bluuebunny/crossref_metadata_2025 huggingface dataset:
Succinct k-mer Sets Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform *
Authors: Alanko Jarno N. , Puglisi Simon J. , Vuohtoniemi Jaakko
Published: May 2022

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. This is a lossy but computationally convenient representation of the information in the string, with many applications in high-throughput bioinformatics. In this work, we define the notion of the Spectral Burrows-Wheeler Transform (SBWT), which is a sequence of subsets of the alphabet of the string encoding the k-spectrum of the string. The SBWT is a distillation of the ideas found in the BOSS and Wheeler graph data structures. We explore multiple different approaches to index the SBWT for membership queries on the underlying k-spectrum. We identify subset rank queries as the essential subproblem, and propose four succinct index structures to solve it. One of the approaches essentially leads to the known BOSS data structure, while the other three offer attractive time-space trade-offs and support simpler query algorithms that rely only on fast rank queries. The most general approach involves a novel data structure we call the subset wavelet tree, which we find to be of independent interest. All of the approaches are also amendable to entropy compression, which leads to good space bounds on the sizes of the data structures. Using entropy compression, we show that the SBWT can support membership queries on the k-spectrum of a single string in O(k) time and (n + k)(log σ + 1/ ln 2) + o((n + k)σ) bits of space, where n is the number of distinct substrings of length k in the input and σ is the size of the alphabet. This improves from the time O(k log σ) achieved by the BOSS data structure. We show, via experiments on a range of genomic data sets, that the simplicity of our new indexes translates into large performance gains in practice over prior art.
Changes in ProteinN-Glycosylation Regulation Occur in the Human Parkinsonian Brain in a Region-Specific Manner
Authors: Lúcia Rebelo Ana , Drake Richard R. , Marchetti-Deschmann Martina , Saldova Radka , Pandit Abhay
Published: May 2022

Parkinson’s Disease (PD) associated state of neuroinflammation due to the aggregation of aberrant proteins is widely reported. One type of post-translational modification involved in protein stability is glycosylation. Here, we aimed to characterise the human Parkinsonian nigro-striatalN-glycome, and related transcriptome/proteome, and its correlation with endoplasmic reticulum stress and unfolded protein response (UPR), providing a comprehensive characterisation of the PD molecular signature. Significant changes were seen upon PD: 3% increase in sialylation and 5% increase in fucosylation in both regions, and 2% increase in oligomannosylatedN-glycans in the substantia nigra. In the latter, a decrease in the mRNA expression of sialidases and an upregulation in the UPR pathway were also seen. To show the correlation between these, we also describe anin vitrofunctional study where changes in specific glycosylation trait enzymes (inhibition of sialyltransferases) led to impairments in cell mitochondrial activity, changes in glyco-profile and upregulation in UPR pathways. This complete characterisation of the human nigro-striatalN-glycome provides an insight into the glycomic profile of PD through a transversal approach while combining the other PD “omics” pieces, which can potentially assist in the development of glyco-focused therapeutics.
Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma gondii
Authors: Yin Deqi , Jiang Ning , Cheng Chang , Sang Xiaoyu , Feng Ying , Chen Ran , Chen Qijun
Published: May 2022

The biology of Toxoplasma gondii, the causative pathogen of one of the most wide-spread parasitic diseases remains poorly understood. Lactate, which is derived from glucose metabolic pathways, is considered to be not only an energy source in a variety of organisms including Toxoplasma gondii, but also a regulatory molecule that participates in gene activation and protein functioning. Lysine lactylation is a type of posttranslational modifications (PTMs) that was recently associated with chromatin remodeling, but lysine lactylation of histone and non-histone proteins has not yet been studied in T. gondii. To examine the prevalence and function of lactylation in T. gondii parasites, we mapped the lactylome of proliferating tachyzoite cells and found 1964 lactylation sites on 955 proteins in the T. gondii RH strain. The lactylated proteins were distributed in multiple subcellular compartments and were closely related to a wide variety of biological processes, including mRNA splicing, glycolysis, aminoacyl-tRNA biosynthesis, RNA transport, and multiple signaling pathways. We also performed chromatin immunoprecipitation sequencing (ChIP-seq) analysis with a lactylation specific antibody, the results revealed that histone H4K12la and H3K14la were enriched in the promoter and exon regions of Toxoplasma gondii genes associated with microtubule-based movement and cell invasion. We further confirmed the de-lactylase activity of histone deacetylase TgHDACs 2, 3, and 4, and that treatment with anti-histone acetyltransferase (TgMYST-A) antibodies profoundly reduced protein lactylation in the parasites. This study offers the first dataset of the global lactylation proteome and provides a basis for further dissection of the functional biology of Toxoplasma gondii.
Parieto-frontal Oscillations Show Hand Specific Interactions with Top-Down Movement Plans
Authors: Blohm G. , Cheyne D.O. , Crawford J.D.
Published: May 2022

