bluuebunny/crossref_metadata_2025 huggingface dataset:
A transmissible γδ intraepithelial lymphocyte hyperproliferative phenotype is associated with the intestinal microbiota and confers protection against acute infection
Authors: Jia Luo , Wu Guojun , Alonso Sara , Zhao Cuiping , Lemenze Alexander , Lam Yan Y. , Zhao Liping , Edelblum Karen L.
Published: July 2021

Intraepithelial lymphocytes expressing the γδ T cell receptor (γδ IELs) serve as a first line of defense against luminal microbes. Although the presence of an intact microbiota is dispensable for γδ IEL development, several microbial factors contribute to the maintenance of this sentinel population. However, whether specific commensals influence population of the γδ IEL compartment under homeostatic conditions has yet to be determined. We identified a novel γδ IEL hyperproliferative phenotype that arises early in life and is characterized by expansion of multiple Vγ subsets. Horizontal transfer of this hyperproliferative phenotype to mice harboring a phenotypically normal γδ IEL compartment was prevented following antibiotic treatment, thus demonstrating that the microbiota is both necessary and sufficient for the observed increase in γδ IELs. Further, we identified a group of unique gut bacteria represented by 5 amplicon sequence variants (ASV) which are strongly associated with γδ IEL expansion. Using intravital microscopy, we find that hyperproliferative γδ IELs also exhibit increased migratory behavior leading to enhanced protection against bacterial infection. These findings reveal that transfer of a specific group of commensals can regulate γδ IEL homeostasis and immune surveillance, which may provide a novel means to reinforce the epithelial barrier.
A workflow for rapid unbiased quantification of fibrillar feature alignment in biological images
Authors: Marcotti Stefania , Freitas Deandra Belo de , Troughton Lee D , Kenny Fiona N , Shaw Tanya , Stramer Brian M , Oakes Patrick W
Published: July 2021

Measuring the organisation of the cellular cytoskeleton and the surrounding extracellular matrix (ECM) is currently of wide interest as changes in both local and global alignment can highlight alterations in cellular functions and material properties of the extracellular environment. Different approaches have been developed to quantify these structures, typically based on fibre segmentation or on matrix representation and transformation of the image, each with its own advantages and disadvantages.

Here we presentAFT - Alignment by Fourier Transform, a workflow to quantify the alignment of fibrillar features in microscopy images exploiting 2D Fast Fourier Transforms (FFT). Using pre-existing datasets of cell and ECM images, we demonstrate our approach and compare and contrast this workflow with two other well-known ImageJ algorithms to quantify image feature alignment. These comparisons reveal thatAFThas a number of advantages due to its grid-based FFT approach. 1) Flexibility in defining the window and neighbourhood sizes allows for performing a parameter search to determine an optimal length scale to carry out alignment metrics. This approach can thus easily accommodate different image resolutions and biological systems. 2) The length scale of decay in alignment can be extracted by comparing neighbourhood sizes, revealing the overall distance that features remain anisotropic. 3) The approach is ambivalent to the signal source, thus making it applicable for a wide range of imaging modalities and is dependent on fewer input parameters than segmentation methods. 4) Finally, compared to segmentation methods, this algorithm is computationally inexpensive, as high-resolution images can be evaluated in less than a second on a standard desktop computer. This makes it feasible to screen numerous experimental perturbations or examine large images over long length scales.

Implementation is made available in both MATLAB and Python for wider accessibility, with example datasets for single images and batch processing. Additionally, we include an approach to automatically search parameters for optimum window and neighbourhood sizes, as well as to measure the decay in alignment over progressively increasing length scales.
Cross immunity protection and antibody dependent enhancement: A distributed delay dynamic model
Authors: Steindorf Vanessa , Oliva Sergio , Wu Jianhong
Published: July 2021

