bluuebunny/crossref_metadata_2025 huggingface dataset:
Decreased overall neuronal activity in a rodent model of impaired consciousness during absence seizures
Authors: McCafferty Cian , Gruenbaum Benjamin , Tung Renee , Li Jing-Jing , Salvino Peter , Vincent Peter , Kratochvil Zachary , Ryu Jun Hwan , Khalaf Aya , Swift Kohl , Akbari Rashid , Islam Wasif , Antwi Prince , Johnson Emily Ann , Vitkovskiy Petr , Sampognaro James , Freedman Isaac , Kundishora Adam , Sanganahalli Basavaraju G. , Herman Peter , Hyder Fahmeed , Crunelli Vincenzo , Depaulis Antoine , Blumenfeld Hal
Published: April 2021

Absence seizures are characterized by a brief behavioural impairment including apparent loss of consciousness. Neuronal mechanisms determining the behavioural impairment of absence seizures remain unknown, and their elucidation might highlight therapeutic options for reducing seizure severity. However, recent studies have questioned the similarity of animal spike-wave-discharges (SWD) to human absence seizures both behaviourally and neuronally. Here, we report that Genetic Absence Epilepsy Rats from Strasbourg recapitulate the decreased neuroimaging signals and loss of consciousness characteristic of human absence seizures. Overall neuronal firing is decreased but rhythmic in the somatosensory cortex and thalamus during these seizures. Interestingly, individual neurons in both regions tend to consistently express one of four distinct patterns of seizure-associated activity. These patterns differ in firing rate dynamics and in rhythmicity during seizure. One group of neurons showed a transient initial peak in firing at SWD onset, accounting for the brief initial increase in overall neuronal firing seen in cortex and thalamus. The largest group of neurons in both cortex and thalamus showed sustained decreases in firing during SWD. Other neurons showed either sustained increases or no change in firing. These findings suggest that certain classes of cortical and thalamic neurons may be particularly responsible for the paroxysmal oscillations and consequent loss of consciousness in absence epilepsy.
Developmental stage- and site-specific transitions in lineage specification and gene regulatory networks in human hematopoietic stem and progenitor cells
Authors: Roy Anindita , Wang Guanlin , Iskander Deena , O’Byrne Sorcha , Elliott Natalina , O’Sullivan Jennifer , Buck Gemma , Heuston Elisabeth F. , Wen Wei Xiong , Meira Alba Rodriguez , Hua Peng , Karadimitiris Anastasios , Mead Adam J , Bodine David , Roberts Irene , Psaila Bethan , Thongjuea Supat
Published: April 2021

Human hematopoiesis is a dynamic process that startsin utero4 weeks post-conception. Understanding the site- and stage-specific variation in hematopoiesis is important if we are to understand the origin of hematological disorders, many of which occur at specific points in the human lifespan. To unravel how the hematopoietic stem/progenitor cell (HSPC) compartments change during human ontogeny and the underlying gene regulatory mechanisms, we compared 57,489 HSPCs from 5 different tissues spanning 4 developmental stages through the human lifetime. Single-cell transcriptomic analysis identified significant site- and developmental stage-specific transitions in cellular architecture and gene regulatory networks. Uncommitted stem cells showed progression from cycling to quiescence and increased inflammatory signalling during ontogeny. We demonstrate the utility of this dataset for understanding aberrant hematopoiesis through comparison to two cancers that present at distinct timepoints in postnatal life – juvenile myelomonocytic leukemia, a childhood cancer, and myelofibrosis, which classically presents in older adults.
Quantifying ERK-activity in response to inhibition of the BRAFV600E-MEK-ERK cascade using mathematical modelling
Authors: Hamis Sara , Kapelyukh Yury , McLaren Aileen , Henderson Colin J. , Wolf C. Roland , Chaplain Mark A.J.
Published: April 2021

Background

Simultaneous inhibition of multiple components of the BRAF-MEK-ERK cascade (vertical inhibition) has become a standard of care for treating BRAF-mutant melanoma. However, the molecular mechanism of how vertical inhibition synergistically suppresses intracellular ERK-activity, and consequently cell proliferation, are yet to be fully elucidated.

Methods

We develop a mechanistic mathematical model that describes how the mutant BRAF-inhibitor, dabrafenib, and the MEK-inhibitor, trametinib, affect BRAFV600E-MEK-ERK signalling. The model is based upon a system of chemical reactions that describes cascade signalling dynamics. Using mass action kinetics, the chemical reactions are re-expressed as ordinary differential equations which are parameterised byin vitrodata and solved numerically to obtain the temporal evolution of cascade component concentrations.

Results

The model provides a quantitative method to compute how dabrafenib and trametinib can be used in combination to synergistically inhibit ERK-activity in BRAFV600E-mutant melanoma cells. The model elucidates molecular mechanisms of vertical inhibition of the BRAFV600E-MEK-ERK cascade and delineates how elevated BRAF concentrations generate drug resistance to dabrafenib and trametinib. The computational simulations further suggest that elevated ATP levels could be a factor in drug resistance to dabrafenib.

