bluuebunny/crossref_metadata_2025 huggingface dataset:
How woodcocks produce the most brilliant white plumage patches among the birds
Authors: Dunning Jamie , Patil Anvay , D’Alba Liliana , Bond Alexander L , Debruyn Gerben , Dhinojwala Ali , Shawkey Matthew , Jenni Lukas
Published: December 2022

Until recently, and when compared with diurnal birds that use contrasting plumage patches and complex feather structures to convey visual information, communication in nocturnal species was considered to follow acoustic and chemical channels. However, many nocturnal birds have evolved intensely white plumage patches within otherwise inconspicuous plumages. We used spectrophotometry, electron microscopy, and optical modelling to explain the mechanisms producing bright white tail feather tips of the Eurasian woodcockScolopax rusticola. Their diffuse reflectance was ∼30% higher than any previously measured feather. This intense reflectance is the result of incoherent light scattering from a disordered nanostructure composed of keratin and air within the barb rami. In addition, the flattening, thickening, and arrangement of those barbs creates a Venetian-blind-like macrostructure that enhances the surface area for light reflection. We suggest that the woodcocks have evolved these bright white feather patches for long-range visual communication in dimly lit environments.
Propagated circulating tumor cells uncovers the role of NFκB and COP1 in metastasis
Authors: Xiao Jerry , Sharma Utsav , Arab Abolfazl , Miglani Sohit , Bhalla Sonakshi , Suguru Shravanthy , Suter Robert , Mukherji Reetu , Lippman Marc E. , Pohlmann Paula R. , Zeck Jay , Marshall John L. , Weinberg Benjamin A. , He Aiwu Ruth , Noel Marcus S. , Schlegel Richard , Goodarzi Hani , Agarwal Seema
Published: December 2022

Circulating tumor cells (CTCs), a population of cancer cells that represents the seeds of metastatic nodules, are a promising model system for studying metastasis. However, expansion of patient-derived CTCsex vivois challenging and dependent on the collection of high numbers of CTCs, which are ultra-rare. Here, we report the development of a combined CTC and CTC-derived xenograft (CDX) platform for expanding and studying patient-derived CTCs from metastatic colon, lung, and pancreatic cancers. Propagated CTCs yielded a highly aggressive population of cells that could be used to routinely and robustly establish primary tumors and metastatic lesions in CDXs. Differential gene analysis of the resultant CTC models emphasized a role for NF-kB signaling as a pan-cancer signaling pathway involved in metastasis. Furthermore, metastatic CTCs were identified through a prospective 5-gene signature (BCAR1, COL1A1, IGSF3, RRAD, and TFPI2). Whole-exome sequencing of CDX models and metastases further identified mutations in constitutive photomorphogenesis protein 1 (COP1) as a potential driver of metastasis. These findings illustrate the utility of the combined patient-derived CTC model and provide a glimpse of the promise of CTCs in identifying drivers of cancer metastasis.
Daily membrane capacitance changes in mouse neurons
Authors: Severin Daniel , Moreno Cristián , Tran Trinh , Wesselborg Christian , Shirley Sofia , Kirkwood Alfredo , Golowasch Jorge
Published: December 2022

Capacitance of biological membranes is determined by the properties of the lipid portion of the membrane, as well as morphological features of a cell. In neurons, membrane capacitance is a determining factor of synaptic integration, action potential propagation speed and firing frequency due to its direct effect on the membrane time constant. Besides slow changes associated with increased morphological complexity during postnatal maturation, neuron membrane capacity is largely considered a stable, non-regulated constant magnitude. Here we report that in two excitatory neuronal cell types, pyramidal cells of mouse primary visual cortex and granule cells of the hippocampus, the membrane capacitance significantly changes between the start and the end of a daily light cycle. The changes are large, nearly two-fold in magnitude in pyramidal cells, but are not observed in cortical parvalbumin-expressing inhibitory interneurons. We discuss potential functional implications and plausible mechanisms.
Computing Absolute Binding Affinities by Streamlined Alchemical Free Energy Perturbation (SAFEP)
Authors: Santiago-McRae Ezry , Ebrahimi Mina , Sandberg Jesse W. , Brannigan Grace , Hénin Jérôme
Published: December 2022

Free Energy Perturbation (FEP) is a powerful but challenging computational technique for estimating differences in free energy between two or more states. This document is intended both as a tutorial and as an adaptable protocol for computing free energies of binding using free energy perturbations in NAMD. We present the Streamlined Alchemical Free Energy Perturbation (SAFEP) framework. SAFEP shifts the computational frame of reference from the ligand to the binding site itself. This both simplifies the thermodynamic cycle and makes the approach more broadly applicable to superficial sites and other less common geometries. As a practical example, we give instructions for calculating the absolute binding free energy of phenol to lysozyme. We assume familiarity with standard procedures for setting up, running, and analyzing molecular dynamics simulations using NAMD and VMD. While simulation times will vary, the human tasks should take no more than 3 to 4 hours for a reader without previous training in free energy calculations or experience with the VMD Colvars Dashboard. Sample data are provided for all key calculations both for comparison and readers’ convenience.
The role of human superior colliculus in affective experiences during visual and somatosensory stimulation
Authors: Chen Danlei , Kragel Philip A. , Savoca Paul W. , Wald Lawrence L. , Bianciardi Marta , Wager Tor D. , Quigley Karen S. , Satpute Ajay B. , Barrett Lisa Feldman , Theriault Jordan E.
Published: December 2022