To generate a hand-specific reach plan, the brain must integrate hand-specific signals with the desired movement strategy. Although various neurophysiology / imaging studies have investigated hand-target interactions in simple reach-to-target tasks, the whole-brain timing and distribution of this process remain unclear, especially for more complex, instruction-dependent motor strategies. Previously, we showed that a pro/anti-pointing instruction influences magnetoencephalographic (MEG) signals in frontal cortex that then propagate recurrently through parietal cortex (Blohm et al., 2019). Here, we contrasted left versus right hand pointing in the same task to investigate 1) which cortical regions of interest show hand specificity, and 2) which of those areas interact with the instructed motor plan. Eight bilateral areas – the parietooccipital junction (POJ), superior parietooccipital cortex (SPOC), supramarginal gyrus (SMG), middle / anterior interparietal sulcus (mIPS/aIPS), primary somatosensory / motor cortex (S1/M1), and dorsal premotor cortex (PMd) – showed hand-specific changes in beta band power, with four of these (M1, S1, SMG, aIPS) showing robust activation before movement onset. M1, SMG, SPOC, and aIPS showed significant interactions between contralateral hand specificity and the instructed motor plan, but not with bottom-up target signals. Separate hand / motor signals emerged relatively early and lasted through execution, whereas hand-motor interactions only occurred close to movement onset. Taken together with our previous results, these findings show that instruction-dependent motor plans emerge in frontal cortex and interact recurrently with hand-specific parietofrontal signals before movement onset to produce hand-specific motor behaviors.

Impact Statement

The brain must generate different motor signals, depending which hand is used. The distribution and timing of hand use / instructed motor plan integration is not understood at the whole-brain level. Using whole-brain MEG recordings we show that different sub-networks involved in action planning code for hand usage (alpha and beta frequencies) and integrating hand use information into a hand-specific motor plan (beta band). The timing of these signals indicates that frontal cortex first creates a general motor plan and then integrates hand-specific frontoparietal information to produce a hand-specific motor plan.
Mechanosensor Piezo1 Mediates Bimodal Patterns of Intracellular Signaling
Authors: Pan Yijia , Shi Linda Zhixia , Preece Daryl , Gomez-Godinez Veronica , Yoon Chi Woo , Lu Shaoying , Carmona Christopher , Woo Seung-Hyun , Chien Shu , Berns Michael W. , Liu Longwei , Wang Yingxiao
Published: May 2022

Piezo1 belongs to mechano-activatable cation channels serving as biological force sensors. However, the molecular events downstream of Piezo1 activation remain unclear. In this study, we used biosensors based on fluorescence resonance energy transfer (FRET) to investigate the dynamic modes of Piezo1-mediated signaling and revealed a bimodal pattern of Piezo1-induced intracellular calcium signaling. Laser-induced shockwaves (LIS) and its associated shear stress can mechanically activate Piezo1 to induce transient intracellular calcium (Ca[i]) elevation, accompanied by an increase in FAK activity. Interestingly, multiple pulses of shockwave stimulation caused a more sustained calcium increase and a decrease of FAK activity. Similarly, tuning the degree of Piezo1 activation by titrating either the dosage of Piezo1 ligand Yoda1 or the expression level of Piezo1, produced a similar bimodal pattern of FAK responses. Specifically, a low degree of Piezo1 activation (transient mode) leads to a transient Ca[i] response with FAK activation, whereas a high degree of Piezo1 activation (sustained mode) causes a sustained Ca[i] response with FAK suppression. Further investigation revealed that SHP2 serves as an intermediate regulator mediating this bimodal pattern in Piezo1 sensing and signaling. These results suggest that the degrees of Piezo1 activation induced by both mechanical LIS and chemical ligand stimulation may determine downstream signaling characteristics.
Root-specific activation of plasma membrane H+-ATPase 1 enhances plant growth and shoot accumulation of nutrient elements under nutrient-poor conditions in Arabidopsis thaliana
Authors: Monden Kota , Kamiya Takehiro , Sugiura Daisuke , Suzuki Takamasa , Nakagawa Tsuyoshi , Hachiya Takushi
Published: May 2022

Plasma membrane (PM) H+-ATPase contributes to nutrient uptake and stomatal opening by creating proton gradient across the membrane. Previous studies report that a dominant mutation in the OPEN STOMATA2 locus (OST2-2D) constitutively activates Arabidopsis PM H+-ATPase 1 (AHA1), which enlarges proton motive force for root nutrient uptake. However, the stomatal opening is also constitutively enhanced in the ost2-2D, causing drought hypersensitivity. To develop plants with improved nutrient acquisition and normal stomatal movement, we generated grafted plants (scion/rootstock : Col-0 (WT)/ost2-2D), and compared their growth and nutrient element content with those of control plants (WT/WT) under two nutrient regimes. WT/ost2-2D shoots had larger weights, rosette diameter, leaf blade area, and content of C, N, K, Ca, S, P, Mg, Na, Mn, B, Co, and Mo under nutrient-poor conditions compared with WT/WT shoots. The root weights and primary root length were greater in WT/ost2-2D plants than in WT/WT plants under both nutrient conditions. These results suggest that root-specific activation of PM H+-ATPase enhances root nutrient uptake, which accelerates the plant growth under nutrient-poor condition. Our study presents a novel approach to improving nutrient uptake efficiency in crops and vegetable for the implementation of low-input sustainable agriculture.
Improving communications in PPE: A solution for landline telephone communication.
Authors: Coats Timothy J , Pallett Edward , Mangat Jasdip , Chung Emma
Published: May 2022

