bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanoscale dynamics of streptococcal adhesion to AGE-modified collagen
Authors: Leiva-Sabadini Camila , Tiozzo-Lyon Paola , Hidalgo-Galleguillos Luis , Rivas Lina , Robles Agustín I , Fierro Angélica , Barrera Nelson P , Bozec Laurent , Schuh Christina MAP , Aguayo Sebastian
Published: October 2022

The adhesion of initial colonizers such asStreptococcus mutansto collagen is critical for dentinal and root caries progression. One of the most described pathological and aging-associated changes in collagen – including dentinal collagen – is the generation of advanced glycation end-products (AGEs) such as methylglyoxal (MGO)-derived AGEs. Despite previous reports suggesting that AGEs alter bacterial adhesion to collagen, the biophysics driving oral streptococcal attachment to MGO-modified collagen remains largely understudied. Thus, the aim of this work was to unravel the dynamics of the initial adhesion ofS. mutansto type-I collagen in the presence and absence of MGO-derived AGEs, by employing bacterial cell force-spectroscopy with atomic force microscopy (AFM). Type-I collagen gels were treated with 10mM MGO to induce AGE formation, which was characterized with microscopy and ELISA. Subsequently, AFM cantilevers were functionalized with livingS. mutansUA 159 orS. sanguinisSK 36 cells and probed against collagen surfaces to obtain force-curves displaying bacterial attachment in real-time, from which the adhesion force, number of events, Poisson analysis, and contour and rupture lengths for each individual detachment event were computed. Furthermore, in-silico docking studies between the relevantS. mutansUA 159 collagen-binding protein SpaP and collagen were computed, in the presence and absence of MGO. Overall, results showed that MGO modification increased both the number and adhesion force of single-unbinding events betweenS. mutansand collagen, without altering the contour or rupture lengths. Both experimental and in-silico simulations suggest that this effect is due to increased specific and non-specific forces and interactions betweenS. mutansUA 159 and MGO-modified collagen substrates. In summary, these results suggest that collagen alterations due to glycation and AGE formation may play a role in early bacterial adherence to oral tissues, associated with conditions such as aging or chronic hyperglycemia, amongst others.
Junctophilin-2 promotes cardiomyocyte survival by blocking MURF1-mediated Junctin ubiquitination and proteasome-dependentdegradation
Authors: Ji Xiaoyun , Huang Yifan , Ni Rui , Zheng Dong , Fan Guo-Chang , Jones Douglas L , Song Long-Sheng , Chakrabarti Subrata , Su Zhaoliang , Peng Tianqing
Published: October 2022

Aims

Junctophilin-2 is required for the development, maturation and integrity of the t-tubule system and the gating stability of RyR2 in cardiomyocytes. This study investigated whether and how junctophilin-2 maintained junctin, a scaffold protein stabilizing RyR2, to prevent cardiomyocyte death under stress.

Methods

Cardiomyocytes were exposed to conditions of stress including palmitate, doxorubicin, or hypoxia/re-oxygenation. Adenoviral vectors were employed to manipulate expression of junctophilin-2 and junctin in cardiomyocytes. Molecular/cellular/biochemical analyses were conducted.

Results

Different conditions of stress decreased junctophilin-2 expression through aberrant autophagy and concomitantly induced a reduction of junctin protein in cardiomyocytes. Over-expression of junctophilin-2 preserved the protein levels of junctin and attenuated cytosolic Ca2+and apoptosis in cardiomyocytes under stress. Knockdown of junctophilin-2 reproduced the detrimental phenotypes of stress in cardiomyocytes. Notably, over-expression of junctin prevented cardiomyocyte death under stress whereas knockdown of junctin offset the protective effects conferred by junctophilin-2 over-expression. Mechanistically, junctophilin-2 blocked MURF1-junctin interaction thereby preventing junctin ubiquitination and proteasome-dependent degradation. Mass spectrometry analysis identified multiple ubiquitination sites on the junctin protein and the non-ubiquitinated junctin mutant (K8A/K102A/K107A/K140A) was resistant to degradation.

Conclusions

This study uncovers an unrecognized role of junctophilin-2 in preventing junctin ubiquitination and degradation in maintaining cytosolic Ca2+homeostasis. Both junctophilin-2 and junctin represent two new survival factors of cardiomyocytes and thus, may be new therapeutic targets for cardiac protection.
Hypothalamic melanin-concentrating hormone neurons integrate food-motivated appetitive and consummatory processes
Authors: Subramanian Keshav S. , Lauer Logan Tierno , Hayes Anna M. R. , Décarie-Spain Léa , McBurnett Kara , Donohue Kristen N. , Kao Alicia E. , Bashaw Alexander G. , Burdakov Denis , Noble Emily E. , Schier Lindsey A. , Kanoski Scott E.
Published: October 2022