The superior colliculus is often studied for its role in visually guided behaviors, but research in non-human animals indicates it is a midbrain hub for processing sensory information from multiple domains, including interoception (which is associated with affect). We used ultra-high field 7-Tesla fMRI to extend this work to humans, modeling superior colliculus BOLD signal intensity during visual or somatosensory stimulation (N = 40 in each sensory modality), both under aversive and neutral affective intensity. As hypothesized, the superior colliculus showed increased BOLD signal intensity in the dorsal and ventral subregions during visual and somatosensory stimulation, respectively. The entire superior colliculus also showed increased BOLD signal intensity during aversive compared to neural conditions. The superior colliculus BOLD signal intensity also correlated with a preregistered set of brain regions involved in visual, somatosensory, and interoceptive processing.
Supercomputer framework for reverse engineering firing patterns of neuron populations to identify their synaptic inputs
Authors: Chardon Matthieu K. , Wang Y. Curtis , Garcia Marta , Besler Emre , Beauchamp J. Andrew , D’Mello Michael , Powers Randall K. , Heckman Charles J.
Published: December 2022

In this study, we develop new reverse engineering (RE) techniques to identify the organization of the synaptic inputs generating firing patterns of populations of neurons. We tested these techniquesin silicoto allow rigorous evaluation of their effectiveness, using remarkably extensive parameter searches enabled by massively-parallel computation on supercomputers. We chose spinal motoneurons as our target neural system, since motoneurons process all motor commands and have well established input-output properties. One set of simulated motoneurons was driven by 300,000+ simulated combinations of excitatory, inhibitory, and neuromodulatory inputs. Our goal was to determine if these firing patterns had sufficient information to allow RE identification of the input combinations. Like other neural systems, the motoneuron input-output system is likely non-unique. This non-uniqueness could potentially limit this RE approach, as many input combinations can produce similar outputs. However, our simulations revealed that firing patterns contained sufficient information to sharply restrict the solution space. Thus, our RE approach successfully generated estimates of the actual simulated patterns of excitation, inhibition, and neuromodulation, with variances accounted for ranging from 75% to 90%. It was striking that nonlinearities induced in firing patterns by the neuromodulation inputs did not impede RE, but instead generated distinctive features in firing patterns that aided RE. These simulations demonstrate the potential of this form of RE analysis. It is likely that the ever-increasing capacity of supercomputers will allow increasingly accurate RE of neuron inputs from their firing patterns from many neural systems.
Genetic and phylogenetic features of the repetitive ITS copies in theHirsutella sinensisgenome and the genomically independent AT-biasedOphiocordyceps sinensisgenotypes
Authors: Li Xiu-Zhang , Li Yu-Ling , Wang Ya-Nan , Zhu Jia-Shi
Published: December 2022

It has been hypothesized that AT-biased genotypes ofOphiocordyceps sinensisare generated through repeat-induced point mutation (RIP) and coexist as permanently nonfunctional internal transcribed spacer (ITS) pseudogenes in the genome ofHirsutella sinensis(GC-biased Genotype #1 ofO. sinensis). This study examined theH. sinensisgenome, which contains multiple repetitive ITS copies (GC content: 64.7±0.33%) with multiple insertion/deletion and transversion alleles, which were not generated through RIP mutagenesis that theoretically causes cytosine-to-thymine (C-to-T) and guanine-to-adenine (G-to-A) transitions. The repetitive ITS copies in theH. sinensisgenome were found to be genetically and phylogenetically distinct from the AT-biasedO. sinensisgenotypes (GC content: 51.1±1.69%), which possess multiple transition alleles. The sequences of Genotypes #2–17, both GC- and AT-biased, are absent from theH. sinensisgenome; these genotypes belong to interindividualO. sinensisfungi and differentially occur in different compartments of naturalCordyceps sinensis,with dynamic alterations in abundance occurring in an asynchronous, disproportional manner duringC. sinensismaturation. Metatranscriptomic analyses of naturalC. sinensisrevealed the transcriptional silencing of 5.8S genes in allC. sinensis- colonizing fungi, includingH. sinensis. The transcription assay reported by Liet al. [1] provided unsound, controversial evidence indicating that the 5.8S genes of AT-biased genotypes are nonfunctional pseudogenes. In addition to the single ITS locus analysis, repetitive genomic copies were also examined at multiple loci in theH. sinensisgenome, and approximately 8.2% of the authentic genes had repetitive copies, including various transitions, transversions, and insertions/deletions. The transcripts for the repetitive copies, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in theH. sinensistranscriptome. These results are inconsistent with those of RIP mutagenesis, which generates pseudogenic, nonfunctional, repetitive copies. In conclusion, AT-biased genotypes ofO. sinensismight have evolved through evolutionary mechanisms from a common ancestor over the long course of evolution, in parallel with GC-biased Genotype #1H. sinensis.
Investigation on the Effectiveness ofLactobacillus plantarumin Enhancing the Folate content ofInjeramade with Different Cereals
Authors: Tamene Aynadis , Baye Kaleab , Mekuriyaw Tesfaye
Published: December 2022

