bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for a selective link between cooperation and individual recognition
Authors: Tumulty James P. , Miller Sara E. , Van Belleghem Steven M. , Weller Hannah I. , Jernigan Christopher M. , Vincent Sierra , Staudenraus Regan J. , Legan Andrew W. , Polnaszek Timothy J. , Uy Floria M. K. , Walton Alexander , Sheehan Michael J.
Published: September 2021

The ability to recognize and discriminate among others is a frequent assumption of models of the evolution of cooperative behavior. At the same time, cooperative behavior has been proposed as a selective agent favoring the evolution of individual recognition abilities. While theory predicts that recognition and cooperation may co-evolve, data linking recognition abilities and cooperative behavior with fitness or evidence of selection are elusive. Here, we provide evidence of a fitness link between individual recognition and cooperation in the paper waspPolistes fuscatus. Nest founding females in northern populations frequently form cooperative multiple foundress nests and possess highly variable facial patterns that mediate individual recognition. We describe a dearth of cooperative nesting, low phenotypic diversity, and a lack of individual recognition in southern populations. In a common garden experiment, northern co-foundress associations successfully reared offspring while all cooperative southern groups failed to rear any offspring, suggesting a fitness link between individual recognition and successful cooperation. Consistent with a selective link between individual recognition and cooperation, we find that rates of cooperative co-nesting correlate with identity-signaling color pattern diversity across the species’ range. Moreover, genomic evidence of recent positive selection on cognition loci likely to mediate individual recognition is substantially stronger in northern compared to southernP. fuscatuspopulations. Collectively, these data suggest that individual recognition and cooperative nesting behavior have co-evolved inP. fuscatusbecause recognition helps mediate conflict among co-nesting foundresses. This work provides evidence of a specific cognitive phenotype under selection because of social interactions, supporting the idea that social behavior can be a key driver of cognitive evolution.
Depside and depsidone synthesis in lichenized fungi comes into focus through a genome-wide comparison of the olivetoric and physodic acid chemotype of Pseudevernia furfuracea
Authors: Singh Garima , Armaleo Daniele , Grande Francesco Dal , Schmitt Imke
Published: September 2021

Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are Non-Reducing Polyketide Synthases (NR-PKSs), and cytochrome P450s (CytP450). However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acyl synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for the synthesis of olivetoric and physodic acid, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for olivetoric and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for physodic and olivetoric acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.
Intersegmental coordination of the central pattern generator via interleaved electrical and chemical synapses in zebrafish spinal cord
Authors: Kim Lae Un , Riecke Hermann
Published: September 2021

A significant component of the repetitive dynamics during locomotion in vertebrates is generated within the spinal cord. The legged locomotion of mammals is most likely controled by a hierarchical, multi-layer spinal network structure, while the axial circuitry generating the undulatory swimming motion of animals like lamprey is thought to have only a single layer in each segment. Recent experiments have suggested a hybrid network structure in zebrafish larvae in which two types of excitatory interneurons (V2a-I and V2a-II) both make first-order connections to the brain and last-order connections to the motor pool. These neurons are connected by electrical and chemical synapses across segments. Through computational modeling and an asymptotic perturbation approach we show that this interleaved interaction between the two neuron populations allows the spinal network to quickly establish the correct activation sequence of the segments when starting from random initial conditions and to reduce the dependence of the intersegmental phase difference (ISPD) of the oscillations on the swimming frequency. The latter reduces the frequency dependence of the waveform of the swimming motion. In the model the reduced frequency dependence is largely due to the different impact of chemical and electrical synapses on the ISPD and to the significant spike-frequency adaptation that has been observed experimentally in V2a-II neurons, but not in V2a-I neurons. Our model makes experimentally testable predictions and points to a benefit of the hybrid structure for undulatory locomotion that may not be relevant for legged locomotion.
Atria: An Ultra-fast and Accurate Trimmer for Adapter and Quality Trimming
Authors: Chuan Jiacheng , Zhou Aiguo , Hale Lawrence Richard , He Miao , Li Xiang
Published: September 2021

Background

As Next Generation Sequencing takes a dominant role in terms of output capacity and sequence length, adapters attached to the reads and low-quality bases hinder the performance of downstream analysis directly and implicitly, such as producing false-positive single nucleotide polymorphisms (SNP), and generating fragmented assemblies. A fast trimming algorithm is in demand to remove adapters precisely, especially in read tails with relatively low quality.

Findings

We present a trimming program named Atria. Atria matches the adapters in paired reads and finds possible overlapped regions with a super-fast and carefully designed byte-based matching algorithm (O(n)time withO(1)space). Atria also implements multi-threading in both sequence processing and file compression and supports single-end reads.

Conclusions

Atria performs favorably in various trimming and runtime benchmarks of both simulated and real data with other cutting-edge trimmers. We also provide an ultra-fast and lightweight byte-based matching algorithm. The algorithm can be used in a broad range of short-sequence matching applications, such as primer search and seed scanning before alignment.