The lateral hypothalamic area (LHA) integrates homeostatic processes and reward-motivated behaviors. Here we show that LHA neurons that produce melanin-concentrating hormone (MCH) are dynamically responsive to both food-directed appetitive and consummatory processes. Specifically, our results reveal that MCH neuron Ca+2activity increases in response to both discrete and contextual food-predictive cues and is correlated with food-motivated responses. MCH neuron activity also increases during eating and this response is highly predictive of caloric consumption and declines throughout a meal, thus supporting a role for MCH neurons in the positive feedback consummatory process known as appetition. These physiological MCH neural responses are functionally-relevant as chemogenetic MCH neuron activation promotes appetitive behavioral responses to food-predictive cues and increases meal size. Finally, MCH neuron activation enhances preference for a noncaloric flavor paired with intragastric glucose. Collectively, these data identify a hypothalamic neural population that orchestrates both food-motivated appetitive and intake-promoting consummatory processes.
The C-terminal domain of RNase H and the C-terminus amino acid residue regulate virus release and autoprocessing of a defective HIV-1 possessing M50I and V151I changes in integrase
Authors: Imamichi Tomozumi , Chen Qian , Hao Ming , Chang Weizhong , Yang Jun
Published: October 2022

Previously, we reported that an HIV-1 variant containing Met-to-Ile change at codon 50 and Val-to-Ile mutation at codon 151 of integrase (IN), HIV(IN:M50I/V151I), was an impaired virus. Despite the mutations being in IN, the virus release was significantly suppressed (p < 0.0001) and the initiation of autoprocessing was inhibited; the mechanism of the defect remains unknown. In the current study, we attempted to identify the critical domains or amino acid (aa) residue(s) that promote defects in HIV(IN:M50I/V151I), using a series of variants, including truncated or aa-substituted RNase H (RH) or IN. The results demonstrated that virus release and the initiation of autoprocessing were regulated by the C-terminal domains (CTDs) of RH and IN. Further studies illustrated that Asp at codon 109 of RH CTD and Asp at the C terminus of IN induces the defect. This result indicated that the CTD of RH and IN in GagPol and particular aa positions in RH and IN regulated the virus release and the initiation of autoprocessing, and these sites could be potential targets for the developing new therapies.
The regulatory landscape of the yeast phosphoproteome
Authors: Leutert Mario , Barente Anthony S. , Fukuda Noelle K. , Rodriguez-Mias Ricard A. , Villén Judit
Published: October 2022

The cellular ability to react to environmental fluctuations depends on signaling networks that are controlled by the dynamic activities of kinases and phosphatases. To gain insight into these stress-responsive phosphorylation networks, we generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses inSaccharomyces cerevisiaeexposed to 101 environmental and chemical perturbations. We report phosphosites on 59% of the yeast proteome, with 18% of the proteome harboring a phosphosite that is regulated within 5 minutes of stress exposure. We identify shared and perturbation-specific stress response programs, uncover dephosphorylation as an integral early event, and dissect the interconnected regulatory landscape of kinase-substrate networks, as we exemplify with TOR signaling. We further reveal functional organization principles of the stress-responsive phosphoproteome based on phosphorylation site motifs, kinase activities, subcellular localizations, shared functions, and pathway intersections. This information-rich map of 25,000 regulated phosphosites advances our understanding of signaling networks.

Highlights

Ultra-deep reference yeast phosphoproteome covers 36,000 phosphorylation sites and reveals general principles of eukaryotic protein phosphorylation.

High-dimensional quantitative atlas of early phosphoproteomic responses of yeast across 101 environmental and chemical perturbations identifies 25,000 regulated perturbation-phosphosite pairs.

Identification of shared and perturbation-specific stress response phosphorylation programs reveals the importance of dephosphorylation as an early stress response.

Dissection of the TOR signaling network uncovers subnetworks with differential stress responsiveness and points of pathway cross-talk

Identification of functional organization of the phosphoproteome by dimensionality reduction and co-regulation analysis.
Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis)
Authors: Wang Yongsheng , Wang Huihui , Wang Huiyuan , Zhou Ruifan , Wu Ji , Zhang Zekun , Jin Yandong , Li Tao , Kohnen Markus V. , Liu Xuqing , Wei Wentao , Chen Kai , Gao Yubang , Ding Jiazhi , Zhang Hangxiao , Liu Bo , Lin Chentao , Gu Lianfeng
Published: October 2022