Background. Emergency care staff wearing elastomeric respiratory PPE report difficulties in communicating by telephone. We developed and tested an affordable technological solution aimed at improving telephone call intelligibility in staff wearing PPE.
Methods. A novel headset was created to enable a throat microphone and bone conduction headset to be used in combination with a standard hospital emergency alert telephone system. Speech intelligibility of a ED staff member wearing PPE was compared between the proposed headset and current practice by simultaneously recording a short-version of the Modified Rhyme Test and a Key Sentences Test. Recordings were played back to a group of blinded ED staff listening to pairs of recordings under identical conditions. The proportion of correctly identified words was compared using a paired t-test.
Results. Fifteen ED staff correctly identified a mean of 73% (SD 9%) words for speech communicated via the throat microphone system, compared to only 43% (SD 11%) of words for standard practice (paired t-test, p<0.001).
Conclusions. Introduction of a suitable headset can significantly improve speech intelligibility during emergency alert telephone calls.
Background noise in an Emergency Department: an observational study from staff and patient perspectives
Authors: Emar Murad , Smith Ella , Coats Timothy J
Published: May 2022

Background and importance

Noise is a contributing factor to mis-communication, poor sleep patterns and stress in healthcare. There has been little research on noise in the Emergency Department (ED).

Objective(s)

(1) To identify the noise levels experienced by staff and patients in different areas of an emergency department over the 24 hour cycle, (2) to examine the impact of cubicle doors on the background noise experienced by the patient, and (3) to assess the impact of monitor alarms on staff and patient noise levels.

Design

Observational study.

Setting

A large urban teaching hospital Emergency Department.

Measures and analysis

Using a standard protocol monitoring of staff and patient experience of noise was carried out in 3 areas of the ED (a resuscitation room, an area of patient cubicles with solid doors and and an area of patient cubicles with curtains).

The overall distributions of noise levels in each area were described and circadian variation plotted. The proportion of time that background noise was above key cutoff values known to impair communication was calculated (45dB and 65dB).

Non-parametric methods were used to compare: (1) a patient cubicle with curtains compared to a solid door, (2) having the door open or closed, and (3) staff and patient exposure a monitor alarm.

Main results

Noise was greater than 45dB for staff between 76% and 96% of the time (30% to 100% for patients). There was little difference across the 24hr cycle. A door decreased the noise experienced by patients, but only if left closed. In the resuscitation rooms monitor alarms were much louder for patients than for staff.

Conclusion

Noise levels likely to impair communication are present in the ED for most of the time. Staff awareness and improved design of both buildings and equipment might mitigate this negative acoustic environment.
Modelling the impact of combining HIV prevention interventions on HIV dynamics in fishing communities in Uganda
Authors: Kremer Cécile , Kamali Anatoli , Kuteesa Monica , Seeley Janet , Hens Niel , Nsubuga Rebecca N
Published: May 2022

Background

In countries with mature generalized HIV epidemics such as Uganda, there are still groups of individuals that are disproportionately affected. These most at risk populations (MARPs) have high HIV prevalence compared to the general population. Among the MARPs in Uganda are fishing communities, which make up about 10% of the population.

Methods

We investigated the impact of combined HIV prevention interventions on HIV transmission dynamics in high-risk fishing communities in Uganda using a deterministic compartmental model. The model was calibrated to seroprevalence data from a census performed in 2014. To account for remaining uncertainty in the calibrated model parameters, an additional 50 000 simulated scenarios were modelled to investigate the impact of combined interventions.

Results

The projected HIV incidence decreased from 1.87 per 100 PY without intervention scale-up to 0.25 per 100 PY after 15 years (2014-2029) of intervention scale-up. A potential combination achieving this 87% reduction in incidence included condom use in about 60% of sexual acts, 23% of susceptible men circumcised, 87% of people living with HIV aware of their status, 75% of those on ART, and about 3% of susceptible individuals on oral PrEP. Uncertainty analysis revealed relative reductions in incidence ranging from 30.9% to 86.8%. Sensitivity analyses suggested that condom use and early ART were the most important intervention components.

Conclusions

Reducing HIV incidence, and consequently prevalence and AIDS-related mortality, in these high-risk fishing communities in Uganda is attainable in the long-run with a combination prevention package. Our projected intervention coverage levels are well within the national targets set by the Uganda government and close to reaching the UNAIDS 95-95-95 goal to end AIDS by 2030.
Assessing the knowledge and practices of primary healthcare workers on malaria diagnosis and related challenges in view of COVID-19 outbreak in a Nigerian Southwestern Metropolis
Authors: Ayandipo Esther , Babatunde Deborah , Afolayan Oladipo , Kalejaye Olabisi , Obembe Taiwo
Published: May 2022

Background

The clinical features of COVID-19 and malaria are interrelated. Due to the similarity of symptoms between the two disease states, patients can be incorrectly diagnosed with the other ailment in areas with limited health resources. There is a dearth of knowledge of co-infection between COVID-19 and malaria from healthcare providers’ perspective. Hence, this study assessed the ability of primary healthcare workers to diagnose malaria infection correctly from COVID-19 infection.

