with 101, 103, 105, 106, and 107 microconidia per gram of soil. The inoculum density positively associated with leaf and stem yellows, and rhizome discolouration, and negatively associated with root length and rhizome weight. The lowest threshold required for plant infection was 101 microconidia per gram of soil, which may provide an important basis for outbreaks of Foz in the field. This finding adds significantly to the knowledge of the impact of soil health to ginger production thereby contributing to the integrated management of Foz. When used at a high dose, this method can facilitate reliable and accurate screening of Foz susceptible ginger genotypes in a controlled environment.
Percutaneous Intramyocardial Septal Cryoablation for Hypertrophic Cardiomyopathy: A Canine Model with 6 months Follow-up
Authors: Lu Xiaonan , Li Jing , Hsi David H. , Zhang Juan , Han Yupeng , Ta Shengjun , Wang Jing , He Jing , Zhao Jia , Hao Chao , Yao Lu , Ou Xumei , Shan Bo , Wang Bo , Zhao Xueli , Hu Rui , Liu Liwen
Published: August 2023

BACKGROUND

Echocardiography-guided percutaneous intramyocardial septal radiofrequency ablation (PIMSRA, Liwen procedure) is a novel treatment option for hypertrophic obstructive cardiomyopathy (HOCM). The safety and feasibility of using this procedure for cryoablation are unknown.

OBJECTIVE

To establish a canine model for echocardiography-guided percutaneous intramyocardial septal cryoablation (PIMSCA).

METHODS

Eight canines underwent PIMSCA and had electrocardiography, echocardiography, myocardial contrast echocardiography (MCE), (ECG), serological and pathological examinations during the preoperative, immediate postoperative, and in 6-month follow-up.

RESULTS

All eight canines underwent successful cryoablation and continued to be in sinus rhythm during ablation and without malignant arrhythmias. MCE showed that ablation area had decreased myocardial perfusion after procedure. Troponin I levels were significantly elevated [0.010 (0.005, 0.297) ng/mL vs. 3.122 (1.152,7.990) ng/mL, p < 0.05)]. At follow-up 6-months after procedure, all animals were alive, with thinning of the interventricular septum (7.26 ± 0.52 mm vs. 3.86 ± 0.29 mm, p < 0.05). Echocardiography showed no significant decrease in left ventricular ejection fractions (LVEF) (54.32 ± 2.93 %vs. 54.70 ± 2.47 %, p > 0.05) or changes by pulse-wave Doppler E/A (1.17 ± 0.43 vs. 1.07 ± 0.43, p > 0.05), E/e’(8.09 ± 1.49 vs. 10.05 ±2.68, p > 0.05). Pathological findings proved effective cryoablation in myocardial tissues. We observed pericardial effusions and premature ventricular complexes (PVCs) associated with the procedure.

CONCLUSION

Our findings provide preliminary evidence of the safety and feasibility of PIMSACA in interventricular septum reduction, which provides a potentially new treatment option for HOCM.
Structural elucidation and antiviral activity of cathepsin L inhibitors with carbonyl and epoxide warheads
Authors: Falke Sven , Lieske Julia , Herrmann Alexander , Loboda Jure , Günther Sebastian , Reinke Patrick YA , Ewert Wiebke , Karničar Katarina , Usenik Aleksandra , Lindič Nataša , Sekirnik Andreja , Tsuge Hideaki , Turk Vito , Chapman Henry N , Hinrichs Winfried , Ebert Gregor , Turk Dušan , Meents Alke
Published: August 2023

Emerging RNA viruses including SARS-CoV-2 continue to be a major threat around the globe. The cell entry of SARS-CoV-2 particles via the endosomal pathway involves the cysteine protease cathepsin L (CatL) among other proteases. CatL is rendered as a promising drug target in the context of different viral and lysosome-related diseases. Hence, drug discovery and structure-based optimization of inhibitors is of high pharmaceutical interest. We herein verified and compared the anti-SARS-CoV-2 activity of a set of carbonyl and succinyl-epoxide-based inhibitors, which have previously been identified as cathepsin inhibitors. Calpain inhibitor XII (CI-XII), MG-101 and CatL inhibitor IV (CLI-IV) possess antiviral activity in the very low nanomolar IC50range in Vero E6 cells. Experimental structural data on how these and related compounds bind to CatL are however notably lacking, despite their therapeutic potential. Consequently, we present and compare crystal structures of CatL in complex with 14 compounds, namely BOCA (N-BOC-2-aminoacetaldehyde), CLI-IV, CI-III, CI-VI, CI-XII, the main protease α-ketoamide inhibitor 13b, MG-101, MG-132 as well as E-64d (aloxistatin), E-64, CLIK148, CAA0225, TC-I (CID 16725315) and TPCK at resolutions better than 2 Å. Overall, the presented data comprise a broad and solid basis for structure-guided understanding and optimization of CatL inhibitors towards protease drug development.
Functional Domains of Substance Use and Trauma: A Systematic Review of Neuroimaging Studies
Authors: Hinojosa Cecilia A. , Sitar Siara I. , Zhao Joshua C. , Barbosa Joshua D. , Hien Denise A. , Welsh Justine W. , Fani Negar , van Rooij Sanne J.H.
Published: August 2023

In a framework for substance use concerning trauma, Hien and colleagues suggested three domains: reward salience, executive function, and negative emotionality. In this PRISMA-guided systematic review, we explored the neural correlates of these domains in individuals who use substances with or without trauma exposure. We included 45 studies utilizing tasks of interest in alcohol, tobacco, and cannabis use groups.