Circular RNAs are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GA) and auxins (NAA) remain unknown. Here, we systematically identified and characterized expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We determined details regarding the function of circRNAs, including their roles in regulating microRNA-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect microRNA-mediated cleavage of circRNAs. Finally, we present a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with gibberellins (GA) and auxins (NAA). Collectively, our study uncovers important features of circRNAs including overall characteristics, biogenesis, function, and microRNA-mediated degradation of circRNAs in moso bamboo.
Century-long timelines of herbarium genomes predict plant stomatal response to climate change
Authors: Lang Patricia L.M. , Erberich Joel M. , Lopez Lua , Weiß Clemens L. , Amador Gabriel , Fung Hannah F. , Latorre Sergio M. , Lasky Jesse R. , Burbano Hernán A. , Expósito-Alonso Moisés , Bergmann Dominique
Published: October 2022

Dissecting plant responses to the environment is key to understanding if and how plants adapt to anthropogenic climate change. Stomata, plants’ pores for gas exchange, are expected to decrease in density following increased CO2concentrations, a trend already observed in multiple plant species. However, it is unclear if such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191A. thalianahistorical herbarium specimens collected over the last 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a polygenic score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the last centuries without requiring direct phenotype observation of historical samples. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes have already responded to climate change through adaptive evolution.

One sentence summary

Using a molecular-knowledge based genetic phenotype proxy, historical whole-genomeA. thalianatimelines compared with contemporary data indicate a shift of stomatal density following climate-associated predictions.
PhenoScore: AI-based phenomics to quantify rare disease and genetic variation
Authors: Dingemans Alexander J M , Hinne Max , Truijen Kim M G , Goltstein Lia , van Reeuwijk Jeroen , de Leeuw Nicole , Schuurs-Hoeijmakers Janneke , Pfundt Rolph , Diets Illja J , den Hoed Joery , de Boer Elke , Coenen-van der Spek Jet , Jansen Sandra , van Bon Bregje W , Jonis Noraly , Ockeloen Charlotte , Vulto-van Silfhout Anneke T , Kleefstra Tjitske , Koolen David A , Van Esch Hilde , Lyon Gholson J , Alkuraya Fowzan S , Rauch Anita , Marom Ronit , Baralle Diana , van der Sluijs Pleuntje J , Santen Gijs W E , Kooy R Frank , van Gerven Marcel A J , Vissers Lisenka E L M , de Vries Bert B A
Published: October 2022

While both molecular and phenotypic data are essential when interpreting genetic variants, prediction scores (CADD, PolyPhen, and SIFT) have focused on molecular details to evaluate pathogenicity — omitting phenotypic features. To unlock the full potential of phenotypic data, we developed PhenoScore: an open source, artificial intelligence-based phenomics framework. PhenoScore combines facial recognition technology with Human Phenotype Ontology (HPO) data analysis to quantify phenotypic similarity at both the level of individual patients as well as of cohorts. We prove PhenoScore’s ability to recognize distinct phenotypic entities by establishing recognizable phenotypes for 25 out of 26 investigated genetic syndromes against clinical features observed in individuals with other neurodevelopmental disorders. Moreover, PhenoScore was able to provide objective clinical evidence for two distinctADNP-related phenotypes, that had already been established functionally, but not yet phenotypically. Hence, PhenoScore will not only be of use to unbiasedly quantify phenotypes to assist genomic variant interpretation at the individual level, such as for reclassifying variants of unknown clinical significance, but is also of importance for detailed genotype-phenotype studies.
Vague retellings of personal narratives in temporal lobe epilepsy
Authors: D’Aprano Fiore , Malpas Charles B. , Roberts Stefanie E. , Saling Michael M.
Published: October 2022

Aside from deficits identified in lexical retrieval, individuals with temporal lobe epilepsy (TLE) exhibit clinical oddities, such as circumstantiality in their language production. This becomes particularly evident when elicitation tasks impose minimal structure, or when impersonal narratives are retold over consecutive occasions. Personal reminiscence is highly specific and localised in time, placing specific demands on cognitive-linguistic systems. It is presumed that the nature of this elicitation paradigm will produce a unique psycholinguistic phenotype in those with TLE. Among controls there is a compression of output for impersonal narratives, but the opposite effect when personal narratives are retold. To investigate the micro- and macrolinguistic processes underpinning personal discourse production in TLE, we examined the elicited language output of in 15 surgically naïve individuals with TLE and 14 healthy controls. Participants were asked to recall and re-tell an autobiographical memory on four immediately consecutive occasions, representing an alternative unstructured elicitation. Following transcription and coding of output, a detailed multi-level discourse analysis of output volume, fluency, cohesion, and coherence was conducted. There were significant group by trial interactions for the number of novel units, the number of non-progression units, and for the proportion of non-progression to novel content. As anticipated, a distinctly different pattern emerged in TLE when compared with controls who did not compress their output volume across repetitions but instead produced greater novelty, and a more coherent and refined account over time. Individuals with TLE consistently told a less distinct story across repetitions, with disturbances in fluency, cohesion, and coherence. This reflects a reduced capacity to produce a coherent mental representation, in all likelihood related to the neurolinguistic demands of recalling and retelling specific personal events.
Microbial diversity and community dynamics in an active, high CO2subsurface rift ecosystem
Authors: Lipus Daniel , Jia Zeyu , Sondermann Megan , Bussert Robert , Bartholomäus Alexander , Yang Sizhong , Wagner Dirk , Kallmeyer Jens
Published: October 2022

The Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO2concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H2during earthquakes may provide substrates for methanogenic and chemolithotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 240 m deep drill core, running across six lithostratigraphic zones. In addition, we evaluated diversity as well as metabolic attributes of bacterial and archaeal communities. Our investigation revealed a distinct low biomass community, with a surprisingly diverse Archaea population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis revealed sulfate and sodium concentrations as high as 1000 mg L−1in sediment samples from a depth between 50 and 100 m and in weathered rock samples collected below 200 m.

Most microbial signatures could be assigned to common soil and water bacteria, which together with the occurrence of freshwater Cyanobacteria at specific depths, emphasize the heterogenous, groundwater movement driven nature of this terrestrial subsurface environment. Although not as frequently and abundantly as initially expected, our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur cycling taxa likeThiohalophilusandDesulfosporosinuswere specifically enriched at depths below 100 m. The detection of methanogenic, halophilic, and ammonia oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO2and when available H2, as a primary energy source.
Physico-chemical characterization of single bacteria and spores using optical tweezers
Authors: Nilsson Daniel P.G. , Jonsmoen Unni Lise , Malyshev Dmitry , Öberg Rasmus , Wiklund Krister , Andersson Magnus
Published: October 2022

Spore-forming pathogenic bacteria are adapted for adhering to surfaces, and their endospores can tolerate strong chemicals making decontamination difficult. Understanding the physico-chemical properties of bacteria and spores is therefore essential in developing antiadhesive surfaces and disinfection techniques. However, measuring physico-chemical properties in bulk does not show the heterogeneity between cells. Characterizing bacteria on a single-cell level can provide mechanistic clues usually hidden in bulk measurements. This paper shows how optical tweezers can be applied to characterize single bacteria and spores, and how physico-chemical properties related to adhesion, fluid dynamics, biochemistry, and metabolic activity can be assessed.
A quorum of mechano-sensing fungal consortia
Authors: García-Navarrete M. , Sanchis D. Ruiz , Sánchez-Muñoz I. , González-Ruiz S. , Avdovic M. , Atienza-Sanz S. , Wabnik K.
Published: October 2022

Bacteria use Quorum sensing (QS) to coordinate gene expression in dense cell populations. Here, we show that eukaryoteS. Cerevisiaeuses an alternative strategy, the quorum mechano-sensing (QMS), to resolve growth conflicts in the fungal consortia. QMS connects the biomechanical signal perception through adhesin FLO11 and transmembrane histidine kinase SLN1, triggering an intracellular signaling cascade for the cell density-dependent regulation of gene expression. Both cis and trans interactions of FLO11 are required for the inhibition of SLN1 and involve the extracellular fibronectin type III-like domain of FLO11. Genetic deletion of FLO11 removes inhibition of SLN1, associated with the spontaneous activation of gene expression whereas overproduction of FLO11 strengthens the inhibitory effect of FLO11 on SLN1. Therefore, adjusting the amount of FLO11 directly scales with the level of SLN1 inhibition, forecasting the outcome of growth competition at the macroscopic scale. Furthermore, the integration of an orthogonal synthetic circuit downstream of SLN1 allows for QMS-controlled regulation of gene expression in cell populations. Our study reveals a molecular pathway connecting FLO11 adhesion to SLN1-dependent intracellular regulation of gene expression in fungi. FLO11 and SLN1 coordinate kin recognition and growth conflict resolution through gene expression in dense fungal populations. This study challenges the classical view of chemically-driven QS and provides new strategies for controlling population growth through quorum mechano-sensing.
Transposons repressed by H3K27me3 were co-opted as cis-regulatory elements of H3K27me3 controlled protein coding genes during evolution of plants
Authors: Hisanaga Tetsuya , Romani Facundo , Wu Shuangyang , Kowar Teresa , Lintermann Ruth , Jamge Bhagyshree , Montgomery Sean A. , Axelsson Elin , Dierschke Tom , Bowman John L. , Fujiwara Takayuki , Hirooka Shunsuke , Miyagishima Shin-ya , Dolan Liam , Schubert Daniel , Berger Frédéric
Published: October 2022

The mobility of transposable elements (TEs) contributes to evolution of genomes1,2. Meanwhile, their uncontrolled activity causes genomic instability and therefore expression of TEs is silenced by host genomes3,4. TEs are marked with DNA and H3K9 methylation that are associated with silencing in flowering plants5, animals, and fungi6. Yet, in distantly related eukaryotes TEs are instead marked by H3K27me3 deposited by the Polycomb Repressive Complex 2 (PRC2)7–11, an epigenetic mark associated with gene silencing in multicellular eukaryotes12–15. It was therefore proposed that the ancestral activity of PRC2 was the deposition of H3K27me3 to silence TEs16.

