bluuebunny/crossref_metadata_2025 huggingface dataset:
A Human Liver Organoid Screening Platform for DILI Risk Prediction
Authors: Zhang Charles J. , Meyer Sophia R. , O’Meara Matthew J. , Huang Sha , Capeling Meghan M. , Ferrer-Torres Daysha , Childs Charlie J. , Spence Jason R. , Fontana Robert J. , Sexton Jonathan Z.
Published: August 2021

Background and Aims

Drug-induced liver injury (DILI), both intrinsic and idiosyncratic, causes frequent morbidity, mortality, clinical trial failures and post-approval withdrawal. This suggests an unmet need for improved in vitro models for DILI risk prediction that can account for diverse host genetics and other clinical factors. In this study, we evaluated the utility of human liver organoids (HLOs) for high-throughput DILI risk prediction and in an organ-on-chip system.

Methods

HLOs were derived from 3 separate iPSC lines and benchmarked on two platforms for their ability to model in vitro liver function and identify hepatotoxic compounds using biochemical assays for albumin, ALT, and AST, microscopy-based morphological profiling, and single-cell transcriptomics: 1) HLOs dispersed in 384-well formatted plates and exposed to a library of compounds. 2) HLOs adapted to a liver-on-chip system.

Results

Dispersed HLOs derived from the 3 iPSC lines had similar DILI predictive capacity to intact HLOs in a high-throughput screening format allowing for measurable IC50 values of compound cytotoxicity. Distinct morphological differences were observed in cells treated with drugs exerting differing mechanisms of toxicity.

On-chip HLOs significantly increased albumin production, CYP450 expression, and ALT/AST release when treated with known DILI drugs compared to dispersed HLOs and primary human hepatocytes. On-chip HLOs were able to predict the synergistic hepatotoxicity of tenofovir-inarigivir and showed steatosis and mitochondrial perturbation via phenotypic and transcriptomic analysis with exposure to FIAU and acetaminophen, respectively.

Conclusions

The high throughput and liver-on-chip system exhibit enhanced in vivo-like function and demonstrate the potential utility of these platforms for hepatotoxicity risk assessment. Tenofovir-inarigivr associated hepatotoxicity was observed and correlates with the clinical manifestation of DILI observed in patients.

LAY SUMMARY

Idiosyncratic (spontaneous, patient-specific) drug-induced liver injury (DILI) is difficult to study due to the lack of liver models that function as human liver tissue and are adaptable for large-scale drug screening. Human liver organoids grown from patient stem cells respond to known DILI-causing drugs in both a high-throughput and on a physiological “chip” culture system. These platforms show promise in their use as predictive model for novel drugs before entering clinical trials.
Genome-wide local ancestry and direct evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus)
Authors: Ward James A. , McHugo Gillian P. , Dover Michael J. , Hall Thomas J. , Ismael Ng’ang’a Said , Sonstegard Tad S. , Bradley Daniel G. , Frantz Laurent A. F. , Salter-Townshend Michael , MacHugh David E.
Published: August 2021

The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humplessBos taurus(taurine) and humpedBos indicus(zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of a human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here we assess whether ancestry at mitochondrially-targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially-targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.

GRAPHICAL SUMMARY

Highlights

•

Using high-density genome-wide SNP data, we present evidence for mitonuclear coevolution in hybrid African cattle.

•

We observe a significant increase of taurine ancestry across multiple hybrid populations at mitochondrially-targeted nuclear genes.

•

Our results provide support for the hypothesis of mitonuclear incompatibility between the zebu nuclear genome and the taurine mitochondrial genome.
Methylmalonic acid impairs cell respiration and glutamate uptake in C6 rat glioma cells
Authors: Costa Renata T. , Santos Marcella B. , Alberto-Silva Carlos , Carrettiero Daniel C. , Ribeiro César A.J.
Published: August 2021

Methylmalonic acidemia is an organic acidemia caused by deficient activity of L-methylmalonyl-CoA mutase or its cofactor cyanocobalamin and it is biochemically characterized by an accumulation of methylmalonic acid (MMA) in tissue and body fluids of patients. The main clinical manifestations of this disease are neurological and observable symptoms during metabolic decompensation are encephalopathy, cerebral atrophy, coma, and seizures, which commonly appear in newborns. This study aimed to investigate the toxic effects of MMA in a glial cell line presenting astrocytic features. Astroglial C6 cells were exposed to MMA (0.1-10mM) for 24 or 48 hours and cell viability, glucose consumption and oxygen consumption rate, as well as glutamate uptake and ATP content were analyzed. The possible preventive effects of bezafibrate were also evaluated. MMA significantly reduced cell viability after 48-hour period and increased glucose consumption during the same period of incubation. Regarding the energy homeostasis, MMA significantly reduced respiratory parameters of cells after 48-hour exposition, indicating that cell metabolism is compromised at resting and reserve capacity state, which might influence the cell capacity to meet energetic demands. Glutamate uptake and ATP content were also compromised after exposition to MMA, which can be influenced energy metabolism impairment, affecting the functionality of the astroglial cells. Our findings suggest that these effects could be involved in the pathophysiology of neurological dysfunction of this disease.
Cryptococcus neoformans melanization incorporates multiple catecholamines to produce polytypic melanin
Authors: Baker Rosanna P. , Chrissian Christine , Stark Ruth E. , Casadevall Arturo
Published: August 2021