Availability & Implementation

The Atria executables, source code, and benchmark scripts are available athttps://github.com/cihga39871/Atriaunder the MIT license.
A unique form of collective epithelial migration is crucial for tissue fusion in the secondary palate and can overcome loss of epithelial apoptosis
Authors: Teng Teng , Teng Camilla , Kaartinen Vesa , Bush Jeffrey O.
Published: September 2021

Tissue fusion is an oft-employed process in morphogenesis which often requires the removal of the epithelia intervening multiple distinct primordia to form one continuous structure. In the mammalian secondary palate, a midline epithelial seam (MES) forms between two palatal shelves and must be removed to allow mesenchymal confluence. Abundant apoptosis and cell extrusion in this epithelial seam support their importance in its removal. However, by genetically disrupting the intrinsic apoptotic regulators BAX and BAK within the MES, we find a complete loss of cell death and cell extrusion, but successful removal of the MES, indicating that developmental compensation enables fusion. Novel static and live imaging approaches reveal that the MES is removed through a unique form of collective epithelial cell migration in which epithelial trails and islands stream through the mesenchyme to reach the oral and nasal epithelial surfaces. These epithelial trails and islands begin to express periderm markers while retaining expression of the basal epithelial marker ΔNp63, suggesting their migration to the oral and nasal surface is concomitant with their differentiation to an epithelial intermediate. Live imaging reveals anisotropic actomyosin contractility within epithelial trails that drives their peristaltic movement, and genetic loss of non-muscle myosin IIA-mediated actomyosin contractility results in dispersion of epithelial collectives and dramatic failure of normal MES migration. These findings demonstrate redundancy between cellular mechanisms of morphogenesis and reveal a crucial role for a unique form of collective epithelial migration during tissue fusion.
LIFE-Seq: A universal Large Integrated DNA Fragment Enrichment Sequencing strategy for transgene integration in genetically modified organisms
Authors: Zhang Hanwen , Li Rong , Guo Yongkun , Zhang Yuchen , Zhang Dabing , Yang Litao
Published: September 2021

Molecular characterisation of genetically modified organisms (GMOs) yields basic information on exogenous DNA integration, including integration sites, entire inserted sequences and structures, flanking sequences and copy number, providing key data for biosafety assessment. However, there are few effective methods for deciphering transgene integration, especially for large DNA fragment integration with complex rearrangement, inversion, and tandem repeats. Herein, we developed a universal Large Integrated DNA Fragments Enrichment strategy combined with PacBio Sequencing (LIFE-Seq) for deciphering transgene integration in GMOs. Universal tilling DNA probes targeting transgenic elements and exogenous genes facilitate specific enrichment of large inserted DNA fragments associated with transgenes from plant genomes, followed by PacBio sequencing. LIFE-Seq were evaluated using six GM events and four crop species. Target DNA fragments averaging ∼6275 bp were enriched and sequenced, generating ∼26,352 high fidelity reads for each sample. Transgene integration structures were determined with high repeatability and sensitivity. Compared with whole-genome sequencing, LIFE-Seq achieved better data integrity and accuracy, greater universality, and lower cost, especially for transgenic crops with complex inserted DNA structures. LIFE-Seq could be applied in molecular characterisation of transgenic crops and animals, and complex DNA structure analysis in genetics research.
Genome-wide transcriptional profiling uncovers a similar oligodendrocyte-related transcriptional response to acute and chronic alcohol drinking in the amygdala
Authors: Narendra Sharvari , Klengel Claudia , Hamzeh Bilal , Patel Drasti , Otten Joy , Lardenoije Roy , Newman Emily L. , Miczek Klaus A. , Klengel Torsten , Ressler Kerry J. , Suh Junghyup
Published: September 2021

Alcohol intake progressively increases after prolonged consumption of alcohol, but relatively few new therapeutics targeting development of alcohol use disorder (AUD) have been validated. Here, we conducted a genome-wide RNA-sequencing (RNA-seq) analysis in mice exposed to different modes (acute vs chronic) of ethanol drinking. We focused on transcriptional profiles in the amygdala including the central and basolateral subnuclei, a brain area previously implicated in alcohol drinking and seeking, demonstrating distinct gene expression patterns and canonical pathways induced by both acute and chronic intake. Surprisingly, both drinking modes triggered similar transcriptional changes, including up-regulation of ribosome-related/translational pathways and myelination pathways, and down-regulation of chromatin binding and histone modification. Notably, multiple genes that were significantly regulated in mouse amygdala with alcohol drinking, including Atp2b1, Slc4a7, Nfkb1, Nts, and Hdac2, among others had previously been associated with human AUD via GWAS or other genomic studies. In addition, analyses of hub genes and upstream regulatory pathways predicted that voluntary ethanol consumption affects epigenetic changes via histone deacetylation pathways, oligodendrocyte and myelin function, and oligodendrocyte-related transcriptional factor, Sox17.

