bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic diversity and aero-tolerance in anammox bacteria from geochemically distinct aquifers
Authors: Mosley Olivia E. , Gios Emilie , Weaver Louise , Close Murray , Daughney Chris , van der Raaij Rob , Martindale Heather , Handley Kim M. 
Published: September 2021

AbstractBackgroundAnaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon poor environments. Yet, the diversity and prevalence of anammox bacteria in the terrestrial subsurface – a typically oligotrophic environment – is little understood across different geochemical conditions. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analysed 16S rRNA genes, metagenomes and metatranscriptomes, and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells distributed over 1 240 km2.ResultsData indicate that anammox-associated bacteria (class Brocadiae) and the anammox process are prevalent in aquifers (identified in aquifers with sandy-gravel, sand-silt and volcanic lithologies). While Brocadiae diversity decreased with increasing DO, Brocadiae 16S rRNA genes and hydrazine synthase genes and transcripts (hydrazine synthase, hzsB) were detected across a wide range of bulk groundwater dissolved oxygen (DO) concentrations (0 – 10 mg/L). Anammox genes and transcripts (hzsB) correlated significantly with those involved in bacterial and archaeal ammonia oxidation (ammonia monooxygenase, amoA), which could represent a major source of nitrite for anammox. Differences in anammox community composition were strongly associated with DO and bore depth (and to a lesser extent pH and phosphate), revealing niche differentiation among anammox bacteria in groundwater that was largely driven by water oxygen contents, and not ammonium/nitrite. Eight Brocadiae genomes (63-95% estimated completeness) reconstructed from a subset of groundwater sites belong to 2 uncharacterized families and 6 novel species (based on average nucleotide identity). Distinct groups of these genomes dominated the anammox-associated community at dysoxic and oxic sites, further reflecting the influence of DO on Brocadiae composition. Six of the genomes (dominating dysoxic or oxic sites) have genes characteristic of anammox (hydrazine synthase and/or dehydrogenase). These genes, in addition to aerotolerance genes, belonging to four Brocadiae genomes, were transcriptionally active, although transcript numbers clearly highest in dyoxic groundwater.ConclusionsOur findings indicate anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, and that this is likely supported by nitrite from aerobic ammonia oxidation. Results provide an insight into the distribution and activity of anammox bacteria across distinct aquifer physicochemisties.
Modulation of optical speaker using biogenic guanine platelets floating in water
Authors: Iwasaka Masakazu 
Published: September 2021

AbstractMicrophones are miniature devices for sound detection. Various technologies have been developed to transfer sound properties onto other physical quantities, e.g., electricity. Over the past three decades, many studies have reported on optical sensing of sound. Most of these studies were performed via application of light interference at the edges of optical fibers. Several studies have reported on detection of sounds in the air or objects causing mechanical vibrations based on light interference. This work proposes an optical speaker which is a method to reconstruct and modulate sound from the power spectrum of light that has been reflected by guanine platelets floating in water droplet. The water droplet containing fish guanine platelets was placed on a piezoelectric membrane and acoustic vibration from the membrane propagated inside the droplet. A photomultiplier tube (PMT) then collected the light reflected from the water droplet. Without post-analysis of the measured light intensity, the analog output voltage from the PMT clearly sounded an audio speaker. In addition, it was found that the guanine platelets reflecting light operated as an audio equalizer.
Assessing the zoonotic potential of a novel bat morbillivirus
Authors: Ikegame Satoshi , Carmichael Jillian C. , Wells Heather , O’Brien Robert L. Furler , Acklin Joshua A. , Chiu Hsin-Ping , Oguntuyo Kasopefoluwa Y. , Cox Robert M. , Patel Aum R. , Kowdle Shreyas , Stevens Christian S. , Eckley Miles , Zhan Shijun , Lim Jean K. , Veit Ethan C. , Evans Matthew , Hashiguchi Takao , Durigon Edison , Schountz Tony , Epstein Jonathan H. , Plemper Richard K. , Daszak Peter , Anthony Simon J. , Lee Benhur 
Published: September 2021

