bluuebunny/crossref_metadata_2025 huggingface dataset:
Expanding the role of village malaria workers in Cambodia: implementation and evaluation of four health education packages
Authors: Betrian Mipharny , Umans Dafne , Vanna Moul , Ol Sam , Adhikari Bipin , Davoeung Chan , Callery James J , Sovann Yok , Peto Thomas J , Maude Richard J , van der Pluijm Rob W , Bunreth Voeunrung , Grobusch Martin P. , van Vugt Michèle , Lubell Yoel , von Seidlein Lorenz , Dondorp Arjen M , Sovannaroth Siv , Lek Dysoley , Tripura Rupam
Published: March 2023

Background

Early access to correct diagnosis and appropriate treatment is essential for malaria elimination, and in Cambodia this relies on village malaria workers (VMWs). Decreasing malaria transmission leave VMWs with diminished roles. Activities related to the control of other health conditions could keep these community health workers relevant.

Methods

During 2022, 120 VMWs attended training at local health centres on four health education packages: 1. hygiene and sanitation; 2. disease surveillance; 3. management of mild illness; 4. vaccination and antenatal care. All training and evaluation sessions were documented through meeting minutes, and 19 focus group discussions (FGDs) were conducted among VMWs and health centre personnel. Audio-records of FGDs were transcribed and translated in English and underwent thematic analysis.

Results

VMWs reported strong interest in the training and welcomed the expansion of their roles thus assuring their continued relevance. VMWs prioritized disease surveillance and management of mild illness among the available training packages because these topics were seen as most relevant. While training was considered comprehensible and important, the low literacy among VMWs was an impediment suggesting training materials need to be delivered visually. Since VMWs have limited resources, incentives could ensure that VMWs are motivated to undertake additional roles and responsibilities.

Conclusions

The transformation of VMWs into community health workers with roles beyond malaria is a promising approach for sustaining health care provision in remote areas. Training needs to consider the low scientific literacy, time constraints and limited resources of VMWs.
Deep learning model for prenatal congenital heart disease (CHD) screening generalizes to the community setting and outperforms clinical detection
Authors: Athalye Chinmayee , van Nisselrooij Amber , Rizvi Sara , Haak Monique , Moon-Grady Anita J. , Arnaout Rima
Published: March 2023

Objective

Congenital heart defects (CHD) are still missed despite nearly universal prenatal ultrasound screening programs, which may result in severe morbidity or even death. Deep machine learning (DL) can automate image recognition from ultrasound. The aim of this study was to apply a previously developed DL model trained on images from a tertiary center, to fetal ultrasound images obtained during the second-trimester standard anomaly scan in a low-risk population.

Methods

All pregnancies with isolated severe CHD in the Northwestern region of the Netherlands between 2015 and 2016 with available stored images were evaluated, as well as a sample of normal fetuses’ examinations from the same region. We compared initial clinical diagnostic accuracy (made in real time), model accuracy, and performance of blinded human experts with access only to the stored images (like the model). We analyzed performance by study characteristics such as duration, quality (independently scored by study investigators), number of stored images, and availability of screening views.

Results

A total of 42 normal fetuses and 66 cases of isolated CHD at birth were analyzed. Of the abnormal cases, 31 were missed and 35 were detected at the time of the clinical anatomy scan (sensitivity 53 percent). Model sensitivity and specificity was 91 and 93 percent, respectively. Blinded human experts (n=3) achieved sensitivity and specificity of 55±10 percent (range 47-67 percent) and 71±13 percent (range 57-83 percent), respectively. There was a statistically significant difference in model correctness by expert-grader quality score (p=0.04). Abnormal cases included 19 lesions the model had not encountered in its training; the model’s performance (15/19 correct) was not statistically significantly different on previously encountered vs. never before seen lesions (p=0.07).

Conclusions

A previously trained DL algorithm out-performed human experts in detecting CHD in a cohort in which over 50 percent of CHD cases were initially missed clinically. Notably, the DL algorithm performed well on community-acquired images in a low-risk population, including lesions it had not been previously exposed to. Furthermore, when both the model and blinded human experts had access to stored images alone, the model outperformed expert humans. Together, these findings support the proposition that use of DL models can improve prenatal detection of CHD.
Deep audio embeddings for vocalisation clustering
Authors: Best Paul , Marxer Ricard , Paris Sébastien , Glotin Hervé
Published: March 2023