Overall, our results suggest that the transcriptional landscape in the central and basolateral subnuclei of the amygdala is sensitive to voluntary alcohol drinking. They provide a unique resource of gene expression data for future translational studies examining transcriptional mechanisms underlying the development of AUD due to alcohol consumption.
Characterization of the Endogenous DAF-12 Ligand and Its Use as an Anthelmintic Agent inStrongyloides stercoralis
Authors: Wang Zhu , Cheong Mi Cheong , Tsien Jet , Deng Heping , Qin Tian , Stoltzfus Jonathan D. C. , Jaleta Tegegn G. , Li Xinshe , Lok James B. , Kliewer Steven A. , Mangelsdorf David J.
Published: September 2021

A prevalent feature ofStrongyloides stercoralisis a life-long and potentially lethal infection that is due to the nematode parasite’s ability to autoinfect and, thereby, self-replicate within its host. Here, we investigated the role of the parasite’s nuclear receptor,Ss-DAF-12, in governing infection. We identified Δ7-DA as the endogenousSs-DAF-12 ligand and elucidated the hormone’s biosynthetic pathway. Genetic loss of function of the ligand’s rate-limiting enzyme demonstrated that Δ7-DA synthesis is necessary for parasite reproduction, whereas its absence is required for development of infectious larvae. Availability of the ligand permitsSs-DAF-12 to function as an on/off switch governing autoinfection, making it vulnerable to therapeutic intervention. In a preclinical model of hyperinfection, pharmacologic activation of DAF-12 suppressed autoinfection and markedly reduced lethality. Moreover, when Δ7-DA was administered with ivermectin, the current but limited drug of choice for treating strongyloidiasis, the combinatorial effects of the two drugs resulted in a near cure of the disease.
The spliced leader RNA silencing (SLS) pathway in Trypanosoma brucei is induced by perturbations of endoplasmic reticulum, Golgi, or mitochondrial proteins factors and functional analysis of SLS inducing kinase, PK3
Authors: Okalang Uthman , Bar-Ner Bar Mualem , Rajan K. Shanmugha , Friedman Nehemya , Aryal Saurav , Egarmina Katarina , Hope Ronen , Khazanov Netaly , Senderowitz Hanoch , Alon Assaf , Fass Deborah , Michaeli Shulamit
Published: September 2021

In the parasite Trypanosoma brucei, the causative agent of human African sleeping sickness, all mRNAs are trans-spliced to generate a common 5’ exon derived from the spliced leader RNA (SL RNA). Perturbations of protein translocation across the endoplasmic reticulum (ER) induce the spliced leader RNA silencing (SLS) pathway. SLS activation is mediated by a serine-threonine kinase, PK3, which translocates from the cytosolic face of the ER to the nucleus, where it phosphorylates the TATA binding protein TRF4, leading to the shut-off of SL RNA transcription, followed by induction of programmed cell death. Here, we demonstrate that SLS is also induced by depletion of the essential ER resident chaperones BiP and calreticulin, ER oxidoreductin 1 (ERO1), and the Golgi-localized quiescin sulfhydryl oxidase (QSOX1). Most strikingly, silencing of Rhomboid-like 1(TIMRHOM1) involved in mitochondrial protein import, also induces SLS. The PK3 kinase, which integrates SLS signals, is modified by phosphorylation on multiple sites. To determine which of the phosphorylation events activate PK3, several individual mutations or their combination were generated. These mutations failed to completely eliminate the phosphorylation or translocation of the kinase to the nucleus. The structure of PK3 kinase and its ATP binding domain were therefore modeled. A conserved phenylalanine at position 771 was proposed to interact with ATP, and the PK3F771L mutation completely eliminated phosphorylation under SLS, suggesting that the activation involves most if not all the phosphorylation sites. The study suggests that the SLS occurs broadly in response to failures in protein sorting, folding, or modification across multiple compartments.
Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle
Authors: Hoces Daniel , Lan Jiayi , Wenfei Sun , Geiser Tobias , Cappio Barazzone Elisa , Arnoldini Markus , Nowok Sven , Macpherson Andrew J , Stecher Bärbel , Zenobi Renato , Hardt Wolf-Dietrich , Wolfrum Christian , Slack Emma
Published: September 2021

The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiome to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat-mass than germ-free or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure and respiratory quotient using a novel isolator-housed metabolic cage system which allows long-term measurements without contamination risk. This demonstrated that microbiota- released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and germ-free mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well-integrated into appetite control. We also observed no significant difference in energy expenditure per gram lean mass between the different microbiota groups, suggesting that cumulative very small differences in energy balance, or altered energy storage must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: in germ-free mice the respiratory exchange ratio was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied germ-free mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a germ-free-like drop in liver glycogen storage during the light cycle and both liver and plasma metabolomes of OligoMM12 mice clustered closely with germ-free mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle, and which are absent in the OligoMM12 consortium.
Intercellular crosstalk regulating ARRB2/RARRES1 is involved in transition from fibrosis to cancer
Authors: Schierwagen Robert , Dietrich Peter , Heinzen Judith , Klein Sabine , Uschner Frank E. , Ortiz Cristina , Tyc Olaf , Torres Sandra , Hieber Christoph , Kraus Nico , Premont Richard T. , Grünewald Leon D. , Poisson Johanne , Rautou Pierre-Emmanuel , Kristiansen Glen , Gracia-Sancho Jordi , Poglitsch Marko , Ludwig-Portugall Isis , Walther Thomas , Trautwein Christian , Abdullah Zeinab , Münch Christian , Welsch Christoph , Fernandez Mercedes , Zeuzem Stefan , Moreau Richard , Hellerbrand Claus , Rombouts Krista , Kastenmüller Wolfgang , Diehl Anna Mae , Trebicka Jonel
Published: September 2021