Injera is an Ethiopian fermented pancake-like flatbread made from different cereals. The aim of the study was to investigate the effect of injera making process using different cereals (tef, sorghum, wheat and barley) on folate content and to evaluate the effectiveness of Lactobacillus plantarum (L. plantarum) in enhancing folate of injera made with different cereals. Cereals were used alone or in combination (tef and sorghum (1:1), wheat and sorghum (3:1), sorghum (100 %) and Barley (100 %). L. plantarum previously isolated from tef dough and ersho were used as starters. Folate content of flour, dough and injera was determined by microbiological assay. The contribution of consumption of injera made with different cereals to the folate requirement of children and women of reproductive age was evaluated. Acceptability of injera was estimated by 30 adult healthy volunteers using a 9-point hedonic scale. Among the studied cereals, the highest average folate content (49.9 μg/100 g) was observed in 100 % sorghum flour and the least (32.2 μg/100 g) in 100 % barley flour, on dry weight basis. After fermentation, the highest average folate content (60.1 μg/100 g) was observed in 100 % sorghum dough fermented with L. plantarum and the least (27.6 μg/100 g) was observed in the same dough but fermented with ersho. The average folate contents (fresh weight basis) of 100 % sorghum, wheat & sorghum (3:1), tef & sorghum (1:1) and 100 % barley injeras fermented with L. plantarum were 14.48 μg/100 g, 15.45 μg/100 g, 13.23 μg/100 g and 13.13 μg/100 g, respectively. Consumption of L. plantarum fermented injera made with different cereals can contribute up to 8 % of the recommended folate intake of women of reproductive age. Injera made with tef and sorghum blend (1:1) and fermented with L. plantarum was highly accepted.
Unconditioned and Conditioned Anxiolytic Effects of Sodium Valproate on Flavor Neophobia and Fear Conditioning
Authors: Cintado María Ángeles , González-Tirado Gabriel , Cárcel Lucía , De la Casa Luis Gonzalo
Published: December 2022

In three experiments with rats, we analyzed the potential anxiolytic effects of sodium valproate, an anticonvulsant drug that has shown additional pharmacodynamic effects in animal models, including anxiolytic action. Since previous results have revealed that injecting valproate before allowing animals to consume a novel flavor solution resulted in an attenuation of neophobia, we predicted a similar effect when the novel flavor is presented on a drug-free trial in the presence of a context previously associated with the drug. In line with this hypothesis, in our first experiment we observed a reduction in neophobia to a novel flavor for those animals tested in the presence of the context associated with Sodium Valproate. However, a control group that received the drug before being allowed access to the novel flavor showed a significant reduction in consumption. Experiment 2 revealed that the unconditioned effects of the drug include a deleterious effect on the animals’ locomotor activity that probably interferes with drinking behavior. Finally, in a third experiment, we directly tested the potential anxiolytic properties of sodium valproate by injecting the drug before implementing a fear conditioning procedure. These findings are explained in terms of the unconditioned anxiolytic action of the drug and the formation of an association between the context and the effects of the drug that evokes a conditioned response reminiscent of such anxiolytic effect.
Rapid Audiovisual Integration Guides Predictive Actions
Authors: Kreyenmeier Philipp , Schroeger Anna , Cañal-Bruland Rouwen , Raab Markus , Spering Miriam
Published: December 2022

Natural movements, such as catching a ball or capturing prey, typically involve multiple senses. Yet, laboratory studies on human movements commonly focus solely on vision and ignore sound. Here we ask how visual and auditory signals are integrated to guide interceptive movements. Human observers tracked the brief launch of a simulated baseball, randomly paired with batting sounds of varying intensities, and made a quick pointing movement at the ball. Movement endpoints revealed systematic overestimation of target speed when ball launch was paired with a loud versus a quiet sound, even though sound was never informative. This effect was modulated by the availability of visual information: sounds biased interception when ball presentation time was short. Continuous eye movements uncovered that sound affected interception within 125 ms of ball launch and revealed a correction of the sound-induced bias when more visual information was available. Our findings suggest that auditory and visual signals are integrated to guide interception and that this integration process must occur early at a site that receives auditory and visual signals within an ultrashort timespan.
Global soil metagenomics reveals ubiquitous yet previously-hidden predominance ofDeltaproteobacteriain nitrogen-fixing microbiome
Authors: Masuda Yoko , Mise Kazumori , Xu Zhenxing , Zhang Zhengcheng , Shiratori Yutaka , Senoo Keishi , Itoh Hideomi
Published: December 2022

Biological nitrogen fixation is a fundamental process sustaining all life on earth. In the soil,Alphaproteobacteria, Betaproteobacteria, andCyanobacteriaare traditionally considered the major groups of nitrogen fixation population. This conventional knowledge has been accumulated by numerous PCR amplicon surveys for nitrogenase genes. However, this prevalent view appears to be inconsistent with results of recent PCR-free meta-omics investigations. Here, we show the global distribution and diversity of terrestrial diazotrophic microbiome, updated by fully leveraging the planetary collections of soil metagenomes along with recently expanded culture collections. After extensive analysis of 1,445 soil metagenomic samples, we proved that the previously-undervaluedAnaeromyxobacteraceaeandGeobacteraceaewithinDeltaproteobacteriaare ubiquitous and predominant groups of diazotrophic microbiome in the soils, spanning a broad spectrum of environments, with different geographic origins and land usage types, including aerobic (croplands, grasslands) and anaerobic ones (paddy soils, sediments). Our results delineate a revised scheme of soil nitrogen fixation, which is inclusive of both conventional diazotrophs and the so far undervaluedDeltaproteobacteria.
A weighted quantile sum regression with penalized weights and two indices
Authors: Renzetti Stefano , Gennings Chris , Calza Stefano
Published: December 2022