The study of non-human animals’ communication systems generally relies on the transcription of vocal sequences using a finite set of discrete units. This set is referred to as a vocal repertoire, which is specific to a species or a sub-group of a species. When conducted by human experts, the formal description of vocal repertoires can be laborious and/or biased. This motivates computerised assistance for this procedure, for which machine learning algorithms represent a good opportunity. Unsupervised clustering algorithms are suited for grouping close points together, provided a relevant representation. This paper therefore studies a new method for encoding vocalisations, allowing for automatic clustering to alleviate vocal repertoire characterisation. Borrowing from deep representation learning, we use a convolutional auto-encoder network to learn an abstract representation of vocalisations. We report on the quality of the learnt representation, as well as of state of the art methods, by quantifying their agreement with expert labelled vocalisation types from 7 datasets of other studies across 6 species (birds and marine mammals). With this benchmark, we demonstrate that using auto-encoders improves the relevance of vocalisation representation which serves repertoire characterisation using a very limited number of settings. We also publish a Python package for the bioacoustic community to train their own vocalisation auto-encoders or use a pretrained encoder to browse vocal repertoires and ease unit wise annotation.
Improving the sensitivity of fluorescence-based immunoassays by time-resolved and spatial-resolved measurements
Authors: Kremer Ran , Roth Shira , Bross Avital , Danielli Amos , Noam Yair
Published: March 2023

Detection of target molecules, such as proteins, antibodies, or specific DNA sequences, is critical in medical laboratory science. Commonly used assays rely on tagging the target molecules with fluorescent probes. These are then fed to high-sensitivity detection systems. Such systems typically consist of a photodetector or camera and use time-resolved measurements that require sophisticated and expensive optics. Magnetic modulation biosensing (MMB) is a novel, fast, and sensitive detection technology that has been used successfully to detect viruses such as Zika and SARS-CoV-2. While this powerful tool is known for its high analytical and clinical sensitivity, the current signal-processing method for detecting the target molecule and estimating its dose is based on time-resolved measurements only.

To improve the MMB-system performance, we propose here a novel signal processing algorithm that uses both temporally and spatially resolved measurements. We show that this combination significantly improves the sensitivity of the MMB-based assay. To evaluate the new method statistically, we performed multiple dose responses of Human Interleukin 9 (IL −8) on different days. Compared to standard time-resolved methods, the new algorithm provides a 2-3 fold improvement in detection limit and a 25% improvement in quantitative resolution.
ATR-FTIR spectra of polysaccharide isolated fromEuphorbia caducifoliaand its chemical modifications: A study of Principal component analysis
Authors: Venumadhav Kusuma , Seshagirirao Kottapalli
Published: March 2023

Polysaccharides are the carbohydrates composed of same or different types of saccharides in an organized manner with glycosidic bonds. These are useful for various industrial applications mainly in food and pharmaceutical companies. Modifications of the polysaccharides change its structure and lead to the physical as well as functional differences. Mostly, chemical methods are used to modify its structure to study the structure-activity relationship in interest towards its physical properties like solubility and biological activities among various types of molecular modifications. In this study, a polysaccharide isolated from stems ofEuphorbia caducifoliaand modified its structure chemically by substituting different groups by sulfonation, carboxymethylation, acetylation and phosphorylation with various degree of substitutions. Molecular modifications of the polysaccharides showed the impact on water solubility as a physiochemical property. Thus, ATR-FTIR spectroscopy was employed along with a chemometric analysis, i.e., Principal components analysis (PCA) to understand and identify the chemical moieties differed from the unmodified polysaccharide. From PCA analysis, PC1and PC2components suffice to differentiate the modified polysaccharides with its native form.
Purification and characterization of a novel anti-tumour galactose binding lectin fromEuphorbia caducifolialatex
Authors: Venumadhav Kusuama , Seshagirirao Kottapalli
Published: March 2023

A galactose specific lectin was isolated from the latex ofEuphorbia caducifoliato investigate the therapeutical aspects protein. Protein was purified from latex serum with two different affinity matrices and confirmed to contain 8 isoforms called isolectin with a molecular weight of 32 and 32.5 kDa. Preliminary studies state the specificity towards galactose, but its affinity with lactose is more favourable even at low concentrations. Circular spectrometry suggests the predominance β conformation is high in comparison to others as like most of the other latex lectins. Haemagglutination activity of the protein with different thermal and pH ranges shows maximum activity at pH 6-8 and 60-70°C. In therapeutically, it is noticed that the galactose specific lectin showed mitogenicity with human macrophages and anti-cancer properties on human cervical cancer cells.
A Consensus Model of Glucose-Stimulated Insulin Secretion in the Pancreaticβ-Cell
Authors: Deepa Maheshvare M. , Raha Soumyendu , König Matthias , Pal Debnath
Published: March 2023