Progressive fibrogenesis in chronic liver injury is often associated with cancer development. Beta-arrestin-2 (ARRB2) is a regulator of the profibrotic Angiotensin II type 1 receptor (AGTR1). The role of ARRB2 in liver fibrosis and in the transition from fibrosis to cancer is not fully understood and was investigated in this study.

This study demonstrates that upregulation of the retinoic acid receptor responder 1 (RARRES1) in HSC mediated by ARRB2 leads to fibrosis. This process is driven by exosomal ARRB2 transfer to HSC, major fibrosis contributors, from injured hepatocytes, which highly express ARRB2. By contrast, downregulation of RARRES1 in hepatocytes induces malignant transformation and hepatocellular carcinoma (HCC) development. Consequently, Arrb2-deficient mice show higher number and size of liver tumors than wild-type mice in a hepatocellular carcinoma model with fibrosis. The identified relationship between ARRB2 and RARRES1 was observed in at least two species, including human cells and tissues in fibrosis and HCC and has a predictive value for survival in cancer patients. This study describes the discovery of a novel molecular pathway mediating the transition from fibrosis to cancer offering potential diagnostics and therapeutics.
Flexible Path Planning Through Vicarious Trial and Error
Authors: Krichmar Jeffrey L. , Ketz Nicholas A. , Pilly Praveen K. , Soltoggio Andrea
Published: September 2021

Abstract

Flexible planning is necessary for reaching goals and adapting when conditions change. We introduce a biologically plausible path planning model that learns its environment, rapidly adapts to change, and plans efficient routes to goals. Unlike prior models of hippocampal replay, our model addresses the decision-making process when faced with uncertainty. We tested the model in simulations of human and rodent navigation in mazes. Like the human and rat, the model was able to generate novel shortcuts, and take detours when familiar routes were blocked. Similar to rodent hippocampus recordings, the neural activity of the model resembles neural correlates of Vicarious Trial and Error (VTE) during early learning or during uncertain conditions. Similar to rodent studies, after learning, the neural activity resembles forward replay or preplay predicting a future route, and VTE activity decreases. We suggest that VTE, in addition to weighing possible outcomes, is a way in which an organism may gather information for future use.
Host- and age-dependent transcriptional changes in Mycobacterium tuberculosis cell envelope biosynthesis genes after exposure to human alveolar lining fluid
Authors: Allué-Guardia Anna , Garcia-Vilanova Andreu , M. Olmo-Fontánez Angélica , Peters Jay , Maselli Diego J. , Wang Yufeng , Turner Joanne , Schlesinger Larry S. , Torrelles Jordi B.
Published: September 2021

Tuberculosis (TB) infection, caused by the airborne pathogen Mycobacterium tuberculosis (M.tb), resulted in almost 1.4 million deaths in 2019 and the number of deaths is predicted to increase by 20% over the next 5 years due to the COVID-19 pandemic. Upon reaching the alveolar space, M.tb comes in close contact with the lung mucosa before and after its encounter with host alveolar compartment cells. Our previous studies show that homeostatic innate soluble components of the alveolar lining fluid (ALF) can quickly alter the cell envelope surface of M.tb upon contact, defining subsequent M.tb-host cell interactions and infection outcomes in vitro and in vivo. We also demonstrated that ALF from 60+ year old elders (E-ALF) vs. healthy 18- to 45-year-old adults (A-ALF) is dysfunctional with loss of homeostatic capacity and impaired innate soluble responses linked to high local oxidative stress. In this study, a targeted transcriptional assay demonstrates that M.tb exposure to human ALF alters the expression of its cell envelope genes. Specifically, our results indicate that A-ALF-exposed M.tb upregulates cell envelope genes associated with lipid, carbohydrate, and amino acid metabolism, as well as genes associated with redox homeostasis and transcriptional regulators. Conversely, M.tb exposure to E-ALF shows lesser transcriptional response, with most of the M.tb genes unchanged or downregulated. Overall, this study indicates that M.tb responds and adapts to the lung alveolar environment upon contact, and that the host ALF status determined by factors such as age might play an important role in determining infection outcome.
Riparian forest restoration as sources of biodiversity and ecosystem functions in anthropogenic landscapes
Authors: Antonini Y , Beirão MV , Costa FV , Azevedo CSv , Wojakowski MM , Kozovits AR , Pires MRS , Sousa HC de , Messias MCTB , Fujaco MA , Leite MGP , Vidigal JP , Monteiro GF , Dirzo R
Published: September 2021

Abstract

Restoration of tropical riparian forests is challenging, since these ecosystems are the most diverse, dynamic, and complex physical and biological terrestrial habitats. This study tested whether biodiversity can predict ecosystem functions in a human-impacted tropical riparian forest.