AbstractMorbilliviruses are amongst the most contagious viral pathogens that infect mammals. Metagenomic surveys have identified numerous morbillivirus sequences in bats, but no full-length authentic morbillivirus has been isolated or characterized from bats. Here we detail the discovery of full-length Myotis Bat Morbillivirus (MBaMV) from a bat surveillance program in Brazil. After determining that MBaMV utilizes bat CD150 but not human CD150 as an entry receptor, we generated an infectious clone of MBaMV using reverse genetics. MBaMV exhibited features consistent with other morbilliviruses, including pleomorphic virions, P-editing and the rule-of-six. MBaMV replicated well in human epithelial cell lines in a nectin-4 dependent manner. Surprisingly, MBaMV was able to infect human macrophages in a CD150-independent manner. However, MBaMV was restricted by cross-neutralizing human sera and did not evade the human innate immune system, indicating that while zoonotic spillover into humans may be possible, MBaMV replication in humans would likely be restricted.
Pharmacological rescue of tumor intrinsic STING expression and immune response in LKB1-mutant lung cancer via the IAP-JAK regulatory axis
Authors: Shu Changfa , Jin Rui , Niu Qiankun , Cicka Danielle , Doyle Sean , Wahafu Alafate , Fan Dacheng , Zheng Xi , Du Yuhong , Ivanov Andrey A. , Doxie Deon B , Dhodapkar Kavita M , Carlisle Jennifer , Owonikoko Taofeek , Ramalingam Suresh , Sica Gabriel , Dhodapkar Madhav V , Zhou Wei , Mo Xiulei , Fu Haian 
Published: September 2021

SummaryHarnessing the power of the immune system to treat cancer has become a core clinical approach. However, rewiring of intrinsic circuitry enables tumor cells to escape immune attacks, leading to therapeutic failure. Pharmacological strategies to reverse tumor genotype-dictated therapeutic resistance are urgently needed to advance precision immunotherapy. Here, we identify antagonists of Inhibitor of Apoptosis Protein (IAP) as potent sensitizers that restore immune-dependent killing of LKB1-mutant lung cancer cells. Mechanistic studies reveal an LKB1-IAP-JAK trimolecular complex that bridges the LKB1-mutant genotype with IAP-dependency and a STING-deficiency-mediated immune resistance phenotype. Ultimately, inhibition of IAP re-establishes JAK-regulated STING expression and DNA sensing pathway as well as enhanced cytotoxic immune cell infiltration and selective immune-dependent anti-tumor activity in an LKB1-mutant immune-competent mouse model. Thus, IAP-JAK-modulatory strategies, like IAP inhibitors, offer promising immunotherapy adjuvants to re-establish the responsiveness of “immunologically-cold” LKB1-mutant tumors to immune checkpoint inhibitors or STING-directed therapies.
Discovery of frog virus 3 microRNAs and their roles in evasion of host antiviral responses
Authors: Todd Lauren A. , Katzenback Barbara A. 
Published: September 2021

AbstractFrog virus 3 (FV3, genus Ranavirus) causes devastating disease in amphibian populations and is capable of subverting host immune responses. Evidence suggests that virus-encoded microRNAs (v-miRNAs) are implicated in host immunoevasion tactics. Thus, we sought to discover FV3-encoded v-miRNAs and to uncover their putative roles in immunoevasion. Small RNA libraries were generated from FV3-infected Xela DS2, a Xenopus laevis dorsal skin epithelial-like cell line, at 24- and 72-hours post-infection (hpi). We discovered 43 FV3 v-miRNAs and identified that 15 are upregulated at 24 hpi, while 18 are upregulated at 72 hpi. Target prediction analyses revealed that FV3 v-miRNAs target host genes involved in key antiviral signaling pathways, while gene ontology analyses suggest that FV3 v-miRNAs may broadly impact host cell function. This is the first study to experimentally detect mature v-miRNAs produced by FV3. Our findings highlight the possibility that ranaviral v-miRNAs facilitate immunoevasion of frog antiviral responses.
Cofilin Regulates Filopodial Structure and Flexibility in Neuronal Growth Cones
Authors: Hylton Ryan , Heebner Jessica , Grillo Michael , Swulius Matthew 
Published: September 2021