The pancreas plays a critical role in maintaining glucose homeostasis through the secretion of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by the pancreaticβ-cell is the main mechanism for reducing elevated plasma glucose. Here we present a systematic modeling workflow for the development of kinetic pathway models using the Systems Biology Markup Language (SBML). Steps include retrieval of information from databases, curation of experimental and clinical data for model calibration and validation, integration of heterogeneous data including absolute and relative measurements, unit normalization, data normalization, and model annotation. An important factor was the reproducibility and exchangeability of the model, which allowed the use of various existing tools. The workflow was applied to construct the first consensus model of GSIS in the pancreaticβ-cell based on experimental and clinical data from 39 studies spanning 50 years of pancreatic, islet, andβ-cell research in humans, rats, mice, and cell lines. The model consists of detailed glycolysis and equations for insulin secretion coupled to cellular energy state (ATP/ADP ratio). Key findings of our work are that in GSIS there is a glucose-dependent increase in almost all intermediates of glycolysis. This increase in glycolytic metabolites is accompanied by an increase in energy metabolites, especially ATP and NADH. One of the few decreasing metabolites is ADP, which, in combination with the increase in ATP, results in a large increase in ATP/ADP ratios in theβ-cell with increasing glucose. Insulin secretion is dependent on ATP/ADP, resulting in glucose-stimulated insulin secretion. The observed glucose-dependent increase in glycolytic intermediates and the resulting change in ATP/ADP ratios and insulin secretion is a robust phenomenon observed across data sets, experimental systems and species. Model predictions of the glucose-dependent response of glycolytic intermediates and insulin secretion are in good agreement with experimental measurements. Our model predicts that factors affecting ATP consumption, ATP formation, hexokinase, phosphofructokinase, and ATP/ADP-dependent insulin secretion have a major effect on GSIS. In conclusion, we have developed and applied a systematic modeling workflow for pathway models that allowed us to gain insight into key mechanisms in GSIS in the pancreaticβ-cell.
S-acylation and tonoplast localization of the Geminivirus Rep-Interacting Kinase/SnRK1-Activating Kinase (GRIK/SnAK) proteins differentially regulate salt and energy stress responses in Arabidopsis
Authors: Crepin Nathalie , Rolland Filip
Published: March 2023

SnRK1 and SnRK3.11/SOS2 are key protein kinases in plant cellular energy and salt stress signaling, respectively. Using cellular assays, we confirm that the GRIK/SnAK (Geminivirus Rep-Interacting Kinase/SnRK1-Activating Kinase) proteins act as their main activating upstream kinases in Arabidopsis, catalyzing T-loop phosphorylation on the SnRK1α1 T175 and SOS2 T168 residues. Remarkably, SnRK1α1 phosphorylation on the neighbouring S176 residue competes with GRIK-mediated T175 phosphorylation to negatively regulate SnRK1 activity. Cellular assays and transgenic plants also revealed that the GRIK proteins, via N-terminal S-acylation, are predominantly localized at the tonoplast, where they interact with SnRK1α1 and SOS2. We optimized a leaf mesophyll protoplast-based Acyl PEG Exchange (APE) protocol to further explore GRIK protein S-acylation and tonoplast recruitment and identified the amino acid residues involved. GRIK1 tonoplast localization is likely mediated by initial membrane sampling via N-terminal domain hydrophobicity and local S-acylation, independently of a secretory pathway. Finally,grik1-1 grik2-1double KO mutants complemented with a non-S-acylatable mutant GRIK1 protein exhibit increased salt sensitivity (reduced SOS2 activity) but hyperactive SnRK1 signaling, demonstrating the differential importance of GRIK subcellular localization for Arabidopsis salt and energy stress responses.
The inactive X chromosome accumulates widespread epigenetic variability with age
Authors: Liu Yunfeng , Sinke Lucy , Jonkman Thomas H. , Slieker Roderick C. ,   BIOS Consortium, van Zwet Erik W. , Daxinger Lucia , Heijmans Bastiaan T.
Published: March 2023

Background

Loss of epigenetic control is a hallmark of aging. Among the most prominent roles of epigenetic mechanisms is the inactivation of one of two copies of the X chromosome in females through DNA methylation. Hence, age-related disruption of X-chromosome inactivation (XCI) may contribute to the ageing process in women.

Methods

We analyzed 9,777 CpGs on the X chromosome in whole blood samples from 2343 females and 1688 males. We replicated findings in duplicate using one whole blood and one purified monocyte data set (in total, 991/924 females/males). We used double generalized linear models (DGLM) to detect age-related differentially methylated CpGs (aDMCs), whose mean methylation level differs with age, and age-related variable methylated CpGs (aVMCs), whose methylation level becomes more variable with age.

Results

In females, aDMCs were relatively uncommon (n=33) and preferentially occurred in regions known to escape XCI. In contrast, many CpGs (n=987) were found to display an increased variance with age (aVMCs). Of note, the replication rate of aVMCs was also high in purified monocytes (95%), indicating that their occurrence may be independent of cell composition. aVMCs accumulated in CpG islands and regions subject to XCI. Although few aVMCs were associated with X-linked genes in all females studied, an exploratory analysis suggested that such associations may be more common in old females. In males, aDMCs (n=316) were primarily driven by cell composition, while aVMCs replicated well (94%) but were infrequent (n=37).