Greater reward, lesser regulation of inhibitory processes, and mixed findings of negative emotionality processes in individuals who use substances versus controls were found. Specifically, greater orbitofrontal cortex, ventral tegmental area, striatum, amygdala, and hippocampal activation was found in response to reward-related tasks, and reduced activation was found in the inferior frontal gyrus and hippocampus in response to inhibition-related tasks. No studies in trauma-exposed individuals met our review criteria.

Future studies examining the role of trauma-related factors are needed and should explore inhibition- and negative-emotionality domains in individuals who use substances to uncover alterations in these domains that place an individual at greater risk for developing SUD.
Artemisitene protected against murine schistosomiasis japonica through anti-parasite activity and immune regulation
Authors: Liu Meng-ke , Chen Xu-yang , Tang Juan-juan , Liu Zhi-peng , Lin Gui-ying , Cai Jun-ling , Chen Zuo-ming , Yan Yu-yun , Ji Xiao-fang , Yang Zhong-jin , Li Zi
Published: August 2023

Schistosoma japonicum(Sj) infection induced liver granulomatous inflammation and fibrosis. As an active artemisinin analog, the implication of artemisitene (ATT) in schistosomiasis were unclear. Herein, we found that ATT significantly reduced the count of total adult worms and eggs, and increased the count of single males, injured the tegument in the surface ofSjadult worms & gynecophoral canal of males. The transcription of 98 genes in females and 48 genes in males were significantly changed, and these genes were closely related to cellular anatomical entity through gene ontology analysis. So, ATT might possess anti-parasite activity. Meanwhile, ATT treatment significantly lowered the level of glutamic oxaloacetic transaminase (AST) and glutamic pyruvic transaminase (ALT) in sera, the size of mesenteric lymph node, and granuloma, the collagen area and α-SMA expression level in the liver. Liver transcriptome and multi-cytokines analysis indicated its immune regulation effect. Flow cytometry verified that the count of eosinophils in the liver were significantly increased, while the frequency of neutrophils, M1/M2 and Th1/Th2 index were significantly decreased. Therefore, we provided strong evidence that ATT has therapeutic potential throughSjclearance and anti-liver disease. Tegument development injury and immune regulation including type 2 immunity enhancement might be the mechanisms.

Author summary

Currently, there were still 290 million people worldwide who were infected bySchistosoma, and the treatment for schistosomiasis relies majorly on the use of a single drug-praziquantel. In this study, we described for the first time that artemisinin-derived artemisitene (ATT), chemically remarkably different from praziquantel, possessed the therapeutic effects on murine schistosomiasis japonica. ATT displayed both anti-Schistsosoma japonicumand anti-liver inflammation & liver fibrosis effect. Through RNA-seq and scanning electronic microscope of adult female & male worms from hepatoportal veins with or without ATT treatment, we found that the mechanisms of ATT’s anti-parasites could be through injuring tegument development and then interrupting adult worms’ especially adult female worms’ clearance by immune cells such as eosinophils. Moreover, through RNA-seq of liver total RNA, ELISA of multi-cytokines in liver lysates and flow cytometry analysis of liver single cells, we found that the anti-liver diseases’ efficacy of ATT was associated with immune regulation especially type 2 immunity enhancement. Therefore, ATT possessed the therapeutic potential against schistosomiasis japonica and further researches were necessary for its future clinical use.
Skeletons in the closet? – Using a bibliometric lens to visualise phytochemical and pharmacological activities linked toSceletium, a mood enhancer
Authors: Reddy Kaylan , Stafford Gary I. , Makunga Nokwanda P.
Published: August 2023

