bluuebunny/crossref_metadata_2025 huggingface dataset:
Chimera alert! The threat of chimeric sequences causing inaccurate taxonomic classification of phytoplasma strains
Authors: Tiwarekar Bhavesh , Kirdat Kiran , Sathe Shivaji , Foissac Xavier , Yadav Amit
Published: April 2023

The 16S rRNA gene is a primary marker used to study bacterial taxonomy, particularly for bacteria with ‘Candidatus’ status, where it serves as a primary reference sequence for identification. Despite its usefulness, ensuring the authenticity of publicly available sequences has always posed a challenge. To address this issue, multiple tools and databases with curated collections of reference 16S rRNA gene sequences were established. However, even with these efforts, many sequence chimeras still exist. These chimeric gene sequences are formed by the fusion of sequence parts from multiple organisms and can arise from errors during PCR amplification or sequencing. The objective of this study was to identify chimeric sequences from a dataset of over 4500 phytoplasma 16S rRNA gene sequences using multiple tools. The tools ChimeraSlayer and UCHIME identified 12 and 11 chimeric sequences, respectively. Notably, these sequences included the reference 16S rRNA gene sequence of ‘Ca. Phytoplasma wodyetiae’ strain Bangi-2 (KC844879) and ‘Ca. Phytoplasma allocasuarinae’ (AY135523). The study’s outcomes indicated the existence of chimeric 16S rRNA gene sequences, emphasizing the threat posed by such sequences in correctly assigning taxonomic status to phytoplasma strains. These findings underscore the importance of rigorously verifying the authenticity of 16S rRNA gene sequences to ensure their accuracy in identifying and classifying bacterial species.
Effect of temperature on mosquito olfaction
Authors: Lahondère Chloé , Vinauger Clément , Liaw Jessica E. , Tobin Kennedy K.S. , Joiner Jillian M. , Riffell Jeffrey A.
Published: April 2023

Mosquitoes use a wide range of cues to find a host to feed on, eventually leading to the transmission of pathogens. Among them, olfactory cues (e.g., host emitted odors, including CO2, and skin volatiles) play a central role in mediating host seeking behaviors. While mosquito olfaction can be impacted by many factors, such as the physiological state of the insect (e.g., age, reproductive state), the impact of environmental temperature on the olfactory system remains unknown. In this study, we quantified the behavioral responses ofAedes aegyptimosquitoes, vectors of dengue, yellow fever and Zika viruses, to host and plant related odors under different environmental temperatures.
A late Neanderthal reveals genetic isolation in their populations before extinction
Authors: Slimak Ludovic , Vimala Tharsika , Seguin-Orlando Andaine , Metz Laure , Zanolli Clément , Joannes-Boyau Renaud , Frouin Marine , Arnold Lee J. , Demuro Martina , Devièse Thibaut , Comeskey Daniel , Buckley Michael , Camus Hubert , Muth Xavier , Lewis Jason E. , Bocherens Hervé , Yvorra Pascale , Tenailleau Christophe , Duployer Benjamin , Coqueugniot Hélène , Dutour Olivier , Higham Thomas , Sikora Martin
Published: April 2023

Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations’ structure, mostly indicating that late European Neanderthals belonged to a single metapopulation with no significant evidence of deep population structure. Here we report the discovery of a late Neanderthal individual, nicknamed “Thorin”, from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of their final technological traditions in this region ∼50-42 thousand years ago. Thorin’s genome reveals a deep divergence with other late Neanderthals. Thorin belonged to a population with small group size that showed no genetic introgression with other known late European Neanderthals, revealing genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the Neanderthals’ disappearance.

One Sentence Summary

A new French Neanderthal fossil and its genome reveal complex population dynamics during the past 100,000 years.
Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack
Authors: Nobori Tatsuya , Monell Alexander , Lee Travis A. , Zhou Jingtian , Nery Joseph , Ecker Joseph R.
Published: April 2023

Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that critically impacts plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present cell atlases with gene regulatory logic involving transcription factors, putativecis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integrating our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic with pathogen cells. Our study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.
High methane flux in a tropical peatland post-fire is linked to homogenous selection of diverse methanogenic archaea
Authors: Bandla Aditya , Akhtar Hasan , Lupascu Massimo , Sukri Rahayu Sukmaria , Swarup Sanjay
Published: April 2023