Background

New statistical methodologies were developed in the last decade to face the challenges of estimating the effects of exposure to multiple chemicals. Weighted Quantile Sum (WQS) regression is a recent statistical method that allows estimating a mixture effect associated with a specific health effect and identifying the components that characterize the mixture effect.

Objectives

In this study, we propose an extension of WQS regression that estimates two mixture effects of chemicals on a health outcome in the same model through the inclusion of two indices with the introduction of a penalization term.

Methods

To evaluate the performance of this new model we performed both a simulation study and a real case study where we assessed the effects of nutrients on obesity among adults using the National Health and Nutrition Examination Survey (NHANES) data.

Results

The method showed good performance in estimating both the regression parameter and the weights associated with the single elements when the penalized term was set equal to the magnitude of the Akaike information criterion of the unpenalized WQS regression. The two indices further helped to give a better estimate of the parameters (Positive direction Median Error (PME): 0.017; Negative direction Median Error (NME): -0.023) compared to the standard WQS (PME: -0.141; NME: 0.078). In the case study, WQS with two indices was able to find a significant effect of nutrients on obesity in both directions identifying caffeine and magnesium as the main actors in the positive and negative association respectively.

Discussion

Through this work, we introduced an extension of the WQS regression that showed the possibility to improve the accuracy of the parameter estimates when considering a mixture of elements that can have both a protective and a harmful effect on the outcome; and the advantage of adding a penalization term when estimating the weights.
Artificial intelligence-assisted meta-analysis of the frequency ofACEI/D polymorphisms in centenarians and other long-lived individuals
Authors: Li Lingxuan , Murakami Shin
Published: December 2022

Current research on the angiotensin-converting-enzyme (ACE) gene has yielded controversial results on whether different ACE polymorphisms are linked with human longevity. ACE polymorphisms are a risk factor for Alzheimer’s disease and age-onset diseases that may contribute to the mortality of older people. Our goal is to consolidate existing studies with assistance from artificial intelligence and machine-learning-assisted software to come to a more precise understanding of the role of the ACE gene in human longevity. The I (insertion) and D (deletion) polymorphisms in the intron are correlated with the levels of circulating ACE; homozygous D (DD) is high and homozygous I (II) is low. Here, we performed a detailed meta-analysis of the I and D polymorphisms using centenarians (100+ years old), long-lived subjects (85+ years old), and control groups. ACE genotype distribution was analyzed across a total of 2,054 centenarians and 12,074 controls, as well as 1,367 long-lived subjects between the ages of 85-99, using the inverse variance and random effects methods. The ACE DD genotype was found to be favored in centenarians (OR: 1.41 [95% CI: 1.19-1.67], P < 0.0001) with a heterogeneity of 32%, and the II genotype slightly favored the control groups (OR: 0.81 [95% CI: 0.66-0.98], P = 0.03) with a heterogeneity of 28%, corroborating results from previous meta-analyses. Novel to our meta-analysis, the ID genotype was found to be favored in control groups (OR: 0.86 [95% CI: 0.76-0.97], P = 0.01) with a heterogeneity of 0%. The long-lived group showed a similar positive association between the DD genotype and longevity (OR: 1.34 [95% CI: 1.21-1.48, P < 0.0001) and a negative association between the II genotype and longevity (OR: 0.79 [95% CI: 0.70-0.88], P < 0.0001). The long-lived ID genotype did not show significant findings (OR: 0.93 [95% CI: 0.84-1.02], P = 0.79). In conclusion, the results suggest a significant positive association of the DD genotype with human longevity. However, despite the previous study, the results do not confirm a positive association of the ID genotype with human longevity. We suggest a few paradoxical observations: (1) inhibition of ACE can increase longevity in model systems from nematodes to mammals, seemingly opposite to the finding in humans; (2) exceptional longevity associated with homozygous DD is also associated age-related diseases with higher mortality risks in homozygous DD. We discuss ACE, longevity, and age-related diseases.
Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters
Authors: Lalanne Jean-Benoît , Regalado Samuel G. , Domcke Silvia , Calderon Diego , Martin Beth , Li Tony , Suiter Chase C. , Lee Choli , Trapnell Cole , Shendure Jay
Published: December 2022

