bluuebunny/crossref_metadata_2025 huggingface dataset:
Drosophila centrocortin is dispensable for centriole duplication but contributes to centrosome separation
Authors: Mehta Dipen S. , Ryder Pearl V. , Lee Jina , Zein-Sabatto Hala , Lerit Dorothy A.
Published: September 2021

Centrosomes are microtubule-organizing centers that duplicate exactly once to organize the bipolar mitotic spindle required for error-free mitosis. Prior work indicated that Drosophila centrocortin (cen) is required for normal centrosome separation, although a role in centriole duplication was not closely examined. Through time-lapse recordings of rapid syncytial divisions, we monitored centriole duplication and the kinetics of centrosome separation in control versus cen null embryos. Our data suggest that although cen is dispensable for centriole duplication, it contributes to centrosome separation.
Hopanoids confer robustness to physicochemical variability in the niche of the plant symbiont Bradyrhizobium diazoefficiens
Authors: Tookmanian Elise , Junghans Lisa , Kulkarni Gargi , Ledermann Raphael , Saenz James , Newman Dianne K.
Published: September 2021

Climate change poses a threat to soil health and agriculture, but the potential effects of climate change on soil bacteria that can help maintain soil health are understudied. Rhizobia are a group of bacteria that increase soil nitrogen content through a symbiosis with legume plants. The soil and symbiosis are potentially stressful environments, and the soil will likely become even more stressful as the climate changes. Many rhizobia within the bradyrhizobia clade, like Bradyrhizobium diazoefficiens, possess the genetic capacity to synthesize hopanoids, steroid-like lipids similar in structure and function to cholesterol. Hopanoids are known to protect against stresses relevant to the niche of B. diazoefficiens. Paradoxically, mutants unable to synthesize the extended class of hopanoids participate in similarly successful symbioses compared to the wild type, despite being delayed in root nodule initiation. Here, we show that in B. diazoefficiens, the in vitro growth defects of extended hopanoid deficient mutants can be at least partially compensated for by the physicochemical environment, specifically by optimal osmotic and divalent cation concentrations. Through biophysical measurements, we show that extended hopanoids confer robustness to environmental variability. These results help explain the discrepancy between previous in vitro and in planta results and indicate that hopanoids may provide a greater fitness advantage to rhizobia in the variable soil environment than the more controlled environment within root nodules. To improve the legume-rhizobia symbiosis through either bioengineering or strain selection, it will be important to consider the full lifecycle of rhizobia, from the soil to the symbiosis.

Importance

Rhizobia, such as B. diazoefficiens, play an important role in the nitrogen cycle by making nitrogen gas bioavailable through symbiosis with legume plants. As climate change threatens soil health, this symbiosis has reentered the spotlight as a more sustainable source of soil nitrogen than the energy-intensive Haber-Bosch process. Efforts to use rhizobia as biofertilizers have been effective; however, long term integration of rhizobia into the soil community has been less successful. This work represents a small step towards improving the legume-rhizobia symbiosis by identifying a cellular component—hopanoid lipids—that confers robustness to environmental stresses rhizobia are likely to encounter in soil microenvironments as sporadic desiccation and flooding events become more common.
Descriptive epidemiology of COVID-19 deaths during the first wave of pandemic in India - a single center experience
Authors: Tendulkar Prakash , Pragya  , Panda Prasan Kumar , Bhadoria Ajeet Singh , Kulshreshtha Poorvi
Published: September 2021

Background

With the looming threat of recurrent waves of COVID-19 in the presence of mutated strains, it’s of paramount importance to understand the demographic and clinical attributes of COVID-19 related mortalities in each pandemic waves. This could help policy makers, public health experts, and clinicians to better plan preventive and management strategies to curb COVID-19 related mortality.

Method

This was a hospital record based, retrospective cross-sectional descriptive study, at a tertiary care hospital in Rishikesh, India. The study included all deceased patients between March 2020 and January 2021 (first wave) who tested positive for SARS-CoV-2 by RT-PCR and were hospitalized. The study was done to describe demography, clinical presentation, laboratory parameters, treatment given and associated complications of all COVID-19 deaths.

Result

Out of 424 mortalities, 298 (70.38%) were males and 126 (29.62%) were females. Mean age of patients was 55.85 ± 16.24 years, out of which 19.5 percent were less than 45 years old, 33.6 percent were 45 to 60 years old and 41.8% were more than 60 years old. Comorbidity in the form of type 2 diabetes mellitus was present in 41.4% [95% CI (41.4-51.1)], hypertension in 39.8% [95% CI (35.1-44.6)], and coronary artery disease in 15.2% [95% CI (11.8-18.8)]. At the time of presentation, shortness of breath was present in 73.6% [95% CI (69.1 -77.7)], fever in 64.92% [95% CI (60.1-69.4)], and cough in 46.1%, [95% CI (41.1-50.8)]. Deranged laboratory parameters were lymphopenia in 90.2% [95% CI (86.8-92.7)], transaminitis in 59.7% [95% CI (54.8-64.3)], and hypercreatinemia in 37.7% [95% CI (33.1-42.5)]. Complications manifested were acute respiratory distress syndrome in 78.3% [95% CI (74-82.1)] and shock in 54.7% [95% CI (49.8-59.5)]. Median time duration between onset of symptom and hospital admission was 5 days (IQR = 3 - 5 days) and median length of hospital stay was 9 days (IQR = 4 - 14 days).