AbstractCofilin is best known for its ability to sever actin filaments, and facilitate cytoskeletal recycling inside of cells. At higher concentrations, in vitro, cofilin stabilizes a more flexible, hyper-twisted state of actin known as “cofilactin”, but a structural role for cofilactin, in situ, has not been observed. Combining cryo-electron tomography and live-cell imaging in neuronal growth cones, we show that filopodial actin bundles can switch between a fascin-linked and a cofilin-decorated state, composed of hyper-twisted cofilactin filaments. These cofilactin bundles contribute to the flexibility of filopodial actin networks, thus regulating growth cone searching dynamics. Our results provide mechanistic insight into the processes underlying proper brain development, as well as fundamentals of cytoskeletal mechanics inside confined cellular spaces.
Genetically diverse mouse models of SARS-CoV-2 infection reproduce clinical variation in type I interferon and cytokine responses in COVID-19
Authors: Robertson Shelly J. , Bedard Olivia , McNally Kristin L. , Shaia Carl , Clancy Chad , Lewis Matthew , Broeckel Rebecca M. , Chiramel Abhilash I. , Shannon Jeffrey G. , Sturdevant Gail L. , Rosenke Rebecca , Anzick Sarah L. , Forte Elvira , Preuss Christoph , Baker Candice N. , Harder Jeffrey , Brunton Catherine , Munger Steven , Bruno Daniel P. , Lack Justin B. , Leung Jacqueline M. , Shamsaddini Amirhossein , Gardina Paul , Sturdevant Daniel E. , Sun Jian , Martens Craig , Holland Steven M. , Rosenthal Nadia A. , Best Sonja M. 
Published: September 2021

ABSTRACTInflammation in response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection drives severity of coronavirus disease 2019 (COVID-19) and is influenced by host genetics. To understand mechanisms of inflammation, animal models that reflect genetic diversity and clinical outcomes observed in humans are needed. We report a mouse panel comprising the genetically diverse Collaborative Cross (CC) founder strains crossed to human ACE2 transgenic mice (K18-hACE2) that confers susceptibility to SARS-CoV-2. Infection of CC x K18- hACE2 resulted in a spectrum of survival, viral replication kinetics, and immune profiles. Importantly, in contrast to the K18-hACE2 model, early type I interferon (IFN-I) and regulated proinflammatory responses were required for control of SARS-CoV-2 replication in PWK x K18-hACE2 mice that were highly resistant to disease. Thus, virus dynamics and inflammation observed in COVID-19 can be modeled in diverse mouse strains that provide a genetically tractable platform for understanding anti-coronavirus immunity.One Sentence SummaryGenetically diverse mice model a spectrum of clinically relevant innate immune responses to SARS-CoV-2 infection.
Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage
Authors: Avery Ellen G. , Bartolomaeus Hendrik , Rauch Ariana , Chen Chia-Yu , N’Diaye Gabriele , Löber Ulrike , Bartolomaeus Theda U. P. , Fritsche-Guenther Raphaela , Rodrigues André F. , Tsvetkov Dmitry , Todiras Mihail , Park Joon-Keun , Markó Lajos , Maifeld András , Bader Michael , Kempa Stefan , Kirwan Jennifer A. , Forslund Sofia K. , Müller Dominik N. , Wilck Nicola 
Published: September 2021

AbstractAimsHypertension (HTN) can lead to heart and kidney damage. The gut microbiota has been linked to HTN, although it is difficult to estimate its significance due to the variety of other features known to influence HTN. In the present study, we used germ-free (GF) and colonized (COL) littermate mice to quantify the impact of microbial colonization on organ damage in HTN.Methods and resultsFour-week-old male GF C57BL/6J littermates were randomized to remain GF or receive microbial colonization. HTN was induced by subcutaneous infusion with angiotensin (Ang) II (1.44mg/kg/d) and 1% NaCl in the drinking water; sham-treated mice served as control. Renal damage was exacerbated in GF mice, whereas cardiac damage was more comparable between COL and GF, suggesting that the kidney is more sensitive to microbial influence. Multivariate analysis revealed a larger effect of HTN in GF mice. Serum metabolomics demonstrated that the colonization status influences circulating metabolites relevant to HTN. Importantly, GF mice were deficient in anti-inflammatory fecal short-chain fatty acids (SCFA). Flow cytometry showed that the microbiome has an impact on the induction of anti-hypertensive myeloid-derived suppressor cells and pro-inflammatory Th17 cells in HTN. In vitro inducibility of Th17 cells was significantly higher for cells isolated from GF than conventionally raised mice.ConclusionsMicrobial colonization status of mice had potent effects on their phenotypic response to a hypertensive stimulus, and the kidney is a highly microbiota-susceptible target organ in HTN. The magnitude of the pathogenic response in GF mice underscores the role of the microbiome in mediating inflammation in HTN.Translation PerspectiveTo assess the potential of microbiota-targeted interventions to prevent organ damage in hypertension, an accurate quantification of microbial influence is necessary. We provide evidence that the development of hypertensive organ damage is dependent on colonization status and suggest that a healthy microbiota provides anti-hypertensive immune and metabolic signals to the host. In the absence of normal symbiotic host-microbiome interactions, hypertensive damage to the kidney in particular is exacerbated. We suggest that hypertensive patients experiencing perturbations to the microbiota, which are common in CVD, may be at a greater risk for target-organ damage than those with a healthy microbiome.
Kalium rhodopsins: Natural light-gated potassium channels
Authors: Govorunova Elena G. , Gou Yueyang , Sineshchekov Oleg A. , Li Hai , Wang Yumei , Brown Leonid S. , Xue Mingshan , Spudich John L. 
Published: September 2021