Conclusions

Age-related DNA methylation differences at the inactive X chromosome are dominated by the accumulation of variability.
Degenerated CRISPRs widely regulate Cas expression to balance immunity and cost
Authors: Liu Chao , Wang Rui , Li Jie , Cheng Feiyue , Shu Xian , Zhao Huiwei , Xue Qiong , Yu Haiying , Wu Aici , Wang Lingyun , Hu Sushu , Zhang Yihan , Yang Jun , Xiang Hua , Li Ming
Published: March 2023

CRISPR RNAs (crRNAs) and Cas proteins together provide prokaryotes with adaptive immunity against genetic invaders. How Cas expression is fine-tuned to avoid energy burden while satisfying the dynamic need of crRNAs remains poorly understood. Here we experimentally demonstrated widespread degenerated mini-CRISPRs encode CreR (Cas-regulating)RNAs to mediate autorepression of type I-B, I-E and V-A Cas proteins, based on their partial complementarity tocaspromoters. This autorepression decreases energy burden and autoimmune risks, thus mitigating the fitness cost on host cell, and remarkably, senses and responds to alterations in the volume of canonical crRNAs, which compete with CreR for Cas proteins. Moreover, CreR-guided Cas autorepression can be subverted by diverse anti-CRISPR (Acr) proteins that destruct Cas proteins, which in turn replenishes the weapon depot. Our data unveil a general degenerated crRNA-guided autorepression paradigm for diverse Cas effectors, which highlights the intricate (self-)regulation of CRISPR-Cas and its transcriptional counterstrategy against Acr attack.
AlphaPeptStats: an open-source Python package for automated, scalable and industrial-strength statistical analysis of mass spectrometry-based proteomics
Authors: Krismer Elena , Strauss Maximilian T , Mann Matthias
Published: March 2023

The widespread application of mass spectrometry (MS)-based proteomics in biomedical research increasingly requires robust, transparent and streamlined solutions to extract statistically reliable insights. Existing, popular tools were generally developed for specific uses in academic environments and did not fully embrace current open-source principles and best practices of software engineering. We have designed and implemented AlphaPeptStats, an inclusive python package with broad functionalities for normalization, imputation, visualization, and statistical analysis of proteomics data. It modularly builds on the established stack of Python scientific libraries, and is accompanied by a rigorous testing framework with 98% test coverage. It imports the output of a range of popular search engines. Data can be filtered and normalized according to user specifications. At its heart, AlphaPeptStats provides a wide range of robust statistical algorithms such as t-tests, ANOVA, PCA, hierarchical clustering and multiple covariate analysis, all in an automatable manner. Data visualization capabilities include heat maps, volcano plots, scatter plots in publication-ready format. AlphaPeptStats advances proteomic research through its robust tools that enable researchers to manually or automatically explore complex datasets to identify interesting patterns and outliers.
Incomplete transcripts dominate theMycobacterium tuberculosistranscriptome
Authors: Ju Xiangwu , Li Shuqi , Froom Ruby , Wang Ling , Lilic Mirjana , Campbell Elizabeth A. , Rock Jeremy M. , Liu Shixin
Published: March 2023

Mycobacterium tuberculosis(Mtb) is a bacterial pathogen that causes tuberculosis, an infectious disease that inflicts major health and economic costs around the world1. Mtb encounters a diversity of environments during its lifecycle, and responds to these changing environments by reprogramming its transcriptional output2. However, the transcriptomic features of Mtb remain poorly characterized. In this work, we comprehensively profile the Mtb transcriptome using the SEnd-seq method that simultaneously captures the 5’ and 3’ ends of RNA3. Surprisingly, we find that the RNA coverage for most of the Mtb transcription units display a gradual drop-off within a 200-500 nucleotide window downstream of the transcription start site, yielding a massive number of incomplete transcripts with heterogeneous 3’ ends. We further show that the accumulation of these short RNAs is mainly due to the intrinsically low processivity of the Mtb transcription machinery rather than trans-acting factors such as Rho. Finally, we demonstrate that transcription-translation coupling plays a critical role in generating full-length protein-coding transcripts in Mtb. In sum, our results depict a mycobacterial transcriptome that is dominated by incomplete RNA products, suggesting a distinctive set of transcriptional regulatory mechanisms that could be exploited for new therapeutics.
Disease Modifying Osteoarthritis Drug Discovery Using A Temporal Phenotypic Reporter In 3D Aggregates of Primary Human Chondrocytes
Authors: Cruz Maria A. , Gronowicz Scott , Karimzadeh Makan , Martyniak Kari , Medam Ramapaada , Kean Thomas J.
Published: March 2023

Osteoarthritis is a significant and growing problem with no disease modifying drugs in the clinic. Current screening platforms typically use 2D culture, immortalized or non-human cells in a hyperoxic environment. To challenge this paradigm and identify new drugs, we engineered primary human chondrocytes with a secreted luciferase reporter under the control of the articular cartilage marker, type II collagen. We then successfully screened a natural product library using a high throughput model with COL2A1-Gaussia luciferase primary human chondrocyte reporter cells in 3D aggregates under physioxia. We identified several candidate compounds that increased type II collagen over controls, with aromoline being the best candidate. Aromoline is a bisbenzylisoquinoline alkaloid that has been studied for its anti-proliferative, anti-inflammatory, and anti-microbial properties, and we are the first to explore its effects on chondrocytes and chondrogenesis. In silico analysis of predicted targets narrowed by RNA-Seq data on expression provided an unexpected initial candidate target protein: the dopamine receptor D4 (DRD4). The researchers confirmed upregulation in the expression of DRD4 and type II collagen after treatment with aromoline. This novel approach combining in silico and in vitro methods provides a platform for drug discovery in a challenging and under-researched area. In conclusion, a novel drug (aromoline) and target receptor (dopamine receptor D4) were identified as stimulating type II collagen, with the goal to treat or prevent osteoarthritis.
The 1/f-like behavior of neural field spectra are a natural consequence of noise driven brain dynamics
Authors: Kramer Mark A. , Chu Catherine J.
Published: March 2023