Conclusions

The model can be used to systematically motivate which dabrafenib-trametinib dose-combinations, for treating BRAFV600E-mutated melanoma, warrant experimental investigation.
Mesoporous silica particles functionalized with newly extracted fish oil (Omeg@Silica) inhibit lung cancer cell growth
Authors: Di Sano Caterina , D’Anna Claudia , Scurria Antonino , Lino Claudia , Pagliaro Mario , Ciriminna Rosaria , Pace Elisabetta
Published: April 2021

Omeg@Silicamicroparticles consisting of whole fish oil rich in omega-3 lipids, vitamin D3and zeaxanthin extracted with biobased limonene from anchovy fillet leftovers (AnchoisOil) encapsulated within mesoporous silica particles are highly effective in modulating oxidative stress, mitochondrial damage or in promoting antitumor effects in lung cancer cells. A panel of three different human non-small cell lung cancer (NSCLC) cell lines (A549, Colo 699 and SKMES) was used. Cancer cells were treated withAnchoisOildispersed in ethanol (10 and 15 μg/ml) or encapsulated in silica, and cell cycle, reactive oxigen species (ROS) and mitochondrial stress (MitoSOX) assessed by flow cytometry. The effects on long-term proliferation (clonogenic assay) were also evaluated. The sub-micronOmeg@Silicamicroparticles were more effective than fish oil alone in increasing ROS and mitocondrial damage, in altering cell cycle as well as in reducing colony formation ability in the tested lung cancer cell lines. These results suggest thatOmeg@Silicamesoporous silica functionalized with whole fish oil has antitumor effects in NSCLC cell lines and support its investigation in lung cancer therapy.
Single-cell analysis reveals MHCII expressing keratinocytes in pressure ulcers with worse healing outcomes
Authors: Li Dongqing , Cheng Shangli , Pei Yu , Sommar Pehr , Kärner Jaanika , Herter Eva K. , Toma Maria A. , Zhang Letian , Pham Kim , Cheung Yuen Ting , Chen Xingqi , Eidsmo Liv , Deng Qiaolin , Landén Ning Xu
Published: April 2021

Pressure ulcer (PU) is a chronic wound often seen in spinal cord injury patients and other bed-bound individuals, particularly in the elderly population. Despite its association with high mortality, the pathophysiology of PU remains poorly understood. Here, we compared single-cell transcriptomic profiles of human epidermal cells from PU wound edges with those from uninjured skin and acute wounds (AWs) in healthy donors. We identified significant shifts in the cell composition and gene expression patterns in PU. In particular, we found that major histocompatibility complex class II (MHCII) expressing keratinocytes were enriched in patients with worse healing outcomes. Furthermore, we showed that the IFNγ in PU-derived wound fluid could induce MHCII expression in keratinocytes and that these wound fluid-treated keratinocytes inhibited autologous T cell activation. In line with this observation, we found that T cells from PUs enriched with MHCII+ keratinocytes produced fewer inflammatory cytokines. Overall, our study provides a high-resolution molecular map of human PU compared to AW and intact skin, providing new insights into PU pathology and the future development of tailored wound therapy.
A model of the CA1 field rhythms
Authors: I.E. Mysin
Published: April 2021

We propose a model of the main rhythms in the hippocampal CA1 field: theta rhythm, slow, middle, and fast gamma rhythms, and ripples oscillations. We have based this on data obtained from animals behaving freely. We have considered the modes of neuronal discharges and the occurrence of local field potential (LFP) oscillations in the theta and non-theta states at different inputs from the CA3 field, the medial entorhinal cortex, and the medial septum. In our work, we tried to reproduce the main experimental phenomena about rhythms in the CA1 field: the coupling of neurons to the phase of rhythms, cross-rhythm phase-phase and phase-amplitude coupling. Using computational experiments, we have proved the hypothesis that the descending phase of the theta rhythm in the CA1 field is formed by the input from the CA3 field via the Shaffer collaterals, and the ascending phase of the theta rhythm is formed by the inhibitory postsynaptic potentials from CCK basket cells. The slow gamma rhythm is coupled to the descending phase of the theta rhythm, since it also depends on the arrival of the signal via the Shaffer collaterals. The middle gamma rhythm is formed by the excitatory postsynaptic potentials of the principal neurons of the third layer of the entorhinal cortex, corresponds to experimental data. We were able to unite in a single mathematical model several theoretical ideas about the mechanisms of rhythmic processes in the CA1 field of the hippocampus.
Focal DNA hypo-methylation in cancer is mediated by transcription factors binding
Authors: Detilleux Dylane , Spill Yannick G , Balaramane Delphine , Weber Michaël , Bardet Anaïs Flore
Published: April 2021

Aberrant DNA methylation has emerged as a hallmark of cancer cells and profiling their epigenetic landscape has widely been carried out in many types of cancer. However, the mechanisms underlying changes in DNA methylation remain elusive. Transcription factors, initially thought to be repressed from binding by DNA methylation, have recently emerged as potential drivers of DNA methylation patterns. Here we perform a rigorous bioinformatic analysis integrating the massive amount of data available from The Cancer Genome Atlas to identify transcription factors driving aberrant DNA methylation. We predict TFs known to be involved in cancer as well as novel candidates to drive hypo-methylated regions such as FOXA1 and GATA3 in breast cancer, FOXA1 and TWIST1 in prostate cancer and NFE2L2 in lung cancer. We also predict TFs that lead to hyper-methylated regions upon TF loss such as EGR1 in several cancer types. Finally, we validate experimentally that FOXA1 and GATA3 mediate hypo-methylated regions in breast cancer cells. Our work shows the importance of TFs as upstream regulators shaping DNA methylation patterns in cancer.
Surrogate production of genome edited sperm from a different subfamily by spermatogonial stem cell transplantation
Authors: Zhang Fenghua , Li Xianmei , Hao Yongkang , Li Yi , Ye Ding , He Mudan , Wang Houpeng , Zhu Zuoyan , Sun Yonghua
Published: April 2021