Tropical peatlands in South-East Asia are some of the most carbon dense ecosystems in the world. Recurrent wildfires in repurposed peatlands release massive amounts of carbon and other greenhouse gases, strongly alter peat geochemistry and physicochemical conditions. However, little is known about the impact of fire on peat microbiome composition, microbial guilds contributing to greenhouse gas emissions, and their predictability based on environmental conditions. Here, we address this gap by studying peat microbiomes from fire-affected and intact areas of a tropical peatland in Brunei using high-throughput sequencing and ecological process modelling at the community and clade levels. We show that fire disrupts depth-stratification of peat microbiomes with the strongest effects observed at 1m below the surface. The enrichment of specific taxa and methanogenic archaea at such depths suggests an adaptation to low-energy conditions post-fire. Finally, fire shifts archaeal community composition and clades containing abundant methanogens in a homogeneous manner that can be predicted from environmental conditions and functional traits. Together, our findings provide a biological basis for earlier work which reported elevated methane flux 2-3 years post-fire and show that such changes follow predictable trajectories with important implications for post-fire microbiome forecasting and ecosystem recovery efforts.
Spatiotemporal Genomic Profiling of Intestinal Metaplasia Reveals Clonal Dynamics of Gastric Cancer Progression
Authors: Huang Kie Kyon , Ma Haoran , Uchihara Tomoyuki , Sheng Taotao , Chong Roxanne Hui Heng , Zhu Feng , Srivastava Supriya , Tay Su Ting , Sundar Raghav , Tan Angie Lay Keng , Ong Xuewen , Lee Minghui , Ho Shamaine Wei Ting , Lesluyes Tom , Van Loo Peter , Chua Joy Shijia , Ramnarayanan Kalpana , Ang Tiing Leong , Khor Christopher , Lee Jonathan Wei Jie , Tsao Stephen Kin Kwok , Teh Ming , Chung Hyunsoo , So Jimmy Bok Yan , Yeoh Khay Guan , Tan Patrick , Cancer Consortium Singapore Gastric
Published: April 2023

Intestinal metaplasia (IM) is a pre-malignant condition of the gastric mucosa associated with increased gastric cancer (GC) risk. We analyzed 1256 gastric samples (1152 IMs) from 692 subjects through a prospective 10-year study. We identified 26 IM driver genes in diverse pathways including chromatin regulation (ARID1A) and intestinal homeostasis (SOX9), largely occurring as small clonal events. Analysis of clonal dynamics between and within subjects, and also longitudinally across time, revealed that IM clones are likely transient but increase in size upon progression to dysplasia, with eventual transmission of somatic events to paired GCs. Single-cell and spatial profiling highlighted changes in tissue ecology and lineage heterogeneity in IM, including an intestinal stem-cell dominant cellular compartment linked to early malignancy. Expanded transcriptome profiling revealed expression-based molecular subtypes of IM, including a body-resident “pseudoantralized” subtype associated with incomplete histology, antral/intestinal cell types,ARID1Amutations, inflammation, and microbial communities normally associated with the healthy oral tract. We demonstrate that combined clinical- genomic models outperform clinical-only models in predicting IMs likely to progress. Our results raise opportunities for GC precision prevention and interception by highlighting strategies for accurately identifying IM patients at high GC risk and a role for microbial dysbiosis in IM progression.
Comprehensive insight into the alterations in the gut microbiome and the intestinal barrier as a consequence of iron deficiency anaemia
Authors: Soriano-Lerma Ana , García-Burgos María , Barton Wiley , Muñoz-Alférez María José , Crespo-Pérez Jorge Valentín , Soriano Miguel , López-Aliaga Inmaculada , Cotter Paul D. , García-Salcedo José Antonio
Published: April 2023

Background

Iron is an essential micronutrient for all living organisms, and as such, iron deficiency is the top leading cause of anaemia. Iron supplements have been shown to be detrimental to the gut microbiome and the intestinal epithelium, triggering dysbiosis and an impaired gut barrier. However, a comprehensive analysis of these two aspects have not been performed during IDA. This study aims to delve further into the analysis of the gut microbiome in an animal model of IDA and to relate microbial changes to the biological processes occurring in the colonic epithelium, with a special focus on the gut barrier. This in-depth analysis might mean a step forward minimising the negative impact of iron supplements on intestinal health during IDA.

Methods

IDA was experimentally induced in an animal model through the use of an iron deficient diet. Shotgun sequencing was used to gain insight into alterations of the gut microbiome in the most affected intestinal region during IDA, the colon. Histological analyses, mRNA sequencing (RNA-Seq), qPCR and immunofluorescence were used to study transcriptionally deregulated processes in the colonic epithelium. Determinations of lipopolysaccharide and bacteria-specific immunoglobulins were performed to assess microbial translocation.

Results

Microbial metabolism in the colon shifted towards an increased production of certain amino acids, short chain fatty acids and nucleotides, withClostridiumspecies being enriched during IDA. Structural alterations of the colonic epithelium were shown by histological analysis. RNA-Seq revealed a downregulation of extracellular matrix-associated genes and proteins and an overall underdeveloped epithelium. Increased levels of serum LPS in the anaemic animals and an increased immune response against IDA dysbiotic bacteria support an impairment in the integrity of the gut barrier.