Consistent observations across recording modalities, experiments, and neural systems find neural field spectra with 1/f-like scaling, eliciting many alternative theories to explain this universal phenomenon. We show that a general dynamical system with stochastic drive and minimal assumptions generates 1/f-like spectra consistent with the range of values observedin vivo, without requiring a specific biological mechanism or collective critical behavior.
Sperm production is negatively associated with muscle and sperm telomere length in a highly polyandrous species
Authors: Morbiato Elisa , Cattelan Silvia , Pilastro Andrea , Grapputo Alessandro
Published: March 2023

Life history theory suggests that aging is one of the costs of reproduction. Accordingly, a higher reproductive allocation is expected to increase the deterioration of both the somatic and the germinal lines through enhanced telomere attrition. In most species, males’ reproductive allocation mainly regards traits that increase mating and fertilization success, i.e. sexually selected traits. In the current study, we tested the hypothesis that a higher investment in sexually selected traits is associated with a reduced telomere length in the guppy (Poecilia reticulata), an ectotherm species characterized by strong pre- and postcopulatory sexual selection. We first measured telomere length in both the soma and the sperm over the course of guppy’s lifespan to see if there was any variation in telomere length associated with age. Secondly, we investigated whether a greater expression of pre- and postcopulatory sexually selected traits is linked to shorter telomere length in both the somatic and the sperm germinal lines, and in young and old males. We found that telomeres lengthened with age in the somatic tissue, but there was no age-dependent variation in telomere length in the sperm cells. Telomere length in guppies was significantly and negatively correlated with sperm production in both tissues and life stages considered in this study. Our findings indicate that telomere erosion in male guppies is more strongly associated with their reproductive investment (sperm production) rather than their age, suggesting a trade-off between reproduction and maintenance is occurring at each stage of males’ life in this species.
Heterospecific developmental models highlight the role ofFBXO32in neural crest lineages and the significance of its variant in pediatric melanoma
Authors: Alexandra Vargas , Clémence Guillermain , Tatiana Gorojankina , Sophie Creuzet
Published: March 2023

Melanoma is a rare sporadic pediatric cancer caused byde novogenetic accidents. To analyze the involvement ofFBXO32of unknown biological significance, we set up original developmental invivo,ex vivo, andin vitromodels to unmask the biological role ofFBXO32in cephalic and trunk neural crest lineages. We show thatFBXO32silencing impairs melanocyte proliferation, differentiation, and vascularization. In rescue experiments, co-electroporation with the human wild-type gene compensates for the silencing of the endogenous gene and restores normal melanocyte phenotypes. By contrast, co-electroporation with the human variant,FBXO32G139S, alters melanocyte differentiation, pigment synthesis, triggers migration to the dermis, and favors angiotropism. Transcriptomic analysis reveals targets associated with melanocyte transformation, cytoskeleton remodeling, and focal adhesion. We show thatFBXO32orchestrates unexpected interactions withASIPfor melanogenesis andBAP1for the post-translational ubiquitination system. We proposeFBXO32as a tumor suppressor gene capable of preventing the onset of pediatric melanoma.
Influence of visual perception on movement decisions by an ungulate prey species
Authors: Newman Blaise A. , Dyal Jordan R. , Miller Karl V. , Cherry Michael J. , D’Angelo Gino J.
Published: March 2023

Visual perception is dynamic and depends on physiological properties of a species’ visual system and physical characteristics of the environment. White-tailed deer (Odocoileus virginianus) are most sensitive to short- and mid-wavelength light (e.g., blue and green). Wavelength enrichment varies spatially and temporally across the landscape. We assessed how the visual perception of deer influences their movement decisions. From August-September 2019, we recorded 10-min locations from 15 GPS collared adult male deer in Central Florida. We used Hidden-Markov models to identify periods of movement by deer and subset these data into three time periods based on temporal changes in light environments. We modeled resource selection during movement using path-selection functions and simulated 10 available paths for every used path. We developed five a priori models and used 10-fold cross validation to assess our top model’s performance for each time period. During the day, deer selected to move through woodland shade, avoided forest shade, and neither selected nor avoided small gaps. At twilight, deer avoided wetlands as cloud cover increased but neither selected nor avoided other cover types. Visual cues and signals are likely more conspicuous to deer in short-wavelength-enriched woodland shade during the day, while at twilight in long-wavelength-enriched wetlands during cloud cover, visual cues are likely less conspicuous. The nocturnal light environment did not influence resource selection and likely has little effect on deer movements because it’s relatively homogenous. Our findings suggest visual perception relative to light environments is likely an underappreciated driver of behaviors and decision-making by an ungulate prey species.