Melanin is a major virulence factor in pathogenic fungi that enhances the ability of fungal cells to resist immune clearance. Cryptococcus neoformans is an important human pathogenic fungus that synthesizes melanin from exogenous tissue catecholamine precursors during infection, but the type of melanin made in cryptococcal meningoencephalitis is unknown. We analyzed the efficacy of various catecholamines found in brain tissue in supporting melanization using animal brain tissue and synthetic catecholamine mixtures reflecting brain tissue proportions. Solid-state NMR spectra of the melanin pigment produced from such mixtures yielded more melanin than expected if only the preferred constituent dopamine had been incorporated, suggesting uptake of additional catecholamines. Probing the biosynthesis of melanin using radiolabeled catecholamines revealed that C. neoformans melanization simultaneously incorporated more than one catecholamine, implying that the pigment was polytypic in nature. Nonetheless, melanin derived from individual or mixed catecholamines had comparable ability to protect C. neoformans against ultraviolet light and oxidants. Our results indicate that melanin produced during infection differs depending on the catecholamine composition of tissue and that melanin pigment synthesized in vivo is likely to accrue from the polymerization of a mixture of precursors. From a practical standpoint our results strongly suggest that using dopamine as a polymerization precursor is capable of producing melanin pigment comparable to that produced during infection. On a more fundamental level our findings uncover additional structural complexity for natural cryptococcal melanin by demonstrating that pigment produced during human infection is likely to be composed of polymerized moieties derived from chemically different precursors.
Mitochondrial pyruvate supports lymphoma proliferation by fueling a non-canonical glutamine metabolism pathway
Authors: Wei Peng , Bott Alex J. , Cluntun Ahmad A. , Morgan Jeffrey T. , Cunningham Corey N. , Schell John C. , Ouyang Yeyun , Ficarro Scott B. , Marto Jarrod A. , Danial Nika N. , DeBerardinis Ralph J. , Rutter Jared
Published: August 2021

The fate of pyruvate, which is modulated by the activity of the mitochondrial pyruvate carrier (MPC), is a defining metabolic feature in many cancers. Diffuse large B-cell lymphomas (DLBCLs) are a genetically and metabolically heterogeneous cancer. Although MPC expression and activity differed between DLBCL subgroups, mitochondrial pyruvate was uniformly consumed by glutamate pyruvate transaminase 2 (GPT2) to support α-ketoglutarate production as part of glutaminolysis. This led us to discover that glutamine exceeds pyruvate as a carbon source for the tricarboxylic acid (TCA) cycle in DLBCLs. Furthermore, we found that MPC inhibition unexpectedly leads to decreased glutaminolysis, which is contrary to previous observations in other cell types. We also discovered that MPC inhibition and depletion only decreased DLBCL proliferation in an extracellular matrix (ECM) environment and in vivo xenografts, but not in the typical DLBCL suspension environment. We also have found that the metabolic profile of DLBCL cells in ECM is markedly different from cells in suspension environment. Thus, we report that besides the canonical glutamate dehydrogenase (GDH)-mediated glutaminolysis, the non-canonical GPT2 mediated consumption and assimilation of glutamine and pyruvate in DLBCLs enables their proliferation in an extracellular environment-dependent manner.

HIGHLIGHTS

Glutamine, but not glucose, is a major carbon source for the tricarboxylic acid cycle in diffuse large B-cell lymphomas.

Mitochondrial pyruvate supports glutaminolysis in diffuse large B-cell lymphomas by supplying pyruvate for glutamate pyruvate transaminase 2-mediated α -ketoglutarate production.

Mitochondrial pyruvate carrier inhibition leads to decreased glutaminolysis in diffuse large B-cell lymphomas.

α -ketoglutarate production is important for diffuse large B-cell lymphoma proliferation in a solid extracellular matrix environment.