Dengue fever is endemic in tropical and sub-tropical countries, and some of the important features of Dengue fever spread continues to pose challenges for mathematical modelling. Here, we propose a system of integro-differential equations (IDE) to study the disease transmission dynamics that involves multiserotypes and cross immunity. Our main objective is to incorporate and analyze the effect of a general time delay term describing acquired cross immunity protection and the effect of antibody dependent enhancement (ADE), both characteristics of Dengue fever. We perform qualitative analysis of the model and obtain results to show the stability of the epidemiologically important steady solutions that is completely determined by the basic reproduction number and the invasion reproduction number. We establish the global dynamics, by constructing suitable Lyapunov functions. We also conduct some numerical experiments to illustrate bifurcation structures, indicating the occurrence of periodic oscillations for specific range of values of a key parameter representing the ADE.
OPUS-Rota4: A Gradient-Based Protein Side-Chain Modeling Framework Assisted by Deep Learning-Based Predictors
Authors: Xu Gang , Wang Qinghua , Ma Jianpeng
Published: July 2021

Accurate protein side-chain modeling is crucial for protein folding and protein design. In the past decades, many successful methods have been proposed to address this issue. However, most of them depend on the discrete samples from the rotamer library, which may have limitations on their accuracies and usages. In this study, we report an open-source toolkit for protein side-chain modeling, named OPUS-Rota4. It consists of three modules: OPUS-RotaNN2, which predicts protein side-chain dihedral angles; OPUS-RotaCM, which measures the distance and orientation information between the side chain of different residue pairs; and OPUS-Fold2, which applies the constraints derived from the first two modules to guide side-chain modeling. In summary, OPUS-Rota4 adopts the dihedral angles predicted by OPUS-RotaNN2 as its initial states, and uses OPUS-Fold2 to refine the side-chain conformation with the constraints derived from OPUS-RotaCM. In this case, we convert the protein side-chain modeling problem into a side-chain contact map prediction problem. OPUS-Fold2 is written in Python and TensorFlow2.4, which is user-friendly to include other differentiable energy terms into its side-chain modeling procedure. In other words, OPUS-Rota4 provides a platform in which the protein side-chain conformation can be dynamically adjusted under the influence of other processes, such as protein-protein interaction. We apply OPUS-Rota4 on 15 FM predictions submitted by Alphafold2 on CASP14, the results show that the side chains modeled by OPUS-Rota4 are closer to their native counterparts than the side chains predicted by Alphafold2.
Neural and computational processes of accelerated perceptual awareness and decisions: A 7T fMRI Study
Authors: Kalhan Shivam , McFadyen Jessica , Tsuchiya Naotsugu , Garrido Marta I.
Published: July 2021

Rapidly detecting salient information in our environments is critical for survival. Visual processing in subcortical areas like the pulvinar and amygdala have been shown to facilitate unconscious processing of salient stimuli. It is unknown, however, if and how these areas might interact with cortical networks to facilitate faster conscious perception of salient stimuli. Here we investigated these neural processes using 7T functional Magnetic Resonance Imaging (fMRI) in concert with computational modelling while participants (n = 32) engaged in a breaking continuous flash suppression paradigm (bCFS) in which fearful and neutral faces are initially suppressed from conscious perception but then eventually “breakthrough” into awareness. We found that participants reported faster breakthrough times for fearful faces compared to neutral faces. Drift-diffusion modelling suggested that perceptual evidence was accumulated at a faster rate for fearful faces compared to neutral faces. For both neutral and fearful faces, faster response times coincided with greater activity in the amygdala (specifically within its subregions, including superficial, basolateral and amygdalo-striatal transition area) and the insula. Faster rates of evidence accumulation coincided with greater activity in frontoparietal regions and the occipital lobe, as well as the amygdala. Overall, our findings suggest that hastened perceptual awareness of salient stimuli recruits the amygdala and, more specifically, is driven by accelerated evidence accumulation in fronto-parietal and visual areas. In sum, we have uncovered and mapped distinct neural computations that accelerate perceptual awareness of visually suppressed faces.
Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provide Insight into N Uptake from Forest Soil
Authors: Rivera Pérez Carmen Alicia , Janz Dennis , Schneider Dominik , Daniel Rolf , Polle Andrea
Published: July 2021