Conclusion

During first pandemic wave, COVID-19 related mortality was 2.37 times higher among males, 2.14 times in age group >60 than <45 years. Most common associated comorbidities (>40%) were type 2 diabetes mellitus and hypertension. Most common associated symptoms (>60%) were shortness of breath and fever. Lymphopenia was seen in >90% cases while liver involvement in 60% and kidney in 38% cases. Median hospital stay was doubled the pre-hospital illness.
Gene signatures and host-parasite interactions revealed by dual single-cell profiling of Plasmodium vivax liver infection
Authors: Mancio-Silva Liliana , Gural Nil , Wadsworth Marc H. , Butty Vincent L. , Hughes Travis K. , March Sandra , Nerurkar Niketa , Roobsoong Wanlapa , Fleming Heather E. , Whittaker Charlie , Levine Stuart S. , Sattabongkot Jetsumon , Shalek Alex K. , Bhatia Sangeeta N.
Published: September 2021

Malaria-causing P. vivax parasites can linger in the human liver for weeks to years, and then reactivate to cause recurrent blood-stage infection. While an important target for malaria eradication, little is known about the molecular features of the replicative and non-replicative states of intracellular P. vivax parasites, or the human host-cell responses to them. Here, we leverage a bioengineered human microliver platform to culture Thai clinical isolates of P. vivax in primary human hepatocytes and conduct transcriptional profiling of infected cultures. By coupling enrichment strategies with bulk and single-cell analyses, we captured both parasite and host transcripts in individual hepatocytes throughout the infection course. We defined host- and state-dependent transcriptional signatures and identified previously unappreciated populations of replicative and non-replicative parasites, sharing features with sexual transmissive forms. We found that infection suppresses transcription of key hepatocyte function genes, and that P. vivax elicits an innate immune response that can be manipulated to control infection. Our work provides an extendible framework and resource for understanding host-parasite interactions and reveals new insights into the biology of malaria dormancy and transmission.
The Shigella type III effector protein OspB is a cysteine protease
Authors: Wood Thomas E. , Westervelt Kathleen A. , Yoon Jessica M. , Eshleman Heather D. , Levy Roie , Burnes Henry , Slade Daniel J. , Lesser Cammie F. , Goldberg Marcia B.
Published: September 2021

The type III secretion system is required for virulence of many pathogenic bacteria. Bacterial effector proteins delivered into target host cells by this system modulate host signaling pathways and processes in a manner that promotes infection. Here, we define the activity of the effector protein OspB of the human pathogen Shigella spp., the etiological agent of shigellosis and dysenteric disease. Using the yeast Saccharomyces cerevisiae as a model organism, we show that OspB sensitizes cells to inhibition of TORC1, the central regulator of growth and metabolism. In silico analyses reveal that OspB bears structural homology to bacterial cysteine proteases, and we define a conserved cysteine-histidine catalytic dyad required for OspB function. Using yeast genetic screens, we identify a crucial role for the arginine N-degron pathway in the growth inhibition phenotype and show that inositol hexakisphosphate is an OspB cofactor. We find that a yeast substrate for OspB is the TORC1 component Tco89p, proteolytic cleavage of which generates a C-terminal fragment that is targeted for degradation via the arginine N-degron pathway; processing and degradation of Tco89p is required for the OspB phenotype. In all, we demonstrate that the Shigella T3SS effector OspB is a cysteine protease and decipher its interplay with eukaryotic cell processes.

Importance

Shigella spp. are important human pathogens and one of the leading causes of diarrheal mortality worldwide, especially in children. Virulence depends on the Shigella type III secretion system (T3SS), and definition of the roles of the bacterial effector proteins secreted by the T3SS is key to understanding Shigella pathogenesis. The effector protein OspB has been shown to contribute to a range of phenotypes during infection, yet the mechanism of action is unknown. Here, we show that OspB possesses cysteine protease activity in both yeast and mammalian cells, and that enzymatic activity of OspB depends on a conserved cysteine-histidine catalytic dyad. We determine how its protease activity sensitizes cells to TORC1 inhibition in yeast, finding that OspB cleaves a component of yeast TORC1, and that the degradation of the C-terminal cleavage product is responsible for OspB mediated hypersensitivity to TORC1 inhibitors. Thus, OspB is a cysteine protease that depends on a conserved cysteine-histidine catalytic dyad.
Retrovirus-induced leukemia – hijack of T-cell activation mechanisms revealed by single-cell analysis
Authors: Tan Benjy Jek Yang , Sugata Kenji , Reda Omnia , Matsuo Misaki , Uchiyama Kyosuke , Miyazato Paola , Hahaut Vincent , Yamagishi Makoto , Uchimaru Kaoru , Suzuki Yutaka , Ueno Takamasa , Suzushima Hitoshi , Katsuya Hiroo , Tokunaga Masahito , Uchiyama Yoshikazu , Nakamura Hideaki , Sueoka Eisaburo , Utsunomiya Atae , Ono Masahiro , Satou Yorifumi
Published: September 2021