Conclusions

IDA negatively impacts the gut microbiome and the intestinal barrier, triggering an increased microbial translocation. This study emphasizes the deterioration of gut health during IDA and the fact that it should be addressed when treating the disease.
Universal method for generating knockout mice in multiple genetic backgrounds using zygote electroporation
Authors: Tamari Tomohiro , Ikeda Yoshihisa , Morimoto Kento , Kobayashi Keiko , Mizuno-Iijima Saori , Ayabe Shinya , Kuno Akihiro , Mizuno Seiya , Yoshiki Atsushi
Published: April 2023

Genetically engineered mouse models are essential tools for understanding mammalian gene functions and disease pathogenesis. Genome editing allows for the generation of these models in multiple inbred strains of mice without backcrossing. Zygote electroporation dramatically removed the barrier for introducing the CRISPR-Cas9 complex in terms of cost and labour. However, the editing conditions and protocols to produce knockout lines have been optimised for a limited number of strains or stocks. Here, we demonstrate a novel and universal approach for generating knockout mice in multiple inbred strains. By combining in vitro fertilisation and electroporation, we obtained founders for knockout alleles in 8 common inbred strains. Long-read sequencing analysis detected not only intended mutant alleles but also differences in read frequency of intended and unintended alleles among strains. Successful germline transmission of knockout alleles demonstrated that our novel approach can establish mutant mice targeting the same locus in multiple inbred strains for phenotyping analysis, contributing to reverse genetics and human disease research.

Summary statement

Universal method for zygote genome editing in multiple inbred mouse strains allows for generation of novel mutant mice for understanding mammalian gene function and human disease pathogenesis.
The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis
Authors: Planells Jordi , Jordán-Pla Antonio , Jain Shruti , Guadalupe Juan José , Proux-Wera Estelle , Euler Anne von , Pelechano Vicent , Visa Neus
Published: April 2023

Chromatin-associated RNAs (caRNAs) modulate chromatin organization and function. The RNA exosome degrades different types of nuclear transcripts, but its role in chromatin has not been addressed. Here we have usedDrosophila melanogasterS2 cells as a model system to identify the repertoire of caRNAs and establish the role of the exosome in their regulation. We have analyzed both unique and repetitive sequences, and combining RNA-seq and ATAC-seq we show that the simultaneous depletion of the exosome catalytic subunits RRP6 and DIS3 not only affects caRNA levels but also changes the local chromatin accessibility at specific loci. We have identified a group of exosome-sensitive genes that are involved in developmental regulation and are characterized by a balanced chromatin state in which Polycomb and Trithorax factors coexist. Our results reveal that RNA degradation by the exosome is an important mechanism for the homeostasis of such balanced chromatin states. Given that eukaryotic genomes are repetitive to a large extent, we have also analyzed repetitive caRNAs (rep-caRNAs) and we show that the exosome is needed to control repcaRNA levels and to maintain the degree of chromatin packaging in repetitive genomic regions. This role is particularly relevant in the pericentromeric regions where the exosome is required to silence LTR elements and maintain centromere organization.
Clostridium butyricumandClostridium tyrobutyricum: angle or devil for Necrotizing enterocolitis?
Authors: Tao Ruizhi , Zong Gangfan , Pan Yehua , Li Hongxing , Cheng Peng , Deng Rui , Chen Wenxing , Wang Aiyun , Xia Shishan , Tang Weibing , Lu Yin , Wei Zhonghong
Published: April 2023

Background

Necrotizing enterocolitis (NEC), high incidence and case-fatality rate among premature neonates, is a frustrating gastrointestinal disease which hard to eradicate currently for its unclear pathogenesis and mechanisms. What has been conformed is that the gut microbes dysbiosis happens before the occurrence of NEC, providing robust evidence for the usage of probiotic therapy. Hence, we mainly concentrated on two probiotics: Clostridium butyricum and Clostridium tyrobutyricum especially after the breakthrough in discovering that several clostridia species have associations with NEC.

Result

To verify whether these two clostridia are pathogenic or probiotic, we compared the phenotypic traits of NEC mice treated with two clostridia. Our results proof that treatment with C. tyrobutyricum recovers the intestinal barrier integrity and alleviates inflammatory immune response of NEC, while treatment with C. butyricum aggrevates the intestinal barrier damage and promotes immune disorder including the number of macrophages, monocytes and neutrophils in Intestinal lamina propria. Further analysis of gut micrbiome implies that the positive effect of C. tyrobutyricum treatment is in association with the increase of Akkermansia muciniphila. Meanwhile, C. butyricum treatment decreases the level of A. muciniphila, which accounts for the negative effect to NEC.

Conclusion

This study sheds light on that treatment with C. tyrobutyricum but not C. butyricum is entitled to protect against NEC development potentially. The mechanisms behind the opposite effect on NEC may result in different modulation on the level of A. muciniphila, which is deeply associated with intestinal homoeostasis. Briefly, through improving the abundance of A. muciniphila to alleviate intestinal inflammation and enhance intestinal barrier integrity, C. tyrobutyricum supplement may become a promising therapy for NEC.
Deep Learning and Transfer Learning for Brain Tumor Detection and Classification
Authors: Rustom Faris , Parva Pedram , Ogmen Haluk , Yazdanbakhsh Arash
Published: April 2023