Mitochondrial pyruvate carrier activity supports diffuse large B-cell lymphoma proliferation in a solid extracellular matrix environment and in mouse xenografts.
Optical Cellular Micromotion: A New Paradigm to Measure Tumour Cells Invasion in 3D Tumour Environments
Authors: Guo Zhaobin , Yang Chih-Tsung , Chien Chia-Chi , Selth Luke A. , Bagnaninchi Pierre O. , Thierry Benjamin
Published: August 2021

Measuring tumour cell invasiveness through three-dimensional (3D) tissues, particularly at the single cell level, can provide important mechanistic understanding and assist in identifying therapeutic targets of tumour invasion. However, current experimental approaches, including standard in vitro invasion assays, have limited physiological relevance and offer insufficient insight about the vast heterogeneity in tumour cell migration through tissues. To address these issues, here we report on the concept of optical cellular micromotion, where digital holographic microscopy (DHM) is used to map the optical thickness fluctuations at sub-micron scale within single cells. These fluctuations are driven by the dynamic movement of subcellular structures including the cytoskeleton and inherently associated with the biological processes involved in cell invasion within tissues. We experimentally demonstrate that the optical cellular micromotion correlates with tumour cells motility and invasiveness both at the population and single cell levels. In addition, the optical cellular micromotion significantly reduced upon treatment with migrastatic drugs that inhibit tumour cell invasion. These results demonstrate that micromotion measurements can rapidly and non-invasively determine the invasive behaviour of single tumour cells within tissues, yielding a new and powerful tool to assess the efficacy of approaches targeting tumour cell invasiveness.

Significance Statement

Tumour cells invasion through tissues is a key hallmark of malignant tumour progression and its measurement is essential to unraveling biological processes and screening for new approaches targeting cell motility. To address the limitations of current approaches, we demonstrate that sub-micron scale mapping of the dynamic optical thickness fluctuations within single cells, referred to as optical cellular micromotion, correlates with their motility in ECM mimicking gel, both at the population and single cell levels. We anticipate that 3D optical micromotion measurement will provide a powerful new tool to address important biological questions and screen for new approaches targeting tumour cell invasiveness.
Thermosynechococcus switches the direction of phototaxis by a c-di-GMP dependent process with high spatial resolution
Authors: Nakane Daisuke , Enomoto Gen , Wilde Annegret , Nishizaka Takayuki
Published: August 2021

Many cyanobacteria, which use light as an energy source via photosynthesis, show directional movement towards or away from a light source. However, the molecular and cell biological mechanisms for switching the direction of movement remain unclear. Here, we visualized type IV pilus-dependent cell movement in the rod-shaped thermophilic cyanobacterium Thermosynechococcus vulcanus using optical microscopy at physiological temperature and light conditions. Positive and negative phototaxis were controlled on a short time scale of 1 min. The cells smoothly moved over solid surfaces towards green light, but the direction was switched to backward movement when we applied additional blue light illumination. The switching was mediated by three photoreceptors, SesA, SesB and SesC, which have cyanobacteriochrome photosensory domains and synthesis/degradation activity of the bacterial second messenger cyclic dimeric GMP (c-di-GMP). Our results suggest that the decision-making process for directional switching in phototaxis involves light-dependent changes in the cellular concentration of c-di-GMP. Furthermore, we reveal that rod-shaped cells can move perpendicular to the light vector, indicating that the polarity can be controlled not only by pole-to-pole regulation but also within-a-pole regulation. This study provides insights into previously undescribed rapid bacterial polarity regulation via second messenger signalling with high spatial resolution.
A promiscuity locus confers Lotus burttii nodulation with rhizobia from five different genera
Authors: Zarrabian Mohammad , Montiel Jesús , Sandal Niels , Jin Haojie , Lin Yen-Yu , Klingl Verena , Marín Macarena , James Euan , Parniske Martin , Stougaard Jens , Andersen Stig U.
Published: August 2021

Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil dwelling organisms and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, where the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity QTL to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for host-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions.
Development and Characterization of a Weaned Pig Model of Shiga Toxin–Producing E. coli-Induced Gastrointestinal Disease
Authors: Boeckman Justin X. , Sprayberry Sarah , Korn Abby , Suchodolski Jan S. , Paulk Chad , Genovese Kenneth , Rech Raquel R. , Giaretta Paula R. , Blick Anna , Callaway Todd , Gill Jason J.
Published: August 2021

Post-weaning enteropathies in swine caused by pathogenic E. coli, such as post-weaning diarrhea (PWD) or edema disease (ED), remain a significant problem for the swine industry. Reduction in the use of antibiotics over concerns of antibiotic resistance and public health concerns, necessitate the evaluation of effective antibiotic alternatives to prevent significant loss of livestock and/or reductions in swine growth performance. For this purpose, an appropriate piglet model of enterotoxigenic E. coli enteropathy is required. In this study, we attempted to induce clinical signs of post-weaning disease in a piglet model using a one-time acute or lower daily chronic dose of a Shiga toxin–producing and enterotoxigenic E. coli strain. The induced disease state was monitored by determining fecal shedding and colonization of the challenge strain, animal growth performance, cytokine levels, fecal calprotectin, histology, fecal metabolomics, and fecal microbiome shifts. The most informative analyses were colonization and shedding of the pathogen, serum cytokines, metabolomics, and targeted metagenomics to determine dysbiosis. Histopathological changes of the gastrointestinal (GI) tract and tight junction leakage as measured by fecal calprotectin concentrations were not observed. Chronic dosing was similar to the acute regimen suggesting that a high dose of pathogen, as used in many studies, may not be necessary. The piglet disease model presented here can be used to evaluate alternative PWD treatment options. Furthermore, this relatively mild disease model presented here may be informative for modeling human chronic gastrointestinal diseases, such as inflammatory bowel disease, which otherwise require invasive procedures for study.