Human T-cell leukemia virus type 1 (HTLV-1) mainly infects CD4+T-cells and induces chronic, persistent infection in infected individuals with some progressing to develop adult T-cell leukemia/lymphoma (ATL). Whilst HTLV-1 alters cellular differentiation, activation and survival, it is unknown whether and how these changes contribute to malignant transformation of infected T-cells. In this study, we used single-cell RNA-Seq and TCR-Seq to investigate T-cell differentiation and HTLV-1-mediated transformation processes. We analyzed 87,742 single cells from peripheral blood of 12 infected and 3 uninfected individuals. Using multiple independent bioinformatic methods, we demonstrated that naïve T-cells dynamically change into activated T-cells including infected cells, which seamlessly transitioned into ATL cells characterized by clonally expanded, highly-activated T-cells. Notably, the more activated ATL cells are, the more they acquire Treg signatures. Intriguingly, HLA class II genes were uniquely induced in infected cells, further upregulated in ATL cells and was induced by viral protein Tax. Functional assays revealed that by upregulating HLA class II, HTLV-1-infected cells can act as tolerogenic antigen presenting cells (APCs) to induce anergy of antigen specific T-cells. In conclusion, our study revealed the in vivo mechanisms of HTLV-1-mediated transformation and immune escape at single-cell level.

Graphical Abstract
Attention-based deep multiple instances learning for classifying circular RNA and other long non-coding RNA
Authors: Liu Yunhe , Fu Qiqing , peng Xueqing , Zhu Chaoyu , Liu Gang , Liu Lei
Published: September 2021

Circular RNA (circRNA) is a distinguishable circular formed long non-coding RNA (lncRNA), which has specific roles in transcriptional regulation, multiple biological processes. The identification of circRNA from other lncRNA is necessary for relevant research. In this study, we designed attention-based multi-instance learning (MIL) network architecture, which can be fed with raw sequence, to learn the sparse features in sequences and accomplish the identification task for circRNAs. The model outperformed previously reported models. Following the effectiveness validation of the attention score by the handwritten digit dataset, the key sequence loci underlying circRNAs recognition were obtained based on the corresponding attention score. Moreover, the motif enrichment analysis of the extracted key sequences identified some of the key motifs for circRNA formation. In conclusion, we designed a deep learning network architecture suitable for gene sequence learning with sparse features and implemented to the circRNA identification, and the network has a strong representation capability with its indication of some key loci.
Skin specimen as an alternative to brain tissue for post mortem rabies diagnosis in animals to scale up animal rabies surveillance
Authors: Aparna Sujatha , Swapna Abraham Susan , Ajithkumar GS , Chintha Sujatha , Prathiush PR , Nandakumar S , Baby Joseph
Published: September 2021

Background

Detection of the virus or some of its specific components using WHO and OIE recommended standard laboratory tests is the only way to get a reliable diagnosis of rabies. Brain tissue is the preferred specimen for post-mortem diagnosis of rabies in both humans and animals. Higher biosecurity requirements, skill and transportation facilities required for collection and transport of brain or whole carcass to the laboratory is one of the reasons for the poor rabies surveillance in animals. Point of care testing with simple, reliable and easy to operate devices would be an ideal approach for providing rapid results.

Methods

The study evaluated diagnostic performance of two reference tests, DFAT and RTPCR on skin specimen, to assess its suitability as an alternative of brain tissue for post mortem rabies diagnosis in animals. Brain tissue and skin sample belonging to different species of animals (n=90) collected at necropsy were compared using Fluorescent Antibody Test and RT PCR, internationally approved methods for rabies diagnosis.

Results

Validation of RT-PCR on skin and DFAT on skin in comparison with DFAT on brain as gold standard gave a sensitivity of 98% (95% CI:94.1-100) and 80% (95% CI:71.8-88.2) respectively. Specificity was 100% in both tests.

Conclusion

The findings highlight the potential of skin specimen for improving rabies surveillance in animals especially in resource poor countries.

Author Summary

The present study was undertaken to define a reliable protocol for diagnosing animal rabies using skin specimen, a superficial tissue sample which is collected in a non-invasive manner for post-mortem diagnosis. Our aim was to design a protocol to replace the classical post-mortem diagnostic method that uses brain biopsy with an ultimate target of stepping up rabies surveillance in animals. Brain tissue and skin sample belonging to different species of animals collected at necropsy were compared using Fluorescent Antibody Test and RT PCR, internationally approved methods for rabies diagnosis. The study established that RT PCR on skin specimen is rapid, sensitive and specific, opening its potential as an ideal rabies surveillance tool overcoming the logistical challenges of carcass transportation to reference laboratories and alleviating biosafety concerns associated with brain collection. The study highlights the potential of skin specimen for improving rabies surveillance in animals especially in resource poor countries.
Visualizing Antineoplastic Activity with a Whole Organism Drosophila melanogaster Screen
Authors: Agbedanu Prince Nii , Sprague Tristan A.
Published: September 2021

Cancer is a disease characterized by high mitosis rates with a loss of regulation. Many antineoplastics, those drugs used to treat cancer, act by slowing or halting mitosis. We are developing a whole-organism screening protocol to identify novel antineoplastics. After exposing Drosophila melanogaster eggs and larva to a compound, their growth rate and population decrease if mitosis inhibition or arrest occur. We screened several compounds from the National Cancer Institute’s (NCI) Developmental Therapeutics Program (DTP). Our screen successfully identified two compounds, toyocamycin and stictic acid, previously identified as possible antineoplastics. Toyocamycin killed a fraction of the population proportional to the dose concentration resulting in full mortality at 100 and 200 µM. At low doses, toyocamycin also slowed larval development by a mean of one day. RNAseq showed that no genes were differentially expressed in mature flies after toyocamycin exposure was halted. Stictic acid delayed larval growth by an equal or greater margin compared to toyocamycin. These results demonstrate that decreases in Drosophila growth or population can predict a compound’s antineoplastic activity and toxicity.
The dengue virus non-structural protein 1 (NS1) interacts with the putative epigenetic regulator DIDO1 to promote flavivirus replication
Authors: Caraballo Gerson I. , Rosales Romel , Viettri Mercedes , Ding Siyuan , Greenberg Harry B. , Ludert Juan E.
Published: September 2021