Convolutional neural networks (CNNs) are powerful tools that can be trained on image classification tasks and share many structural and functional similarities with biological visual systems and mechanisms of learning. In addition to serving as a model of biological systems, CNNs possess the convenient feature of transfer learning where a network trained on one task may be repurposed for training on another, potentially unrelated, task. In this retrospective study of public domain MRI data, we investigate the ability of neural network models to be trained on brain cancer imaging data while introducing a unique camouflage animal detection transfer learning step as a means of enhancing the network’s tumor detection ability. Training on glioma and normal brain MRI data, post-contrast T1-weighted and T2-weighted, we demonstrate the potential success of this training strategy for improving neural network classification accuracy. Qualitative metrics such as feature space and DeepDreamImage analysis of the internal states of trained models were also employed, which show improved generalization ability by the models following camouflage animal transfer learning. Image sensitivity functions further this investigation by allowing us to visualize the most salient image regions from a network’s perspective while learning. Such methods demonstrate that the networks not only ‘look’ at the tumor itself when deciding, but also at the impact on the surrounding tissue in terms of compressions and midline shifts. These results suggest an approach to brain tumor MRIs that is comparatively similar to that of trained radiologists while also exhibiting a high sensitivity to subtle structural changes resulting from the presence of a tumor. These findings present an opportunity for further research and potential use in a clinical setting.
Characterization of Target Gene Regulation by the Two Epstein-Barr Virus Oncogene LMP1 Domains Essential for B-cell Transformation
Authors: Mitra Bidisha , Beri Nina Rose , Guo Rui , Burton Eric M. , Murray-Nerger Laura A. , Gewurz Benjamin E.
Published: April 2023

The Epstein-Barr virus (EBV) oncogene latent membrane protein 1 (LMP1) mimics CD40 signaling and is expressed by multiple malignancies. Two LMP1 C-terminal cytoplasmic tail regions, termed transformation essential sites (TES) 1 and 2, are critical for EBV transformation of B lymphocytes into immortalized lymphoblastoid cell lines (LCL). However, TES1 versus TES2 B-cell target genes have remained incompletely characterized, and whether both are required for LCL survival has remained unknown. To define LCL LMP1 target genes, we profiled transcriptome-wide effects of acute LMP1 CRISPR knockout (KO) prior to cell death. To then characterize specific LCL TES1 and TES2 roles, we conditionally expressed wildtype, TES1 null, TES2 null or double TES1/TES2 null LMP1 alleles upon endogenous LMP1 KO. Unexpectedly, TES1 but not TES2 signaling was critical for LCL survival. The LCL dependency factor cFLIP, which plays obligatory roles in blockade of LCL apoptosis, was highly downmodulated by loss of TES1 signaling. To further characterize TES1 vs TES2 roles, we conditionally expressed wildtype, TES1 and/or TES2 null LMP1 alleles in two Burkitt models. Systematic RNAseq analyses revealed gene clusters that responded more strongly to TES1 versus TES2, that respond strongly to both or that are oppositely regulated. Robust TES1 effects on cFLIP induction were again noted. TES1 and 2 effects on expression of additional LCL dependency factors, including BATF and IRF4, and on EBV super-enhancers were identified. Collectively, these studies suggest a model by which LMP1 TES1 and TES2 jointly remodel the B-cell transcriptome and highlight TES1 as a key therapeutic target.

Importance

Epstein-Barr virus (EBV) causes multiple human cancers, including B-cell lymphomas. In cell culture, EBV converts healthy human B-cells into immortalized ones that grow continuously, which model post-transplant lymphomas. Constitutive signaling from two cytoplasmic tail domains of the EBV oncogene Latent Membrane Protein 1 (LMP1) is required for this transformation, yet there has not been systematic analysis of their host gene targets. We identified that only signaling from the membrane proximal domain is required for survival of these EBV-immortalized cells and that its loss triggers apoptosis. We identified key LMP1 target genes, whose abundance changed significantly with loss of LMP1 signals, or that were instead upregulated in response to switching on signaling by one or both LMP1 domains in an EBV-uninfected human B-cell model. These included major anti-apoptotic factors necessary for EBV-infected B-cell survival. Bioinformatics analyses identified clusters of B-cell genes that respond differently to signaling by either or both domains.
OGG1 and MUTYH repair activities promote telomeric 8-oxoguanine induced cellular senescence
Authors: Rosa Mariarosaria De , Barnes Ryan P. , Nyalapatla Prasanth R. , Wipf Peter , Opresko Patricia L.
Published: April 2023

Telomeres are prone to formation of the common oxidative lesion 8-oxoguanine (8oxoG), and the acute production of 8oxoG damage at telomeres is sufficient to drive rapid cellular senescence. OGG1 and MUTYH glycosylases initiate base excision repair (BER) at 8oxoG sites to remove the lesion or prevent mutation. Here, we show OGG1 loss or inhibition, or MUTYH loss, partially rescues telomeric 8oxoG-induced senescence, and loss of both glycosylases results in a near complete rescue. Loss of these glycosylases also suppresses 8oxoG-induced telomere fragility and dysfunction, indicating that single-stranded break (SSB) intermediates arising downstream of glycosylase activity impair telomere replication. The failure to initiate BER in glycosylase-deficient cells suppresses PARylation at SSB intermediates and confers resistance to the synergistic effects of PARP inhibitors on damage-induced senescence. Our studies reveal that inefficient completion of 8oxoG BER at telomeres triggers cellular senescence via SSB intermediates which impair telomere replication and stability.
Diethylcarbamazine elicits Ca2+signals through TRP-2 channels that are potentiated by emodepside inBrugia malayimuscles
Authors: Williams Paul D. E. , Kashyap Sudhanva S. , Robertson Alan P. , Martin Richard J.
Published: April 2023