Summary Statement

We assessed how visual perception of white-tailed deer influences movement decisions. Our findings suggest visual perception relative to light environments represents an underappreciated driver of decision-making by ungulate prey species.
Altered cell wall hydroxycinnamate composition impacts leaf and canopy-level CO2-uptake and water-use in rice
Authors: Pathare Varsha S. , Panahabadi Rahele , Sonawane Balasaheb V. , Apalla Anthony Jude , Koteyeva Nouria , Bartley Laura E. , Cousins Asaph B.
Published: March 2023

Cell wall properties can play a major role in determining photosynthetic carbon-uptake and water-use through impacts on mesophyll conductance (CO2diffusion from substomatal cavities into photosynthetic mesophyll cells) and leaf hydraulic conductance (water movement from xylem, through leaf tissue to stomata). Consequently, modification of cell wall properties is proposed as a major path for improving photosynthesis and crop water-use efficiency. We tested this using two independent transgenic rice lines that overexpress the riceOsAT10gene (a “BAHD” CoA acyltransferase) which altered cell wall hydroxycinnamic acid content (greaterpara-coumaric acid and lower ferulic acid). Plants were grown under high and low water-levels and traits related to leaf anatomy, cell wall composition, gas exchange and hydraulics, plant biomass, and canopy-level water-use were measured. Alteration of hydroxycinnamic acid content led to significant decreases in mesophyll cell wall thickness (−14%), and increased mesophyll conductance (+120%) and photosynthesis (+22%). However, concomitant increases in stomatal conductance negated increased photosynthesis, resulting in no change in intrinsic water-use efficiency (ratio of photosynthesis/stomatal conductance). The leaf hydraulic conductance was also unchanged; however, the transgenics showed small, but significant increase in above-ground biomass (+12.5%), and canopy-level water-use efficiency (+8.8%; ratio of above-ground biomass/ water-used) and performed better under low water-level. Our results demonstrate that changes in cell wall composition, specifically hydroxycinnamic acid content, can increase mesophyll conductance and photosynthesis in C3cereal crops like rice. However, attempts to improve photosynthetic water-use efficiency will need to enhance mesophyll conductance and photosynthesis whilst maintaining or decreasing stomatal conductance.
Differential contribution of nitrifying prokaryotes to groundwater nitrification
Authors: Krüger Markus , Chaudhari Narendrakumar , Thamdrup Bo , Overholt Will , Bristow Laura , Taubert Martin , Küsel Kirsten , Jehmlich Nico , von Bergen Martin , Herrmann Martina
Published: March 2023

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genusNitrospiraand their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMXamoAgenes accounted on average for 16 to 75% of the total groundwateramoAgenes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated withNitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.
Self-supervised deep learning of gene-gene interactions for improved gene expression recovery
Authors: Wei Qingyue , Islam Md Tauhidul , Zhou Yuyin , Xing Lei
Published: March 2023

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to gain biological insights at the cellular level. However, due to technical limitations of the existing sequencing technologies, low gene expression values are often omitted, leading to inaccurate gene counts. The available methods, including state-of-the-art deep learning techniques, are incapable of imputing the gene expressions reliably because of the lack of a mechanism to explicitly consider the underlying biological knowledge of the system. Here we tackle the problem in two steps to exploit the gene-gene interactions of the system: (i) we reposition the genes in such a way that their spatial configuration reflects their interactive relationships; and (ii) we use a self-supervised 2D convolutional neural network to extract the contextual features of the interactions from the spatially configured genes and impute the omitted values. Extensive experiments with both simulated and experimental scRNA-seq datasets are carried out to demonstrate the superior performance of the proposed strategy against the existing imputation methods.
La-related protein 4 is enriched in vaccinia virus factories and is required for efficient viral replication in primary human fibroblasts
Authors: Dhungel Pragyesh , Belhaouari Djamal Brahim , Yang Zhilong
Published: March 2023

In addition to the 3’-poly(A) tail, vaccinia virus mRNAs synthesized after viral DNA replication (post-replicative mRNAs) possess a 5’-poly(A) leader that confers a translational advantage in virally infected cells. These mRNAs are synthesized in viral factories, the cytoplasmic compartment where vaccinia virus DNA replication, mRNA synthesis, and translation occur. However, a previous study indicates that the poly(A)-binding protein (PABPC1)-which has a well-established role in RNA stability and translation-is not present in the viral factories. This prompts the question of whether another poly(A)-binding protein engages vaccinia virus post-replicative mRNA in viral factories. In this study, we found that La-related protein 4 (LARP4), a poly(A) binding protein, was enriched in viral factories in multiple types of cells during vaccinia virus infection. Further studies showed that LARP4 enrichment in the viral factories required viral post-replicative gene expression and functional decapping enzymes encoded by vaccinia virus. We further showed that knockdown of LARP4 expression in human foreskin fibroblasts (HFFs) significantly reduced vaccinia virus post-replicative gene expression and viral replication. Interestingly, the knockdown of LARP4 expression also reduced 5’-poly(A) leader-mediated mRNA translation in vaccinia virus-infected and uninfected HFFs. Together, our results identified a poly(A)-binding protein, LARP4, enriched in the vaccinia virus viral factories and facilitates viral replication and mRNA translation.