Dengue virus (DENV) NS1 is a multifunctional protein essential for viral replication. To gain insights into NS1 functions in mosquito cells, the protein interactome of DENV NS1 in C6/36 cells was investigated using a proximity biotinylation system and mass spectrometry. Approximately 14% of the 817 identified proteins coincide with interactomes obtained in vertebrate cells, including ontology groups of the oligosaccharide transferase complex, the chaperonin containing TCP-1, and nuclear import and export, vesicle localization and ribosomal proteins. Notably, other protein pathways such as epigenetic regulation and RNA silencing, not previously reported in vertebrate cells, were also found in the NS1 interactome in mosquito cells. Due to the novel interaction observed for NS1 and DIDO1 (Death Inducer-Obliterator 1), we further explored the role of DIDO1 in viral replication. Interactions between NS1 and DIDO1were corroborated in infected C6/36 and Aag2 cells, by colocalization and proximity ligation assays. Silencing DIDO1 expression in C6/36 and Aag2 cells results in a significant reduction in DENV and ZIKV replication and progeny production. Comparison of transcription analysis of mock or DENV infected C6/36 silenced for DIDO1, revealed variations in multiple gene expression pathways, including pathways associated with DENV infection such as RNA surveillance, IMD and Toll. These results suggest that DIDO1 is a host factor involved in the negative modulation of the antiviral response and necessary for flavivirus replication. Our findings uncover novel mechanisms of NS1 to promote DENV and ZIKV replication and add to the understanding of NS1 as a multifunctional protein.

ABSTRACT IMPORTANCE

Dengue is the most important mosquito-borne viral disease to humans. Dengue virus NS1 is a multifunctional protein essential for replication and modulation of innate immunity. To gain insights into NS1 functions, the protein interactome of dengue virus NS1 in Aedes albopictus cells was investigated using a proximity biotinylation system and mass spectrometry. Several protein pathways, not previously observed in vertebrate cells, such as epigenetic regulation and RNA silencing, were found as part of the NS1 interactome in mosquito cells. Among those, DIDO1 was found to be a necessary host factor for dengue and Zika virus replication in vertebrate and mosquito cells. Transcription analysis of infected mosquito cells silenced for DIDO1, revealed alterations of the IMD and Toll pathways, part of the antiviral response in mosquitoes. The results suggest that DIDO1 is a host factor involved in modulation of the antiviral response and necessary for flavivirus replication.
A genetically linked pair of NLR immune receptors show contrasting patterns of evolution
Authors: Shimizu Motoki , Hirabuchi Akiko , Sugihara Yu , Abe Akira , Takeda Takumi , Kobayashi Michie , Hiraka Yukie , Kanzaki Eiko , Oikawa Kaori , Saitoh Hiromasa , Langner Thorsten , Banfield Mark J. , Kamoun Sophien , Terauchi Ryohei
Published: September 2021

Throughout their evolution, plant nucleotide-binding leucine-rich-repeat receptors (NLRs) have acquired widely divergent unconventional integrated domains that enhance their ability to detect pathogen effectors. However, the functional dynamics that drive the evolution of NLRs with integrated domains (NLR-IDs) remain poorly understood. Here, we reconstructed the evolutionary history of an NLR locus prone to unconventional domain integration and experimentally tested hypotheses about the evolution of NLR-IDs. We show that the rice (Oryza sativa) NLR Pias recognizes the effector AVR-Pias of the blast fungal pathogen Magnaporthe oryzae. Pias consists of a functionally specialized NLR pair, the helper Pias-1 and the sensor Pias-2, that is allelic to the previously characterized Pia pair of NLRs: the helper RGA4 and the sensor RGA5. Remarkably, Pias-2 carries a C-terminal DUF761 domain at a similar position to the heavy metal–associated (HMA) domain of RGA5. Phylogenomic analysis showed that Pias-2/RGA5 sensor NLRs have undergone recurrent genomic recombination within the genus Oryza, resulting in up to six sequence-divergent domain integrations. Allelic NLRs with divergent functions have been maintained trans-species in different Oryza lineages to detect sequence-divergent pathogen effectors. By contrast, Pias-1 has retained its NLR helper activity throughout evolution and is capable of functioning together with the divergent sensor-NLR RGA5 to responds to AVR-Pia. These results suggest that opposite selective forces have driven the evolution of paired NLRs: highly dynamic domain integration events maintained by balancing selection for sensor NLRs, in sharp contrast to purifying selection and functional conservation of immune signaling for helper NLRs.