The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays, resulting in accurate measurement of reporter expression over a >10,000-fold range of activity with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode circularization, thesesingle-cellquantitativeexpressionreporters (scQers) provide high-contrast readouts analogous to classicin situassays, but entirely from sequencing. Screening >200 enhancers in a multicellularin vitromodel of early mammalian development, we identified numerous autonomous and cell-type-specific elements, including constituents of theSox2control region exclusively active in pluripotent cells, endoderm-specific enhancers, including nearFoxa2andGata4, and a compact pleiotropic enhancer at theLamc1locus. scQers can be mobilized in developmental systems to quantitatively characterize native, perturbed, and synthetic enhancers at scale, with high sensitivity and at single-cell resolution.
Evaluation of the safety, immunogenicity and efficacy of a new live-attenuated lumpy skin disease vaccine in India
Authors: Kumar Naveen , Barua Sanjay , Kumar Ram , Khandelwal Nitin , Kumar Amit , Verma Assim , Singh Lokender , Godara Bhagraj , Chander Yogesh , Riyesh Thachamvally , Sharma Deepak Kumar , Pathak Anubha , Kumar Sanjay , Dedar Ramesh Kumar , Mehta Vishal , Gaur Mitesh , Bhardwaj Bhupendra , Vyas Vithilesh , Chaudhary Sarjeet , Yadav Vijaypal , Bhati Adrish , Kaul Rakesh , Bashir Arif , Andrabi Anjum , Yousuf Raja Wasim , Koul Abhimanyu , Kachhawa Subhash , Gurav Amol , Gautam Siddharth , Tiwari Hari Audh , Gupta Madhurendu K. , Kumar Rajender , Misri Jyoti , Kumar Ashok , Mohanty Ashok Kumar , Nandi Sukdeb , Singh Karam Pal , Pal Yash , Dutt Triveni , Tripathi Bhupendra N.
Published: December 2022

Lumpy skin disease (LSD) was reported for the first time in India in 2019 and since then, it has become endemic. Since a homologous (LSD-virus based) vaccine was not available in the country, goatpox virus (GPV)-based heterologous vaccine was authorized for mass immunization against LSD in cattle. This study describes the evaluation of safety, immunogenicity and efficacy of a new live-attenuated LSD vaccine developed using an Indian field strain (LSDV/India/2019/Ranchi). The virus was attenuated by continuous passage (P=50) in Vero cells. The vaccine (50thLSDV passage in Vero cells, named as Lumpi-ProVacInd) did not induce any local or systemic reaction upon its experimental inoculation in calves (n=10). At day 30 post-vaccination (pv), the vaccinated animals were shown to develop antibody- and cell-mediated immune response and exhibited complete protection upon virulent LSDV challenge. We observed a minimum Neethling response (0.018% animals; 5 out of 26940 animals) of the vaccine in field trials among 26940 animals. There was no significant reduction in the milk yield in lactating animals (n=10108), besides there was no abortion or any other reproductive disorder in the pregnant animals (n=2889). Sero-conversion was observed in 85.18% animals in the field by day 30 pv.
Patient-derived tumoroids of advanced high-grade neuroendocrine neoplasms mimic patient chemotherapy responses and guide the design of personalized combination therapies
Authors: April-Monn Simon L. , Detjen Katharina , Kirchner Philipp , Bräutigam Konstantin , Trippel Mafalda A. , Grob Tobias , Statzer Cyril , Maire Renaud S. , Kollàr Attila , Chouchane Aziz , Kunze Catarina A. , Horst David , Sadowski Martin C. , Schrader Jörg , Marinoni Ilaria , Wiedenmann Bertram , Perren Aurel
Published: December 2022

There are no therapeutic predictive biomarkers or representative preclinical models for high-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN), a highly aggressive, fatal, and heterogeneous epithelial malignancy. We established patient-derived (PD) tumoroids from biobanked tissue samples of advanced high-grade GEP-NEN patients and applied this model for targeted rapidex vivopharmacotyping, next-generation sequencing, and perturbational profiling. We used tissue-matched PD tumoroids to profile individual patients, comparedex vivodrug response to patients’ clinical response to chemotherapy, and investigated treatment-induced adaptive stress responses.

PD tumoroids recapitulated biological key features of high-grade GEP-NEN and mimicked clinical response to cisplatin and temozolomideex vivo. When we investigated treatment-induced adaptive stress responses in PD tumoroids in silico, we discovered and functionally validated Lysine demethylase 5A and interferon-beta, which act synergistically in combination with cisplatin. Sinceex vivodrug response in PD tumoroids matched clinical patient responses to standard-of-care chemotherapeutics for GEP-NEN, our rapid and functional precision oncology approach could expand personalized therapeutic options for patients with advanced high-grade GEP-NEN.
eEF2 improves dense connective tissue repair and healing outcome by regulating cellular death, autophagy, apoptosis, proliferation and migration
Authors: Chen Junyu , Wang Jin , Wu Xinjie , Simon Nils , Svensson Camilla I , Yuan Juan , Hart David A , Ahmed Aisha S , Ackermann Paul W
Published: December 2022