Importance

Post-weaning diarrhea remains a significant problem in swine production and appropriate models of pathogenesis are needed to test alternative treatment options. In this study, we present an E. coli induced piglet model for post-weaning diarrhea, and also explore its translational potential as a model for human intestinal inflammation. Our study here presents two firsts to our knowledge. 1) The first simultaneous analysis of the intestinal microbiome and metabolome through fecal sampling of piglets challenged with Shiga toxin–producing E. coli. This is valuable given the limited metabolomics data from swine in various disease states. 2) A comparison of the clinical signs caused by a daily chronic vs one-time dosing regimen of E. coli. This comparison is key as infection by pathogenic E. coli in real-world settings likely occurs from chronic exposure to contaminated food, water, or environment rather than the highly concentrated dose of pathogen that is commonly given in the literature.
Current attitudes towards HIV viral load self-testing: thematic analysis of a consultation with potential end-users
Authors: Gliddon Harriet D , McKendry Rachel A , Gibbs Jo
Published: August 2021

Background

HIV viral load (VL) is key to monitoring response to antiretroviral therapy. A number of point-of-care HIV VL tests are in development. These tests could be repurposed for HIV VL self-testing.

Methods

We held a patient and public involvement (PPI) consultation for people living with HIV to explore the prospect of HIV viral load self-testing. We conducted a thematic analysis on the data from this consultation.

Results

Key themes were access, convenience, usability, technical aspects, technology potential, connectivity and confidentiality. Attendees expressed significant appetite for decentralised HIV care, including HIV VL self-testing.

Conclusions

This PPI consultation can help researchers developing HIV viral load self-testing technology to better understand the needs of potential end users. Our findings will help guide the development and implementation of HIV VL self-testing.
Training and Development Needs Assessment in a large NIHR Biomedical Research Centre: A Survey
Authors: Bell Karen , Shah Syed Ghulam Sarwar , Henderson Lorna R. , Kiparoglou Vasiliki
Published: August 2021

Objective

To assess the training and development needs of researchers and support staff affiliated to the NIHR Oxford Biomedical Research Centre (BRC), one of the largest BRCs in England, and to find out about their past experiences of training.

Design

A cross-sectional online questionnaire survey.

Setting and Participants

A convenience sample of clinicians, nurses, midwives, allied health professionals, researchers and support staff (N=798) affiliated with the NIHR Oxford Biomedical Research Centre.

Primary and secondary outcome measures

The primary outcome measure was the type of training and the secondary outcome measures were the duration, location and timing of training.

Results

The response rate was 24%. Of 189 respondents, 114 were women (60%) and 75 men (40%). Respondents included research scientists (31%), medical doctors and dentists (17%), nurses and midwives (16%) and research managers and administrators (16%). Seventy-one percent respondents (n=134) reported attending at least one training activity in the last year and the most wanted training was leadership skills (25%), followed by research grant and fellowship writing (18%) and statistical analysis (16%). An ideal length of a training course was half a day (41%), whole day (25%) and 1-2 hours (22%). The most preferred time of the day for training was morning (60%) and afternoon (22%) and the favoured delivery style of training was an interactive workshop (52%), lecture/talk (25%), online (9%) and practical activities (9%). The main barriers to attending training courses were the lack of time (n-18%), work commitments (13%), and childcare responsibilities (6%).

Conclusions

Translational researchers and supporting affiliates want short, easily accessible, interactive training sessions, particularly leadership training skills and grant and fellowship writing. However, practical elements are important too e.g. in a convenient location during the working day. Work commitment is the biggest obstacle in doing training.

Strengths and limitations of this study

This survey was done to develop and revamp the NIHR Oxford BRC’s training programme that met the training and development needs of our researchers and research support staff.

Leadership skills, research grant and fellowship writing, statistical analysis were the most wanted training.

The lack of time, work commitments, and childcare responsibilities were the main barriers to attending training courses.

Our findings have limited generalisability because the study is based on the responses of participants who are affiliated with only one NIHR BRC; hence, these findings could not be generalised to other NIHR BRCs.