We explored the effects of several biodiversity components (taxonomic or functional groups) on different ecosystem functions associated with restored riparian forests

Overall, 49% of the biodiversity components showed positive effects on ecosystem functions, each component to a different degree. In general, our results showed that both taxonomic and functional biodiversity had strong effects on ecosystem functions indicating that floral and faunal biodiversity enhanced the multifunctionality of these restored riparian tropical forests.

These findings indicate that in restored riparian forests, recovery of biodiversity is followed by improvement in important ecosystem functions that are the basis for successful restoration. Future research and policy for restoration programs must focus on restoring elementary faunal and floral components of biodiversity in order to promote ecosystem multifunctionality.
Foot-and-mouth disease virus localisation on follicular dendritic cells and sustained induction of neutralising antibodies is dependent on binding to complement receptors (CR2/CR1)
Authors: Gordon Lucy , Mabbott Neil , Wells Joanna , Kulik Liudmila , Juleff Nick , Charleston Bryan , Perez-Martin Eva
Published: September 2021

Previous studies have shown after the resolution of acute infection and viraemia, foot- and-mouth disease virus (FMDV) capsid proteins and/or genome are localised in the light zone of germinal centres of lymphoid tissue in cattle and African buffalo. The pattern of staining for FMDV proteins was consistent with the virus binding to follicular dendritic cells (FDCs). We have now demonstrated a similar pattern of FMDV protein staining in mouse spleens after acute infection and showed FMDV proteins are colocalised with FDCs. Blocking antigen binding to complement receptor type 2 and 1 (CR2/CR1) prior to infection with FMDV significantly reduced the detection of viral proteins on FDCs and FMDV genomic RNA in spleen samples. Blocking the receptors prior to infection also significantly reduced neutralising antibody titres. Therefore, the binding of FMDV to FDCs and sustained induction of neutralising antibody responses are dependent on FMDV binding to CR2/CR1 in mice.

Author Summary

Foot and mouth disease virus causes a highly contagious acute vesicular disease, resulting in more than 50% of cattle, regardless of vaccination status, and almost 100% of African buffalo becoming persistently infected for long periods (months) of time. Yet, the mechanisms associated with establishment of persistent infections are still poorly understood. Infected animals are characterised by the presence of long-lived neutralising antibody titres, which contrast with the short-lived response induced by vaccination. We have used a mouse model to understand how foot and mouth disease virus is trapped and retained in the spleen for up to 28 days post infection and how the absence of antigen in the germinal centre prevents a sustainable neutralising antibody response, in the mouse. Our results highlight the importance of targeting antigen to FDCs to stimulate potent neutralising antibody responses after vaccination.
ShareLoc – an open platform for sharing localization microscopy data
Authors: Bai Jiachuan , Ouyang Wei , Singh Manish Kumar , Leterrier Christophe , Barthelemy Paul , Barnett Samuel F.H. , Klein Teresa , Sauer Markus , Kanchanawong Pakorn , Bourg Nicolas , Cohen Mickael M. , Lelandais Benoît , Zimmer Christophe
Published: September 2021

Novel insights and more powerful analytical tools can emerge from the reanalysis of existing data sets, especially via machine learning methods. Despite the widespread use of single molecule localization microscopy (SMLM) for super-resolution bioimaging, the underlying data are often not publicly accessible. We developed ShareLoc (https://shareloc.xyz), an open platform designed to enable sharing, easy visualization and reanalysis of SMLM data. We discuss its features and show how data sharing can improve the performance and robustness of SMLM image reconstruction by deep learning.
Structural origins of Escherichia coli RNA polymerase open promoter complex stability
Authors: Saecker Ruth M. , Chen James , Chiu Courtney E. , Malone Brandon , Sotiris Johanna , Ebrahim Mark , Yen Laura Y. , Eng Edward T. , Darst Seth A.
Published: September 2021