AbstractWe report a family of K+channels, kalium channelrhodopsins (KCRs) from a fungus-like protist. Previously known potassium channels, widespread and mainly ligand- or voltage-gated, share a conserved pore-forming domain and K+-selectivity filter. KCRs differ in that they are light-gated and they have independently evolved an alternative K+selectivity mechanism. The KCRs are potent, highly selective of K+over Na+, and open in less than 1 millisecond following photoactivation. Their permeability ratio PK/PNaof ∼ 20 make KCRs powerful hyperpolarizing tools that suppress excitable cell firing upon illumination, demonstrated here in mouse cortical neurons. KCRs enable specific optogenetic photocontrol of K+gradients promising for the study and potential treatment of potassium channelopathies such as epilepsy, Parkinson’s disease, and long-QT syndrome and other cardiac arrhythmias.One-Sentence SummaryPotassium-selective channelrhodopsins long-sought for optogenetic research and therapy of neurological and cardiac diseases.
The isolation and characterization of Taphrina betulina and other yeasts residing in the Betula pendula phylloplane
Authors: Christita Margaretta , Sipilä Timo P. , Overmyer Kirk 
Published: September 2021

AbstractThe phylloplane is an important microbial habitat and a reservoir of organisms that affect plant health, both positively and negatively. Taphrina betulina is the causative agent of birch witches’ broom disease. Taphrina are dimorphic, invading theirs hosts in a filamentous form and residing in the host phyllosphere in their non-infectious yeast form. As such, they are widely accepted to be found a resident yeasts on their hosts, even on healthy tissues; however, there is little experimental data to support this. With the aim of exploring the local infection ecology of T. betulina, we had isolated yeasts from the phylloplane of birch, using three classes of samples; from infected symptom bearing leaves inside brooms, healthy leaves from branches away from brooms on broom bearing trees, and symptom-free leaves from symptom-free trees. Isolations yielded 224 yeast strains, representing 11 taxa, including T. betulina, which was the most common isolate and was found in all sample classes, including asymptomatic leaves. Genotyping with two genetic markers revealed genetic diversity among these T. betulina isolates, with seven distinct genotype differentiated by the markers used. Of the 57 T. betulina strains, 22 representative strains were selected for further studies and preliminarily characterized, revealing differences in size and the ability to produced compounds with activity to activate the signalling pathway for the plant hormone auxin.
Identifying critical transcriptional targets of the MYC oncogene using a novel competitive precision genome editing (CGE) assay
Authors: Pihlajamaa Päivi , Kauko Otto , Sahu Biswajyoti , Kivioja Teemu , Taipale Jussi 
Published: September 2021

AbstractMYC is an oncogenic transcription factor that controls major pathways promoting cell growth and proliferation. MYC has been implicated in the regulation of large number of genes, but the exact target genes responsible for its proliferative effects are still not known. Here, we use a novel competitive genome editing (CGE) assay for studying the functional consequence of precise mutations of MYC binding sites on cell proliferation. The CGE method is based on precision genome editing, where a CRISPR/Cas9-induced DNA break is repaired using a template that either reconstitutes the original feature or introduces an altered sequence. Both types of repair templates harbor sequence tags that allow direct comparison between cells that carry original and mutant features and generate a large number of replicate cultures. The CGE method overcomes the limitations of CRISPR/Cas9-technology in analyzing the effect of genotype on phenotype, namely the difficulty of cutting DNA exactly at the intended site, and the decreased cell proliferation caused by the DNA cuts themselves. Importantly, it provides a powerful method for studying subtle effects elicited by mutation of individual transcription factor binding sites. We show here that E-box mutations at several MYC target gene promoters resulted in reduced cellular fitness, demonstrating a direct correlation between MYC-regulated cellular processes and MYC binding and identifying important transcriptional targets responsible for its functions.
Programmable mammalian translational modulators by CRISPR-associated proteins
Authors: Kawasaki Shunsuke , Ono Hiroki , Hirosawa Moe , Kuwabara Takeru , Saito Hirohide 
Published: September 2021