Mineral nitrogen (N) is a major nutrient showing strong fluctuations in the environment due to anthropogenic activities. Acquisition and translocation of N to forest trees is achieved by highly diverse ectomycorrhizal fungi (EMF) living in symbioses with their host roots. Here, we examined colonized root tips to characterize the entire root-associated fungal community by DNA metabarcoding-Illumina sequencing of the fungal ITS2 molecular marker and used RNA sequencing to target metabolically active fungi and the plant transcriptome after N application. The study was conducted with beech (Fagus sylvaticaL), a dominant tree species in central Europe, grown in native forest soil. We demonstrate strong enrichment of15N from nitrate or ammonium in the ectomycorrhizal roots by stable isotope labeling. The relative abundance of the EMF members in the fungal community was correlated with their transcriptional abundances. The fungal metatranscriptome covered KEGG and KOG categories similar to model fungi and did not reveal significant changes related to N metabolization but species-specific transcription patterns, supporting trait stability. In contrast to the resistance of the fungal metatranscriptome, the transcriptome of the host exhibited dedicated nitrate- or ammonium-responsive changes with upregulation of transporters and enzymes required for nitrate reduction and drastic enhancement of glutamine synthetase transcript levels, indicating channeling of ammonium into the pathway for plant protein biosynthesis. Our results support that self-composed fungal communities associated with tree roots buffer nutritional signals in their own metabolism but do not shield plants from high environmental N.

IMPORTANCE

Although EMF are well known for their role in supporting tree N nutrition, the molecular mechanisms underlying N flux from the soil solution into the host through the ectomycorrhizal pathway remain widely unknown. Furthermore, ammonium and nitrate availability in the soil solution is subject to constant oscillations that create a dynamic environment for the tree roots and associated microbes during N acquisition. Therefore, it is important to understand how root-associated mycobiomes and the tree roots handle these fluctuations. We studied the response of the symbiotic partners by screening their transcriptomes after a sudden environmental flux of nitrate or ammonium. We show that the fungi and the host respond asynchronously, with the fungi displaying resistance to increased nitrate or ammonium, and the host dynamically metabolizing the supplied N sources. This study provides insights into the molecular mechanisms of the symbiotic partners operating under N enrichment in a multidimensional symbiotic system.
Coordinated activation of both TGFβ and BMP canonical pathways regulates autophagy and tissue regeneration in acetaminophen induced liver injury
Authors: Stavropoulos Athanasios , Divolis Georgios , Manioudaki Maria , Gavriil Ariana , Kloukina Ismini , Perrea Despina N. , Sountoulidis Alexandros , Ford Ethan , Doulou Athanasia , Apostolidou Anastasia , Katsantoni Elena , Ritvos Olli , Germanidis Georgios , Xilouri Maria , Sideras Paschalis
Published: July 2021

Transforming Growth Factor-βs (TGFβs)/Activins and Bone Morphogenetic Proteins (BMPs) have been implicated in numerous aspects of hepatic pathophysiology. However, the way by which hepatocytes integrate and decode the interplay between the TGFβ/Activin and BMP branches in health and disease is still not fully understood. To address this, TGFβ/BMP Smad- responsive double transgenic reporter mice were generated and utilized to map patterns of TGFβ- and/or BMP-pathway activation during acetaminophen- induced liver injury. TGFβ signaling was blocked either pharmacologically or by Smad7 over-expression and the transcriptomes of canonical TGFβ- and/or BMP4-treated hepatospheres and Smad7-treated livers were analyzed to highlight TGFβ-superfamily-regulated pathways and processes. Acetaminophen administration led to dynamically evolving, stage- and context-specific, patterns of hepatic TGFβ/Activin and BMP-reporter expression. TGFβ-superfamily signaling was activated in an autophagy prone zone at the borders between healthy and injured tissue. Inhibition of TGFβ-superfamily signaling attenuated autophagy, exacerbated liver histopathology, and finally led to accelerated tissue-recovery. Hallmarks of this process were the paraptosis-like cell death and the attenuation of immune and reparatory cell responses. Transcriptomic analysis highlighted autophagy as a prominent TGFβ1- and BMP4-regulated process and recognizedTrp53inp2as the top TGFβ-superfamily-regulated autophagy-related gene. Collectively, these findings implicate the coordinated activation of both canonical TGFβ-superfamily signalling branches in balancing autophagic response and tissue-reparatory and -regenerative processes upon acetaminophen-induced hepatotoxicity, highlighting opportunities and putative risks associated with their targeting for treatment of hepatic diseases.
EZH2 inhibition enhances TRAIL responses in multiple myeloma but not in quiescent cells
Authors: Arhoma Amal , Southan Jenny , Chantry Andrew D , Haywood-Small Sarah L , Cross Neil A
Published: July 2021