The first step of gene expression in all organisms requires opening the DNA duplex to expose one strand for templated RNA synthesis. In Escherichia coli, promoter DNA sequence fundamentally determines how fast the RNA polymerase (RNAP) forms “open” complexes (RPo), whether RPo persists for seconds or hours, and how quickly RNAP transitions from initiation to elongation. These rates control promoter strength in vivo but their structural origins remain largely unknown. Here we use cryo-electron microscopy to determine structures of RPo formed de novo at three promoters with widely differing lifetimes at 37°C: λPR (t1/2 ∼ 10 hours), T7A1 (t1/2 ∼ 4 minutes), and a point mutant in λPR (λPR-5C) (t1/2 ∼ 2 hours). Two distinct RPo conformers are populated at λPR, likely representing productive and unproductive forms of RPo observed in solution studies. We find that changes in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1) globally alter the network of DNA-RNAP interactions, base stacking, and strand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond the bubble to upstream and downstream DNA. After expanding the transcription bubble by one base (T7A1), the nontemplate-strand “scrunches” inside the active site cleft; the template-strand bulges outside the cleft at the upstream edge of the bubble. The structures illustrate how limited sequence changes trigger global alterations in the transcription bubble that modulate RPo lifetime and affect the subsequent steps of the transcription cycle.
Pathogenic, but not non-pathogenic,Rickettsiaevade inflammasome-dependent IL-1 responses to establish an intracytosolic replication niche
Authors: Voss Oliver H. , Cobb Jennifer , Gaytan Hodalis , Díaz Natalia Rivera , Sanchez Rigoberto , DeTolla Louis , Rahman M. Sayeedur , Azad Abdu F.
Published: September 2021

Rickettsiaspecies (spp.) are strict obligate intracellular bacteria, with some being pathogenic in their mammalian host, including humans. One critical feature of these stealthy group of pathogens is their ability to manipulate hostile cytosolic environments to their benefits. Although our understanding ofRickettsiacell biology and pathogenesis are evolving, the mechanisms by which pathogenicRickettsiaspp. evade host innate immune detection remains elusive. Here, we showed that disease severity in wild-type (WT) C57BL/6J mice infected withR. typhi(etiologic agent of murinetyphus) andR. rickettsii(etiologic agent of Rocky Mountain Spotted Fever), but not with non-pathogenicR. montanensis, correlated with levels of bacterial burden as detected in the spleens, as well as the serum concentrations of pro-inflammatory cytokine IL-1α and to a lesser extent IL- 1β. Antibody-mediated neutralization of IL-1α confirmed a key role in controlling mortality rates and bacterial burdens of rickettsiae-infectedWTmice. As macrophages are a primary source of both IL-1α and IL-1β cytokines, we determined the mechanism of the anti-rickettsial activities using bone-marrow-derived macrophages. We found that pathogenicR. typhiandR. rickettsii, but not non-pathogenicR. montanensis, eluded pro- IL-1α induction and benefited pre-dominantly from the reduced IL-1α secretion, via a Caspase-11-Gsdmd-dependent pathway, to facilitate intracytosolic replication. Adoptative transfer experiments identified that IL-1α secretion by macrophages was critical for controlling rickettsiosis inWTmice. In sum, we identified a previously unappreciated pathway by which pathogenic, unlike non-pathogenic, rickettsiae preferentially target the Caspase-11-Gsdmd-IL-1α signaling axis in macrophages thus supporting their replication within the host.

IMPORTANCE

Currently, no vaccines are available to prevent rickettsioses, while vector-borne rickettsial infections in humans are on the rise globally. In fact, the insufficient understanding of how pathogenicRickettsiaspecies circumvent host immune defense mechanisms has significantly hindered the development of more effective therapeutics. Here, we identified a previously unappreciated role for the Caspase-11-Gsdmd-IL-1α signaling axis, to limiting the replication of pathogenicR. rickettsiaandR. typhispecies in murine macrophages and wild-type (WT) C57BL/6J mice. Adoptative transfer studies further identified IL-1α-secreting macrophages as critical mediators in controlling rickettsial infection inWTmice. Collectively, these findings provide insight into the potential mechanism of how pathogenic, but not non-pathogenicRickettsiaspp., benefit from a reduction in the Caspase-11-Gsdmd-mediated release of IL-1α to support host colonization.
A redox cycle with complex II promotes sulfide quinone oxidoreductase dependent H2S oxidation
Authors: Kumar Roshan , Landry Aaron P. , Guha Arkajit , Vitvitsky Victor , Lee Ho Joon , Seike Keisuke , Reddy Pavan , Lyssiotis Costas A. , Banerjee Ruma
Published: September 2021

The dueling roles of H2S as an endogenously synthesized respiratory substrate and as a toxin, raise questions as to how it is cleared when the electron transport chain is inhibited. Sulfide quinone oxidoreductase (SQOR) is a mitochondrial inner membrane flavoprotein that catalyzes the first step in the H2S oxidation pathway and uses coenzyme Q (CoQ) as an electron acceptor. However, complex IV poisoning by H2S inhibits complex III-dependent recycling of CoQH2, which is needed to sustain H2S oxidation. We have discovered that under these conditions, reversal of complex II activity using fumarate as an electron acceptor, establishes a new redox cycle with SQOR. The purine nucleotide cycle and the malate aspartate shuttle are sources of fumarate in H2S treated cells, which accumulate succinate. Complex II knockdown decreases the efficiency of H2S clearance and increases recovery time to the basal respiration rate in H2S treated cells. In contrast, attenuation of complex I, which is a major competitor for the mitochondrial CoQ pool, has the opposite effects. Targeted knockout of complex II in murine intestinal epithelial cells that are routinely exposed to microbiota derived H2S, decreases serum, urine, and fecal thiosulfate, a product of H2S oxidation. Our study identifies a metabolic reprogramming response to H2S that furnishes fumarate as an alternate electron acceptor and supports H2S oxidation independent of complex IV activity. Complex II-linked redox cycling of SQOR has important implications for gut H2S metabolism as colonocytes are routinely exposed to high concentrations of this gas derived from the microbiota.