Filarial nematode infections are a major health concern in several countries. Lymphatic filariasis is caused byWucheria bancroftiandBrugia spp.affecting over 120 million people. Heavy infections can lead to elephantiasis having serious effects on individuals’ lives. Although current anthelmintics are effective at killing the microfilariae in the bloodstream, they have little to no effect against adult parasites found in the lymphatic system. The anthelmintic diethylcarbamazine is one of the central pillars of lymphatic filariasis control. Recent studies have reported that diethylcarbamazine can open Transient Receptor Potential (TRP) channels on the muscles of adult femaleBrugia malayileading to contraction and paralysis. Diethylcarbamazine has synergistic effects in combination with emodepside onBrugiainhibiting motility: emodepside is an anthelmintic that has effects on filarial nematodes and is under trials for treatment of river blindness. Here we have studied the effects of diethylcarbamazine on singleBrugiamuscle cells by measuring the change in Ca2+fluorescence in the muscle using Ca2+-imaging techniques. Diethylcarbamazine interacts with the TRPC orthologue receptor TRP-2 to promote Ca2+entry into theBrugiamuscle cells which can activate SLO-1 Ca2+activated K+channels, the putative target of emodepside. A combination of diethylcarbamazine and emodepside leads to a bigger Ca2+signal than when either compound is applied alone. Our study shows that diethylcarbamazine targets TRP channels to promote Ca2+entry that is increased by emodepside activation of SLO-1 channels.
Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics
Authors: Chan Tsz Fung , Rui Xinyue , Conti David V. , Fornage Myriam , Graff Mariaelisa , Haessler Jeffrey , Haiman Christopher , Highland Heather M. , Jung Su Yon , Kenny Eimear , Kooperberg Charles , Marchland Loic Le , North Kari E. , Tao Ran , Wojcik Genevieve , Gignoux Christopher R. ,   PAGE Consortium, Chiang Charleston W. K. , Mancuso Nicholas
Published: April 2023

The heritability explained by local ancestry markers in an admixed populationprovides crucial insight into the genetic architecture of a complex disease or trait. Estimation ofcan be susceptible to biases due to population structure in ancestral populations. Here, we present a novel approach, Heritability estimation from Admixture Mapping Summary STAtistics (HAMSTA), which uses summary statistics from admixture mapping to infer heritability explained by local ancestry while adjusting for biases due to ancestral stratification. Through extensive simulations, we demonstrate that HAMSTAestimates are approximately unbiased and are robust to ancestral stratification compared to existing approaches. In the presence of ancestral stratification, we show a HAMSTA-derived sampling scheme provides a calibrated family-wise error rate (FWER) of ∼5% for admixture mapping, unlike existing FWER estimation approaches. We apply HAMSTA to 20 quantitative phenotypes of up to 15,988 self-reported African American individuals in the Population Architecture using Genomics and Epidemiology (PAGE) study. We observein the 20 phenotypes range from 0.0025 to 0.033 (mean), which translates toranging from 0.062 to 0.85 (mean). Across these phenotypes we find little evidence of inflation due to ancestral population stratification in current admixture mapping studies (mean inflation factor of 0.99 +/-0.001). Overall, HAMSTA provides a fast and powerful approach to estimate genome-wide heritability and evaluate biases in test statistics of admixture mapping studies.
Fecal metagenomics to identify biomarkers of food intake in healthy adults: Findings from randomized, controlled, nutrition trials
Authors: Shinn Leila M. , Mansharamani Aditya , Baer David J. , Novotny Janet A. , Charron Craig S. , Khan Naiman A. , Zhu Ruoqing , Holscher Hannah D.
Published: April 2023

Background

Undigested components of the human diet affect the composition and function of the microorganisms present in the gastrointestinal tract. Techniques like metagenomic analyses allow researchers to study functional capacity, thus, revealing the potential of using metagenomic data for developing objective biomarkers of food intake.

Objective

As a continuation of our previous work using 16S and metabolomic datasets, we aimed to utilize a computationally intensive, multivariate, machine learning approach to identify fecal Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) categories as biomarkers that accurately classify food intake.

Design

Data were aggregated from five controlled feeding studies that studied the individual impact of almonds, avocados, broccoli, walnuts, barley, and oats on the adult gastrointestinal microbiota. DNA from pre-and post-intervention fecal samples underwent shotgun genomic sequencing. After pre-processing, sequences were aligned and functionally annotated with DIAMOND v2.0.11.149 and MEGAN v6.12.2, respectively. After count normalization, the log of the fold change ratio for resulting KOs between pre-and post-intervention of the treatment group against its corresponding control was utilized to conduct differential abundance analysis. Differentially abundant KOs were used to train machine learning models examining potential biomarkers in both single-food and multi-food models.