Significance statement

Plants have evolved sophisticated defense mechanisms to fend off pathogens. Plant nucleotide-binding leucine-rich repeat receptor (NLR) proteins play crucial roles in detecting pathogen molecules inside plant cells and mounting defense responses. Here, we identified the Pias gene from rice, which encodes the NLR pair Pias-1 “helper” and Pias-2 “sensor.” These proteins function together to detect the pathogen molecule AVR-Pias of Magnaporthe oryzae and defend against rice blast disease. Pias is allelic to the previously reported Pia gene. A comparison of Pias/Pia alleles among Oryza species showed that Pias/Pia helper is evolutionarily and functionally conserved, whereas the Pias/Pia sensor shows highly dynamic evolution, with various host domains integrated into similar positions, allowing it to detect a wide variety of pathogen molecules.
Automated Model-Predictive Design of Synthetic Promoters to Control Transcriptional Profiles in Bacteria
Authors: Fleur Travis La , Hossain Ayaan , Salis Howard M.
Published: September 2021

Transcription rates are regulated by the interactions between RNA polymerase, sigma factor, and promoter DNA sequences in bacteria. However, it remains unclear how non-canonical sequence motifs collectively control transcription rates. Here, we combined massively parallel assays, biophysics, and machine learning to develop a 346-parameter model that predicts site-specific transcription initiation rates for any σ70 promoter sequence, validated across 17396 bacterial promoters with diverse sequences. We applied the model to predict genetic context effects, design σ70 promoters with desired transcription rates, and identify undesired promoters inside engineered genetic systems. The model provides a biophysical basis for understanding gene regulation in natural genetic systems and precise transcriptional control for engineering synthetic genetic systems.

One-Sentence Summary

A 346-parameter model predicted DNA’s interactions with RNA polymerase initiation complex, enabling accurate transcription rate predictions and automated promoter design in bacterial genetic systems.
Hydrogen-deuterium exchange mass spectrometry of Mtr4 with diverse RNAs reveals substrate-dependent dynamics and interfaces in the arch
Authors: Zhang Naifu , Olsen Keith J , Ball Darby , Johnson Sean J , D’Arcy Sheena
Published: September 2021

Mtr4 is a eukaryotic RNA helicase required for RNA decay by the nuclear exosome. Previous studies have shown how RNA enroute to the exosome threads through the highly conserved helicase core of Mtr4. Mtr4 also contains an arch domain, although details of potential interactions between the arch and RNA have been elusive. To understand the interaction of Saccharomyces cerevisiae Mtr4 with various RNAs, we have characterized RNA binding in solution using hydrogen-deuterium exchange mass spectrometry, and affinity and unwinding assays. We have identified RNA interactions within the helicase core that are consistent with existing structures and do not vary between tRNA, single-stranded RNA, and double-stranded RNA constructs. We have also identified novel RNA interactions with a region of the arch known as the fist or KOW. These interactions are important for RNA unwinding and vary in strength depending on RNA structure and length. They account for Mtr4 discrimination between different RNAs. These interactions further drive Mtr4 to adopt a closed conformation characterized by reduced dynamics of the arch arm and intra-domain contacts between the fist and helicase core.
Parasite-probiotic interactions in the gut: Bacillus sp. and Enterococcus faecium regulate type-2 inflammatory responses and modify the gut microbiota of pigs during helminth infection
Authors: Myhill Laura J. , Stolzenbach Sophie , Mejer Helena , Krych Lukasz , Jakobsen Simon R. , Kot Witold , Skovgaard Kerstin , Canibe Nuria , Nejsum Peter , Nielsen Dennis S. , Thamsborg Stig M. , Williams Andrew R.
Published: September 2021

Dietary probiotics may enhance gut health by directly competing with pathogenic agents and through immunostimulatory effects. These properties are recognized in the context of bacterial and viral pathogens, but less is known about interactions with eukaryotic pathogens such as parasitic worms (helminths). In this study we investigated whether two probiotic mixtures (comprised of Bacillus amyloliquefaciens, B. subtilis, and Enterococcus faecium [BBE], or Lactobacillus rhamnosus LGG and Bifidobacterium animalis subspecies Lactis Bb12 [LB]) could modulate helminth infection kinetics as well as the gut microbiome and intestinal immune responses in pigs infected with the nodular worm Oesophagostomum dentatum. We observed that neither probiotic mixture influenced helminth infection levels. BBE, and to a lesser extent LB, changed the alpha- and beta-diversity indices of the colon and faecal microbiota, notably including an enrichment of faecal Bifidobacterium spp. by BBE. However, these effects were muted by concurrent O. dentatum infection. BBE (but not LB) significantly attenuated the O. dentatum-induced upregulation of genes involved in type-2 inflammation and restored normal lymphocyte ratios in the ileo-caecal lymph nodes that were altered by infection. Moreover, inflammatory cytokine release from blood mononuclear cells and intestinal lymphocytes was diminished by BBE. Collectively, our data suggest that selected probiotic mixtures can play a role in maintaining immune homeostasis during type 2-biased inflammation. In addition, potentially beneficial changes in the microbiome induced by dietary probiotics may be counteracted by helminths, highlighting the complex inter-relationships that potentially exist between probiotic bacteria and intestinal parasites.
Genomically hardwired regulation of gene activity orchestrates cellular iron homeostasis in Arabidopsis
Authors: Hsieh En-Jung , Lin Wen-Dar , Schmidt Wolfgang
Published: September 2021