To test this hypothesis we obtained mutants deprived of PRC2 activity and used genomics to analyze the role of PRC2 in extant species along the lineage of Archaeplastida. While in the red algaCyanidioschyzon merolaemore TEs than genes were repressed by PRC2, an opposite trend was observed in bryophytesMarchantia polymorphaandAnthoceros agrestis. In the red alga, TEs silenced by H3K27me3 are in subtelomeres but in bryophytes, TEs and genes marked by H3K27me3 form coregulated transcriptional units. The latter trend was also observed in the flowering plantArabidopsis thaliana, and we identified cis-elements recognised by transcription factors in TEs flanking genes repressed by PRC2.

Together with the silencing of TEs by PRC2 in ciliates that diverged early from an ancestor common with Archaeplastida, our findings support the hypothesis that PRC2 deposited H3K27me3 to silence TEs in early lineages of eukaryotes. During evolution, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation that control networks of genes regulated by PRC2.

Highlights

H3K27me3 marks a decreasing proportion of TEs during evolution of plants

The polycomb repressive complex 2 represses TEs in red algae and bryophytes

H3K27me3-marked TEs in flowering plants contain transcription factor binding sites

Transcription factors bind TEs and regulate networks of genes controlled by PRC2
Exposing New Taxonomic Variation with Inflammation – A Murine Model-Specific Genome Database for Gut Microbiome Researchers
Authors: Leleiwi Ikaia , Rodriguez-Ramos Josue , Shaffer Michael , Sabag-Daigle Anice , Kokkinias Katherine , Flynn Rory M , Daly Rebecca A , Kop Linnea FM , Solden Lindsey M , Ahmer Brian M. M. , Borton Mikayla A , Wrighton Kelly C
Published: October 2022

Background

The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminatedSalmonellainteractions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.

Results

Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated andSalmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~42.4 Gbps/sample), we reconstructed 2,281 bacterial and 4,129 viral draft genomes.Salmonellachallenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of theAlistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation resistant strains.

Conclusions

This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on howSalmonellaremodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches.Salmonella-induced inflammation suppressedAlistipesand other dominant members, while rarer commensals likeLactobacillusandEnterococcusendure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.
3D point cloud of normalized difference vegetation index (NDVI) of segmented fruit and leaves in apple production
Authors: Tsoulias Nikos , Saha Kowshik Kumar , Zude-Sasse Manuela
Published: October 2022

A feasible method to analyse fruit at the plant considering its position, size, and maturity are requested in precise production management. The present study proposes the employment of light detection and ranging (LiDAR) to measure the position, quality-related size, and maturity-related chlorophyll of fruit.

During fuit development, apples were analysed in the laboratory (n = 270) with two LiDAR laser scanners measuring at 660 and 905 nm. From the two 3D point clouds, the normalized difference vegetation index (NDVI) was calculated. The correlation analysis with chemically analysed fruit chlorophyll content showed R2= 0.81 and 0.02 % RMSE.

The method was validated on 3D point clouds of 12 fruit trees in the orchard. Segmentation of individual apples was carried out during fruit development on five measuring dates, validated with manual rating (n = 4632). The non-invasively obtained field data showed good calibration performance capturing fruit position, fruit size, fruit NDVI of R2= 0.99, R2= 0.97, R2= 0.71, respectively, considering the related reference data.

For 3D data of leaves, earlier shown analysis of leaf area and leaf chlorophyll by means of LiDAR was confirmed. The new approach of non-invasive laser scanning provided physiologically and agronomically valuable time series data on differences in fruit chlorophyll affected by the leaf area to fruit ratio, as well as differences of fruit chlorophyll in different growing position at the tree. Resulting, the method provides a tool for production management, e.g. crop load management, and integration in harvest robots.
Survivin Regulates Intracellular Stiffness and Extracellular Matrix Production in Vascular Smooth Muscle Cells
Authors: Krajnik Amanda , Nimmer Erik , Sullivan Andra , Brazzo Joseph A. , Heo Yuna , Krug Alanna , Kolega John , Heo Su-Jin , Lee Kwonmoo , Weil Brian R. , Kim Deok-Ho , Bae Yongho
Published: October 2022