One Sentence Summary

Reversal of complex II sustains and prioritizes H2S oxidation when respiration is poisoned.
Angiotensin-converting enzyme governs endogenous opioid signaling and synaptic plasticity in nucleus accumbens
Authors: Trieu Brian H. , Remmers Bailey C. , Toddes Carlee , Brandner Dieter D. , Xie Wei , More Swati S. , Rothwell Patrick E.
Published: September 2021

Angiotensin-converting enzyme (ACE) regulates blood pressure by cleaving angiotensin I to produce angiotensin II. In the brain, ACE is expressed at uniquely high levels in the striatonigral pathway, but its central function remains poorly understood. We find that ACE degrades an unconventional enkephalin heptapeptide, Met-enkephalin-Arg-Phe, in the nucleus accumbens of mice. ACE inhibition enhanced mu opioid receptor activation by Met-enkephalin-Arg-Phe, causing a cell type-specific long-term depression of glutamate release onto medium spiny projection neurons expressing the Drd1 dopamine receptor. Systemic ACE inhibition was not intrinsically rewarding, but decreased the conditioned place preference caused by fentanyl administration, and enhanced reciprocal social interaction. Our results raise the enticing prospect that central ACE inhibition can boost endogenous opioid signaling for clinical benefit, while mitigating risk of addiction.
Charged sequence motifs increase affinity towards liquid-liquid phase separation
Authors: Szabó András László , Sánta Anna , Pancsa Rita , Gáspári Zoltán
Published: September 2021

Protein phase separation is a major governing factor in multiple cellular processes, such as those concerning RNA metabolism and RNA-binding proteins. Despite many key observations, the exact structural characteristics of proteins involved in the process are still not fully deciphered. In this work we show that proteins harbouring sequence regions with specific charged residue patterns are significantly associated with liquid-liquid phase separation. In particular, regions with repetitive arrays of alternating charges show the strongest association, whereas segments with generally high charge density and single α-helices also show detectable but weaker connections.
Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care
Authors: Minich David , Madden Christopher , Navarro Mauricio A. , Glowacki Leo , French-Kim Kristen , Chan Willow , Evans Morgan V. , Soares Kilmer , Mrofchak Ryan , Madan Rushil , Ballash Gregory A. , LaPerle Krista , Paul Subhadeep , Vodovotz Yael , Uzal Francisco A. , Martinez Margaret , Hausmann Jennifer , Junge Randall E. , Hale Vanessa L.
Published: September 2021

Background

Enteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium – CZA; Denver Zoo - DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility.

Results

We employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis.

Conclusions

We identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.
SARS-CoV-2 mRNA vaccination elicits robust and persistent T follicular helper cell response in humans
Authors: Mudd Philip A. , Minervina Anastasia A. , Pogorelyy Mikhail V. , Turner Jackson S. , Kim Wooseob , Kalaidina Elizaveta , Petersen Jan , Schmitz Aaron J. , Lei Tingting , Haile Alem , Kirk Allison M. , Mettelman Robert C. , Crawford Jeremy Chase , Nguyen Thi H.O. , Rowntree Louise C. , Rosati Elisa , Klebert Michael K. , Suessen Teresa , Middleton William D. ,   the SJTRC Study Team, Wolf Joshua , Teefey Sharlene A. , O’Halloran Jane A. , Presti Rachel M. , Kedzierska Katherine , Rossjohn Jamie , Thomas Paul G. , Ellebedy Ali H.
Published: September 2021

SARS-CoV-2 mRNA vaccines induce robust anti-spike (S) antibody and CD4+ T cell responses. It is not yet clear whether vaccine-induced follicular helper CD4+ T (TFH) cell responses contribute to this outstanding immunogenicity. Using fine needle aspiration of draining axillary lymph nodes from individuals who received the BNT162b2 mRNA vaccine, we show that frequency of TFH correlates with that of S-binding germinal center B cells. Mining of the responding TFH T cell receptor repertoire revealed a strikingly immunodominant HLADPB1* 04-restricted response to S167-180 in individuals with this allele, which is among the most common HLA alleles in humans. Paired blood and lymph node specimens show that while circulating S-specific TFH cells peak one week after the second immunization, S-specific TFH persist at nearly constant frequencies for at least six months. Collectively, our results underscore the key role that robust TFH cell responses play in establishing long-term immunity by this efficacious human vaccine.
Heat efficiently inactivates coronaviruses inside vehicles
Authors: Karthigeyan Krithika P. , Flanigan Chloe , Machado Denis Jacob , Kiziltas Alper A. , Janies Daniel A. , Chen Jay , Cooke David , Lee Marcia V. , Saif Linda J. , Henegar Sonny , Jahnes Jeff , Mielewski Deborah F. , Kwiek Jesse J.
Published: September 2021