Methods

A multistage sampling technique was used to select health care workers who were directly involved in malaria case management at 261 government-owned primary health facilities in Oyo State. Socio-demographic characteristics of respondents, knowledge & practices, COVID-19 differential diagnosis and challenges that healthcare workers face regarding malaria diagnosis were obtained using a standardized electronic structured questionnaire. Descriptive statistics, bivariate and multivariate analysis were conducted on data collected and significant results were interpreted at a 5% level of significance.

Results

A good percentage of the respondents (81.6%, 74.3%) had good knowledge about malaria and COVID-19 infection. However, the knowledge gained did not translate to practice, as majority (86.2%) of respondents had poor malaria diagnosis practices. Practices relating to COVID-19 differential diagnosis in 69.7% of respondents were also poor. Most of the respondents attributed poor practices to the unavailability of Malaria Rapid Diagnostic Test (mRDT), inadequate training and continuous capacity improvement. Only 12.3% of the respondents had any form of training on malaria diagnosis and treatment in the last five years.

Conclusion

Harmonization of regular trainings and continuous on-the job capacity building is essential to improve case identification, diagnosis and management of both ailments. Also, uninterrupted supplies of essential commodities such as mRDT in laboratories will reduce missed opportunities for malaria diagnosis.
Sex differences in depression and sleep disturbance as inter-related risk factors of diabetes
Authors: Li Clara S. , Porta Rose , Chaudhary Shefali
Published: May 2022

Background

Previous studies identified depression and sleep disturbance as risk factors for diabetes. Sleep disturbance and depression are known to be inter-related. Further, women relative to men are more prone to depression. Here, we investigated how depression and sleep disturbance may jointly influence the risk of diabetes and the effects of sex on these influences.

Methods

Using the data of 21,229 participants from the 2018 National Health Interview Survey, we performed multivariate logistic regression with diabetes diagnosis as the dependent variable, sex, self-reported frequency of weekly depression and nightly sleep duration, and their interactions with sex as independent variables, and age, race, income, body mass index and physical activity as covariates. We employed Bayesian and Akaike Information criteria to identify the best model, evaluated the accuracy of the model in predicting diabetes using receiver operating characteristic analysis, and computed the odds ratios of these risk factors.

Results

In the two best models, depression frequency and sleep hours interact with sex in determining the diagnosis of diabetes, with higher depression frequency and nightly duration of sleep longer or shorter than 7 to 8 hours associated with higher likelihood of diabetes. The two models both predicted diabetes at an accuracy (area under the receiver operating characteristic curve) of 0.86. Further, these effects were stronger in men than in women at each depression and sleep level.

Conclusions

Depression and sleep inter-relatedly rather than independently contributes to diabetes. Depression and sleep hours associate with diabetes more significantly in men than in women. The current findings indicate a sex-dependent relationship between depression, sleep disturbance and diabetes risk and add to a growing body of evidence linking mental and physical health.
A Mesoscale Agent Based Modeling Framework For Flow-mediated Infection Transmission In Indoor Occupied Spaces
Authors: Mukherjee Debanjan , Wadhwa Gauri
Published: May 2022

The ongoing Covid-19 pandemic, and its associated public health and socioeconomic burden, has reaffirmed the necessity for a comprehensive understanding of flow-mediated infection transmission in occupied indoor spaces. This is an inherently multiscale problem, and suitable investigation approaches that can enable evidence-based decision-making for infection control strategies, interventions, and policies; will need to account for flow physics, and occupant behavior. Here, we present a mesoscale infection transmission model for human occupied indoor spaces, by integrating an agent-based human interaction model with a flow physics model for respiratory droplet dynamics and transport. We outline the mathematical and algorithmic details of the modeling framework, and demonstrate its validity using two simple simulation scenarios that verify each of the major sub-models. We then present a detailed case-study of infection transmission in a model indoor space with 60 human occupants; using a systematic set of simulations representing various flow scenarios. Data from the simulations illustrate the utility and efficacy of the devised mesoscale model in resolving flow-mediated infection transmission; and elucidate key trends in infection transmission dynamics amongst the human occupants.
PGC-1β and ERRα promote glutamine metabolism and colorectal cancer survival via transcriptional regulation of PCK2
Authors: Frodyma Danielle E. , Troia Thomas C. , Rao Chaitra , Svoboda Robert A. , Berg Jordan A. , Shinde Dhananjay D. , C.Thomas Vinai , Lewis Robert E. , Fisher Kurt W.
Published: May 2022