Multiple Myeloma is a plasma cell malignancy for which there is currently no cure, despite many novel therapies. TRAIL (Tumour necrosis factor-related apoptosis inducing ligand) is a promising anti-tumour agent although TRAIL-insensitive cells readily emerge when used as a single agent and its effects are limited due to many TRAIL-resistant cells which emerge soon after treatment. EZH2 is a H3K27 histone methyltransferase found to be overexpressed in many cancers including Multiple Myeloma. We tested the hypothesis that epigenetic reprogramming using the EZH2 inhibitor GSK343 would enhance TRAIL sensitivity, overcome TRAIL resistance, and target TRAIL-resistant quiescent cell populations. We show that GSK343 is a potent TRAIL sensitiser in TRAIL-sensitive RPMI 8226, NCI-H 929 and U266, and in TRAIL-resistant OPM-2 and JJN3, the latter showing very potent synergistic induction of apoptosis, primarily via caspase-8 activation but also via caspase-9. GSK343-enhancement of TRAIL responses was further enhanced in a 3D cell culture model of Multiple Myeloma in NCI-H 929 and U266. We show that in TRAIL-resistant sub-populations of Multiple Myeloma cells, GSK343 responses were completely attenuated in RPMI 8226 although synergistic enhancement of apoptosis was observed in NCI-H 929. Furthermore, following isolation of PKH26Hi quiescent cell populations, TRAIL responses and enhancement of TRAIL responses by GSK343 were completely attenuated. These studies show that EZH2 inhibition enhances TRAIL responses both in TRAIL-sensitive and TRAIL-resistant MM cell lines suspension culture and also in 3D cell culture to model the semi-solid Multiple Myeloma lesions in bone. Pre-existing TRAIL resistance was also enhanced by EZH2, and although synergistic enhancement of TRAIL responses by GSK343 was seen in NCI-H 929, responses were completely lost in TRAIL-resistant RPMI 8226 and also in quiescent cells. These studies highlight that although EZH2 inhibitors enhance TRAIL responses, acquired TRAIL resistance, and the presence of quiescent cells may mediate TRAIL-insensitivity in response to GSK343.
Combined impacts of climate and land use change and the future restructuring of Neotropical bat biodiversity
Authors: Gonçalves Fernando , Sales Lilian P. , Galetti Mauro , Pires Mathias M.
Published: July 2021