Importance

Poxviruses are a family of large DNA viruses comprising members infecting a broad range of hosts, including many animals and humans. Poxvirus infections can cause deadly diseases in humans and animals. Vaccinia virus, the prototype poxvirus, encodes over 200 open reading frames (ORFs). Over 90 of vaccinia virus ORFs are transcribed post-viral DNA replication. All these mRNAs contain a 5’-poly(A) leader, as well as a 3’-poly(A) tail. They are synthesized in viral factories, where vaccinia virus DNA replication, mRNA synthesis and translation occur. However, surprisingly, the poly(A) binding protein (PABPC1) that is important for mRNA metabolism and translation is not present in the viral factories, suggesting other poly(A) binding protein(s) may be present in viral factories. Here we found another poly(A)-binding protein, La-related protein 4 (LARP4), is enriched in viral factories during vaccinia virus infection. We also showed that LARP4 enrichment in the viral factories depends on viral post-replicative gene expression and functional viral decapping enzymes. The knockdown of LARP4 expression in human foreskin fibroblasts (HFFs) significantly reduced vaccinia virus post-replicative gene expression and viral replication. Overall, this study identified a poly(A)-binding protein that plays an important role in vaccinia virus replication.
Spatial Transcriptomics Arena (STAr): an Integrated Platform for Spatial Transcriptomics Methodology Research
Authors: Jiang Xi , Luo Danni , Fernández Esteban , Yang Jie , Li Huimin , Jin Kevin W. , Zhan Yuanchun , Yao Bo , Bedi Suhana , Xiao Guanghua , Zhan Xiaowei , Li Qiwei , Xie Yang
Published: March 2023

The emerging field of spatially resolved transcriptomics (SRT) has revolutionized biomedical research. SRT quantifies expression levels at different spatial locations, providing a new and powerful tool to interrogate novel biological insights. An essential question in the analysis of SRT data is to identify spatially variable (SV) genes; the expression levels of such genes have spatial variation across different tissues. SV genes usually play an important role in underlying biological mechanisms and tissue heterogeneity. Currently, several computational methods have been developed to detect such genes; however, there is a lack of unbiased assessment of these approaches to guide researchers in selecting the appropriate methods for their specific biomedical applications. In addition, it is difficult for researchers to implement different existing methods for either biological study or methodology development.

Furthermore, currently available public SRT datasets are scattered across different websites and preprocessed in different ways, posing additional obstacles for quantitative researchers developing computational methods for SRT data analysis. To address these challenges, we designed Spatial Transcriptomics Arena (STAr), an open platform comprising 193 curated datasets from seven technologies, seven statistical methods, and analysis results. This resource allows users to retrieve high-quality datasets, apply or develop spatial gene detection methods, as well as browse and compare spatial gene analysis results. It also enables researchers to comprehensively evaluate SRT methodology research in both simulated and real datasets. Altogether, STAr is an integrated research resource intended to promote reproducible research and accelerate rigorous methodology development, which can eventually lead to an improved understanding of biological processes and diseases. STAr can be accessed athttps://lce.biohpc.swmed.edu/star/.
Novel method for collecting hippocampal interstitial fluid extracellular vesicles (EV-ISF) reveals sex-dependent changes in microglial EV proteome in response to Aβ pathology
Authors: Pait Morgan C. , Kaye Sarah D , Su Yixin , Kumar Ashish , Singh Sangeeta , Gironda Stephen C , Vincent Samantha , Anwar Maria , Carroll Caitlin M , Snipes J Andy , Lee Jingyun , Furdui Cristina M , Deep Gagan , Macauley Shannon L.
Published: March 2023

Brain-derived extracellular vesicles (EVs) play an active role in Alzheimer's disease (AD), relaying important physiological information about their host tissues. Circulating EVs are protected from degradation, making them attractive AD biomarkers. However, it is unclear how circulating EVs relate to EVs isolated from disease-vulnerable brain regions. We developed a novel method for collecting EVs from the hippocampal interstitial fluid (ISF) of live mice. EVs (EVISF) were isolated via ultracentrifugation and characterized by nanoparticle tracking analysis, immunogold labeling, and flow cytometry. Mass spectrometry and proteomic analyses were performed on EVISF cargo. EVISF were 40-150 nm in size and expressed CD63, CD9, and CD81. Using a model of cerebral amyloidosis (e.g. APPswe,PSEN1dE9 mice), we found protein concentration increased but protein diversity decreased with A deposition. Genotype, age, and Aβ deposition modulated proteostasis- and immunometabolic-related pathways. Changes in the microglial EVISF proteome were sexually dimorphic and associated with a differential response of plaque associated microglia. We found that female APP/PS1 mice have more amyloid plaques, less plaque associated microglia, and a less robust- and diverse- EVISF microglial proteome. Thus, in vivo microdialysis is a novel technique for collecting EVISF and offers a unique opportunity to explore the role of EVs in AD.
Genomic analysis of cultivated infant microbiomes identifiesBifidobacterium2’-fucosyllactose utilization can be facilitated by co-existing species
Authors: Lou Yue Clare , Rubin Benjamin E. , Schoelmerich Marie C. , DiMarco Kaden , Borges Adair L. , Rovinsky Rachel , Song Leo , Doudna Jennifer A. , Banfield Jillian F.
Published: March 2023