Previous studies have shown that Peroxisome Proliferator-Activated Receptor Gamma, Coactivator 1 Beta (PGC-1β) and Estrogen-Related Receptor Alpha (ERRα) are over-expressed in colorectal cancer and promote tumor survival. In this study, we show that amino acid motif LRELL on PGC-1β is responsible for the physical interaction with ERRα and promotes ERRα mRNA and protein expression. We used RNAsequencing to determine the genes regulated by both PGC-1β & ERRα and found that mitochondrial Phosphoenolpyruvate Carboxykinase 2 (PCK2) was the gene that decreased most significantly after depletion of both genes. Depletion of PCK2 in colorectal cancer cells was sufficient to reduce anchorage-independent growth and inhibit glutamine utilization by the TCA cycle. Lastly, shRNA-mediated depletion of ERRα decreased anchorage-independent growth and glutamine metabolism, which could not be rescued by plasmid derived expression of PCK2. These findings suggest that transcriptional control of PCK2 is one mechanism used by PGC-1β and ERRα to promote glutamine metabolism and colorectal cancer cell survival.
Human primed and naïve PSCs are both competent in differentiating into bona fide trophoblast stem cells
Authors: Viukov Sergey , Shani Tom , Bayerl Jonathan , Sheban Daoud , Stelzer Yonatan , Novershtern Noa , Hanna Jacob
Published: May 2022

Cells of the trophoblast lineage constitute the major part of placental tissues in higher mammals. Recent derivation of human trophoblast stem cells (TSC) from placental cytotrophoblasts (CT) and from human naïve PSCs opens new opportunities for studying development and function of human placenta. Several recent reports have suggested that naïve human PSCs retain an exclusive potential to give rise to bona fide TSCs. Here we report that inhibition of TGFβ pathway and avoiding WNT stimulation, leads to direct and robust conversion of primed human pluripotent stem cells into TSCs. Systematic side by side comparative analysis showed that the latter are equivalent to previously derived TSC lines. Primed PSC derived TSC lines exhibit self-renewal, are able to differentiate into the main trophoblast lineages, and present RNA and epigenetic profiles that are indistinguishable from the TSC lines derived from placenta or naïve PSCs. Our findings underscore a residual plasticity in primed human PSCs that allows converting directly into pre-implantation extra-embryonic cell lineages.

Highlights

Primed human PSCs readily convert into TSCs upon inhibition of TGF pathway

CHIR inhibits conversion to TSC in primed but not in naive hPSCs

Primed human PSC derived TSCs line are indistinguishable from placental and naïve derived TSCs

YAP is sufficient for TSC induction from hPSCs and necessary for TSC maintenance.
Complexity of enhancer networks predicts cell identity and disease genes revealed by single-cell multi-omics analysis
Authors: Hong Danni , Lin Hongli , Liu Lifang , Shu Muya , Dai Jianwu , Lu Falong , Tong Mengsha , Huang Jialiang
Published: May 2022

Many enhancers exist as clusters in the genome and control cell identity and disease genes; however, the underlying mechanism remains largely unknown. Here, we introduce an algorithm, eNet, to build enhancer networks by integrating single-cell chromatin accessibility and gene expression profiles. Enhancer network is a gene regulation model we proposed that not only delineates the mapping between enhancers and target genes, but also quantifies the underlying regulatory relationships among enhancers. The complexity of enhancer networks is assessed by two metrics: the number of enhancers and the frequency of predicted enhancer interactions (PEIs) based on chromatin co-accessibility. We apply eNet algorithm to a human blood dataset and find cell identity and disease genes tend to be regulated by complex enhancer networks. The network hub enhancers (enhancers with frequent PEIs) are the most functionally important in enhancer networks. Compared with super-enhancers, enhancer networks show better performance in predicting cell identity and disease genes. The establishment of enhancer networks drives gene expression during lineage commitment. Applying eNet in various datasets in human or mouse tissues across different single-cell platforms, we demonstrate eNet is robust and widely applicable. Thus, we propose a model of enhancer networks containing three modes: Simple, Multiple and Complex, which are distinguished by their complexity in regulating gene expression.

Taken together, our work provides an unsupervised approach to simultaneously identify key cell identity and disease genes and explore the underlying regulatory relationships among enhancers in single cells, without requiring the cell type identity in advance.

Highlights

eNet, a computational method to build enhancer network based on scATAC-seq and scRNA-seq data

Cell identity and disease genes tend to be regulated by complex enhancer networks, where network hub enhancers are functionally important

Enhancer network outperforms the existing models in predicting cell identity and disease genes, such as super-enhancer and enhancer cluster

We propose a model of enhancer networks in gene regulation containing three modes: Simple, Multiple and Complex
Humanized CAR T cells targeting p95HER2
Authors: Román Macarena , Rius-Ruiz Irene , Grinyó-Escuer Ariadna , Duro-Sánchez Santiago , Escorihuela Marta , Moessner Ekkehard , Klein Christian , Arribas Joaquín
Published: May 2022

Redirection of T lymphocytes against tumor-associated or tumor-specific antigens, via bispecifc T cells engagers (BiTEs) or chimeric antigen receptors (CARs), is a successful therapeutic strategy against certain hematologic malignancies. In contrast, so far it has failed against solid tumors. Given the scarcity of tumor-specific antigens, the vast majority of BiTEs and CAR Ts developed to date have been directed against tumor-associated antigens. These are expressed in some normal tissues and, as a consequence, frequent and serious side effects caused by on-target off-tumor activity have limited the use of BiTEs and CARs in the clinic. P95HER2 is a fragment of the tyrosine kinase receptor HER2 expressed in more than 30% of HER2-amplified tumors. It has been previoulsy shown that p95HER2 is a tumor-specific antigen. Here we present the generation of CARs targeting p95HER2. p95HER2 CAR T cells show remarkable activity against p95HER2-expressing cells in vitro and in vivo. Further, they are also effective against lung and brain metastasis. These tumor-specific CAR T cells could be used in the near future to deliver additional anti-tumor therapies in a safe manner.
Structural basis for substrate selection by the SARS-CoV-2 replicase
Authors: Malone Brandon F. , Perry Jason K. , Olinares Paul Dominic B. , Chen James , Appelby Todd K. , Feng Joy Y. , Bilello John P. , Ng Honkit , Sotiris Johanna , Ebrahim Mark , Chua Eugene Y.D. , Mendez Joshua H. , Eng Ed T. , Landick Robert , Chait Brian T. , Campbell Elizabeth A. , Darst Seth A.
Published: May 2022