Vascular dysfunction is a common cause of cardiovascular diseases characterized by the narrowing and stiffening of arteries, such as atherosclerosis, restenosis, and hypertension. Arterial narrowing results from the aberrant proliferation of vascular smooth muscle cells (VSMCs) and their increased synthesis and deposition of extracellular matrix (ECM) proteins. These, in turn, are modulated by arterial stiffness, but the mechanism for this is not fully understood. We found that survivin (an inhibitor of apoptosis) is an important regulator of stiffness-mediated ECM synthesis and intracellular stiffness in VSMCs. Whole-transcriptome analysis and cell culture experiments showed that survivin expression is upregulated in injured femoral arteries in mice and in human VSMCs cultured on stiff fibronectin-coated hydrogels. Suppressed expression of survivin in human VSMCs and mouse embryonic fibroblasts decreased the stiffness-mediated expression of ECM components implicated in arterial stiffness, namely, collagen-I, fibronectin, and lysyl oxidase. By contrast, expression of these proteins was upregulated by the overexpression of survivin in human VSMCs cultured on soft hydrogels. Atomic force microscopy analysis showed that suppressed or enhanced expression of survivin decreases or increases intracellular stiffness, respectively. These findings suggest a novel mechanism by which survivin modulates arterial stiffness.
A High Fraction of Oral Bacteria in the Feces Indicates Gut Microbiota Depletion with Implications for Human Health
Authors: Liao Chen , Rolling Thierry , Djukovic Ana , Fei Teng , Mishra Vishwas , Liu Hongbin , Lindberg Chloe , Dai Lei , Zhai Bing , Peled Jonathan U. , van den Brink Marcel R.M. , Hohl Tobias M. , Xavier Joao B.
Published: October 2022

The increased relative abundance of oral bacteria detected in fecal samples has been associated with intestinal diseases and digestive disorders. This observation raises two competing hypotheses: either oral bacteria invade the gut bacterial population and expand in the intestine (theExpansionhypothesis), or oral bacteria transit through and their relative increase in feces marks a depletion of the gut bacterial population (theMarkerhypothesis). To address this, we conducted a comprehensive analysis of quantitative microbiome data from mouse experiments and diverse patient cohorts. Our findings consistently support theMarkerhypothesis as the primary explanation. We further establish a robust inverse correlation between the total fraction of oral bacteria and decreased total bacterial abundance in feces. This correlation underlies the associations between the oral bacterial fraction and multiple patient outcomes consistent with a depleted gut microbiota. By distinguishing between the two hypotheses, our study guides the interpretation of microbiome compositional data and their links with human health.
Representations of fricatives in sub-cortical model responses: comparisons with human consonant perception
Authors: Hamza Yasmeen , Farhadi Afagh , Schwarz Douglas M. , McDonough Joyce M. , Carney Laurel H.
Published: October 2022

Fricatives are obstruent sound contrasts made by airflow constrictions in the vocal tract that produce turbulence across the constriction or at a site downstream from the constriction. Fricatives exhibit significant intra/inter-subject and contextual variability. Yet fricatives are perceived with high accuracy. The current study investigated modeled neural responses to fricatives in the auditory nerve (AN) and inferior colliculus (IC), with the hypothesis that response profiles across populations of neurons provide robust correlates to consonant perception. Stimuli were 270 intervocalic fricatives (10 speakers x 9 fricatives x 3 utterances). Computational model response profiles had characteristic frequencies that were log-spaced from 125 Hz to 8 or 20 kHz, to explore the impact of high-frequency responses. Confusion matrices generated by k-nearest-neighbor subspace classifiers were based on the profiles of average rates across characteristic frequencies as feature vectors. Model confusion matrices were compared them with published behavioral data. The modeled AN and IC neural responses provided better predictions of behavioral accuracy than the stimulus spectra, with IC showing better accuracy than AN. Behavioral fricative accuracy was explained by modeled neural response profiles, whereas confusions were only partially explained. Extended frequencies improved accuracy based on the model IC, corroborating the importance of extended high frequencies in speech perception.
A Digital Biomarker for Identifying Changes in Daily Activity Patterns
Authors: Fletcher-Lloyd Nan , Serban Alina-Irina , Kolanko Magdalena , Wingfield David , Wilson Danielle , Nilforooshan Ramin , Barnaghi Payam , Soreq Eyal
Published: October 2022

Malnutrition and dehydration are strongly associated with increased cognitive and functional decline in people living with dementia (PLWD), as well as an increased rate of hospitalisations in comparison to their healthy counterparts. Extreme changes in eating and drinking behaviours can often lead to malnutrition and dehydration, accelerating the progression of cognitive and functional decline and resulting in a marked reduction in quality of life. Unfortunately, there are currently no established methods by which to objectively detect such changes. Here, we present the findings of a quantitative analysis conducted on in-home monitoring data collected from 73 households of PLWD using Internet of Things technologies. The Coronavirus 2019 (COVID-19) pandemic has previously been shown to have dramatically altered the behavioural habits, particularly the eating and drinking habits, of PLWD. Using the COVID-19 pandemic as a natural experiment, we show that there were significant changes in kitchen activities at the group level within a subset of 21 households of PLWD that were continuously monitored for 499 days, with an overall increase in day-time activities and a decrease in night-time activity observed in both single and multiple occupancy households. We further present preliminary results suggesting it is possible to proactively detect episodic and gradual changes in behaviours using remote monitoring data as a proxy for behaviours that cannot be directly measured. Together, these results pave the way to introduce improvements into the monitoring of PLWD in naturalistic settings and for shifting from reactive to proactive care.
Prospective cohort study ofCryptosporidiuminfection and shedding in infants and their households
Authors: Korpe Poonum , Ni Zhanmo , Kabir Mamun , Alam Masud , Ferdous Tahsin , Ara Rifat , Munday Rebecca M. , Haque Rashidul , Duggal Priya
Published: October 2022