Plants from theSceletiumgenus (Aizoaceae) have been traditionally used by the Khoe-Sān people in southern Africa, mainly for thirst and hunger relief, pain reduction and spiritual purposes, particularlySceletium tortuosum. The research on this species has seen rapid growth with advancements in analytical and pharmacological tools. The Web of Science (WoS) database was searched for articles related to ‘Sceletium’ and ‘Mesembrine’. These data were additionally analysed by bibliometric software (VOSviewer) to generate term maps and author associations. The thematic areas with the most citations were, South African Traditional Medicine for mental health (110) and anxiolytic agents (75). Pioneer studies in the genus focused on chemical structural isolation, purification and characterization and techniques such as thin layer chromatography, liquid chromatography (HPLC, UPLC and more recently, LC-MS), gas chromatography mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) to study mesembrine alkaloids. Different laboratories have used a diverse range of extraction and pre-analytical methods that become routinely favoured in the analysis of the main metabolites (mesembrine, mesembranol, mesembranone and Sceletium A4) in their respective experimental settings. In contrast with previous reviews, this paper identified gaps in the research field, being a lack of toxicology assays, a deficit of clinical assessments, too few bioavailability studies and little to no investigation into the minor alkaloid groups found inSceletium. Future studies are likely to see innovations in analytical techniques like leaf spray mass spectrometry and direct analysis in real-time ionization coupled with high-resolution time-of-flight mass spectrometry (DART-HR-TOF-MS) for rapid alkaloid identification and quality control purposes. WhileS. tortuosumhas been the primary focus, studying otherSceletiumspecies may aid in establishing chemotaxonomic relationships and addressing challenges with species misidentification. This research can benefit the nutraceutical industry and conservation efforts for the entire genus. At present, little to no pharmacological information is available in terms of the molecular physiological effects of mesembrine alkaloids in medical clinical settings. Research in these fields is expected to increase due to the growing interest inS. tortuosumas a herbal supplement and the potential development of mesembrine alkaloids into pharmaceutical drugs.
The Role of Binding Site Specificity in the Disaggregation of Aβ42Fibrils through a Synthetic Paratope
Authors: Tiwari Shivam , Mandal Bhubaneswar , Reddy K Anki
Published: August 2023

Amyloid-β(Aβ) fibrils are the characteristic hallmark of Alzheimer’s disease(AD), and most drug development approaches for AD are focused on preventing and reversing the formation of these fibrillar aggregates. Previous studies show that synthetic antibodies have demonstrated great potential to inhibit the Aβaggregation and disaggregate the preformed Aβfibrils. Here, we perform explicit molecular dynamics(MD) simulation to elucidate the molecular mechanism of disaggregation of preformed LS-shaped Aβ42protofibril with a flexible, hairpin-like synthetic paratope (SP) which, in a recent experimental study, has shown promising results. Our simulations demonstrate various potential binding sites for SP on Aβ42protofibril. However, binding of SP at the amyloidogenic core region (KLVFF) shows pronounced structural disruption of Aβ42protofibril. Our results show heavy loss ofβsheet content, dismantling of K28-A42 salt bridge, and destruction of key contacts in the hydrophobic cores of Aβ42protofibril in the presence of SP. We found the aromatic and hydrophobic residues of Aβ42protofibril participating primarily in the binding with SP. Also, we found thatπ−πstacking and hydrophobic interactions are the most dominant mode of interaction between SP and Aβ42protofibril. This work provides a detailed atomistic perspective on the Aβ42protofibril disaggregation mechanism with SP, and the findings can help develop more effective drugs for AD in the future.
Comparative analysis of PB2 residue 627E/K/V in H5 subtypes of avian influenza viruses isolated in birds and mammals
Authors: Briggs Kelsey , Kapczynski Darrell R.
Published: August 2023

Avian influenza viruses (AIV) are naturally found in wild birds, primarily in migratory waterfowl. Although species barriers exist, many AIV have demonstrated the ability to jump from birds into mammalian species. A key contributor to this jump is the adaption of the viral RNA polymerase complex to a new host for efficient replication of its RNA genome. The AIV PB2 gene appears to be essential in this conversion as key residues have been discovered at amino acid position 627 that interact with the host cellular protein, acidic nuclear phosphoprotein 32 family member A (ANP32A). In particular, the conversion of glutamic acid (E) to a lysine (K) is frequently observed at this position following isolation in mammals. The focus of this report was to compare the distribution of PB2 627 residues from different lineages and origins of H5 AIV, determine the prevalence between historical and contemporary sequences, and investigate the ratio of amino acids in avian versus mammalian AIV sequences. Results demonstrate a low prevalence of E627K in H5 non-Goose/Guangdong/1996-lineage (Gs/GD) AIV samples, with a low number of mammalian sequences in general. In contrast, the H5-Gs/GD lineages sequences had an increased prevalence of the E627K mutation and contained more mammalian sequences. An approximate 40 percent conversion of E to K was observed in human sequences of H5 AIV, suggesting a non-exclusive requirement. Taken together, these results expand our understanding of the distribution of these residues within different subtypes of AIV and aid in our knowledge of PB2 mutations in different species.
Unveiling Novel Double-Negative Prostate Cancer Subtypes Through Single-Cell RNA Sequencing Analysis
Authors: Cheng Siyuan , Li Lin , Yeh Yunshin , Shi Yingli , Franco Omar , Corey Eva , Yu Xiuping
Published: August 2023

Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into disease heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising both publicly available cohorts and data generated by our research team, and established the HuPSA (HumanProstateSingle cellAtlas) and the MoPSA (MouseProstateSingle cellAtlas) datasets. Through comprehensive analysis, we identified two novel double-negative PCa populations: KRT7 cells characterized by elevated KRT7 expression, and progenitor-like cells marked by SOX2 and FOXA2 expression, distinct from NEPCa, and displaying stem/progenitor features. Furthermore, HuPSA-based deconvolution allowed for the re-classification of human PCa specimens, validating the presence of these novel subtypes. Leveraging these findings, we developed a user-friendly web application, “HuPSA-MoPSA” (https://pcatools.shinyapps.io/HuPSA-MoPSA/), for visualizing gene expression across all newly-established datasets. Our study provides comprehensive tools for PCa research and uncovers novel cancer subtypes that can inform clinical diagnosis and treatment strategies.