Heat is an established method to inactivate coronaviruses, and there is utility in using heat to reduce viral load on common touch points in vehicles exposed to a person shedding SARS-CoV-2. As SARS-CoV-2 is a Biosafety level (BSL)-3 pathogen, real world testing of heat as a sanitation method for public and private vehicles becomes a challenge, requiring a surrogate coronavirus that can be handled safely outside of a BSL-3 facility. In this study, we used Bovine Coronavirus (BCoV) as a surrogate for SARS-CoV-2 to test the efficacy of heat-based betacoronavirus inactivation. In vitro, a 30-minute exposure to 56°C completely inactivated BCoV in solution, and a 15-minute exposure reduced recovery of BCoV >1000-fold. When heated to 56°C for 15 minutes, the infectivity of BCoV spotted and dried on typical porous and non-porous automobile interior materials was reduced by 99 - 99.99%. When BCoV was spotted and dried on hard plastic (seat) material placed inside an out of service transit bus, 56°C heat for 30 minutes reduced BCoV infectivity 85 - 99.5%. Thus, 56°C is an accessible, rapid, and effective method to inactivate coronaviruses inside motor vehicles.
An ultrasensitive microfluidic approach reveals correlations between the physico-chemical and biological activity of experimental peptide antibiotics
Authors: Cama Jehangir , Al Nahas Kareem , Fletcher Marcus , Hammond Katharine , Ryadnov Maxim G. , Keyser Ulrich F. , Pagliara Stefano
Published: September 2021

Antimicrobial resistance challenges the ability of modern medicine to contain infections. Given the dire need for new antimicrobials, peptide antibiotics hold particular promise. These agents hit multiple targets in bacteria starting with their most exposed regions – their membranes. However, suitable assays to quantify the efficacy of peptide antibiotics at the membrane and cellular level have been lacking. Here, we employ two complementary microfluidic platforms to probe the structure-activity relationships of two experimental series of peptide antibiotics. We reveal strong correlations between each peptide’s physicochemical activity at the membrane level and biological activity at the cellular level by assaying the membranolytic activities of the antibiotics on hundreds of individual giant lipid vesicles, and quantifying phenotypic responses within clonal bacterial populations with single-cell resolution. Our strategy proved capable of detecting differential responses for peptides with single amino acid substitutions between them, and can accelerate the rational design and development of peptide antimicrobials.
The function of α-Catenin mechanosensing in tissue morphogenesis
Authors: Sheppard Luka , Tepass Ulrich
Published: September 2021

α-catenin couples the cadherin-catenin complex to the actin cytoskeleton. The mechanosensitive α-catenin M region undergoes conformational changes upon application of force to recruit binding partners. Here, we took advantage to the tension landscape in the Drosophila embryo to define three different states of α-catenin mechanosensing in support of cell adhesion. Low, medium, and high tension contacts showed α-catenin M region-dependent low, medium, and high levels of Vinculin and Ajuba recruitment. In contrast, Afadin/Canoe acts in parallel to α-catenin at bicellular low and medium tension junctions, but requires an interaction with α-catenin for its tension-sensitive enrichment at high-tension tricellular junctions. Individual M region domains make complex contributions to cell adhesion through their impact on binding partner recruitment, and redundancies with the function of Afadin/Canoe. Our data argue that α-catenin and its interaction partners are part of a cooperative and partially redundant, mechanoresponsive network that supports AJs remodelling during morphogenesis.
Semisynthesis of functional transmembrane proteins in GUVs
Authors: Podolsky K. A. , Masubuchi T. , Debelouchina G. T. , Hui E. , Devaraj N. K.
Published: September 2021

Cellular transmembrane (TM) proteins are essential sentries of the cell facilitating cell-cell communication, internal signaling, and solute transport. Reconstituting functional TM proteins into model membranes remains a challenge due to the difficulty of expressing hydrophobic TM domains and the required use of detergents. Herein, we use a intein-mediated ligation strategy to semisynthesize bitopic TM proteins in synthetic membranes. We have adapted the trans splicing capabilities of split inteins for a native peptide ligation between a synthetic TM peptide embedded in the membrane of giant unilamellar vesicles (GUVs) and an expressed soluble protein. We demonstrate that the extracellular domain of programmed cell death protein 1 (PD-1), a mammalian transmembrane immune checkpoint receptor, retains its function for binding its ligand PD-L1 at a reconstituted membrane interface after ligation to a synthetic TM peptide in GUV membranes. We envision that the construction of full-length TM proteins using orthogonal split intein-mediated semisynthetic protein ligations will expand applications of membrane protein reconstitution in pharmacology, biochemistry, biophysics, and artificial cell development.