Outcomes following human dense connective tissue (DCT) repair are often variable and suboptimal, resulting in compromised function and development of chronic painful degenerative diseases. Moreover, biomarkers and mechanisms that guide good clinical outcomes after DCT injuries are mostly unknown. Here, we characterize the proteomic landscape of DCT repair following human tendon rupture and its association with long-term patient-reported outcome. Moreover, the regulatory mechanisms of relevant biomarkers were assessed partly by gene silencing experiments. A Mass-Spectrometry based proteomic approach quantified a large number (769) of proteins, including 51 differentially expressed proteins among 20 good versus 20 poor outcome patients. A novel biomarker, elongation factor-2 (eEF2) was identified as being strongly prognostic of the 1-year clinical outcome. Further bioinformatic and experimental investigation revealed that eEF2 positively regulated autophagy, cell proliferation and migration, as well as reduced cell death and apoptosis, leading to improved DCT repair and outcomes. Findings of eEF2 as novel prognostic biomarker could pave the way for new targeted treatments to improve healing outcomes after DCT injuries.
Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina)
Authors: Yu Lei , Khachaturyan Marina , Matschiner Michael , Healey Adam , Bauer Diane , Cameron Brenda , Cusson Mathieu , Duffy J. Emmet , Fodrie F. Joel , Gill Diana , Grimwood Jane , Hori Masakazu , Hovel Kevin , Hughes A. Randall , Jahnke Marlene , Jenkins Jerry , Keymanesh Keykhosrow , Kruschel Claudia , Mamidi Sujan , Moksnes Per-Olav , Nakaoka Masahiro , Pennacchio Christa , Reiss Katrin , Rossi Francesca , Ruesink Jennifer L. , Schultz Stewart , Talbot Sandra , Unsworth Richard , Dagan Tal , Schmutz Jeremy , Stachowicz John J. , Van de Peer Yves , Olsen Jeanine L. , Reusch Thorsten B. H.
Published: December 2022

Currents are unique drivers of oceanic phylogeography and so determine the distribution of marine coastal species, along with past glaciations and sea level changes. Here, we reconstruct the worldwide colonization history of eelgrass (Zostera marinaL.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Multiple west to east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival ofZ. marinain the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present since ∼208 Kya (thousand years ago). Mediterranean populations were founded ∼53 Kya while extant distributions along western and eastern Atlantic shores coincide with the end of the Last Glacial Maximum (∼20 Kya). The recent colonization and 5-to 7-fold lower genomic diversity of Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.
De novo design of high-affinity protein binders to bioactive helical peptides
Authors: Vázquez Torres Susana , Leung Philip J. Y. , Lutz Isaac D. , Venkatesh Preetham , Watson Joseph L. , Hink Fabian , Huynh Huu-Hien , Yeh Andy Hsien-Wei , Juergens David , Bennett Nathaniel R. , Hoofnagle Andrew N. , Huang Eric , MacCoss Michael J , Expòsit Marc , Lee Gyu Rie , Levine Paul M. , Li Xinting , Lamb Mila , Korkmaz Elif Nihal , Nivala Jeff , Stewart Lance , Rogers Joseph M. , Baker David
Published: December 2022

Many peptide hormones form an alpha-helix upon binding their receptors1–4, and sensitive detection methods for them could contribute to better clinical management.De novoprotein design can now generate binders with high affinity and specificity to structured proteins5,6. However, the design of interactions between proteins and short helical peptides is an unmet challenge. Here, we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that with the RFdiffusiongenerative model, picomolar affinity binders can be generated to helical peptide targets either by noising and then denoising lower affinity designs generated with other methods, or completelyde novostarting from random noise distributions; to our knowledge these are the highest affinity designed binding proteins against any protein or small molecule target generated directly by computation without any experimental optimization. The RFdiffusiondesigns enable the enrichment of parathyroid hormone or other bioactive peptides in human plasma and subsequent detection by mass spectrometry, and bioluminescence-based protein biosensors. Capture reagents for bioactive helical peptides generated using the methods described here could aid in the improved diagnosis and therapeutic management of human diseases.7,8
Structural basis for BIRC6 to balance apoptosis and autophagy
Authors: Liu Shuo-Shuo , Jiang Tian-Xia , Bu Fan , Zhao Ji-Lan , Wang Guang-Fei , Yang Guo-Heng , Kong Jie-Yan , Qie Yun-Fan , Wen Pei , Fan Li-Bin , Li Ning-Ning , Gao Ning , Qiu Xiao-Bo
Published: December 2022

Caspase-9 is the initiator caspase for the intrinsic apoptotic cell death pathway, and is critical to the activation of effector caspases during apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor of Apoptosis Protein (IAP) BIRC6/BRUCE/Apollon not only inhibits apoptosis, but also promotes ubiquitination of the key autophagic protein LC3 and inhibits autophagy. Here we show that BIRC6 forms an anti-parallel U-shaped dimer in a 3.6-Å cryo-EM structure with multiple previously unannotated domains, including a ubiquitin-like domain, and discover that the mitochondria-derived pro-apoptotic factor Smac/DIABLO binds BIRC6 by interacting with one BIR domain, two carbohydrate-binding modules and two helices in the central cavity. Notably, Smac outcompetes the effector caspase 3 and the pro-apoptotic protease HtrA2, but not caspase 9, for binding BIRC6. BIRC6 strongly inhibits cellular activity of caspase 9, but weakly suppresses that of caspase 3. Meanwhile, BIRC6 binds LC3 through an LC3-interacting region, probably following dimer disruption of this BIRC6 region. Deficiency in LC3 ubiquitination promotes autophagy and autophagic degradation of BIRC6, and inhibits apoptosis. Moreover, induction of autophagy promotes autophagic degradation of both procaspase-9 and active caspase-9, but not of effector caspases. These results are important to understand how the balance between apoptosis and autophagy is regulated under pathophysiological conditions.
Comprehensive Evaluation of Rapamycin’s Specificity as an mTOR Inhibitor
Authors: Artoni Filippo , Grützmacher Nina , Demetriades Constantinos
Published: December 2022