Graph abstract
Assessing the Quality of Hand-Dug Wells in the Sunyani Municipality, Ghana
Authors: Addo Henry Ofosu , Barimah Antwi Joseph , Dun-Dery Elvis J. , Ibrahim Fati , Obeng Mercy O. , Asiamah Christiana , Amegah Kingsley E.
Published: August 2023

Background

Hand-dug well water represents one of the main sources of drinking water for many settlements, especially people without access to treated potable water. However, water from such alternative sources can sometimes be polluted and not conducive for human consumption, due to the presence of pathogenic parasitic organisms. This study assessed the physico-chemical and microbial quality of hand-dug wells in the Sunyani Municipality in Ghana.

Methods

The study was cross-sectional in nature and results were laboratory-based analyses. The study used Global Positioning System (GPS)tracker to locate and sample hand-dug wells within the Sunyani Municipality. Fifteen (15) households with hand-dug wells were randomly selected from fifteen major communities within the Sunyani Municipality. One (1) sample was collected from each of the 15-household hand-dug wells for the study.

Results

Physico-chemical analyses suggest that the temperature of water from all sources ranged between 25.8oC and 270C whiles phenolphthalein alkalinity of all water samples was 0. But the total alkalinity was between 28 to 116 mg/L. Relatively higher concentrations of nitrate were also observed in samples from all locations and most wells were exposed. However, all samples contained 18.2MPN Index/100ml of faecal coliform compared to 0.0MPN Index/100ml of acceptable national limits.

Conclusion

Apart from most samples recording parameters exceeding World Health Organization (WHO) and Ghana Standards Authority recommended levels, majority of wells were exposed and sited around unhygienic environment. Hand-dug well water in the Sunyani Municipality is not completely safe for drinking purposes and requires periodic expert supervision and sample testing.
Fixational Eye Movements Enhance the Precision of Visual Information Transmitted by the Primate Retina
Authors: Wu Eric G. , Brackbill Nora , Rhoades Colleen , Kling Alexandra , Gogliettino Alex R. , Shah Nishal P. , Sher Alexander , Litke Alan M. , Simoncelli Eero P. , Chichilnisky E.J.
Published: August 2023

Fixational eye movements alter the number and timing of spikes transmitted from the retina to the brain, but whether these changes enhance or degrade the retinal signal is unclear. To quantify this, we developed a Bayesian method for reconstructing natural images from the recorded spikes of hundreds of retinal ganglion cells (RGCs) in the macaque retina (male), combining a likelihood model for RGC light responses with the natural image prior implicitly embedded in an artificial neural network optimized for denoising. The method matched or surpassed the performance of previous reconstruction algorithms, and provides an interpretable framework for characterizing the retinal signal. Reconstructions were improved with artificial stimulus jitter that emulated fixational eye movements, even when the eye movement trajectory was assumed to be unknown and had to be inferred from retinal spikes. Reconstructions were degraded by small artificial perturbations of spike times, revealing more precise temporal encoding than suggested by previous studies. Finally, reconstructions were substantially degraded when derived from a model that ignored cell-to-cell interactions, indicating the importance of stimulusevoked correlations. Thus, fixational eye movements enhance the precision of the retinal representation.
Single nucleotide polymorphisms and Zn transport by nuclear ZIP11 shape cancer phenotypes in HeLa cells
Authors: Kim Elizabeth Y. , Verdejo-Torres Odette , Diaz-Rodriguez Karla , Hasanain Farah , Caromile Leslie , Padilla-Benavides Teresita
Published: August 2023

Zinc (Zn) is an essential micronutrient that regulates critical biological processes such as enzymatic function, gene expression, and cell signaling and provides structural stability to proteins. Under physiological conditions, Zn is a divalent cation (Zn2+) in an inactive redox state. Maintaining Zn homeostasis is essential for normal cell development and function, and any dysregulation in supply and transport can lead to pathophysiological conditions. Zn transporters, such as ZIP11, are critical regulators in Zn homeostasis. In mammals, ZIP11 belongs to the GufA subfamily of ZIP transporters and is primarily found in the nucleus and the Golgi apparatus. Our laboratory recently reported an essential role of ZIP11 in maintaining nuclear Zn levels in the cervical cancer cell line HeLa that supports various hallmark phenotypes of cancer. Genomic analysis of publicly available cervical and ovarian cancer patient datasets identified several single-nucleotide polymorphisms (SNPs) in the ZIP11 coding region that correlated with disease severity. We hypothesized that these SNPs might have potentially deleterious consequences as they are in coding regions that could affect ZIP11 function by increasing substrate accessibility, potentially enhancing the carcinogenic phenotype of HeLa cells. In addition, we identified a classic Zn-metal binding site (MBS) composed of three relevant residues which may be required for transmembrane Zn-transport, maintenance of metal homeostasis, and the carcinogenic properties of HeLa cells. To address these questions, we utilized our well-established model of stably knock down (KD)ZIP11in HeLa cells and overexpressed ZIP11 encoding single mutations corresponding to the SNPs and the MBS. Overexpression of ZIP11 encoding SNPs restored the Zn levels and the proliferation, migration, and invasive defects ofZIP11KD cells. On the other hand, cells expressing ZIP11 with single MBS mutations exhibited a phenotype similar to KD cells, suggesting that Zn transport by this transporter is necessary for establishing and maintaining carcinogenic properties. The work highlights the functional relevance of nuclear Zn transport by ZIP11 to maintain homeostasis and support carcinogenic properties in ovarian cancer cells.
A model of calcium-induced calcium release from the sarcoplasmic reticulum in the smooth muscle cell and its investigation by mathematical modeling
Authors: Zhuk P. F. , Karakhim S. O. , Kosterin S. O.
Published: August 2023