The surrogate reproduction technique provides a powerful tool for production of allogenic or xenogeneic gametes derived from endangered species or those with valuable genetic traits. Production of functional donor-derived gametes through intra- or inter-specific spermatogonial stem cell transplantation (SSCT) has been achieved in many species. However, generation of functional gametes from a phylogenetically distant species such as from a different subfamily by SSCT has never been successful. Here, using two small cyprinid fishes, Chinese rare minnow (gobiocypris rarus, for brief:Gr) and zebrafish (danio rerio), which belong to different subfamilies, as donors and recipients for SSCT, we optimized the SSCT technique and successfully obtainedGr-derived sperm carrying targeted genome modifications in zebrafish. We revealed that the transplantedGrspermatogonia supported the host gonadal development and underwent normal spermatogenesis, resulting in a reconstructed fertile testis containingGrspermatids and zebrafish testicular somatic cells. Interestingly, the surrogate spermatozoa resembled those of host zebrafish but not donorGrin morphology and swimming behavior. Finally, we showed thatGr-derived genome edited sperm was successfully produced in zebrafish by cross-subfamily SSCT, when thepou5f3andchdgene knockoutGrSSCs were used as surrogate donors. This is the first report demonstrating the surrogate production of genome edited sperm from a phylogenetically distant species, and this method is feasible to be applied to future breeding of commercial fishes.
Disentangling the effects of past logging and ongoing cryptic anthropogenic disturbance on vegetation structure and composition in Himalayan Foothills, India
Authors: Kaushik Monica , Dutta Sutirtha , Rawat Gopal S. , Singh Pratap , Mohan Dhananjai
Published: April 2021

Most tropical forests have undergone commercial logging. Even where logging has ceased, subsistence harvest of forest resources often persists especially in South-East Asia. Understanding of impacts of frequent forest resources extraction in areas recovering from past selective logging would be essential for designing the appropriate management interventions.

We studied the impacts of current chronic anthropogenic disturbances (hereafter CAD) and past selective logging on vegetation structure, diversity, and regeneration, and the invasion of a non-native shrub,Lantana camara, in three major forest types in the Himalayan foothills, India. We analyzed field data on intensity of CAD and vegetation variables, collected from 269 stratified random plots, using ordination and generalized linear (mixed) modeling approaches.

Our results, based on 2758 adult trees of 54 species, showed that forest types differed in disturbance regimes depending on protection level and availability of fodder tree species. Intensity of CAD depended on proximity to settlements (for livestock related disturbances). Whereas selective logging, including firewood collection, was associated with land protection status. Selective logging reduced the extent of mature forest but facilitated regeneration, thereby promoting secondary forest features such as tree density and canopy cover. In contrast, the interaction between lopping and selective logging was negatively associated with regeneration. Past logging facilitatedL. camarainvasion in Dry and Hill forests but not in Moist forest. Finally, while selective logging marginally enhanced tree diversity, CAD reduced native shrub diversity.

Our study demonstrates that selective logging followed by CAD arrest forest recovery, as evident from the suppression of mature forest elements, loss of shrub biomass, reduced regeneration rate, and facilitation of invasive species. To abate these impacts, alternative livelihood/subsistence options that sustain forests and local communities should be explored. Additionally, CAD management should be site-specific as local ecological contexts modify their impacts on forests.
Comparative anatomy and phylogenetic contribution of intracranial osseous canals and cavities in armadillos and glyptodonts (Xenarthra, Cingulata)
Authors: Le Verger Kévin , González Ruiz Laureano R. , Billet Guillaume
Published: April 2021