Forecasting the effects of global change on biodiversity is necessary to anticipate the threats operating at different scales in space and time. Climate change may create unsuitable environmental conditions, forcing species to move to persist. However, land-use changes create barriers that limit the access of some species to future available habitats. Here, we project the impacts of climate and land-use change on 228 Neotropical bat species by forecasting changes in environmental suitability, while accounting for the effect of habitat type specialization and simulating dispersal across suitable patches. We also identify the most vulnerable ecoregions and those that may offer future stable refugia. We further investigate potential functional changes by analysing the response of different trophic guilds. We found that the range contraction of habitat specialists, especially frugivores, was more frequent and stronger under all simulated scenarios. Projected changes differ markedly across ecoregions. While the Amazon region is likely to undergo high turnover rates in bat composition, the Andean grassland, Cerrado and Chaco might experience the greatest losses. The expansion of habitat generalists, which forage in open areas and commonly establish large colonies in manmade structures, coupled with the range contraction of habitat specialists is projected to homogenize bat communities across the Neotropics. Overall, dispersal will likely be the key for the future of Neotropical bat diversity. Therefore, safeguarding the refugia highlighted here, by expanding and connecting the existing network of protected areas, for example, may allow species to move in response to global change.
Mesalamine Reduces Intestinal ACE2 Expression Without Modifying SARS-CoV-2 Infection or Disease Severity in Mice
Authors: Alvarado David M. , Son Juhee , Thackray Larissa B. , Diamond Michael S. , Ding Siyuan , Ciorba Matthew A. ,   the IBD Investigators Group at Washington University
Published: July 2021

Introduction

Coronavirus Disease 2019 (COVID-19) is an ongoing public health crisis that has sickened or precipitated death in millions. The etiologic agent of COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), infects the intestinal epithelium, and can induce GI symptoms similar to the human inflammatory bowel diseases (IBD). An international surveillance epidemiology study (SECURE-IBD) reported that the standardized mortality ratio trends higher in IBD patients (1.5-1.8) and that mesalamine/sulfasalazine therapy correlates with poor outcome. The goal of our study was to experimentally address the relationship between mesalamine and SARS-CoV-2 entry, replication, and/or pathogenesis.

Methods

Viral infection was performed with a chimeric vesicular stomatitis virus expressing SARS-CoV-2 spike protein and EGFP (VSV-SARS-CoV-2) and SARS-CoV-2 virus derived from an infectious cDNA clone of 2019n-CoV/USA_WA1/2020. Primary human ileal spheroids derived from healthy donors were grown as 3D spheroids or on 2D transwells. We assessed the effect of 10 mM mesalamine (Millipore Sigma) on viral RNA levels, as well as the expression of the SARS-CoV-2 receptor angiotensin II-converting enzyme 2 (ACE2), Transmembrane Serine Protease 2 (TMPRSS2), TMPRSS4, Cathepsin B (CTSB) and CTSL by qRT-PCR. 8-12 week old K18-ACE2 were treated orally with PBS or mesalamine at 200 mg/kg daily. Mice were inoculated intranasally with 1×103 FFU of SARS-CoV-2. Mice were weighed daily and viral titers were determined 7 days post infection (dpi) by qRT-PCR. For the intestinal viral entry model, VSV-SARS-CoV-2 was injected into a ligated intestinal loop of anesthetized K18-ACE2 mice and tissues were harvested 6 hours post-infection.

Results

We found no change in viral RNA levels in human intestinal epithelial cells in response to mesalamine. Expression of ACE2 was reduced following mesalamine treatment in enteroids, while CTSL expression was increased. Mice receiving mesalamine lost weight at similar rates compared to mice receiving vehicle control. Mesalamine treatment did not change viral load in the lung, heart, or intestinal tissues harvested at 7 dpi. Pretreatment with mesalamine did not modulate intestinal entry of the chimeric VSV-SARS-CoV-2 in K18-ACE2 mice.

Conclusions

Mesalamine did not alter viral entry, replication, or pathogenesis in vitro or in mouse models. Mesalamine treatment reduced expression of the viral receptor ACE2 while concurrently increasing CTSL expression in human ileum organoids.
Biocompatible soft hydrogel lens as topical implants for diabetic retinopathy
Authors: Sadasivam Rajkumar , Packirisamy Gopinath , Goswami Mayank
Published: July 2021