A model of calcium-induced calcium release (CICR) from the sarcoplasmic reticulum was developed, simulating the behavior of the smooth muscle cell under conditions of its agonist stimulation. The mathematical model is a system of thirteen differential equations. In the initial (basal) state, the parameters of active and passive transport of Ca2+through both the plasma membrane and the sarcoplasmic reticulum membrane are adjusted.

A study of the model showed that, depending on the model parameters, the cell system can demonstrate two types of calcium concentration changes in the cytosol: a single Ca2+transient and an oscillatory mode.

After stimulation is completed, the cell system returns to the basal state (underin vivoconditions) or goes to a new steady-state level (underin vitroconditions), except when the cell system is in oscillatory mode. It is shown that the sarcoplasmic reticulum can act both as a passive participant in the process of Ca2+accumulation in the smooth muscle cell, acting as a buffer, and play a major role in this process by significantly increasing the Ca2+concentration in the cytosol, which is initiated by Ca2+entry from the extracellular space.

It was found that after stimulation of the smooth muscle cell, the net Ca2+flux from the cytosol increases due to an increase in Ca2+concentration in the cytosol, while the net Ca2+flux into the cytosol first increases due to an increase in the number of open calcium channels located on the membrane of the sarcoplasmic reticulum. It then begins to decrease due to a decrease in the Ca2+concentration gradient across the membrane of the sarcoplasmic reticulum. Therefore, at a certain time point these fluxes become equal and the process of Ca2+accumulation in the cytosol is terminated. Thus, calcium-induced calcium release is terminated spontaneously, resulting in the formation of a single cytosolic Ca2+transient. As a result of calcium-induced calcium release, the sarcoplasmic reticulum is not completely emptied, but retains quite significant amounts of Ca2+.

The possibility of Ca2+redistribution between the three compartments (extracellular space, cytosol and sarcoplasmic reticulum) creates the possibility of oscillation of cytosolic Ca2+concentration. The oscillation amplitude and frequency can remain practically unchanged for a considerable period.

The developed model qualitatively reproduces the results of experimental studies conducted to identify store-operated calcium channels using the inhibitors of the calcium pump of the sarcoplasmic reticulum in a calcium-free medium.
Addressing biases in gene-set enrichment analysis: a case study of Alzheimer’s Disease
Authors: Bakulin Artemy , Teyssier Noam B , Kampmann Martin , Khoroshkin Matvei , Goodarzi Hani
Published: August 2023

Inferring the driving regulatory programs from comparative analysis of gene expression data is a cornerstone of systems biology. Many computational frameworks were developed to address this problem, including our iPAGE (information-theoreticPathwayAnalysis ofGeneExpression) toolset that uses information theory to detect non-random patterns of expression associated with given pathways or regulons1. Our recent observations, however, indicate that existing approaches are susceptible to the biases and artifacts that are inherent to most real world annotations. To address this, we have extended our information-theoretic framework to account for specific biases in biological networks using the concept of conditional information. This novel implementation, called pyPAGE, provides an unbiased way for the estimation of the activity of transcriptional and post-transcriptional regulons.

To showcase pyPAGE, we performed a comprehensive analysis of regulatory perturbations that underlie the molecular etiology of Alzheimer’s disease (AD). pyPAGE successfully recapitulated several known AD-associated gene expression programs. We also discovered several additional regulons whose differential activity is significantly associated with AD. We further explored how these regulators relate to pathological processes in AD through cell-type specific analysis of single cell gene expression datasets.
Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora
Authors: Eglit Yana , Shiratori Takashi , Jerlström-Hultqvist Jon , Williamson Kelsey , Roger Andrew J. , Ishida Ken-Ichiro , Simpson Alastair G. B.
Published: August 2023