Iron (Fe) is an essential micronutrient that plays pivotal roles as electron donor and catalyst across organisms. In plants, variable, often insufficient Fe supply necessitates mechanisms that constantly attune Fe uptake rates and recalibrate cellular Fe homeostasis. Here, we show that short-term (0.5, 6, and 12 h) exposure of Arabidopsis thaliana plants to Fe deficiency triggered massive changes in gene activity governed by transcription and alternative splicing (AS), regulatory layers that were to a large extent mutually exclusive. Such preclusion was not observed for genes that are directly involved in the acquisition of Fe, which appears to be concordantly regulated by both expression and AS. Generally, genes with lower splice site strengths and higher intron numbers were more likely to be regulated by AS, no dependence was on gene architecture was observed for transcriptionally controlled genes. Conspicuously, specific processes were associated with particular genomic features and biased towards either regulatory mode, suggesting that genomic hardwiring is functionally biased. Early changes in splicing patterns were, in many cases, congruent with later changes in transcript or protein abundance, thus contributing to the pronounced transcriptome-proteome discordance observed in plants.
Multiplex Immunohistochemical Phenotyping of T Cells in Primary Prostate Cancer
Authors: Ozbek Busra , Ertunc Onur , Erickson Andrew , Vidal Igor Damasceno , Alexandre Carolina Gomes , Guner Gunes , Hicks Jessica L. , Jones Tracy , Taube Janis M. , Sfanos Karen S. , Yegnasubramanian Srinivasan , De Marzo Angelo M
Published: September 2021

Most prostate cancers are “immune cold” and poorly responsive to immune checkpoint inhibitors. However, the mechanisms responsible for the lack of a robust anti-tumor adaptive immune response in the prostate are poorly understood, which hinders the development of novel immunotherapeutic approaches. In addition, most inflammatory infiltrates in the prostate are centered around benign glands and stroma, which can confound the molecular characterization of the anti-tumor immune response. We analytically validated a chromogenic-based multiplex IHC approach and performed whole slide digital image analysis to quantify T cell subsets from the tumor microenvironment (TME) of primary prostatic adenocarcinomas. We trained a classifier to quantify the densities of eight T cell phenotypes separately in the tumor epithelial and stromal subcompartments. As an initial application, we tested the hypothesis that PTEN loss leads to an altered anti-tumor immune response by comparing matched regions of tumors within the same individual with and without PTEN loss. Our main findings in carcinomas (benign removed) include the following: i) CD4+ T cells are present at higher density than CD8+ T cells; ii) All T cell subsets are present at higher densities in the stromal compartment compared to the epithelial tumor compartment; iii) most CD4+ and CD8+ T cells are PD1+; iv) cancer foci with PTEN loss harbored increased numbers of T cells compared to regions without PTEN loss, in both stromal and epithelial compartments; v) the increases in T cells in PTEN loss regions were associated with ERG gene fusion status. This modular approach can apply to any IHC-validated antibody combination, sets the groundwork for more detailed spatial analyses, can help preserve small tissue samples, and can complement single cell and spatial genomic approaches.
Insights from complex trait fine-mapping across diverse populations
Authors: Kanai Masahiro , Ulirsch Jacob C , Karjalainen Juha , Kurki Mitja , Karczewski Konrad J , Fauman Eric , Wang Qingbo S , Jacobs Hannah , Aguet François , Ardlie Kristin G , Kerimov Nurlan , Alasoo Kaur , Benner Christian , Ishigaki Kazuyoshi , Sakaue Saori , Reilly Steven ,   The BioBank Japan Project,   FinnGen, Kamatani Yoichiro , Matsuda Koichi , Palotie Aarno , Neale Benjamin M , Tewhey Ryan , Sabeti Pardis C , Okada Yukinori , Daly Mark J , Finucane Hilary K
Published: September 2021

Despite the great success of genome-wide association studies (GWAS) in identifying genetic loci significantly associated with diseases, the vast majority of causal variants underlying disease-associated loci have not been identified1–3. To create an atlas of causal variants, we performed and integrated fine-mapping across 148 complex traits in three large-scale biobanks (BioBank Japan4,5, FinnGen6, and UK Biobank7,8; total n = 811,261), resulting in 4,518 variant-trait pairs with high posterior probability (> 0.9) of causality. Of these, we found 285 high-confidence variant-trait pairs replicated across multiple populations, and we characterized multiple contributors to the surprising lack of overlap among fine-mapping results from different biobanks. By studying the bottlenecked Finnish and Japanese populations, we identified 21 and 26 putative causal coding variants with extreme allele frequency enrichment (> 10-fold) in these two populations, respectively. Aggregating data across populations enabled identification of 1,492 unique fine-mapped coding variants and 176 genes in which multiple independent coding variants influence the same trait (i.e., with an allelic series of coding variants). Our results demonstrate that fine-mapping in diverse populations enables novel insights into the biology of complex traits by pinpointing high-confidence causal variants for further characterization.
Machine Learning prediction of cardiac resynchronisation therapy response from combination of clinical and model-driven data
Authors: Khamzin Svyatoslav , Dokuchaev Arsenii , Bazhutina Anastasia , Chumarnaya Tatiana , Zubarev Stepan , Lyubimtseva Tamara , Lebedeva Viktoria , Lebedev Dmitry , Gurev Viatcheslav , Solovyova Olga
Published: September 2021

Abstract

Background

Up to 30%-50% of chronic heart failure patients who underwent cardiac resynchronization therapy (CRT) do not respond to the treatment. Therefore, patient stratification for CRT and optimization of CRT device settings remain a challenge.