Rapamycin is a macrolide antibiotic that functions as an immunosuppressive and anti-cancer agent, and displays robust anti-ageing effects in multiple organisms including humans. Importantly, rapamycin analogs (rapalogs) are of clinical importance against certain cancer types and neurodevelopmental diseases. Although rapamycin is widely perceived as an allosteric inhibitor of mTOR (mechanistic target of rapamycin), the master regulator of cellular and organismal physiology, its specificity has not been thoroughly evaluated so far. In fact, previous studies in cells and in mice suggested that rapamycin may be also acting independently from mTOR to influence various cellular functions. Here, we generated a gene-edited cell line, that expresses a rapamycin-resistant mTOR mutant (mTORRR), and assessed the effects of rapamycin treatment on the transcriptome and proteome of control or mTORRR-expressing cells. Our data reveal a striking specificity of rapamycin towards mTOR, demonstrated by virtually no changes in mRNA or protein levels in rapamycin-treated mTORRRcells, even following prolonged drug treatment. Overall, this study provides the first comprehensive and conclusive assessment of rapamycin’s specificity, with important potential implications for ageing research and human therapeutics.
Network analysis of chromophore binding site in LOV domain
Authors: Panda Rishab , Panda Pritam Kumar , Krishnamoorthy Janarthanan , Kar Rajiv K.
Published: December 2022

Photoreceptor proteins are versatile toolbox for developing biosensors for optogenetic applications. These molecular tools get activated upon illumination of blue light, which in turn offers a non-invasive method for gaining high spatiotemporal resolution and precise control of cellular signal transduction. The Light-Oxygen-Voltage (LOV) domain family of proteins is a well-recognized system for constructing optogenetic devices. Translation of these proteins into efficient cellular sensors is possible by tuning their photochemistry lifetime. However, the bottleneck is the need for more understanding of the relationship between the protein environment and photocycle kinetics. Significantly, the effect of the local environment also modulates the electronic structure of chromophore, which perturbs the electrostatic and hydrophobic interaction within the binding site. This work highlights the critical factors hidden in the protein networks, linking with their experimental photocycle kinetics. It presents an opportunity to quantitatively examine the alternation in chromophore’s equilibrium geometry and identify details which have substantial implications in designing synthetic LOV constructs with desirable photocycle efficiency.
Strategic control of location and ordinal context in visual working memory
Authors: Fulvio Jacqueline M. , Yu Qing , Postle Bradley R.
Published: December 2022

Working memory (WM) requires encoding stimulus identity and context (e.g., where or when stimuli were encountered). To explore the neural bases of the strategic control of context binding in WM, we acquired fMRI while subjects performed delayed recognition of three orientation patches presented serially and at different locations. The recognition probe was an orientation patch with a superimposed digit, and pretrial instructions directed subjects to respond according to its location (location-relevant), to the ordinal position corresponding to its digit (order-relevant), or to just its orientation (relative to all three samples;context-irrelevant). Delay-period signal in PPC was greater for context-relevant than forcontext-irrelevanttrials, and multivariate decoding revealed strong sensitivity to context binding requirements (relevant vs.irrelevant) and to context domain (location-vs.order-relevant) in both occipital cortex and PPC. At recognition, multivariate inverted encoding modeling revealed markedly different patterns in these two regions, suggesting different context-processing functions. In occipital cortex, an active representation of the location of each of the three samples was reinstated, regardless of trial type. The pattern in PPC, in contrast, suggested a trial type-dependent filtering of sample information. These results indicate that PPC exerts strategic control over the representation of stimulus context in visual WM.
Regulation of Nuclear Transcription by Mitochondrial RNA
Authors: Sriram Kiran , Qi Zhijie , Yuan Dongqiang , Malhi Naseeb K. , Liu Xuejing , Calandrelli Riccardo , Luo Yingjun , Jin Shengyan , Shi Ji , Salas Martha , Dang Runrui , Armstrong Brian , Priceman Saul J. , Wang Ping , Liao Jiayu , Natarajan Rama , Zhong Sheng , Chen Zhen B.
Published: December 2022

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, which we termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.
Cleavage of the Jaw1 C-terminal region enhances its augmentative effect on the Ca2+release via inositol 1,4,5-trisphosphate receptors
Authors: Kozono Takuma , Jogano Chifuyu , Okumura Wataru , Sato Hiroyuki , Matsui Hitomi , Takagi Tsubasa , Okumura Nobuaki , Takao Toshifumi , Tonozuka Takashi , Nishikawa Atsushi
Published: December 2022

Jaw1, a tail-anchored protein with 39 carboxyl (C)-terminal amino acids, is oriented to the lumen of the endoplasmic reticulum and outer nuclear membrane. We previously reported that Jaw1, as a member of the KASH protein family, plays a role in maintaining nuclear shape via its C-terminal region. Furthermore, we recently reported that Jaw1 functions as an augmentative effector of Ca2+release from the endoplasmic reticulum by interacting with the inositol 1,4,5-trisphosphate receptors (IP3Rs). Intriguingly, the C-terminal region is partially cleaved, meaning that Jaw1 exists in the cell in at least two forms: uncleaved and cleaved. However, the mechanism of the cleavage event and its physiological significance remain to be determined. In this study, we demonstrate that the C-terminal region of Jaw1 is cleaved after its insertion by the signal peptidase complex (SPC). Particularly, our results indicate that the SPC with the catalytic subunit SEC11A, but not SEC11C, specifically cleaves Jaw1. Furthermore, using a mutant with a deficit in the cleavage event, we demonstrate that the cleavage event enhances the augmentative effect of Jaw1 on the Ca2+release ability of IP3Rs.