‘Kingdom-level’ branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down1–4. Some are completely new discoveries, while others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19thcentury, but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted2.Meteora sporadicaHausmann et al. 20025is a protist with a unique morphology and motility; cells glide over substrates along a long axis of anterior and posterior projections, and have a pair of lateral ‘arms’ that swing back and forth. Originally,Meteorawas described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement ofMeteoraremained unresolved6. Here, we investigated two cultivatedMeteora sporadicaisolates in detail. Transmission electron microscopy showed that the anterior-posterior projections are supported by microtubules originating from a cluster of subnuclear MTOCs. Likewise, the arms are supported by microtubules, and neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be amongst the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests thatMeteoraand Hemimastigophora together represent a morphologically diverse ‘supergroup’, and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.
Neural correlates of confidence during decision formation in a perceptual judgment task
Authors: Ko Yiu Hong , Zhou Andong , Niessen Eva , Stahl Jutta , Weiss Peter H. , Hester Robert , Bode Stefan , Feuerriegel Daniel
Published: August 2023

When we make a decision, we also estimate the probability that our choice is correct or accurate. This probability estimate is termed our degree of decision confidence. Recent work has reported event-related potential (ERP) correlates of confidence both during decision formation (the centro-parietal positivity component; CPP) and after a decision has been made (the error positivity component; Pe). However, there are several measurement confounds that complicate the interpretation of these findings. More recent studies that overcome these issues have so far produced conflicting results. To better characterise the ERP correlates of confidence we presented participants with a comparative brightness judgment task while recording electroencephalography. Participants judged which of two flickering squares (varying in luminance over time) was brighter on average. Participants then gave confidence ratings ranging from “surely incorrect” to “surely correct”. To elicit a range of confidence ratings we manipulated both the mean luminance difference between the brighter and darker squares (relative evidence) and the overall luminance of both squares (absolute evidence). We found larger CPP amplitudes in trials with higher confidence ratings. This association was not simply a by-product of differences in relative evidence (which covaries with confidence) across trials. We did not identify postdecisional ERP correlates of confidence, except when they were artificially produced by pre-response ERP baselines. These results provide further evidence for neural correlates of processes that inform confidence judgments during decision formation.
Pantothenate Kinase 4 controls efficient skeletal muscle energy substrate metabolism via acetyl-CoA
Authors: Miranda-Cervantes Adriana , Fritzen Andreas M. , Raun Steffen H. , Hodek Ondřej , Møller Lisbeth L. V. , Johann Kornelia , Deisen Luisa , Gregorevic Paul , Gudiksen Anders , Artati Anna , Adamski Jerzy , Andersen Nicoline R. , Schjerling Peter , Cebrian-Serrano Alberto , Jähnert Markus , Gottmann Pascal , Burtscher Ingo , Lickert Heiko , Pilegaard Henriette , Schürmann Annette , Tschöp Matthias H. , Moritz Thomas , Müller Timo D. , Sylow Lykke , Kiens Bente , Richter Erik A. , Kleinert Maximilian
Published: August 2023

Metabolic inflexibility in skeletal muscle (SkM) is closely linked to metabolic diseases. Exercise improves metabolic flexibility, rendering it a valuable discovery tool of mechanisms promoting efficient metabolism of glucose and lipids. We herein discover pantothenate kinase 4 (PanK4) as a conserved exercise target with high abundance in SkM. We go on to show that murine musclePank4is dysregulated with high-fat diet feeding, and identify humanPANK4variants that associate with glycemic control and body mass index traits, indicating important roles of PanK4 in glucose metabolism and growth. Consistent with the latter, germline deletion of PanK4 reduces circulating IGF-1 and stunts growth in mice. Deletion specifically in mouse SkM reveals that PanK4 facilitates fatty acid oxidation by acting as a regulator of SkM acetyl-CoA, a key node in metabolism of both glucose and lipids. Consequently, without PanK4, elevated SkM acetyl-CoA levels allosterically gridlock key enzymes required for efficient lipid and glucose utilization, and these SkM metabolic perturbations manifest in whole-body insulin resistance. As proof of principle, we show that an increase in muscle PanK4 lowers SkM acetyl-CoA and increases SkM glucose utilization. Our findings identify PanK4 as a novel regulator of SkM energy substrate metabolism, warranting inclusion in comprehensive strategies against metabolic disease.
Single-protein optical holography
Authors: Thiele Jan Christoph , Pfitzner Emanuel , Kukura Philipp
Published: August 2023

Light scattering by nanoscale objects is a fundamental physical property defined by their scattering cross-section and thus polarisability. Over the past decade, a number of studies have demonstrated single molecule sensitivity, by imaging the interference between coherent scattering from the object of interest with a reference field. This approach has enabled mass measurements of single biomolecules in solution owing to the linear scaling of the image contrast with the molecular polarisability. Nevertheless, all implementations to date based on a common-path interferometer cannot separate and independently tune the reference and scattered light field, prohibiting access to the rich toolbox available to holographic imaging. Here, we demonstrate comparable sensitivity using a non-common path geometry based on a dark-field scattering microscope, similar to a Mach-Zehnder interferometer. We separate the scattering and reference light into four parallel, inherently phase stable detection channels, delivering a five orders of magnitude boost in sensitivity in terms of scattering cross-section over the state-of-the-art, demonstrating detection and mass measurement of single proteins below 100 kDa. Amplitude and phase measurement yields direct information on sample identity and the first experimental determination of the polarisability of single biomolecules.
A scalable, low-cost phenotyping strategy to assess tuber size, shape, and the colorimetric features of tuber skin and flesh in potato breeding populations
Authors: Feldman Max J. , Park Jaebum , Miller Nathan , Wakholi Collins , Greene Katelyn , Abbasi Arash , Rippner Devin A. , Navarre Duroy , Carley Cari Schmitz , Shannon Laura M. , Novy Rich
Published: August 2023