Objective

The main goal of our study is to develop a predictive model of CRT outcome using a combination of clinical data recorded in patients before CRT and simulations of the response to biventricular (BiV) pacing in personalized computational models of the cardiac electrophysiology.

Materials and Methods

Retrospective data from 57 patients who underwent CRT device implantation was utilized. Positive response to CRT was defined by a 10% increase in the left ventricular ejection fraction in a year after implantation. For each patient, an anatomical model of the heart and torso was reconstructed from MRI and CT images and tailored to ECG recorded in the participant. The models were used to compute ventricular activation time, ECG duration and electrical dyssynchrony indices during intrinsic rhythm and BiV pacing from active poles of leads. For building a predictive model of CRT response, we used clinical data recorded before CRT device implantation together with model-derived biomarkers of ventricular excitation in the left bundle branch block mode of activation and under BiV stimulation. Several Machine Learning (ML) classifiers and feature selection algorithms were tested on the hybrid dataset, and the quality of predictors was assessed using the area under receiver operating curve (ROC AUC). The classifiers on the hybrid data were compared with ML models built on clinical data only.

Results

The best ML classifier utilizing a hybrid set of clinical and model-driven data demonstrated ROC AUC of 0.82, an accuracy of 0.82, sensitivity of 0.85, and specificity of 0.78, improving quality over that of ML predictors built on clinical data from much larger datasets. Distance from the LV pacing site to the post-infarction zone and ventricular activation characteristics under BiV pacing were shown as the most relevant model-driven features for CRT response classification.

Conclusion

Our results suggest that combination of clinical and model-driven data increases the accuracy of classification models for CRT outcomes.
PGP1 personal genome assembly - a hybrid assembly dataset using ONT’s PromethION and PacBio’s HiFi sequencing
Authors: Kim Hui-Su , Kim Changjae , Church George , Bhak Jong
Published: September 2021

PGP1 is the first participant of Personal Genome Project. We present the PGP1’s chromosome-scale genome assembly. It was constructed using 255 Gb ultra-long PromethION reads and 97 Gb short paired-end reads. For reducing base calling errors, we corrected PromethION reads using 72 Gb PacBio HiFi reads. 327 Gb Hi-C chromosomal mapping data were utilized to maximize the assembly’s contiguity. PGP1’s contig assembly was 3.01 Gb in length comprising of 4,234 contigs with an N50 value of 33.8 Mb. After scaffolding with Hi-C data and extensive manual curation, we obtained a chromosome-scale assembly that represents 3,880 scaffolds with an N50 value of 142 Mb. From the Merqury assessment, PGP1 assembly achieved a high QV score of Q45.45. For a gene annotation, we predicted 106,789 genes with a liftover from the Gencode 38 and an assembly of transcriptome data.
Prediction of evolutionary constraint by genomic annotations improves prioritization of causal variants in maize
Authors: Ramstein Guillaume P. , Buckler Edward S.
Published: September 2021

Crop improvement through cross-population genomic prediction and genome editing requires identification of causal variants at single-site resolution. Most genetic mapping studies have generally lacked such resolution. In contrast, evolutionary approaches can detect genetic effects at high resolution, but they are limited by shifting selection, missing data, and low depth of multiple-sequence alignments. Here we used genomic annotations to accurately predict nucleotide conservation across Angiosperms, as a proxy for fitness effect of mutations. Using only sequence analysis, we annotated non-synonymous mutations in 25,824 maize gene models, with information from bioinformatics (SIFT scores, GC content, transposon insertion, k-mer frequency) and deep learning (predicted effects of polymorphisms on protein representations by UniRep). Our predictions were validated by experimental information: within-species conservation, chromatin accessibility, gene expression and gene ontology enrichment. Importantly, they also improved genomic prediction for fitness-related traits (grain yield) in elite maize panels (+5% and +38% prediction accuracy within and across panels, respectively), by stringent prioritization of ≤ 1% of single-site variants (e.g., 104 sites and approximately 15deleterious alleles per haploid genome). Our results suggest that predicting nucleotide conservation across Angiosperms may effectively prioritize sites most likely to impact fitness-related traits in crops, without being limited by shifting selection, missing data, and low depth of multiple-sequence alignments. Our approach – Prediction of mutation Impact by Calibrated Nucleotide Conservation (PICNC) – could be useful to select polymorphisms for accurate genomic prediction, and candidate mutations for efficient base editing.
Inverse Problem Reveals Conditions for Characteristic Retinal Degeneration Patterns in Retinitis Pigmentosa under the Trophic Factor Hypothesis
Authors: Roberts Paul A.
Published: September 2021

Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy with a prevalence of about 1 in 4000, affecting approximately 1.5 million people worldwide. Patients with RP experience progressive visual field loss as the retina degenerates, destroying light-sensitive photoreceptor cells (rods and cones), with rods affected earlier and more severely than cones. Spatio-temporal patterns of retinal degeneration in human RP have been well characterised; however, the mechanism(s) giving rise to these patterns have not been conclusively determined. One such mechanism, which has received a wealth of experimental support, is described by the trophic factor hypothesis. This hypothesis suggests that rods produce a trophic factor necessary for cone survival; the loss of rods depletes this factor, leading to cone degeneration. In this paper we formulate a partial differential equation mathematical model of RP in one spatial dimension, spanning the region between the retinal centre (fovea) and the retinal edge (ora serrata). Using this model we derive and solve an inverse problem, revealing for the first time experimentally testable conditions under which the trophic factor mechanism will qualitatively recapitulate the spatio-temporal patterns of retinal regeneration observed in human RP.
Generation of transducible version of a recombinant human HAND2 transcription factor from Escherichia coli
Authors: Haridhasapavalan Krishna Kumar , Sundaravadivelu Pradeep Kumar , Mohapatra Anshuman , Joshi Neha , Das Nayan Jyoti , Thummer Rajkumar P
Published: September 2021