The evolutionary history of the Cingulata, as for many groups, remains a highly debated topic to this day, particularly for one of their most emblematic representatives: the glyptodonts. There is no consensus among morphological and molecular phylogenies relative to their position within Cingulata. As demonstrated by recent works, the study of the internal anatomy constitutes a promising path for enriching morphological matrices for the phylogenetic study of armadillos. However, internal cranial anatomy remains under-studied in the Cingulata. Here we explored and compared the anatomy of intracranial osseous canals and cavities in a diverse sample of extant and extinct cingulates, including the earliest well-preserved glyptodont crania. The virtual 3D reconstruction (using X-ray microtomography) of selected canals, i.e., the nasolacrimal canal, the palatine canal, the sphenopalatine canal, the canal for the frontal diploic vein, the transverse canal, the orbitotemporal canal, the canal for the capsuloparietal emissary vein and the posttemporal canal, and alveolar cavities related to cranial vascularization, innervation or tooth insertion allowed us to compare the locations, trajectories and shape of these structures and to discuss their potential interest for cingulate systematics. We tentatively reconstructed evolutionary scenarios for eight selected traits on these structures, in which glyptodonts often showed a greater resemblance to pampatheres, to the genusProeutatusand/or to chlamyphorines. This latter pattern was partly congruent with recent molecular hypotheses, but more research is needed on these resemblances and on the potential effects of development and allometry on the observed variations. Overall, these comparisons have enabled us to highlight new anatomical variation that may be of great interest to further explore the evolutionary history of cingulates and the origins of glyptodonts on a morphological basis.
A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines
Authors: Chen Ying , Davidson Nadia M. , Wan Yuk Kei , Patel Harshil , Yao Fei , Low Hwee Meng , Hendra Christopher , Watten Laura , Sim Andre , Sawyer Chelsea , Iakovleva Viktoriia , Lee Puay Leng , Xin Lixia , Ng Hui En Vanessa , Loo Jia Min , Ong Xuewen , Ng Hui Qi Amanda , Wang Jiaxu , Koh Wei Qian Casslynn , Poon Suk Yeah Polly , Stanojevic Dominik , Tran Hoang-Dai , Lim Kok Hao Edwin , Toh Shen Yon , Ewels Philip Andrew , Ng Huck-Hui , Iyer N.Gopalakrishna , Thiery Alexandre , Chng Wee Joo , Chen Leilei , DasGupta Ramanuj , Sikic Mile , Chan Yun-Shen , Tan Boon Ooi Patrick , Wan Yue , Tam Wai Leong , Yu Qiang , Khor Chiea Chuan , Wüstefeld Torsten , Pratanwanich Ploy N. , Love Michael I. , Goh Wee Siong Sho , Ng Sarah B. , Oshlack Alicia , Göke Jonathan ,   SG-NEx consortium
Published: April 2021

The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing. To systematically evaluate the ability to study the transcriptome at a resolution of individual isoforms we profiled 5 human cell lines with short read cDNA sequencing and Nanopore long read direct RNA, amplification-free direct cDNA, PCR-cDNA sequencing. The long read protocols showed a high level of consistency, with amplification-free RNA and cDNA sequencing being most similar. While short and long reads generated comparable gene expression estimates, they differed substantially for individual isoforms. We find that increased read length improves read-to-transcript assignment, identifies interactions between alternative promoters and splicing, enables the discovery of novel transcripts from repetitive regions, facilitates the quantification of full-length fusion isoforms and enables the simultaneous profiling of m6A RNA modifications when RNA is sequenced directly. Our study demonstrates the advantage of long read RNA sequencing and provides a comprehensive resource that will enable the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.
Relationship between Deceleration Morphology and Phase Rectified Signal Averaging-based Parameters during Labor
Authors: Rivolta Massimo W. , Barbieri Moira , Stampalija Tamara , Sassi Roberto , Frasch Martin G.
Published: April 2021

During labor, uterine contractions trigger the response of the autonomic nervous system (ANS) of the fetus, producing sawtooth-like decelerations in the fetal heart rate (FHR) series. Under chronic hypoxia, ANS is known to regulate FHR differently with respect to healthy fetuses. In this study, we hypothesized that such different ANS regulation might also lead to a change in the FHR deceleration morphology. The hypothesis was tested in an animal model comprising 7 normoxic and 5 chronically hypoxic fetuses that underwent a protocol of umbilical cord occlusions (UCOs). Deceleration morphologies in the fetal inter-beat time interval (FRR) series were modeled using a trapezoid with four parameters, i.e., baselineb, deceleration deptha, UCO response timeτuand recovery timeτr. Comparing normoxic and hypoxic sheep, we found a clear difference forτu(24.8 ± 9.4 vs 39.8 ± 9.7 s;p <0.05),a(268.1 ± 109.5 vs 373.0 ± 46.0 ms;p <0.1) and Δτ=τu−τr(13.2 ± 6.9 vs 23.9 ± 7.5 s;p <0.05). Therefore, the animal model supported the hypothesis that hypoxic fetuses have a longer response timeτuand larger asymmetry Δτas a response to UCOs. Assessing these morphological parameters during labor is challenging due to non-stationarity, phase desynchronization and noise. For this reason, in the second part of the study, we quantified whether acceleration capacity (AC), deceleration capacity (DC), and deceleration reserve (DR), computed through Phase-Rectified Signal Averaging (PRSA, known to be robust to noise), were correlated with the morphological parameters. DR and DC correlated with Δτandτufor a wide range of the PRSA parameterT(max Pearson’s correlationρ= 0.9,p <0.05, andρ= 0.6,p <0.1, respectively). In conclusion, deceleration morphologies have been found to differ between normoxic and hypoxic sheep fetuses during UCOs. The same difference can be assessed through PRSA based parameters, further motivating future investigations on the translational potential of this methodology on human data.
Assessment of the pollution incident performance of water and sewerage companies in England
Authors: Purnell Sarah , Mills Nick , Davis Keith , Joyce Christopher
Published: April 2021