Tuber size, shape, colorimetric characteristics, and defect susceptibility are all factors that influence the acceptance of new potato cultivars. Despite the importance of these characteristics, our understanding of their inheritance is substantially limited by our inability to precisely measure these features quantitatively on the scale needed to evaluate breeding populations. To alleviate this bottleneck, we developed a low-cost, semi-automated workflow to capture data and measure each of these characteristics using machine vision. This workflow was applied to assess the phenotypic variation present within 189 F1 progeny of the A08241 breeding population. Our results provide an example of quantitative measurements acquired using machine vision methods that are reliable, heritable, and can be used to understand and select upon multiple traits simultaneously in structured potato breeding populations.
Relative importance of MCL-1’s Anti-Apoptotic versus Non-Apoptotic Functionsin vivo
Authors: Brinkmann Kerstin , McArthur Kate , Tee Annli , Kueh Andrew J. , Malelang Shezlie , Wimmer Verena C. , Gibson Leonie , Rowe Caitlin L , Arandjelovic Philip , Dewson Grant , Putoczki Tracey L , Bouillet Philippe , Fu Naiyang , Thomas Tim , Herold Marco J. , Voss Anne K. , Strasser Andreas
Published: August 2023

MCL-1 is an anti-apoptotic member of the BCL-2 protein family that ensures cell survival by blocking the intrinsic apoptotic cell death pathway1. MCL-1 is unique in being essential for early embryonic development and the survival of many cell types, including many cancer cells, which are not affected by the loss of the other anti-apoptotic BCL-2 family members1–4. Non-apoptotic functions of MCL-1 controlling mitochondrial ATP production and dynamics have been proposed to underlie this unique requirement for MCL-15–9. The relative contributions of the anti-apoptoticversusthe non-apoptotic functions of MCL-1 in normal physiology have not been addressed. Here we replaced the coding sequence for MCL-1 with those for the anti-apoptotic proteins BCL-XL, BCL-2 or A1. We hypothesised that BCL-XL, BCL-2 and A1 may substitute for MCL-1 in the inhibition of apoptosis, but that they will not be able to replace MCL-1’s non-apoptotic function. Strikingly,Mcl-1Bcl-xL/Bcl-xLandMcl-1Bcl-2/Bcl-2embryos survived to embryonic day 14.5, greatly surpassing the pre-implantation lethality ofMcl-1−/−embryos at E3.5. This demonstrates that the non-apoptotic functions of MCL-1 are dispensable for early development. However, at later stages of development and life after birth many cell types, particularly ones with high energy demand, were found to require both the anti-apoptotic and the non-apoptotic functions of MCL-1. These findings reveal the relative importance of these distinct functions of MCL-1 in physiology, providing important information for basic biology and the advancement of MCL-1 inhibitors in cancer therapy.
Early life high fructose exposure disrupts microglia function and impedes neurodevelopment
Authors: Wang Zhaoquan , Lipshutz Allie , Liu Zong-Lin , Trzeciak Alissa J. , Miranda Isabella C. , Martínez de la Torre Celia , Schild Tanya , Lazarov Tomi , Rojas Waleska Saitz , Saavedra Pedro H. V. , Romero-Pichardo Jesús E. , Baako Ann , Geissmann Frederic , Faraco Giuseppe , Gan Li , Etchegaray Jon Iker , Lucas Christopher D. , Parkhurst Christopher N. , Zeng Melody Y. , Keshari Kayvan R. , Perry Justin S. A.
Published: August 2023

Despite the success of fructose as a low-cost food additive, recent epidemiological evidence suggests that high fructose consumption by pregnant mothers or during adolescence is associated with disrupted neurodevelopment1–7. An essential step in appropriate mammalian neurodevelopment is the synaptic pruning and elimination of newly-formed neurons by microglia, the central nervous system’s (CNS) resident professional phagocyte8–10. Whether early life high fructose consumption affects microglia function and if this directly impacts neurodevelopment remains unknown. Here, we show that both offspring born to dams fed a high fructose diet and neonates exposed to high fructose exhibit decreased microglial density, increased uncleared apoptotic cells, and decreased synaptic pruningin vivo. Importantly, deletion of the high affinity fructose transporter SLC2A5 (GLUT5) in neonates completely reversed microglia dysfunction, suggesting that high fructose directly affects neonatal development. Mechanistically, we found that high fructose treatment of both mouse and human microglia suppresses synaptic pruning and phagocytosis capacity which is fully reversed in GLUT5-deficient microglia. Using a combination ofin vivoandin vitronuclear magnetic resonance- and mass spectrometry-based fructose tracing, we found that high fructose drives significant GLUT5-dependent fructose uptake and catabolism, rewiring microglia metabolism towards a hypo-phagocytic state. Importantly, mice exposed to high fructose as neonates exhibited cognitive defects and developed anxiety-like behavior which were rescued in GLUT5-deficient animals. Our findings provide a mechanistic explanation for the epidemiological observation that early life high fructose exposure is associated with increased prevalence of adolescent anxiety disorders.
Llgl1 mediates timely epicardial emergence and establishment of an apical laminin sheath around the trabeculating cardiac ventricle
Authors: Pollitt Eric JG , Derrick Christopher J , Sánchez-Posada Juliana , Noël Emily S
Published: August 2023