These findings might inform the training and development programmes in other NIHR BRCs in the country.
Novel Coronavirus Pandemic Impacts Children and Adolescents’ Psychological Well-Being in Heavily Hit Chinese Provinces
Authors: Ma Jing , Ding Jun , Hu Jiawen , Wang Kai , Xiao Shuaijun , Luo Ting , Yu Shuxiang , Liu Chuntao , Xu Yunxuan , Liu Yingxian , Wang Changhong , Guo Suqin , Yang Xiaohua , Song Haidong , Geng Yaoguo , Jin Yu , Chen Huayun , Liu Chunyu
Published: August 2021

Abstracts

In light of the novel coronavirus’s (COVID-19’s) threat to public health worldwide, we sought to elucidate COVID-19’s impacts on the mental health of children and adolescents in China. Through online self-report questionnaires, we aimed to discover the psychological effects of the pandemic and its associated risk factors for developing mental health symptoms in young people.

We disseminated a mental health survey through online social media, WeChat, and QQ in the five Chinese provinces with the most confirmed cases of COVID-19 during the late stage of the country-wide lockdown. We used a self-made questionnaire that queried children and adolescents aged 6 to 18 on demographic information, psychological status, and other lifestyle and COVID-related variables.

A total of 17,740 children and adolescents with valid survey data participated in the study. 10,022 (56.5%), 11,611 (65.5%), 10,697 (60.3%), 6,868 (38.7%), and 6,225 (35.1%) participants presented, respectively, more depressive, anxious, compulsive, inattentive, and sleep-related problems compared to before the outbreak of COVID-19. High school students reported a greater change in depression and anxiety than did middle school and primary school students. Despite the fact that very few children (0.1%) or their family members (0.1%) contracted the virus in this study, the psychological impact of the pandemic was clearly profound. Fathers’ anxiety appeared to have the strongest influence on a children’s psychological symptoms, explaining about 33% of variation in the child’s overall symptoms. Other factors only explained less than 2% of the variance in symptoms once parents’ anxiety was accounted for.

The spread of COVID-19 significantly influenced the psychological state of children and adolescents. It is clear that children and adolescents, particularly older adolescents, need mental health support during the pandemic. The risk factors we uncovered suggest that reducing fathers’ anxiety is particularly critical to addressing young people’s mental health disorders in this time.
Physical Activity Moderates Inflammatory Gene Expression in Rheumatoid Arthritis
Authors: Patterson Sarah L. , Sun Shenghuan , Rychkov Dmitry , Katz Patricia , Tsitsiklis Alexandra , Nakamura Mary C. , Serpa Paula Hayakawa , Langelier Charles R , Sirota Marina
Published: August 2021

Background

While general population studies have shown associations between greater physical activity and lower inflammatory markers, effects of physical activity on inflammatory pathways in rheumatoid arthritis (RA) remain unknown. We aimed to determine whether physical activity independently associates with differential expression of inflammatory genes in RA.

Methods

Data derived from an observational RA cohort. Physical activity was measured with the GT9X ActiGraph Link device. RNA extraction from peripheral blood, sequencing library preparation and transcriptomic analyses were performed using established methods. Genes differentially expressed in the most versus least physically active groups (top versus bottom activity tertiles) were identified using DESeq2 after adjusting for sex, age, race/ethnicity, and disease activity. Ingenuity Pathway Analysis (IPA) was employed to identify canonical biological pathways and upstream regulating cytokines associated with physical activity.

Results

35 participants were enrolled (mean age 56±12 years; 91% female; race/ethnicity 31% white, 9% African American, 9% Asian, 40% Hispanic). 767 genes were differentially expressed (padj<0.1) between high versus low activity groups. The high activity group exhibited downregulation of innate and adaptive immune signaling pathways, including CD40, STAT3, TREM-1, IL-17a, IL-8, toll-like receptor and interferon signaling. Upstream cytokine analysis demonstrated inhibition of TNF-alpha and interferon among individuals in the most active group.

Conclusion

In a racially diverse RA cohort, patients who were more physically active had lower expression of immune signaling pathways implicated in RA pathogenesis, even after adjusting for disease activity, suggesting a potential protective effect of physical activity in RA.
Balancing growth amidst salinity stress – lifestyle perspectives from the extremophyte model Schrenkiella parvula
Authors: Tran Kieu-Nga , Pantha Pramod , Wang Guannan , Kumar Narender , Wijesinghege Chathura , Oh Dong-Ha , Duppen Nick , Li Hongfei , Hong Hyewon , Johnson John C. , Kelt Ross , Matherne Megan G. , Clement Ashley , Tran David , Crain Colt , Adhikari Prava , Zhang Yanxia , Foroozani Maryam , Sessa Guido , Larkin John C. , Smith Aaron P. , Longstreth David , Finnegan Patrick , Testerink Christa , Barak Simon , Dassanayake Maheshi
Published: August 2021