Transcription factor HAND2 has a significant role in vascularization, angiogenesis, and cardiac neural crest development. Also, it is one of the key cardiac factors crucial for the enhanced derivation of functional and mature myocytes from non-myocyte cells. Here, we report the generation of the recombinant human HAND2 fusion protein from the heterologous system. First, we cloned the full-length human HAND2 gene (only protein-coding sequence) after codon optimization along with the fusion tags (for cell penetration, nuclear translocation, and affinity purification) into the expression vector. We then transformed and expressed it in Escherichia coli (E. coli) strain, BL21(DE3). Next, the effect (in terms of expression) of tagging of fusion tags with this recombinant protein at two different terminals was also investigated. Notably, using affinity chromatography, we established the one-step homogeneous purification of human recombinant HAND2 protein; and through circular dichroism spectroscopy, we established that this purified protein had retained its secondary structure. Furthermore, we show that this purified human protein could transduce the human cells and translocate to its nucleus. Prospectively, the purified recombinant HAND2 protein can potentially be a safe and effective molecular tool in the direct cardiac reprogramming process and other biological applications.
Distinct inflammatory and transcriptomic profiles in dominant versus subordinate males in mouse social hierarchies
Authors: Lee Won , Milewski Tyler M. , Dwortz Madeleine F. , Young Rebecca L. , Gaudet Andrew D. , Fonken Laura K. , Champagne Frances A. , Curley James P.
Published: September 2021

Social status is a critical factor determining health outcomes in human and nonhuman social species. In social hierarchies with reproductive skew, individuals compete to monopolize resources and increase mating opportunities. This can come at a significant energetic cost leading to trade-offs between different physiological systems. Particularly, changes in energetic investment in the immune system can have significant short and long-term effects on fitness and health. We have previously found that dominant alpha male mice living in social hierarchies have increased metabolic demands related to territorial defense. In this study, we tested the hypothesis that high-ranking male mice favor energetically inexpensive adaptive immunity, while subordinate mice show higher investment in innate immunity. We housed 12 groups of 10 outbred CD-1 male mice in a social housing system. All formed linear social hierarchies and subordinate mice had higher concentrations of plasma corticosterone (CORT) than alpha males. This difference was heightened in highly despotic hierarchies. Using flow cytometry, we found that dominant status was associated with a significant shift in immunophenotypes towards favoring adaptive versus innate immunity. Using Tag-Seq to profile hepatic and splenic transcriptomes of alpha and subordinate males, we identified genes that regulate metabolic and immune defense pathways that are associated with status and/or CORT concentration. In the liver, dominant animals showed an up-regulation of specific genes involved in major urinary production and catabolic processes, whereas subordinate animals showed an up-regulation of genes promoting biosynthetic processes, wound healing, and proinflammatory responses. In spleen, subordinate mice showed up-regulation of genes facilitating oxidative phosphorylation and DNA repair and CORT was negatively associated with genes involved in lymphocyte proliferation and activation. Together, our findings suggest that dominant and subordinate animals adaptively shift energy investment in immune functioning and gene expression to match their contextual energetic demands.

Highlights

Immunity is shaped by stress and energetic pressures associated with social status

Dominant and subordinate mice favor adaptive and innate immunity, respectively

Dominants increase expression of genes involved in energy production

Wound healing and DNA repair genes are upregulated in subordinates

Genes related to maintaining and signaling social status are upregulated in dominants
Entry to and exit from diapause arrest inCaenorhabditis elegansare both regulated by a steroid hormone pathway
Authors: Zhang Mark G , Sternberg Paul W
Published: September 2021

Diapause arrest in animals such asCaenorhabditis elegansis tightly regulated so that animals make appropriate developmental decisions amidst environmental challenges. Fully understanding diapause requires mechanistic insight of both entry and exit from the arrested state. While a steroid hormone pathway regulates the entry decision intoCaenorhabditis elegansdauer diapause, its role in the exit decision is less clear. A complication to understanding steroid hormonal regulation of dauer has been the peculiar fact that steroid hormone mutants such asdaf-9form partial dauers under normal growth conditions. Here, we corroborate previous findings thatdaf-9mutants remain capable of forming full dauers under unfavorable growth conditions, and we establish that thedaf-9partial dauer state is likely a partially exited dauer that has initiated but cannot complete the dauer exit decision. We show that the steroid hormone pathway is both necessary for and promotes complete dauer exit, and that the spatiotemporal dynamics of steroid hormone regulation during dauer exit resembles that of dauer entry. Overall, dauer entry and dauer exit are distinct developmental decisions that are both controlled by steroid hormone signaling.

Summary Statement

In animals such asCaenorhabditis elegans, a steroid hormone pathway controls both the entry and exit decisions into and out of the developmentally arrested dauer state in response to environmental signaling.