The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC)1. Accordingly, the RTC is a target for clinically approved antiviral nucleoside analogs, including remdesivir2. Faithful synthesis of viral RNAs by the RTC requires recognition of the correct nucleotide triphosphate (NTP) for incorporation into the nascent RNA. To be effective inhibitors, antiviral nucleoside analogs must compete with the natural NTPs for incorporation. How the SARS-CoV-2 RTC discriminates between the natural NTPs, and how antiviral nucleoside analogs compete, has not been discerned in detail. Here, we use cryo-electron microscopy to visualize the RTC bound to each of the natural NTPs in states poised for incorporation. Furthermore, we investigate the RTC with the active metabolite of remdesivir, remdesivir triphosphate (RDV-TP), highlighting the structural basis for the selective incorporation of RDV-TP over its natural counterpart ATP3,4. Our results elucidate the suite of interactions required for NTP recognition, informing the rational design of antivirals. Our analysis also yields insights into nucleotide recognition by the nsp12 NiRAN, an enigmatic catalytic domain essential for viral propagation5. The NiRAN selectively binds GTP, strengthening proposals for the role of this domain in the formation of the 5’ RNA cap6.
Spurious intragenic transcription is a hallmark of mammalian cellular senescence and tissue aging
Authors: Sen P. , Donahue G. , Li C. , Lan Y. , Egervari G. , Robertson N. , Shah P. P. , Kerkhoven E. , Schultz D. C. , Adams P. D. , Berger S. L.
Published: May 2022

Mammalian aging is characterized by the progressive loss of tissue integrity and function manifesting in ill health and increased risk for developing multiple chronic conditions. Accumulation of senescent cells in aging tissues partly contributes to this decline and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. However, the fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal that aberrant transcription initiation inside genes is widespread in senescence and aging. It co-occurs with changes in the chromatin landscape and formation of non-canonical transcription start sites. Interventions that alter spurious transcripts have dramatic consequences on cellular health primarily affecting intracellular signal transduction pathways. We propose that spurious transcription is a conserved hallmark of aging that promotes a noisy transcriptome and degradation of coherent transcriptional networks.
Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen
Authors: Singh Nikhil Kumar , Tralamazza Sabina Moser , Abraham Leen Nanchira , Glauser Gaétan , Croll Daniel
Published: May 2022

Background

Fungi produce a wide range of specialized metabolites (SMs) involved in biotic interactions. Pathways for the production of SMs are often encoded in clusters of tightly arranged genes identified as biosynthetic gene clusters. Such gene clusters can undergo horizontal gene transfers between species and rapid evolutionary change within species. The acquisition, rearrangement and deletion of gene clusters can generate significant metabolome diversity. However, the genetic basis underlying variation in SM production remains poorly understood.

Results

Here, we analyzed metabolite production of a large population of the fungal pathogen of wheat, Zymoseptoria tritici. The pathogen causes major yield losses and shows variation in gene clusters. We performed untargeted ultra-high performance liquid chromatography-high resolution mass spectrometry to profile the metabolite diversity among 102 isolates of the same species. We found substantial variation in the abundance of the detected metabolites among isolates. Integrating whole-genome sequencing data, we performed metabolite genome-wide association mapping to identify loci underlying variation in metabolite production (i.e. metabolite-GWAS). We found that significantly associated SNP reside mostly in coding and gene regulatory regions. Associated genes encode mainly transport and catalytic activities. The metabolite-GWAS identified also a polymorphism in the 3’UTR region of a virulence gene related to metabolite production and showing expression variation.

Conclusions

Taken together, our study provides a significant resource to unravel polymorphism underlying metabolome diversity within a species. Integrating metabolome screens should be feasible for a range of different plant pathogens and help prioritize molecular studies.
Differences in Gut Microbiota Assembly Alter Its Ability to Metabolize Dietary Polysaccharides and Resist Clostridioides difficile Colonization
Authors: Schnizlein Matthew K. , Standke Alexandra K. , Garmo Mark J. , Edwards Summer J. , Young Vincent B.
Published: May 2022