During heart development, the embryonic ventricle becomes enveloped by the epicardium, a layer of mesothelium which adheres to the outer apical surface of the heart. This is concomitant with onset of ventricular trabeculation, where a subset of cardiomyocytes lose apicobasal polarity and delaminate basally from the ventricular wall, projecting into the cardiac lumen to begin building the muscle mass necessary for adult cardiac function. Lethal(2) giant larvae homolog 1 (Llgl1) regulates the formation of apical cell junctions and apicobasal polarity, and we investigated its role in ventricular wall maturation, including trabeculation and epicardial establishment. We found thatllgl1mutant zebrafish embryos exhibit aberrantly positioned cardiomyocytes during early trabeculation, some of which extrude apically into the pericardial space. While investigating apical cardiomyocyte extrusion we identified a basal to apical shift in laminin deposition in the ventricular wall. Initially laminin deposition occurs on the luminal (basal) surface of the heart but concomitant with the onset of trabeculation basal laminin is removed and is instead deposited on the exterior (apical) surface of the ventricle. We find that epicardial cells express several laminin subunits as they adhere to the ventricular wall, and show that the epicardium is required for laminin deposition on the ventricular surface. Inllgl1mutants the timing of the basal-apical laminin shift is delayed, in line with a delay in establishment of the epicardial layer. Analysis of earlier epicardial development reveals that while both Llgl1 and laminin are not required for specification of the proepicardial organ, they are instead required for dissemination of epicardial cells to the ventricular surface. Together our analyses reveal an unexpected role for Llgl1 in correct timing of epicardial development, supporting integrity of the myocardial wall during early trabeculation.
Crowdsourcing and phylogenetic modelling reveal parrot tool use is not rare
Authors: Bastos Amalia P. M. , Claessens Scott , Nelson Ximena J. , Welch David , Atkinson Quentin D. , Taylor Alex H.
Published: August 2023

Studying the prevalence of putatively rare behaviours, such as tool use, is challenging because absence of evidence can arise either from a species’ inability to produce the behaviour or from insufficient research effort. Here, we tackle this challenge by combining crowdsourcing and phylogenetic modelling to approximate actual rates of a rarely observed behaviour based on limited data, targeting tool use in parrots. Crowdsourcing on a social media platform revealed novel instances of tool use in 17 parrot species, more than doubling the confirmed number of tool-using parrot species from 11 (3%) to 28 (7%). Phylogenetic modelling ranked additional species that are most likely to be unobserved tool users, suggesting that between 11% and 17% of extant parrot species may be tool users. These discoveries have implications for inferences about the evolutionary drivers and origins of tool use in parrots, revealing associations with relative brain size and feeding generalism and indicating several genera where tool use was likely an ancestral trait. Overall, our findings challenge the assumption that current sampling effort captures the full distribution of putatively rare animal behaviours. Combining our sampling and analysis methods offers a fruitful approach for investigating the distribution, drivers, and origins of other rare behaviours.

This working paper has not yet been peer-reviewed.
Intein-based thermoregulated meganucleases for biocontainment of genetic material
Authors: Foo Gary W. , Leichthammer Christopher D. , Saita Ibrahim M. , Lukas Nicholas D. , Batko Izabela Z. , Heinrichs David E. , Edgell David R.
Published: August 2023

Limiting the spread of synthetic genetic information outside of the intended use is essential for applications where biocontainment is critical. In particular, biocontainment of engineered probiotics and plasmids that are excreted from the mammalian gastrointestinal tract is needed to prevent escape and acquisition of genetic material that could confer a selective advantage to microbial communities. Here, we built a simple and lightweight biocontainment system that post-translationally activates a site-specific DNA endonuclease to degrade DNA at 18°C and not at higher temperatures. We constructed an orthogonal set of temperature sensitive-meganucleases, or TSMs, by inserting the yeast VMA1 L212P temperature-sensitive intein into the coding regions of LAGLIDADG homing endonucleases. We showed that the TSMs eliminated plasmids carrying the cognate TSM target site from laboratory strains ofEscherichia coliat the permissive 18°C but not at higher restrictive temperatures. Plasmid elimination is dependent on both TSM endonuclease activity and intein splicing. We demonstrated that TSMs eliminated plasmids from theE. coliNissle 1917 strain after passage through the mouse gut when fecal resuspensions were incubated at 18°C but not at 37°C. Collectively, our data demonstrates the potential of thermoregulated meganucleases as a means of restricting engineered plasmids and probiotics to the mammalian gut.