Results

We identified differentially abundant KOs in the almond (n = 54), broccoli (n = 2,474), and walnut (n = 732) groups (q< 0.20), which demonstrated classification accuracies of 80%, 87%, and 86% for the almond, broccoli, and walnut groups, respectively, using a random forest model to classify food intake into each food group’s respective treatment and control arms. The mixed-food random forest achieved 81% accuracy.

Conclusions

Our findings reveal promise in utilizing fecal metagenomics to objectively complement self-reported measures of food intake. Future research on various foods and dietary patterns will expand these exploratory analyses for eventual use in feeding study compliance and clinical settings.
Distinct interactions stabilize EGFR dimers and higher-order oligomers in cell membranes
Authors: Mudumbi Krishna C. , Burns Eric A. , Schodt David J. , Petrova Zaritza O. , Kiyatkin Anatoly , Kim Lucy W. , Mangiacapre Emma M. , Ortiz-Caraveo Irais , Ortiz Hector Rivera , Hu Chun , Ashtekar Kumar D. , Lidke Keith A. , Lidke Diane S. , Lemmon Mark A.
Published: April 2023

The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase (RTK) with important roles in many cellular processes as well as cancer and other diseases. EGF binding promotes EGFR dimerization and autophosphorylation through interactions that are well understood structurally. However, it is not clear how these dimers relate to higher-order EGFR oligomers detected at the cell surface. We used single-particle tracking (SPT) and Förster resonance energy transfer (FRET) imaging to examine how each domain within EGFR contributes to receptor dimerization and the rate of its diffusion in the cell membrane. We show that the EGFR extracellular region is sufficient to drive receptor dimerization, but that the EGF-induced EGFR slow-down seen by SPT requires formation of higher order oligomers, mediated in part by the intracellular tyrosine kinase domain – but only when in its active conformation. Our data thus provide important insight into higher-order EGFR interactions required for EGF signaling.
How individualP. aeruginosacells with diverse stator distributions collectively form a heterogeneous macroscopic swarming population
Authors: de Anda Jaime , Kuchma Sherry L. , Webster Shanice S. , Boromand Arman , Lewis Kimberley A. , Lee Calvin K. , Contreras Maria , Pereira Victor F. Medeiros , Hogan Deborah A. , O’Hern Corey S. , O’Toole George A. , Wong Gerard C.L.
Published: April 2023

Swarming is a macroscopic phenomenon in which surface bacteria organize into a motile population. The flagellar motor that drives swarming inPseudomonas aeruginosais powered by stators MotAB and MotCD. Deletion of the MotCD stator eliminates swarming, whereas deletion of the MotAB stator enhances swarming. Interestingly, we measured a strongly asymmetric stator availability in the WT strain, with MotAB stators produced ∼40-fold more than MotCD stators. However, recruitment of MotCD stators in free swimming cells requires higher liquid viscosities, while MotAB stators are readily recruited at low viscosities. Importantly, we find that cells with MotCD stators are ∼10x more likely to have an active motor compared to cells without, so wild-type, WT, populations are intrinsically heterogeneous and not reducible to MotAB-dominant or MotCD-dominant behavior. The spectrum of motility intermittency can either cooperatively shut down or promote flagellum motility in WT populations. InP. aeruginosa, transition from a static solid-like biofilm to a dynamic liquid-like swarm is not achieved at a single critical value of flagellum torque or stator fraction but is collectively controlled by diverse combinations of flagellum activities and motor intermittencies via dynamic stator recruitment. Experimental and computational results indicate that the initiation or arrest of flagellum-driven swarming motility does not occur from individual fitness or motility performance but rather related to concepts from the ‘jamming transition’ in active granular matter.

Importance

After extensive study, it is now known that there exist multifactorial influences on swarming motility inP. aeruginosa, but it is not clear precisely why stator selection in the flagellum motor is so important or how this process is collectively initiated or arrested. Here, we show that forP. aeruginosaPA14, MotAB stators are produced ∼40-fold more than MotCD stators, but recruitment of MotCD over MotAB stators requires higher liquid viscosities. Moreover, we find the unanticipated result that the two motor configurations have significantly different motor intermittencies, the fraction of flagellum-active cells in a population on average, with MotCD active ∼10x more often than MotAB. What emerges from this complex landscape of stator recruitment and resultant motor output is an intrinsically heterogeneous population of motile cells. We show how consequences of stator recruitment led to swarming motility, and how they potentially relate to surface sensing circuitry.
Comparative analysis of myoglobin in Cetaceans and humans reveals novel regulatory elements and evolutionary flexibility
Authors: Sackerson Charles , Garcia Vivian , Medina Nicole , Maldonado Jessica E. , Daly John , Cartwright Rachel
Published: April 2023