Summary statement

The C-terminal region of Jaw1, a tail-anchored protein, is cleaved by signal peptidase complex and this cleavage event enhances the augmentative effect of Jaw1 on the Ca2+release activity of inositol 1,4,5-trisphosphate receptors
Epidemiological transition in Australia: An analysis of immigration patterns in relation to circulatory system diseases and all-cause mortality in the mid-twentieth century
Authors: Kelleher Cecily C , Kelly Gabrielle E , Segurado Ricardo , Briody Jonathan , Sellers Alexander M , McCalman Janet S
Published: December 2022

Background and Objectives

Circulatory System Diseases (CSD) patterns vary over time and between countries, related to lifestyle risk factors, associated in turn with socio-economic circumstances. Current global CSD epidemics in developing economies are similar in scale to those observed previously in the USA and Australasia. Australia exhibits an important macroeconomic phenomenon as a rapidly transitioning economy with high immigration throughout the 19thand 20thcenturies. We wished to examine how that historical immigration related to CSD patterns subsequently.

Methods and Setting

We provide a novel empirical analysis employing census-derived place of birth by age bracket and sex from 1891 to 1986, in order to map patterns of immigration against CSD mortality rates from 1907 onwards. Age-specific generalised additive models for both CSD mortality in the general population, and all-cause mortality for the foreign-born (FB) only, from 1910 to 1980 were also devised for both males and females.

Results

The % FB fell from 32% in 1891 to 9.8% in 1947. Rates of CSD rose consistently, particularly from the 1940s onwards, peaked in the 1960s, then declined sharply in the 1980s and showed a strong period effect across age groups and genders. The main effects of age and census year and their interaction were highly statistically significant for CSD mortality for males (p < 0.001, each term) and for females (p < 0.001, each term). The main effect of age was statistically significant for all-cause mortality minus net migration rates for the FB males (p =0.005) and for FB females, both age (p < 0.001) and the interaction term (p=0.002) were significant.

Conclusions

We argue our empirical calculations, supported by historical and socio-epidemiological evidence, employing immigration patterns as a proxy for epidemiological transition, affirm the lifecourse hypothesis that both early life circumstances and later life lifestyle drive CSD patterns.

Article Summary

Strengths

An original analysis employing census data and immigration patterns to reinterpret historical trends in CSD in Australia

Relevant to modern public health policy for population approaches to CSD prevention, also integrates lifecourse and lifestyle drivers of trends

Limitations

Historical databases do not categorise either all cause or CSD mortality according to country of origin.

However, data for foreign-born mortality were inferred using novel actuarial type calculations

There are no second-generation data by country of origin, unlike in USA.
Type of refugee accommodation and health of residents: cross-sectional cluster analysis
Authors: Mohsenpour Amir , Dudek Verena , Bozorgmehr Kayvan , Biddle Louise , Razum Oliver , Sauzet Odile
Published: December 2022

Few studies have assessed whether refugees’ health is associated with accommodation characteristics. We aimed to devise a typology of refugee accommodation based on number of inhabitants, degree of housing deterioration and remoteness (distance to amenities) and assess the association with health in multivariate analyses. Accommodations with a moderate occupation, lowest levels of deterioration, and a central urban location showed the best health outcomes in terms of subjective general health status, depression, and general anxiety disorder (GAD). Associations were strongest for GAD and weakest for depression. Our findings inform policymakers on layout and location of refugee collective accommodation centres.
Regions with intermediate DNA methylation are epigenomic hotspots governing behavioral adaptation to changing environments
Authors: Brindley Elizabeth , Taki Faten , Odell Shannon C. , Baker Madelyn R , Toth Judit Gal , Toth Miklos
Published: December 2022

Epigenetic and associated gene expression changes in the brain drive animals’ ability to adapt to changing environments. However, epigenetic attributes of environmental adaptation are unknown. Here we show that exercise, unpredictable stress, and environmental enrichment, conditions that elicit adaptive changes in synaptic plasticity and spatial learning, result in CpG methylation changes in regions that exist in both methylated and unmethylated states (i.e., epigenetically bistable) in hippocampal granule cells. Sustained exposures altered both the epiallelic proportions at these regions and neuronal and behavioral adaptation, indicating their adaptive nature. These malleable regions were enriched in exons and enhancer-associated chromatin marks. Their locations were mostly unique to specific environments but converged on similar synaptic genes. Lastly, manipulating DNA methylation altered epiallelic proportions at bistable regions in granule cells and phenocopied adaptive behavior. We propose that shifts in epiallelic proportions at evolutionarily conserved bistable regions, via gene expression changes, contribute to hippocampal plasticity and behavioral adaptation to changing environments.