Background

Cryptosporidium sppare responsible for significant diarrheal morbidity and mortality in under-five children. There is no vaccine, thus a focus on prevention is paramount. Prior studies suggest that person-to-person spread may be an important pathway for transmission to young children. Here we describe a longitudinal cohort study of 100 families with infants to determine rates of cryptosporidiosis within households during the COVID-19 pandemic.

Methods

Families living in Mirpur, Bangladesh with one infant age 6-8 months were enrolled and followed with weekly illness survey and stool testing for Cryptosporidium for 8 months.

Results

From December 2020 to August 2021, 100 families were enrolled. Forty-four percent of index children, and 35% of siblings had at least oneCryptosporidiuminfection. Shedding ofCryptosporidiumoccurred for a mean of 19 days (sd 8.3 days) in index infants, 16.1 days (sd 11.6) in children 1-5 years, and 16.2 days (sd 12.8) in adults. A longer duration ofCryptosporidiumshedding was associated with growth faltering in infants. There was a spike inCryptosporidiumcases in May 2021, which coincided with a spike in SARS-CoV-2 cases in the region.

Conclusion

In this intensive, longitudinal study ofCryptosporidiuminfection in families we found high rates of cryptosporidiosis in infants and children, and prolonged parasite shedding, especially among malnourished children. These data support that transmission within the household is an important route of exposure for young infants, and that treatment of non-diarrheal infection to interrupt person-to-person transmission within the home may be essential for preventing cryptosporidiosis in infants.

summary

Cryptosporidiosis is a leading cause of morbidity and mortality among children. We followed 100 families with infants living in Bangladesh and studied the incidence ofCryptosporidiuminfection. We found prolongedCryptosporidiumshedding in stool was common among infants and adults.
Two opposing gene expression patterns withinATRXaberrant neuroblastoma
Authors: van Gerven Michael R. , Schild Linda , van Arkel Jennemiek , Koopmans Bianca , Broeils Luuk A. , Meijs Loes A. M. , van Oosterhout Romy , van Noesel Max M. , Koster Jan , van Hooff Sander R. , Molenaar Jan J. , van den Boogaard Marlinde
Published: October 2022

Neuroblastoma is the most common extracranial solid tumor in children. A subgroup of high-risk patients is characterized by aberrations in the chromatin remodeller ATRX that is encoded by 35 exons. In contrast to other pediatric cancer whereATRXpoint mutations are most frequent, multi-exon deletions (MEDs) are the most frequent type ofATRXaberrations in neuroblastoma. Of these MEDs 75% are predicted to produce in-frame fusion proteins, suggesting a potential gain-of-function effect compared to nonsense mutations. For neuroblastoma there are only a few patient-derivedATRXaberrant models. Therefore, we created isogenicATRXaberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid and performed total RNA-sequencing on these and on the patient-derived model. Gene set enrichment analysis (GSEA) showed decreased expression of genes related to both ribosome biogenesis and several metabolic process in our isogenicATRXexon 2-10 MED model systems, the patient-derived MED models and in tumor data containing two patients with anATRXexon 2-10 MED. Interestingly, for our isogenicATRXknock-out and exon 2-13 MED models GSEA revealed an opposite expression pattern characterized by increased expression of genes related to ribosome biogenesis and several metabolic process. Our validations confirmed a potential role of ATRX in the regulation of ribosome homeostasis. In this manner we identified two distinct molecular expression patterns withinATRXaberrant neuroblastomas with important implications for the need of distinct treatment regimens.
Immunity to seasonal coronavirus spike proteins does not protect from SARS-CoV-2 challenge in a mouse model but has no detrimental effect on protection mediated by COVID-19 mRNA vaccination
Authors: Amanat Fatima , Clark Jordan , Carreño Juan Manuel , Strohmeier Shirin , Meade Philip , Bhavsar Disha , Muramatsu Hiromi , Sun Weina , Coughlan Lynda , Pardi Norbert , Krammer Florian
Published: October 2022