Comparison of water and sewerage company pollution performance in relation to severity, frequency and self-reporting of pollution incidents is made difficult by differences in environmental and operational conditions. In England, the deterioration in pollution incident performance across the water industry, makes it important to investigate common trends that could be addressed at national and regional levels. Yet, to date there has been no external peer-reviewed analysis of national pollution incident data in England. This project aimed to analyse available pollution incident data to assess and compare the performance of water and sewerage companies in England. Results indicated that there was significant variation in pollution incident numbers and the severity of the impact on the water environment for different asset types (operational property of the water and sewerage company such as a sewage treatment works). Increasing numbers of pollution incidents from pumping stations and sewage treatment works, were largely responsible for overall increases in pollution incidents. The highest increase in pollution incidents in 2019, was observed from pumping stations. Variation was evident in company self-reporting percentages across asset types. There were significant positive relationships between the self-reporting percentages of pollution incidents and total numbers of reported pollution incidents per 10,000 km sewer length for pumping stations and sewage treatment works. These results indicate that in at least these asset types, an estimated 5% of pollution incidents could go unreported, if not self-reported by the company. Pollution events not reported quickly by companies, can lead to more severe impacts to the water environment so rapid and consistent reporting of incidents is crucial for limiting damage. The results have significance for the water industry internationally, because the issues presented here are not restricted to England. Whilst this research highlighted a number of key areas for more detailed analysis, in the short-term, research should focus on investigating best practice for reporting pollution incidents. It is important to get an accurate baseline of the number of pollution incidents and whether a proportion are currently going unreported. This research should seek to aid the standardisation of reporting practice across the water industry.
Isolation and characterization of novel temperate virusAeropyrumglobular virus 1 infecting hyperthermophilic archaeonAeropyrum
Authors: Yumiya Maho , Fukuyama Yuto , Sako Yoshihiko , Yoshida Takashi
Published: April 2021

We isolate a novel archaeal temperate virus namedAeropyrumglobular virus 1 (AGV1) from the hostAeropyrumculture. Reproduction of AGV1 was induced by adding 20 mM tris-acetate buffer to exponentially growing host cells. Negatively stained virions showed spherical morphology (60 ±2 nm in diameter) similar toGlobuloviridaeviruses. The double-stranded circular DNA genome of AGV1 contains 18,222 bp encoding 34 open-reading frames. No ORFs showed significant similarity withGlobuloviridaeviruses. AGV1 shares three genes, including an integrase gene, with reported spindle-shaped temperate viruses. However we couldn’t detect its integration site in the host genome. Moreover AGV1 seemed not to replicate autonomously because there are no origin recognition boxes in the genome. qPCR results showed that the genome copy number of AGV1 was lower than that of the host genome (10−3copies per host genome). Upon the addition of tris-acetate buffer, a steep increase in the AGV1 genome copy number (9.5–26 copies per host genome at 2 days post-treatment) was observed although clustered regularly interspaced short palindromic repeat (CRISPR) elements of the host genome showed significant matches with AGV1 protospacers. Our findings suggest that AGV1 is a novel globular virus exhibiting an unstable carrier state in the growing host and in that way AGV1 can escape from the host defense system and propagate under stressful host conditions.

Importance

Studying archaeal viruses yields novel insights into the roles of virospheres and viruses in the evolutionary process of their hosts. Here, we isolated a novel spherical virus namedAeropyrumglobular virus 1. AGV1 has integrase gene but its genome is not integrated into the host genome. AGV1 could not replicate autonomously due to the lack of origin recognition boxes and thus its copy number was too low (10−3copies per host genome) without any inducing stimulus. However, upon the addition of tris-acetate buffer, the AGV1 genome copy number steeply increased instead of a perfect sequence match between the spacer of the host CRISPR/Cas system and the protospacer. Our findings suggest that AGV1 can escape from the host defense system and propagate under stressful conditions for the host by establishing an unstable carrier state. These results reveals a novel aspect of host–virus interactions in extreme environments.
Hydrogen sulfide blocks HIV rebound by maintaining mitochondrial bioenergetics and redox homeostasis
Authors: Pal Virender Kumar , Agrawal Ragini , Rakshit Srabanti , Shekar Pooja , Narasimha Murthy Diwakar Tumkur , Vyakarnam Annapurna , Singh Amit
Published: April 2021

A fundamental challenge in HIV eradication is to understand how the virus establishes latency, maintains stable cellular reservoirs, and promotes rebound upon interruption of antiretroviral treatment (ART). Here, we discovered an unexpected role of the ubiquitous gasotransmitter hydrogen sulfide (H2S) in HIV latency and reactivation. We show that reactivation of HIV-1 is associated with down-regulation of the key H2S producing enzyme cystathionine-γ-lyase (CTH) and reduction in endogenous H2S. Genetic silencing of CTH disrupts redox homeostasis, impairs mitochondrial function, and remodels the transcriptome of latent cells to trigger HIV reactivation. Chemical complementation of CTH activity using a slow-releasing H2S donor, GYY4137, suppressed HIV reactivation and diminished virus replication. Mechanistically, GYY4137 blocked HIV reactivation by inducing the Keap1-Nrf2 pathway, inhibiting NF-κB, and recruiting the epigenetic silencer, YY1, to the HIV promoter. In latently infected CD4+T cells from ART-suppressed human subjects, GYY4137 in combination with ART prevented viral rebound and improved mitochondrial bioenergetics. Moreover, prolonged exposure to GYY4137 exhibited no adverse influence on proviral content or CD4+T cell subsets, indicating that diminished viral rebound is due to a loss of transcription rather than a selective loss of infected cells. In summary, this work provides mechanistic insight into H2S-mediated suppression of viral rebound and suggests the inclusion of an H2S donor in the current ART regimen to achieve a functional HIV-1 cure.
General object-based features account for letter perception
Authors: Janini Daniel , Hamblin Chris , Deza Arturo , Konkle Talia
Published: April 2021