Schrenkiella parvula, a leading extremophyte model in Brassicaceae, can grow and complete its life cycle under multiple environmental stresses, including high salinity. While foundational genomic resources have been created for S. parvula, a comprehensive physiological or structural characterization of its salt stress responses is absent. We aimed to identify the influential traits that lead to stress-resilient growth of this species. We examined salt-induced changes in the physiology and anatomy of S. parvula throughout its lifecycle across multiple tissues. We found that S. parvula maintains or even exhibits enhanced growth during various developmental stages at salt stress levels known to inhibit growth in Arabidopsis and most crops. The resilient growth of S. parvula was associated with key traits that synergistically allow continued primary root growth, expansion of xylem vessels across the root-shoot continuum, and a high capacity to maintain tissue water levels by developing larger and thicker leaves while facilitating continued photosynthesis during salt stress. These traits at the vegetative phase were followed by a successful transition to the reproductive phase via early flowering, development of larger siliques, and production of viable seeds during salt stress. Additionally, the success of self-fertilization during early flowering stages was dependent on salt-induced filament elongation in flowers that aborted in the absence of salt. Our results suggest that the maintenance of leaf water status and enhancement of selfing in early flowers to ensure reproductive success, are among the most influential traits that contribute to the extremophyte lifestyle of S. parvula in its natural habitat.

One sentence summary

Schrenkiella parvula salt-resilient growth is facilitated by uncompromised primary root growth, expansion of xylem vessels, maintenance of leaf water status and photosynthesis, and early flowering.
The thymic microenvironment gradually modulates the phenotype of thymus-homing peripheral conventional dendritic cells
Authors: Herppich Susanne , Beckstette Michael , Huehn Jochen
Published: August 2021

Thymic conventional dendritic cells (t-DCs) are crucial for the development of T cells. A substantial fraction of t-DCs originates extrathymically and migrates to the thymus. Here, these cells contribute to key processes of central tolerance like the clonal deletion of self-reactive thymocytes and the generation of regulatory T (Treg) cells. So far, it is only incompletely understood which impact the thymic microenvironment has on thymus-homing conventional DCs (cDCs), which phenotypic changes occur after the entry of peripheral cDCs into the thymus and which functional properties these modulated cells acquire. In the present study, we mimicked the thymus-homing of peripheral cDCs by introducing ex vivo isolated splenic cDCs (sp-DCs) into re-aggregated thymic organ cultures (RTOCs). Already after two days of culture, the transcriptomic profile of sp-DCs was modulated and had acquired certain key signatures of t-DCs. The regulated genes included immunomodulatory cytokines and chemokines as well as co-stimulatory molecules. After four days of culture, sp-DCs appeared to have at least partially acquired the peculiar Treg cell-inducing capacity characteristic of t-DCs. Taken together, our findings indicate that peripheral cDCs possess a high degree of plasticity enabling them to quickly adapt to the thymus-specific microenvironment. We further provide indirect evidence that thymus-specific properties such as the efficient induction of Treg cells under homeostatic conditions can be partially transferred to thymus-homing peripheral cDC subsets.
Long-Read Sequencing of the Zebrafish Genome Reorganizes Genomic Architecture
Authors: Chernyavskaya Yelena , Zhang Xiaofei , Liu Jinze , Blackburn Jessica S.
Published: August 2021

Nanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Although long-read sequencing has been used to resolve several vertebrate genomes, a nanopore-based zebrafish assembly has not yet been released. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers. We used nanopore sequencing to improve upon and resolve the issues plaguing the current zebrafish reference assembly (GRCz11). Our long-read assembly improved the current resolution of the reference genome by identifying 1,697 novel insertions and deletions over 1Kb in length and placing 106 previously unlocalized scaffolds. We also discovered additional sites of retrotransposon integration previously unreported in GRCz11 and observed their expression in adult zebrafish under physiologic conditions, implying they have active mobility in the zebrafish genome and contribute to the ever-changing genomic landscape.
An improved iCLIP protocol
Authors: Lee Flora C. Y. , Chakrabarti Anob M. , Hänel Heike , Monzón-Casanova Elisa , Hallegger Martina , Militti Cristina , Capraro Federica , Sadée Christoph , Toolan-Kerr Patrick , Wilkins Oscar , Turner Martin , König Julian , Sibley Christopher R. , Ule Jernej
Published: August 2021