Seasonal coronaviruses have been circulating widely in the human population for many years. With increasing age, humans are more likely to have been exposed to these viruses and to have developed immunity against them. It has been hypothesized that this immunity to seasonal coronaviruses may provide partial protection against infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and it has also been shown that coronavirus disease 2019 (COVID-19) vaccination induces a back-boosting effects against the spike proteins of seasonal betacoronaviruses. In this study, we tested if immunity to the seasonal coronavirus spikes from OC43, HKU1, 229E or NL63 would confer protection against SARS-CoV-2 challenge in a mouse model, and whether pre-existing immunity against these spikes would weaken the protection afforded by mRNA COVID-19 vaccination. We found that mice vaccinated with the seasonal coronavirus spike proteins had no increased protection as compared to the negative controls. While a negligible back-boosting effect against betacoronavirus spike proteins was observed after SARS-CoV-2 infection, there was no negative original antigenic sin-like effect on the immune response and protection induced by SARS-CoV-2 mRNA vaccination in animals with pre-existing immunity to seasonal coronavirus spike proteins.

Importance

The impact that immunity against seasonal coronaviruses has on both susceptibility to SARS-CoV-2 infection as well as on COVID-19 vaccination is unclear. This study provides insights into both questions in a mouse model of SARS-CoV-2.
Externally applied magnetic force effect on the Couette flow of a viscous incompressible fluid with heat source/sink
Authors: S. Sheeba Juliet , M. Vidhya , A. Govindarajan
Published: October 2022

Purpose

This study aims to investigate the effect of externally applied magnetic force and heat transfer with a heat source/sink on the Couette flow with viscous dissipation in a horizontal rotating channel. The magnetic force is added to the governing equations. The effects of fluid flow parameters are observed under the applied magnetic force. In this system, the magnetic force is applied perpendicular to the plane of the fluid flow. In recent years, the magnetic field has renewed interest in aerospace technology. The physical and theoretical approach in the multidisciplinary field of magneto fluid dynamics (MFD) is applied in the field of aerospace vehicle design.

Design/methodology/approach

Authors use the perturbation method to solve and find the approximate solutions of differential equations. First, convert the partial differential equation to ordinary differential equation and calculate the approximate solutions in two cases. The first solution got by assuming heat generating in the fluid and the second one got when heat absorbing. After applying the external magnetic force, the effects of various fluid parameters velocity, temperature, skin friction coefficient and Nusselt number are found and discussed using tables and graphs.

Findings

It is found that the velocity of the fluid has decreased tendency when the rotation of the fluid and magnetic force on the fluid increases. The temperature of the fluid, Prandtl value and Eckert number increased when the heat source generated heat. When heat absorbs the heat, sink parameter increases and the temperature of the fluid decreases. Also, while heat absorbs, the temperature increases when the Prandtl value and Eckert number increase.

Originality/value

The skin friction coefficient on the surface increases, when the rotation parameter and the magnetic force parameter of the fluid increase. In the case of heat generating, the Nusselt number increased, while the Eckert number and Prandtl numbers increased. Also, the Nusselt number has larger values when the heat source parameter has near the constant temperature, and it has smaller values when the temperature varies. In the case of heat-absorbing, the Nusselt number decreased when the Eckert and Prandtl numbers increased. Also, the Nusselt number varies up and down while the heat absorbing parameter increases.
Effect of emotion induction on potential consumers’ visual attention in beer advertisements: a neuroscience study
Authors: Damião de Paula André Luiz , Lourenção Marina , de Moura Engracia Giraldi Janaina , Caldeira de Oliveira Jorge Henrique
Published: October 2022

Purpose

The study aims to evaluate the effect of inducing emotions (neutral, joy and fear) on the level of visual attention in beer advertisements.

Design/methodology/approach

A between-subject experimental study with a multi-method design was carried out using three neuroscience equipment concomitantly. The electroencephalogram and the electrical conductance sensor on the skin were used to assess the emotions induced in the individuals, while eye-tracking was used to assess the visual attention to beer advertisements. Three independent groups were formed. Each group was induced to one emotion (neutral, joy or fear), and then the level of visual attention was observed in ten stimuli of beer advertisements.

Findings

The results revealed that the induction of joy increased the visual attention to the brand name, while the induction of fear increased the visual attention to both the brand name and product packaging but reduced the visual attention to human faces within the ads.

Research limitations/implications

This paper extends the literature, and to the best of the authors’ knowledge, it is the first study to indicate that induced emotions before ad viewing influence potential consumers’ visual attention.

Practical implications

The findings can serve as a basis for developing advertising campaigns that use emotion induction before ad viewing to increase the visual attention of potential consumers.

Originality/value

To the best of the authors’ knowledge, this is the first study to investigate whether the emotion induction that happens before ad viewing can impact the level of visual attention to advertisements. The study also provides clear and comprehensible implications from marketing practices to improve visual attention to ads.