After years of experience, humans become experts at perceiving letters. Is this visual capacity attained by learning specialized letter features, or by reusing general visual features previously learned in service of object categorization? To explore this question, we first measured the perceptual similarity of letters in two behavioral tasks, visual search and letter categorization. Then, we trained deep convolutional neural networks on either 26-way letter categorization or 1000-way object categorization, as a way to operationalize possible specialized letter features and general object-based features, respectively. We found that the general object-based features more robustly correlated with the perceptual similarity of letters. We then operationalized additional forms of experience-dependent letter specialization by altering object-trained networks with varied forms of letter training; however, none of these forms of letter specialization improved the match to human behavior. Thus, our findings reveal that it is not necessary to appeal to specialized letter representations to account for perceptual similarity of letters. Instead, we argue that it is more likely that the perception of letters depends on domain-general visual features.

AUTHOR SUMMARY

For over a century, scientists have conducted behavioral experiments to investigate how the visual system recognizes letters, but it has proven difficult to propose a model of the feature space underlying this capacity. Here we leveraged recent advances in machine learning to model a wide variety of features ranging from specialized letter features to general object-based features. Across two large-scale behavioral experiments we find that general object-based features account well for letter perception, and that adding letter specialization did not improve the correspondence to human behavior. It is plausible that the ability to recognize letters largely relies on general visual features unaltered by letter learning.
Leveraging probability concepts for genotype by environment recommendation
Authors: Dias Kaio O.G. , dos Santos Jhonathan P.R. , Krause Matheus D. , Piepho Hans-Peter , Guimarães Lauro J.M. , Pastina Maria M. , Garcia Antonio A.F.
Published: April 2021

Statistical models that capture the phenotypic plasticity of a genotype across environments are crucial in plant breeding programs to potentially identify parents, generate offspring, and obtain highly productive genotypes for distinct environments. In this study, our aim is to leverage concepts of Bayesian models and probability methods of stability analysis to untangle genotype-by-environment interaction (GEI). The proposed method employs the posterior distribution obtained with the No-U-Turn sampler algorithm to get Monte Carlo estimates of adaptation and stability probabilities. We applied the proposed models in two empirical tropical datasets. Our findings provide a basis to enhance our ability to consider the uncertainty of cultivar recommendation for global or specific adaptation. We further demonstrate that probability methods of stability analysis in a Bayesian framework are a powerful tool for unraveling GEI given a defined intensity of selection that results in a more informed decision-making process towards cultivar recommendation in multi-environment trials.
NAC transcription factor RD26 is a regulator of root hair morphogenic plasticity
Authors: Kamranfar Iman , Balazadeh Salma , Mueller-Roeber Bernd
Published: April 2021

Root hairs are outgrowths of epidermal cells central for water and nutrient acquisition. Root hair growth is plastically modified by environmental cues. A frequent response to water limitation is active shortening of root hairs, involving largely unknown molecular mechanisms. A root hair-specificcis-regulatory element (RHE) integrates developmental cues with downstream signalling of root hair morphogenesis. Here, we demonstrate NAC transcription factor RD26 to be a key expressional regulator of this drought stress-triggered developmental response inArabidopsis thaliana. RD26 directly repressesRSL4andRSL1, two master transcription regulators of root hair morphogenesis, by binding RHE. RD26 further represses core cell wall modification genes including expansins (EXPA7,EXPA18), hydroxyproline-rich glycoproteins (LRX1), xyloglucan endotransglucosylases/hydrolases (XTH12,13,14,26), class III peroxidases (PRX44) and plasma membrane H+-ATPase (AHA7) through RHE. Of note, several RD26-repressed genes are activated by RSL4. Thus, by repressing RSL4 and numerous cell wall-related genes, RD26 governs a robust gene regulatory network for restricting root hair growth under drought. A similar regulatory network exists in tomato, indicating evolutionary conservation across species.

Significance statement

In plants, root hairs play a vital role for water and nutrient acquisition, soil anchorage, and microbial interactions. During drought stress, root hair growth is suppressed as an adaptive strategy to save cellular energy. We identified NAC transcription factor RD26 as a key regulator of this developmental plasticity in the model plantArabidopsis thaliana. RD26 directly and negatively controls the transcriptional activity of key root hair developmental genes,RSL1andRSL4. Furthermore, RD26 suppresses the expression of several functional genes underlying root hair development including numerous cell wall-related genes. RD26 thus governs a robust gene regulatory network underlying the developmental response to drought stress. A similar regulatory network exists in tomato indicating evolutionary conservation of this mechanism across species.
FACT subunit SUPT16H associates with BRD4 and contributes to silencing of antiviral interferon signaling
Authors: Zhou Dawei , Park Jun-Gyu , Wu Zhenyu , Huang Huachao , Fiches Guillaume N. , Biswas Ayan , Li Tai-Wei , Ma Qin , Martinez-Sobrido Luis , Santoso Netty , Zhu Jian
Published: April 2021