The mammalian gut is home to a vibrant community of microbes. As the gut microbiota has evolved, its members have formed a complex yet stable relationships that prevent non-indigenous microorganisms, such as Clostridioides difficile, from establishing within the gut. Using a bioreactor model of the gut, we characterize how variation in microbial community assembly changes its ability to resist C. difficile. We established diluted microbial communities from healthy human stool in a bioreactor gut model and subsequently challenged them with vegetative C. difficile. 16S rRNA-gene sequencing and selective plating revealed that dilution progressively increases microbiota variability and decreases C. difficile colonization resistance. Using Dirichlet Multinomial Mixtures and linear discriminant analysis of effect size, we identified 19 bacterial taxa, including Bifidobacterium, Bacteroides and Lachnospiraceae, that associate with more resistant community types. Since these taxa are associated with butyrate production, which is tied to C. difficile colonization resistance, we performed another reactor experiment where we increased inulin concentrations prior to C. difficile challenge. Diluted communities concurrently lost their ability to produce additional butyrate in response to inulin, as measured by high performance liquid chromatography, and resist C. difficile colonization. These data demonstrate that a similar level of microbiota cohesiveness is required to prevent C. difficile colonization and metabolize inulin. It also suggests that metabolic activity of butyrate-producing microbes is tied to colonization resistance. Future work can leverage these findings to develop treatments that leverage knowledge of these ecological dynamics to improve efficacy.

Importance

The microbes living in the human large intestine helps create an environment that is resistant to organisms that do not normally reside there, such as the pathogen Clostridioides difficile. Differences in ways in which microbial communities make an environment their home can change their ability to provide that resistance. To study those differences, we use a model of the intestine that incorporates only microbial variables (i.e. no host is involved). By diluting microbial communities to decrease their complexity, we show that communities lose their ability to resist C. difficile at a particular point and, at the same time, their ability to use inulin, a common dietary fiber, in ways that make the environment more toxic to C. difficile. These findings will help future researchers dissect the microbial components that create a resistant intestinal environment.
Determination of heavy metals in blood of nesting Kemp’s Ridley turtles (Lepidochelys kempii) at Rancho Nuevo sanctuary, Tamaulipas, Mexico
Authors: Zavala-Félix Kevin Alan , Reyes-López Miguel Angel , Camacho-Sánchez Fátima Yedith , Acosta-Sánchez Héctor Hugo , Hart Catherine E. , Zavala-Norzagaray Alan A. , Leal-Sepúlveda Valeria , Espinoza-Romo Brenda Aracely , Leal-Moreno Renato , Aguirre A. Alonso , Ley-Quiñónez César Paúl
Published: May 2022

The concentrations of heavy metals and metalloids including As, Zn, Cu, Se, Pb, Hg and Cd, were determined in the blood of nesting Kemp’s ridley turtles (Lepidochelys kempii) at Rancho Nuevo sanctuary, Tamaulipas, Mexico during 2018-2020. The sequential concentrations of metals analyzed were Zn> Se> Cu> As> Pb; while Cd and Hg concentrations were below the limits of detection (0.01 µg g−1). No significant differences were observed between the concentrations of metals (p> 0.05) by year, except Se levels, possibly resulting from recorded seasonal differences in turtle size. No relationships among turtle size vs metal concentration were observed. In conclusion, heavy metals concentrations in the blood of nesting Kemp’s ridley turtles may be a reflex of the ecosystem in which the turtles develop, that is, with low bioavailability of metals observed in the trophic webs in the Gulf of Mexico.
The petrous bone contains high concentrations of osteocytes: one possible reason why ancient DNA is better preserved in this bone
Authors: Ibrahim Jamal , Brumfeld Vlad , Addadi Yoseph , Rubin Sarah , Weiner Steve , Boaretto Elisabetta
Published: May 2022

The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher than in the temporal bone, as well as the cortical bone of the femur. The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also confirm that the petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore conclude that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains up to three times more DNA than other bones, and hence during diagenesis more DNA is likely to be preserved. We also note that the osteocytes in the inner layer of the petrous bone may have a function in hearing.
Cell survival enabled by leakage of a labile metabolic intermediate
Authors: Medina-Carmona Encarnación , Gutierrez-Rus Luis I. , Manssour-Triedo Fadia , Newton Matilda S. , Gamiz-Arco Gloria , Mota Antonio J. , Reiné Pablo , Cuerva Juan Manuel , Ortega-Muñoz Mariano , Andrés-León Eduardo , Ortega-Roldan Jose Luis , Seelig Burckhard , Ibarra-Molero Beatriz , Sanchez-Ruiz Jose M.
Published: May 2022