Crosslinking and Immunoprecipitation (CLIP) is a powerful technique to obtain transcriptome-wide maps of in vivo protein-RNA interactions, which are important to understand the post-transcriptional mechanisms mediated by RNA binding proteins (RBPs). Many variant CLIP protocols have been developed to improve the efficiency and convenience of cDNA library preparation. Here we describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions, and with public eCLIP and iCLIP PTBP1 data. We visualised enriched motifs surrounding the identified crosslink positions and RNA maps of these crosslinks around the alternative exons regulated by PTBP1. Notably, motif enrichment was higher in iiCLIP and iCLIP2 in comparison to public eCLIP and iCLIP, and we show how this impacts the specificity of RNA maps. In conclusion, iiCLIP is technically convenient and efficient, and enables production of highly specific datasets for identifying RBP binding sites.
Fear of parasitism affects the functional role of ecosystem engineers
Authors: Mouritsen Kim N. , Dalsgaard Nina P. , Flensburg Sarah B. , Madsen Josefine C. , Selbach Christian
Published: August 2021

Fear is an integrated part of predator-prey interactions with cascading effects on the structure and function of ecosystems. Fear of parasitism holds a similar ecological potential but our understanding of the underlying mechanisms in host-parasite interactions is limited by lack of empirical examples. Here, we experimentally test if blue musselsMytilus edulisrespond behaviourally to the mere presence of infective transmission stages of the trematodeHimasthla elongataby ceasing filtration activity, thereby avoiding infection. Our results show that blue mussels reduced clearance rates by more than 30% in presences of parasites. The reduced filtration activity resulted in lower infection rates in experimental mussels. The identified parasite-specific avoidance behaviour can be expected to play a significant role in regulating the ecosystem engineering function of blue mussels in coastal habitats.
Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat
Authors: Masoomi-Aladizgeh Farhad , Kamath Karthik Shantharam , Haynes Paul A. , Atwell Brian J.
Published: August 2021

Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian heat-tolerant cotton (Gossypium robinsonii) was exposed to heat events during pollen development, then mature pollen was subjected to deep proteomic analysis using 57,023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads, uninucleate and binucleate microspores were exposed to 36°C or 40°C for 5 d and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using SWATH-MS proteomic analysis, 2,704 proteins were identified and quantified across all pollen samples analyzed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of tetrads to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased mRNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
An integrated model for termination of RNA polymerase III transcription
Authors: Xie Juanjuan , Aiello Umberto , Clement Yves , Haidara Nouhou , Girbig Mathias , Schmitzova Jana , Pena Vlad , Müller Christoph W. , Libri Domenico , Porrua Odil
Published: August 2021

RNA polymerase III (RNAPIII) synthesizes essential and abundant non-coding RNAs such as tRNAs. Controlling RNAPIII span of activity by accurate and efficient termination is a challenging necessity to ensure robust gene expression and to prevent conflicts with other DNA-associated machineries. The mechanism of RNAPIII termination is believed to be simpler than that of other eukaryotic RNA polymerases, solely relying on the recognition of a T-tract in the non-template strand. Here we combine high-resolution genome-wide analyses and in vitro transcription termination assays to revisit the mechanism of RNAPIII transcription termination in budding yeast. We show that T-tracts are necessary but not always sufficient for termination and that secondary structures of the nascent RNAs are important auxiliary cis-acting elements. Moreover, we show that the helicase Sen1 plays a key role in a fail-safe termination pathway. Our results provide a comprehensive model illustrating how multiple mechanisms cooperate to ensure efficient RNAPIII transcription termination.
Invariant neural dynamics drive commands to control different movements
Authors: Athalye Vivek R. , Khanna Preeya , Gowda Suraj , Orsborn Amy L. , Costa Rui M. , Carmena Jose M.
Published: August 2021

It has been proposed that the nervous system has the capacity to generate a wide variety of movements because it re-uses some invariant code. Previous work has identified that dynamics of neural population activity are similar during different movements, where dynamics refer to how the instantaneous spatial pattern of population activity changes in time. Here we test whether invariant dynamics of neural populations are actually used to issue the commands that direct movement. Using a brain-machine interface that transformed rhesus macaques’ motor cortex activity into commands for a neuroprosthetic cursor, we discovered that the same command is issued with different neural activity patterns in different movements. However, these different patterns were predictable, as we found that the transitions between activity patterns are governed by the same dynamics across movements. These invariant dynamics are low-dimensional, and critically, they align with the brain-machine interface, so that they predict the specific component of neural activity that actually issues the next command. We introduce a model of optimal feedback control that shows that invariant dynamics can help transform movement feedback into commands, reducing the input that the neural population needs to control movement. Altogether our results demonstrate that invariant dynamics drive commands to control a variety of movements, and show how feedback can be integrated with invariant dynamics to issue generalizable commands.
The adaptive role of cell death in yeast communities stressed with macrolide antifungals
Authors: Kireeva N. , Sokolov S.S. , Smirnova E.A. , Galkina K.V. , Severin F.F. , Knorre D.A.
Published: August 2021