Human milk oligosaccharides (HMOs) ensure proper infant gut microbiome establishment. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigated microbiome responses to 2’-fucosyllactose (2’FL), a prevalent HMO and infant formula additive, by establishing individualized microbiomes using fecal samples from three different infants as the inocula.Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2’FL. Using metagenomic data, we predicted that extracellular fucosidases encoded by co-existing members such asRuminococcus gnavusinitiate 2’FL breakdown, thus critical forB. breve’sgrowth. Using both targeted co-cultures and by supplementation ofR. gnavusinto one microbiome, we show thatR. gnavuscan promote extensive growth ofB. brevethrough the release of lactose from 2’FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrated that HMO utilization can vary with an individual’s microbiome.
Phage administration with repeated intravenous doses leads to faster phage clearance in mammalian hosts
Authors: Tan Xin , Chen Kai , Jiang Zhihuan , Liu Ziqiang , Wang Siyun , Ying Yong , Zhang Jieqiong , Yuan Shengjian , Huang Zhipeng , Gao Ruyue , Zhao Min , Weng Aoting , Yang Yongqing , Luo Huilong , Zhang Daizhou , Ma Yingfei
Published: March 2023

Objectives

Phage therapy has shown a great promise for the treatment of multidrug-resistant bacterial infections. However, the lack of a thorough and organized understanding of phage-body interactions has limited its clinical application.

Methods

Here, we administered different purified phages (Salmonellaphage SE_SZW1,Acinetobacterphage AB_SZ6, andPseudomonasphage PA_LZ7) intravenously to healthy animals (rats and monkeys) to evaluate the phage-induced host responses and phage pharmacokinetics (PK) with different intravenous (IV) doses in healthy animals. The plasma and the organs were sampled after different IV doses to determine the phage biodistribution, the phage-induced cytokines, and antibodies. The potential side effects of phages on animals were assessed.

Results

A non-compartment model revealed that the plasma phage titer gradually decreased over time following a single dose. Repeated doses caused that the plasma phage titer at 5 minutes dropped 2-3 Log10compared to the first dose regardless of phage types in rats. Host innate immune responses were activated including the upregulated expression (>10-fold) of TNF-αand splenic enlargement following repeated doses. Phage-specific neutralization antibodies in animals receiving phages were detected. Similar results were obtained from monkeys.

Conclusions

The mammalian bodies were well-tolerant to the administered phages. The animal responses to the phages and the phage biodistribution profiles could have a significant impact on the efficacy of phage therapy.
Mammalian cells internalize bacteriophages and utilize them as a food source to enhance cellular growth and survival
Authors: Bichet Marion C. , Adderley Jack , Avellaneda Laura , Gearing Linden J. , Deffrasnes Celine , David Cassandra , Pepin Genevieve , Gantier Michael P. , Lin Ruby CY , Patwa Ruzeen , Moseley Gregory W. , Doerig Christian , Barr Jeremy J.
Published: March 2023

There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate diverse and unexplored symbioses. Yet the impact these bacteriophages may have on mammalian cellular and immunological processes is poorly understood. Here we applied highly purified phage T4, free from bacterial by-products and endotoxins to mammalian cells and analyzed the cellular responses using luciferase reporter and antibody microarray assays. Phage preparations were appliedin vitroto either A549 lung epithelial cells, MDCK-I kidney cells, or primary mouse bone marrow derived macrophages with the phage-free supernatant serving as a comparative control. Highly purified T4 phages were rapidly internalized by mammalian cells and accumulated within macropinosomes but did not activate the inflammatory DNA response TLR9 or cGAS-STING pathways. Following eight hours of incubation with T4 phage, whole cell lysates were analyzed via antibody microarray that detected expression and phosphorylation levels of human signaling proteins. T4 phage internalization led to the activation of AKT-dependent pathways, resulting in an increase in cell metabolism, survival, and actin reorganization, the last being critical for macropinocytosis and potentially regulating a positive feedback loop to drive further phage internalization. T4 phages additionally down-regulated CDK1 and its downstream effectors, leading to an inhibition of cell cycle progression and an increase in cellular growth through a prolonged G1 phase. These interactions demonstrate that highly purified T4 phages do not activate DNA-mediated inflammatory pathways but do trigger protein phosphorylation cascades that promote cellular growth and survival. We conclude that mammalian cells are internalizing bacteriophages as a food source to promote cellular growth and metabolism.