Many metabolic pathways are of ancient origin and have evolved over long periods of time (Noda-Garcia et al., 2018). Yet, new pathways can also emerge in short time scales in response, for instance, to the presence of anthropogenic chemicals in the environment (Copley, 2009). Models of metabolic pathway emergence and evolution often emphasize the acquisition of new reactions through horizontal gene transfer and promiscuous enzyme functionalities (Pál et al., 2005; Schulenburg & Miller, 2014; Copley, 2015; Noda-Garcia et al., 2018; Peracchi, 2018). A fundamentally different mechanism of metabolic innovation is revealed by the evolutionary repair experiments reported here. A block in the proline biosynthetic pathway that compromises cell survival is efficiently rescued by many single mutations (12 at least) in the gene of glutamine synthetase. The mutations cause the leakage to the intracellular milieu of a sequestered phosphorylated intermediate common to the biosynthetic pathways of proline and glutamine, thus generating a new route to proline. Metabolic intermediates may undergo a variety of chemical and enzymatic transformations, but are typically protected as shielded reaction intermediates or through channeling in multi-enzyme complexes and metabolons (Srere, 1987; Huang et al., 2001; Grunwald, 2018; Pareek et al., 2021). Our results show that intermediate leakage can readily occur and contribute to organismal adaptation. Enhanced availability of reactive molecules may enable the generation of new biochemical pathways. We therefore anticipate applications of mutation-induced leakage in metabolic engineering.
SARS-CoV-2 Infects Peripheral and Central Neurons Before Viremia, Facilitated by Neuropilin-1
Authors: Joyce Jonathan D. , Moore Greyson A. , Goswami Poorna , Harrell Telvin L. , Taylor Tina M. , Hawks Seth A. , Green Jillian C. , Jia Mo , Yallayi Neeharika , Leslie Emma H. , Duggal Nisha K. , Thompson Christopher K. , Bertke Andrea S.
Published: May 2022

Neurological symptoms associated with COVID-19, acute and long-term, suggest SARS-CoV-2 affects both central and peripheral nervous systems. Although studies have shown olfactory and hematogenous entry into the brain and neuroinflammation, little attention has been paid to the susceptibility of the peripheral nervous system to infection or to alternative routes of CNS invasion. We show that neurons in the central and peripheral nervous system are susceptible to productive infection with SARS-CoV-2. Infection of K18-hACE2 mice, wild-type mice, golden Syrian hamsters, and primary neuronal cultures demonstrate viral RNA, protein, and infectious virus in peripheral nervous system neurons and satellite glial cells, spinal cord, and specific brain regions. Moreover, neuropilin-1 facilitates SARS-CoV-2 neuronal infection. Our data show that SARS-CoV-2 rapidly invades and establishes a productive infection in the peripheral and central nervous system via direct invasion of neurons prior to viremia, which may underlie some cognitive and sensory symptoms associated with COVID-19.
Art2 mediates selective endocytosis of methionine transporters during adaptation to sphingolipid depletion
Authors: Hepowit Nathaniel L. , Moon Bradley , Dickson Robert C. , MacGurn Jason A.
Published: May 2022

Accumulating evidence in several model organisms indicates that reduced sphingolipid biosynthesis promotes longevity, although underlying mechanisms remain unclear. In yeast, sphingolipid depletion induces a state resembling amino acid restriction, which we hypothesized may be due to altered stability of amino acid transporters at the plasma membrane. To test this, we measured surface abundance for a diverse panel of membrane proteins in the presence of myriocin, a sphingolipid biosynthesis inhibitor. Unexpectedly, we found that surface levels of most proteins examined were either unaffected or increased during myriocin treatment, consistent with an observed decrease in bulk endocytosis. In contrast, sphingolipid depletion triggered selective endocytosis of the methionine transporter Mup1. Unlike methionine-induced Mup1 endocytosis, myriocin triggers Mup1 endocytosis that requires the Rsp5 adaptor Art2, C-terminal lysine residues, and the formation of K63-linked ubiquitin polymers. These findings reveal cellular adaptation to sphingolipid depletion by ubiquitin-mediated remodeling of nutrient transporter composition at the cell surface.
Lysogenized phages of methanotrophic bacteria show a broad and untapped genetic diversity
Authors: Stahn Miranda , Grigonyte Aurelija M. , Orata Fabini D. , Collins David A. , Rieder Liam , Kalyuzhnaya Marina G. , Millard Andrew , Stein Lisa Y. , Sauvageau Dominic
Published: May 2022

Methanotrophs are a unique class of bacteria with the ability to metabolize single-carbon compounds such as methane. They play an important role in the global methane cycle and have great potential as industrial platforms for the bioconversion of methane from industrial waste streams into valuable products, such as biofuels and bioplastics. However, many aspects of methanotroph biology have yet to be elucidated, including the prevalence and impact of lysogenized bacteriophages (phages), which can greatly affect both the ecology and the industrial performance of these bacteria.

The present study investigates the presence of putative prophages in three gammaproteobacterial (Methylobacter marinus A45, Methylomicrobium album BG8, Methylomonas denitrificans FJG1) and two alphaproteobacterial (Methylosinus trichosporium OB3b, Methylocystis sp. Rockwell) methanotrophs using four programs predicting putative phage sequences (PhageBoost, PHASTER, Phigaro, and Island Viewer). Mitomycin C was used to trigger induction of prophages, which was monitored through infection dynamics. Successfully induced phages from M. marinus A45 (MirA1, MirA2), M. album BG8 (MirB1), and M. trichosporium OB3b (MirO1) were isolated and characterized using transmission electron microscopy. Subsequently, bioinformatic analyses (BLAST and phylogenetics) were performed on three induced phages to obtain a profile of their respective genetic makeup. Their broad diversity and differences from previously known phages, based on whole genome and structural gene sequences, suggest they each represent a new phage family, genus and species: “Britesideviridae Inducovirus miraone”, “Patronusviridae Enigmavirus miratwo”, and “Kainiviridae Tripudiumvirus miroone” represented by isolates MirA1, MirA2, and MirO1, respectively.