Microorganisms cooperate with each other to protect themselves from environmental stressors. An extreme case of such cooperation is regulated cell death for the benefit of other cells. Dying cells can provide surviving cells with nutrients or induce their stress-response by transmitting an alarm signal; however, the role of dead cells in microbial communities is unclear. Here we searched for types of stressors the protection from which can be achieved by death of a subpopulation of cells. Thus, we compared the survival of Saccharomyces cerevisiae cells upon exposure to various stressors in the presence of additionally supplemented living versus dead cells. We found that dead cells contribute to yeast community resistance against macrolide antifungals (e.g. amphotericin B [AmB] and filipin) to a greater extent than living cells. Dead yeast cells absorbed more macrolide filipin than control cells because they exposed intracellular sterol-rich membranes. We also showed that, upon the addition of lethal concentrations of AmB, supplementation with AmB-sensitive cells but not with AmB-resistant cells enabled the survival of wild-type cells. Together, our data suggests that cell-to-cell heterogeneity in sensitivity to AmB can be an adaptive mechanism helping yeast communities to resist macrolides, which are naturally occurring antifungal agents.

Importance

Eukaryotic microorganisms harbour elements of programmed cell death (PCD) mechanisms that are homologous to the PCD of multicellular metazoa. However, it is still debated whether microbial PCD has an adaptive role or the processes of cell death are an aimless operation in self-regulating molecular mechanisms. Here, we demonstrated that dying yeast cells provide an instant benefit for their community by absorbing macrolides, which are bacteria-derived antifungals. Our results illustrate the principle that the death of a microorganism can contribute to the survival of its kin and suggest that early plasma membrane permeabilization improves community-level protection. The latter makes a striking contrast to the manifestations of apoptosis in higher eukaryotes, the process by which plasma membranes maintain integrity.
Gene function prediction in five model eukaryotes based on gene relative location through machine learning
Authors: Pazos Obregón Flavio , Silvera Diego , Soto Pablo , Yankilevich Patricio , Guerberoff Gustavo , Cantera Rafael
Published: August 2021

Motiviation

The function of most genes is unknown. The best results in gene function prediction are obtained with machine learning-based methods that combine multiple data sources, typically sequence derived features, protein structure and interaction data. Even though there is ample evidence showing that a gene’s function is not independent of its location, the few available examples of gene function prediction based on gene location relay on sequence identity between genes of different organisms and are thus subjected to the limitations of the relationship between sequence and function.

Results

Here we predict thousands of gene functions in five eukaryotes (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens) using machine learning models trained with features derived from the location of genes in the genomes to which they belong. To the best of our knowledge this is the first work in which gene function prediction is successfully achieved in eukaryotic genomes using predictive features derived exclusively from the relative location of the genes.

Contact

fpazos@iibce.edu.uy

Supplementary information

http://gfpml.bnd.edu.uy
Nuclear soluble cGAS senses DNA virus infection
Authors: Wu Yakun , Song Kun , Hao Wenzhuo , Wang Lingyan , Li Shitao
Published: August 2021

The cytosolic DNA sensor cGAS detects foreign DNA from pathogens or self-DNA from cellular damage and instigates type I interferon (IFN) expression. Recent studies find that cGAS also localizes in the nucleus and binds the chromatin. Despite how cGAS is inhibited in the nucleus is well elucidated, whether nuclear cGAS participates in DNA sensing is not clear. Here, we report that herpes simplex virus 1 (HSV-1) infection caused the release of cGAS from the chromatin into the nuclear soluble fraction. Like its cytosolic counterpart, the leaked nuclear soluble cGAS could sense viral DNA, produce cGAMP, and induce mRNA expression of type I IFN and interferon-stimulated genes. Furthermore, the nuclear cGAS limited HSV-1 infection. Taken together, our study demonstrates that HSV-1 infection releases cGAS from the chromatin tethering and, in turn, the nuclear soluble cGAS activates type I IFN production.
mobileOG-db: a manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements
Authors: Brown Connor L. , Mullet James , Hindi Fadi , Stoll James E. , Gupta Suraj , Choi Minyoung , Keenum Ishi , Vikesland Peter , Pruden Amy , Zhang Liqing
Published: August 2021

Currently available databases of bacterial mobile genetic elements (MGEs) contain both “core” and accessory MGE functional modules, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, limits the usability of these databases for MGE annotation. To overcome this limitation, we analysed 10,776,212 protein sequences derived from seven MGE databases to compile a comprehensive database of 6,140 manually curated protein families that are linked to the “life cycle” (integration, excision, replication/recombination/repair, transfer, and stability/defense) of all major classes of bacterial MGEs. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid, integrative element) derived from the source database, and assign a list of keywords to each entry to delineate different MGE functional modules and to facilitate annotation. The resulting database, mobileOG-db (for mobile orthologous groups), provides a simple and readily interpretable foundation for an array of MGE-centred analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can browse and design, refine, and analyse custom subsets of the dynamic mobilome.