Cetacea and other diving mammals have undergone numerous adaptations to their aquatic environment, among them high levels of the oxygen-carrying intracellular hemoprotein myoglobin in skeletal muscles, especially those responsible for swimming. Hypotheses regarding the mechanisms leading to these high myoglobin levels often invoke exercise, hypoxia, and other physiological pathways that impact gene regulation, and increase myoglobin gene expression. Here we explore an alternative hypothesis: that Cetacean myoglobin genes have evolved high levels of transcription driven by the intrinsic developmental mechanisms that drive muscle cell differentiation. We have used luciferase assays in differentiated C2C12 cells to test this hypothesis. Contrary to our hypothesis, we find that the myoglobin gene from the minke whale,Balaenoptera acutorostrata, has a low level of expression, less than 10% that of humans. This low expression level is broadly shared among Cetaceans, and Artiodactylans. Previous work on regulation of the human gene has identified a core muscle-specific enhancer comprised of two regions, the “AT element” and a C-rich sequence 5’ of the AT element termed the “CCAC-box”. Comparative analysis of the minke whale gene supports the importance of the AT element, but the minke whale CCAC-box ortholog has little effect. Instead, critical positive input has been identified in a G-rich region 3’ of the AT element. Also, a conserved E-box in exon 1 positively affects expression, despite having been assigned a repressive role in the human gene. Last, a novel region 5’ of the core enhancer has been identified, which we hypothesize may function as a boundary element. These results illustrate regulatory flexibility during evolution. They also support the hypothesis that the induction of transcription by physiological signaling pathways, and evolved protein stability are important in leading to the high myoglobin protein levels found in Cetaceans.
The Intestinal Clock Regulates Host Metabolism through the Fiber-Dependent Microbiome and Macronutrient Transcriptome
Authors: Heddes Marjolein , Niu Yunhui , Altaha Baraa , Kleigrewe Karin , Meng Chen , Haller Dirk , Kiessling Silke
Published: April 2023

Circadian disruption, e.g. through shift work, causes microbial dysbiosis and increases the risk of metabolic diseases. Microbial rhythmicity in mice depends on a functional intestinal clock and frequent jetlag as well as high-caloric energy intake induces loss of these oscillations. Similarly, arrhythmic microbiota was found in obese and T2D populations. However, the interplay between the intestinal circadian clock, the microbiome, diet and host metabolism is poorly understood.

In intestinal-specificBmal1knockout mice (Bmal1IEC-/-) we demonstrate the relevance of the intestinal clock in microbiome oscillations and host and microbial nutrient metabolism. Microbiota transfer fromBmal1IEC-/-mice into germ-free recipients led to obesity, reflected by increased bodyweight and fat mass. Western diet-fedBmal1IEC-/-miceincreased bodyweight likely through mechanisms involving the intestinal clock-control of lipid and hexose transporters. Additionally, we identified dietary fiber as novel link between circadian microbial rhythmicity, intestinal clock functioning and host physiology. Thus, revealing the potential of fiber-rich diet intervention as a non-invasive strategy targeting microbial oscillations in metabolic disease prevention.
Temperature-dependent modulation of odor-dependent behavior in three drosophilid fly species of differing thermal preference
Authors: Baleba Steve B. S. , Mahadevan Venkatesh Pal , Knaden Markus , Hansson Bill S
Published: April 2023

Rapid and ongoing climate change increases global temperature and impacts both feeding and reproduction in insects. The sense of smell plays an important underlying role in these behaviors in most insect species. Here, we aimed to investigate how changing temperatures affect odor detection and ensuing behavior in three drosophilid flies:Drosophila novamexicana,D. virilisandD. ezoana, species that have adapted to life in desert, global and subarctic climates, respectively. Using a series of thermal preference assays, we confirmed that the three species indeed exhibit distinct temperature preferences. Next, using single sensillum recording technique, we classified olfactory sensory neurons (OSNs) present in basiconic sensilla on the antenna of the three species and thereby identified ligands for each OSN type. In a series of trap assays we proceeded to establish the behavioral valence of the best ligands and chose guaiacol, methyl salicylate and isopropyl benzoate as representatives of a repellent, attractant and neutral odor. Next, we assessed the behavioral valence of these three odors in all three species across a thermal range (10-35 C), with flies reared at 18°C and 25°C. We found that both developmental and experimental temperatures affected the behavioral performance of the flies. Our study thus reveals temperature-dependent changes in odor-guided behavior in drosophilid flies.
Electron crystallography and dedicated electron-diffraction instrumentation
Authors: Simoncic Petra , Romeijn Eva , Hovestreydt Eric , Steinfeld Gunther , Santiso-Quiñones Gustavo , Merkelbach Johannes
Published: April 2023

Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.
The T2 structure of polycrystalline cubic human insulin
Authors: Triandafillidis Dimitris P. , Karavassili Fotini , Spiliopoulou Maria , Valmas Alexandros , Athanasiadou Maria , Nikolaras George , Fili Stavroula , Kontou Paraskevi , Bowler Matthew W. , Chasapis Christos T. , Von Dreele Robert B. , Fitch Andrew N. , Margiolaki Irene
Published: April 2023