AbstractThe complexity of synthetic genetic circuits relies on repertories of biological circuitry with high orthogonality. Although post-transcriptional circuitry relying on RNA-binding proteins (RBPs) qualifies as a repertory, the limited pool of regulatory devices hinders network modularity and scalability. Here we propose CaRTRIDGE (Cas-Responsive Translational Regulation Integratable into Diverse Genomic Engineering) to repurpose CRISPR-associated (Cas) proteins as translational modulators. We demonstrate that a set of Cas proteins are able to repress (OFF) or activate (ON) the translation of mRNAs that contain a Cas-binding RNA motif in the 5’-UTR. We designed 81 different types of translation OFF and ON switches and verified their functional characteristics. Many of them functioned as efficient translational regulators and showed orthogonality in mammalian cells. By interconnecting these switches, we designed and built artificial circuits, including 60 translational AND gates. Moreover, we show that various CRISPR-related technologies, including anti-CRISPR and split-Cas9 platforms, can be repurposed to control translation. Our Cas-mediated translational regulation is compatible with transcriptional regulation by Cas proteins and increases the complexity of synthetic circuits with fewer elements. CaRTRIDGE builds protein-responsive mRNA switches more than ever and leads to the development of both Cas-mediated genome editing and translational regulation technologies.
A simple method for in situ, multiplexed measurement of RNA degradation by flow cytometry
Authors: Rammohan Jayan , Alperovich Nina , Shao Bin , Ross David 
Published: September 2021

AbstractRNA degradation plays a major role in cellular function, but current methods for measuring RNA degradation require RNA purification or are low throughput. Here we show how a flow-FISH assay can be used for high-throughput, in situ measurement of RNA degradation without RNA purification. We demonstrate how this approach can be used to simultaneously measure RNA degradation rates of different RNA sequences in a single assay and explore how the assay can be used to examine the effect of cellular context on RNA degradation rates. This assay will be generally useful to quantitatively measure how natural and engineered biological function depends on RNA half-life.
m6A modifications regulate intestinal immunity and rotavirus infection
Authors: Wang Anmin , Tao Wanyin , Tong Jiyu , Gao Juanzi , Wang Jinghao , Hou Gaopeng , Qian Cheng , Zhang Guorong , Li Runzhi , Wang Decai , Ren Xingxing , Zhang Kaiguang , Ding Siyuan , Pan Wen , Li Hua-Bing , Flavell Richard , Zhu Shu 
Published: September 2021

AbstractN6-methyladenosine (m6A) is an abundant mRNA modification and affects many biological processes. However, how m6A levels are regulated during physiological or pathological processes such as virus infections, and the in vivo function of m6A in the intestinal immune defense against virus infections are largely unknown. Here, we uncover a novel antiviral function of m6A modification during rotavirus (RV) infection in small bowel intestinal epithelial cells (IECs). We found that rotavirus infection induced global m6A modifications on mRNA transcripts by down-regulating the m6a eraser ALKBH5. Mice lacking the m6A writer enzymes METTL3 in IECs (Mettl3ΔIEC) were resistant to RV infection and showed increased expression of interferons (IFNs) and IFN-stimulated genes (ISGs). Using RNA-sequencing and m6A RNA immuno-precipitation (RIP)-sequencing, we identified IRF7, a master regulator of IFN responses, as one of the primary m6A targets during virus infection. In the absence of METTL3, IECs showed increased Irf7 mRNA stability and enhanced type I and III IFN expression. Deficiency in IRF7 attenuated the elevated expression of IFNs and ISGs and restored susceptibility to RV infection in Mettl3ΔIEC mice. Moreover, the global m6A modification on mRNA transcripts declined with age in mice, with a significant drop from 2 weeks to 3 weeks post birth, which likely has broad implications for the development of intestinal immune system against enteric viruses early in life. Collectively, we demonstrated a novel host m6A-IRF7-IFN antiviral signaling cascade that restricts rotavirus infection in vivo.