Summary/Abstract

FACT (FAcilitatesChromatinTranscription) is a heterodimeric protein complex composed of SUPT16H and SSRP1, and a histone chaperone participating in chromatin remodeling during gene transcription. FACT complex is profoundly regulated, and contributes to both gene activation and suppression. Here we reported that SUPT16H, a subunit of FACT, is acetylated at lysine 674 (K674) of middle domain (MD), which involves TIP60 histone acetyltransferase. Such acetylation of SUPT16H is recognized by bromodomain protein BRD4, which promotes protein stability of SUPT16H. We further demonstrated that SUPT16H-BRD4 associates with histone modification enzymes (EZH2, HDAC1) and affects histone marks (H3K9me3, H3K27me3 and H3ac). BRD4 is known to profoundly regulate interferon (IFN) signaling, while such function of SUPT16H has never been explored. Surprisingly, our results revealed that SUPT16H genetic knockdown via RNAi or pharmacological inhibition by using its inhibitor, curaxin 137 (CBL0137), results in the induction of IFNs and interferon-stimulated genes (ISGs). Through this mechanism, CBL0137 is shown to efficiently inhibit infection of multiple viruses, including Zika, influenza, and SARS-CoV-2. Furthermore, we demonstrated that CBL0137 also causes the remarkable activation of IFN signaling in natural killer (NK) cells, which promotes the NK-mediated killing of virus-infected cells in a co-culture system using human primary NK cells. Overall, our studies unraveled the previously un-appreciated role of FACT complex in regulating IFN signaling in both epithelial and NK cells, and also proposed the novel application of CBL0137 to treat viral infections.
The non-redundant nature of the Axin2 regulatory network in the canonical Wnt signaling pathway
Authors: Moshkovsky Ana R , Kirschner Marc W
Published: April 2021

Axin is one of two essential scaffolds in the canonical Wnt pathway that converts signals at the plasma membrane to signals inhibiting the degradation of β-catenin, leading to its accumulation and specific gene activation. In vertebrates there are two forms of Axin, Axin1 and Axin2, which are similar at the protein level and genetically redundant. We show here that differential regulation of the two genes on the transcriptional and proteostatic level confers robustness and differential responsiveness that can be used in tissue specific regulation. Such subtle features may distinguish other redundant gene pairs that are commonly found in vertebrates through gene knockout experiments.

Significance Statement

The mystery of two functionally redundant Axin genes in all vertebrates are can now be explained by the demonstration that they form a nested proteostatic and transcriptional feedback system that confers regulatory options in different developmental settings, a form of dynamic versatility that may explain the widespread occurrence of closely related seemingly redundant genes with similar functions.
Fast Bayesian inference of phylogenies from multiple continuous characters
Authors: Zhang Rong , Drummond Alexei J. , Mendes Fábio K.
Published: April 2021

Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remains challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counter-parts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods’ properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method’s behavior, and suggest future research venues.
Segment number threshold determines juvenile onset of germline cluster proliferation inPlatynereis dumerilii
Authors: Kuehn Emily , Clausen David S. , Null Ryan W. , Metzger Bria M. , Willis Amy D. , Özpolat B. Duygu
Published: April 2021

Many animals rely on sexual reproduction to propagate by using gametes (oocytes and sperm). Development of sexual characters and generation of gametes are tightly coupled with the growth of an organism.Platynereis dumeriliiis a marine segmented worm which has been used to study germline development and gametogenesis.Platynereishas 4 Primordial Germ Cells (PGCs) that arise early in development and these cells are thought to give rise to germ cell clusters found across the body in the juvenile worms. The germ cell clusters eventually form the gametes. The stages of germline development and how the 4 PGCs become the numerous germ cell clusters are not well-documented in the juvenile stages.Platynereis, like other segmented worms, grows by adding new segments at its posterior end. The number of segments generally reflect the growth state of the worms and therefore is a useful and easily measurable growth state metric. To understand how growth correlates with development and gametogenesis, we investigated germline development across several developmental stages using germline/multipotency markers. We found that segment number predicted the state of germline development and the abundance of germline clusters. Additionally, we found that keeping worms short in segment number via changing external conditions or via amputations supported segment number threshold requirement for germline development. Finally, we asked if these clusters inPlatynereisplay a role in regeneration (as similar free-roaming cells are observed inHydraand planarian regeneration) and found that the clusters were not required for regeneration inPlatynereis, suggesting a strictly germline nature. Overall, these molecular analyses suggest a previously unidentified developmental transition dependent on the growth state in juvenilePlatynereiswhen germline proliferation is substantially increased.
Redox sensitive E2 Rad6 controls cellular response to oxidative stress via K63 ubiquitination of ribosomes
Authors: Simões Vanessa , Harley Lana , Cizubu Blanche K. , Zhou Ye , Pajak Joshua , Snyder Nathan A. , Bouvette Jonathan , Borgnia Mario J. , Arya Gaurav , Bartesaghi Alberto , Silva Gustavo M.
Published: April 2021