The polymorphism of human insulin upon pH variation was characterized via X-ray powder diffraction, employing a crystallization protocol previously established for co-crystallization with phenolic derivatives. Two distinct rhombohedral (R3) polymorphs and one cubic (I213) polymorph were identified with increasing pH, corresponding to the T6, T3R3
f and T2 conformations of insulin, respectively. The structure of the cubic T2 polymorph was determined via multi-profile stereochemically restrained Rietveld refinement at 2.7 Å resolution. This constitutes the first cubic insulin structure to be determined from crystals grown in the presence of zinc ions, although no zinc binding was observed. The differences of the polycrystalline variant from other cubic insulin structures, as well as the nature of the pH-driven phase transitions, are discussed in detail.
Impact of difficult coworkers on employees' turnover intention: the mediating roles of perceived organizational support and affective commitment
Authors: To Wai Ming , Yu Billy T.W.
Published: April 2023

Purpose

This study explores the impact of difficult coworkers on employees' turnover intention. Additionally, this study investigates the roles of employees' attitude toward difficult coworkers, perceived organizational support and affective commitment in the relationship between difficult coworkers and turnover intention.

Design/methodology/approach

Based on the stimulus-organism-response theory, a theoretical model was established that linked difficult coworkers to employees' attitude toward the, then to turnover intention directly and indirectly through perceived organizational support and affective commitment. The model was validated using responses from 343 Chinese employees in Macao's banking industry.

Findings

Results of the partial least squares-structural equation modeling (PLS-SEM) showed that difficult coworkers significantly influenced employees' attitude toward them. Employees' attitude toward difficult coworkers had a small and significant effect on turnover intention while perceived organizational support and affective commitment mediated the relationship between attitude toward difficult coworkers and turnover intention.

Originality/value

The study is the first empirical study to employ the stimulus-organism-response theory to characterize the impact of difficult coworkers on turnover intention. Fortunately, perceived organizational support and affective commitment were able to lessen the impact of difficult coworkers on turnover intention.
Identifying critical challenges to lean construction adoption
Authors: Singh Arpit , Kumar Vimal , Mittal Ankesh , Verma Pratima
Published: April 2023

Purpose

This study aims to set out to identify and evaluate potential obstacles to successfully implementing lean construction (LC) as a result.

Design/methodology/approach

Several indicators were recognized as major obstacles following an exhaustive assessment of the literature and a multicriteria decision analysis based on the analytic hierarchy process (AHP) of information obtained from a questionnaire survey that was directed to practitioners in the Indian construction industry.

Findings

The results of this AHP model suggest that “Managerial” and “Inadequate resources” categories with a priority weight of “0.361” and “0.309” have the highest levels of influence, respectively, while “Inadequate knowledge” and “just in time (JIT)” categories with a priority weight of “0.053” and “0.034” have the lowest levels of influence, respectively.

Research limitations/implications

Construction companies can use the study’s findings as a guide to determine whether they are ready to embrace LC, learn more about the components needed for implementation or investigate any challenges that may arise. These businesses can then create plans to promote the adoption and application of the lean philosophy.

Originality/value

The Indian construction industry may see great success with LC management initiatives. LC concepts have been adopted by many nations, but during the past 20 years, there has only appeared to be a limited amount of lean implementation in the Indian construction industry. It seems that several structural and cultural barriers are preventing its effective implementation. Organizations will not be able to determine what improvement efforts are required, where these efforts should be directed or which initiatives could provide the best outcomes if they are unaware of the elements that influence the effective implementation of LC.
Value-dominant logic: organizational principles
Authors: Mahajan Gautam , Kumar V. , Tregua Marco , Bruni Roberto
Published: April 2023

Purpose

This paper aims to present the seven organizational principles for developing value-dominant logic (VDL) thinking and advancing it toward making a business purposeful and open to a lifestyle of value for humanity at large.

Design/methodology/approach

VDL considers value as rooted on axiology, actor-network theory, the hygge concept and is deployed through seven organizational principles deriving from the original eight VDL principles (Mahajan, 2017).

Findings

It is necessary to consider value in its polysemous meanings as an emergent element and a result of people’s interpretation based on norms and beliefs. At the same time, managers conceptualize businesses to create stimuli for the markets and society and favoring the emergence of a positive and sustainable value. This study explains how organizations and managers can be driven by norms and beliefs and a purpose to make decisions and assume postures and behaviors capable of stimulating the emergence of positive and sustainable value, creating opportunities for humanity at large; this managerial behavior creates conditions for value creation, and it is framed in VDL.

Research limitations/implications

A research agenda is provided that can spawn fruitful research in VDL.

Practical implications

This study develops the theoretical roots for a management approach that will support organizations and managers in interpreting their role as stimulators of value.

Social implications

The study focuses on the well-being and happiness of all the stakeholders.

Originality/value

The study developed organizational principles deeply rooted in the VDL.