Protein ubiquitination is an essential process that rapidly regulates protein synthesis, function, and fate in dynamic environments. Among its non-proteolytic functions, K63 ubiquitin accumulates in yeast cells exposed to oxidative stress, stalling ribosomes at elongation. K63 ubiquitin conjugates accumulate because of redox inhibition of the deubiquitinating enzyme Ubp2, however, the role and regulation of ubiquitin conjugating enzymes in this pathway remained unclear. Here we found that the E2 Rad6 binds and modifies elongating ribosomes during oxidative stress. We elucidated a mechanism by which Rad6 and its human homolog UBE2A are redox-regulated by forming reversible disulfides with the E1 activating enzyme, Uba1. We further showed that Rad6 activity is necessary to regulate translation, antioxidant defense, and adaptation to stress. Finally, we showed that Rad6 is required to induce phosphorylation of the translation initiation factor eIF2α, providing a novel link for K63 ubiquitin, elongation stalling, and the integrated stress response.
Structures of active melanocortin-4 receptor−Gs-protein complexes with NDP-α-MSH and setmelanotide
Authors: Heyder Nicolas A. , Kleinau Gunnar , Speck David , Schmidt Andrea , Paisdzior Sarah , Szczepek Michal , Bauer Brian , Koch Anja , Gallandi Monique , Kwiatkowski Dennis , Bürger Jörg , Mielke Thorsten , Beck-Sickinger Annette , Hildebrand Peter W. , Spahn Christian M. T. , Hilger Daniel , Schacherl Magdalena , Biebermann Heike , Hilal Tarek , Kühnen Peter , Kobilka Brian K. , Scheerer Patrick
Published: April 2021

The melanocortin-4 receptor (MC4R), a hypothalamic master regulator of energy homeostasis and appetite, is a G-protein coupled receptor and a prime target for the treatment of obesity. Here, we present cryo-electron microscopy structures of MC4R− Gs-protein complexes with two recently FDA-approved drugs, the peptide agonists NDP-α-MSH and setmelanotide, with 2.9 Å and 2.6 Å resolution. Together with signaling data, the complex structures reveal the agonist-induced origin of transmembrane helix (TM) 6 regulated receptor activation. In both structures, different ligand binding modes of NDP-α-MSH, a high-affinity variant of the endogenous agonist, and setmelanotide, an anti-obesity drug with biased signaling, underline the key role of TM3 for ligand-specific interactions and of calcium ion as a ligand-adaptable cofactor. The agonist-TM3 interplay subsequently impacts the receptor− Gs-protein interfaces, mainly at intracellular loop 2. These structures reveal mechanistic details of MC4R activation or inhibition and provide important insights into receptor selectivity that will facilitate the development of tailored anti-obesity drugs.
3D Flexible Refinement: Structure and Motion of Flexible Proteins from Cryo-EM
Authors: Punjani Ali , Fleet David J.
Published: April 2021

Single particle cryo-EM excels in determining static structures of biological macromolecules such as proteins. However, many proteins are dynamic, with their motion inherently linked to their function. Recovering the continuous motion and detailed 3D structure of flexible proteins from cryo-EM data has remained an open challenge. We introduce3D Flexible Refinement(3DFlex), a motion-based deep neural network model of continuous heterogeneity. 3DFlex directly exploits the knowledge that conformational variability of a protein is often the result of physical processes that transport density over space and tend to conserve mass and preserve local geometry. From 2D image data, the 3DFlex model jointly learns a single canonical 3D map, latent coordinate vectors that specify positions on the protein’s conformational landscape, and a flow generator that, given a latent position as input, outputs a 3D deformation field. This deformation field convects the canonical map into appropriate conformations to explain experimental images. Applied to experimental data, 3DFlex learns non-rigid motion spanning several orders of magnitude while preserving high-resolution details of secondary structure elements. Further, 3DFlex resolves canonical maps that are improved relative to conventional refinement methods because particle images contribute to the maps coherently regardless of the conformation of the protein in the image. Together, the ability to obtain insight into motion in macromolecules, as well as the ability to resolve features that are usually lost in cryo-EM of flexible specimens, will provide new insight and allow new avenues of investigation into biomolecular structure and function.
Citrullination of a phage displayed human peptidome library reveals the fine specificities of rheumatoid arthritis-associated autoantibodies
Authors: Román-Meléndez Gabriel D. , Monaco Daniel R. , Montagne Janelle M. , Quizon Rachel S. , Konig Maximilian F. , Astatke Mekbib , Darrah Erika , Larman H. Benjamin
Published: April 2021

Post-translational modifications (PTMs) on proteins can be targeted by antibodies associated with autoimmunity. Despite a growing appreciation for their intrinsic role in disease, there is a lack of highly multiplexed serological assays to characterize the fine specificities of PTM-directed autoantibodies. In this study, we used the programmable phage display technology, Phage ImmunoPrecipitation Sequencing (PhIP-Seq), to profile rheumatoid arthritis (RA) associated anti-citrullinated protein antibody (ACPA) reactivities. Using both an unmodified and peptidylarginine deiminases (PAD)-modified phage display library consisting of ~250,000 overlapping 90 amino acid peptide tiles spanning the human proteome, PTM PhIP-Seq robustly identifies antibodies to citrulline-dependent epitopes. PTM PhIP-Seq was used to quantify key differences among RA patients, including PAD isoform specific ACPA profiles, and thus represents a powerful tool for proteome-scale antibody-binding analyses.