Fashioned contact lenses can be converted into novel drug delivery vehicles. Ocular disease like diabetic retinopathy is a major microvascular complication where its early diagnosis and treatment is still a mystery to clinicians. Delivery of pharmaceuticals to the posterior part of eye is quite difficult, with exemption from the injectable formulations. Drug loaded hydrogel like contact lens implants can be utilized in place of commercial contact lens. Such hydrogel lens implants are developed with precise manner in which they are to be inserted as implants in the mice models. The present work is the preliminary outcome of our ongoing research work where the polymerized lens implant can be used as payload carrier for retinopathy. The aim is to propose such appropriate implants suitable for in vivo mice models.
Slow-rising and fast-falling dopaminergic dynamics jointly adjust negative prediction error in the ventral striatum
Authors: Shikano Yu , Yagishita Sho , Tanaka Kenji F. , Takata Norio
Published: July 2021

The greater the reward expectations are, the more different the brain’s physiological response will be. Although it is well-documented that better-than-expected outcomes are encoded quantitatively via midbrain dopaminergic (DA) activity, it has been less addressed experimentally whether worse-than-expected outcomes are expressed quantitatively as well. We show that larger reward expectations upon unexpected reward omissions are associated with the preceding slower rise and following larger decrease (DA dip) in the DA concentration at the ventral striatum of mice. We set up a lever press task on a fixed ratio (FR) schedule requiring five lever presses as an effort for a food reward (FR5). The mice occasionally checked the food magazine without a reward before completing the task. The percentage of this premature magazine entry (PME) increased as the number of lever presses approached five, showing rising expectations with increasing proximity to task completion, and hence greater reward expectations. Fiber photometry of extracellular DA dynamics in the ventral striatum using a fluorescent protein (genetically encoded GPCR-activation-based-DA sensor: GRABDA2m) revealed that the slow increase and fast decrease in DA levels around PMEs were correlated with the PME percentage, demonstrating a monotonic relationship between the DA dip amplitude and degree of expectations. Computational modeling of the lever press task implementing temporal difference errors and state transitions replicated the observed correlation between the PME frequency and DA dip amplitude in the FR5 task. Taken together, these findings indicate that the DA dip amplitude represents the degree of reward expectations monotonically, which may guide behavioral adjustment.
SARS-CoV-2 Exploits Sexually Dimorphic and Adaptive IFN and TNFa Signaling to Gain Entry into Alveolar Epithelium
Authors: Wang Yan , Gurrapu Sreeharsha , Chen Hong , Laudato Sara , Caggiano Emily , Jiang Yan , Ling Hsiang-Hsi , Giancotti Filippo G.
Published: July 2021

Infection of the alveolar epithelium constitutes a bottleneck in the progression of COVID-19 to SARS presumably due to the paucity of viral entry receptors in alveolar epithelial type 1 and 2 cells. We have found that the male alveolar epithelial cells express twice as many ACE2 and TMPRSS2 entry receptors as the female ones. Intriguingly, IFN and TNF-α signaling are preferentially active in male alveolar cells and induce binding of the cognate transcription factors to the promoters and lung-active enhancers ofACE2andTMPRSS2. Cotreatment with IFN-I and III dramatically increases expression of the receptors and viral entry in alveolar epithelial cells. TNFα and IFN-II, typically overproduced during the cytokine storm, similarly collaborate to induce these events. Whereas JAK inhibitors suppress viral entry induced by IFN-I/III, simultaneous inhibition of IKK/NF-κB is necessary to block viral entry induced by TNFα and IFN-II. In addition to explaining the increased incidence of SARS in males, these findings indicate that SARS-Cov-2 hijacks epithelial immune signaling to promote infection of the alveolar epithelium and suggest that JAK inhibitors, singly and in combination with NF-KB inhibitors, may exhibit efficacy in preventing or treating COVID-19 SARS.
Mitochondrial DNA variation across 56,434 individuals in gnomAD
Authors: Laricchia Kristen M. , Lake Nicole J. , Watts Nicholas A. , Shand Megan , Haessly Andrea , Gauthier Laura , Benjamin David , Banks Eric , Soto Jose , Garimella Kiran , Emery James ,   Genome Aggregation Database Consortium, Rehm Heidi L. , MacArthur Daniel G. , Tiao Grace , Lek Monkol , Mootha Vamsi K. , Calvo Sarah E.
Published: July 2021

Databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, genetic databases such as the Genome Aggregation Database (gnomAD) have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three technical challenges: (i) detecting homoplasmic and heteroplasmic variants, present respectively in all or a fraction of mtDNA molecules, (ii) circular mtDNA genome, and (iii) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded samples prone to NUMT misalignment (few mtDNA copies per cell), cell line artifacts (many mtDNA copies per cell), or with contamination and we reported variants with heteroplasmy greater than 10%. We applied this pipeline to 56,434 whole genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. Importantly, we report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mitochondrial population allele frequencies are publicly available at gnomad.broadinstitute.org and will aid in diagnostic interpretation and research studies.
Characterization of BLUF-photoreceptors present in Acinetobacter nosocomialis
Authors: Abatedaga Inés , Mora Bárbara Pérez , Tuttobene Marisel , Müller Gabriela , Biancotti Daiana , Borsarelli Claudio D. , Valle Lorena , Mussi Maria A.
Published: July 2021

Acinetobacter nosocomialis is a Gram-negative opportunistic pathogen, whose ability to cause disease in humans is well recognized. Blue light has been shown to modulate important physiological traits related to persistence and virulence in this microorganism. In this work, we characterized the three Blue Light sensing Using FAD (BLUF) domain-containing proteins encoded in the A. nosocomialis genome, which account for the only “traditional” light sensors present in this microorganism. By focusing on a light-modulated bacterial process such as motility, the temperature dependence of light regulation was studied, as well as the expression pattern and spectroscopic characteristics of the different A. nosocomialis BLUFs. Our results show that the three BLUF-containing proteins encode active photoreceptors, despite only two of them are stable in the light-regulatory temperature range when expressed recombinantly. In vivo, only the A. baumannii’s ortholog AnBLUF65 is expressed, which is active in a temperature range from 15 °C to 37 °C. In turn, AnBLUF46 is an active photoreceptor between 15 °C to 32 °C in vitro, but is not expressed in A. nosocomialis in the conditions tested. Intra-protein interactions were analyzed using 3D models built based on A. baumanni’s photoreceptor, to support spectroscopic data and profile intra-protein residue interactions. A general scheme is presented on how hydrophobic/aromatic interactions may contribute to the stability of dark/light- adapted states, indicating the importance of these interactions in BLUF photoreceptors.
Differential mitochondrial protein interaction profile between human translocator protein and its A147T polymorphism variant
Authors: Asih Prita R , Poljak Anne , Kassiou Michael , Ke Yazi D , Ittner Lars M
Published: July 2021

The translocator protein (TSPO) has been implicated in mitochondrial transmembrane cholesterol transport, brain inflammation, and other mitochondrial functions. It is upregulated in glial cells during neuroinflammation in Alzheimer’s disease. High affinity TSPO imaging radioligands are utilized to visualize neuroinflammation. However, this is hampered by the common A147T polymorphism which compromises ligand binding. Furthermore, this polymorphism has been linked to increased risk of neuropsychiatric disorders, and possibly reduces TSPO protein stability. Here, we used immunoprecipitation coupled to mass-spectrometry (IP-MS) to establish a mitochondrial protein binding profile of wild-type (WT) TSPO and the A147T polymorphism variant. Using mitochondria from human glial cells expressing either WT or A147T TSPO, we identified 30 WT TSPO binding partners, yet only 23 for A147T TSPO. Confirming that A147T polymorphism of the TSPO might confer loss of function, we found that one of the identified interactors of WT TSPO, 14-3-3 theta (YWHAQ), a protein involved in regulating mitochondrial membrane proteins, interacts much less with A147T TSPO. Our data presents a network of mitochondrial interactions of TSPO and its A147T polymorphism variant in human glial cells and indicate functional relevance of A147T in mitochondrial protein networks.
Female Bengalese finches recognize their father’s song as sexually attractive
Authors: Fujii Tomoko G. , Okanoya Kazuo
Published: July 2021

Birdsong is an important communication signal used in mate choice. In some songbirds, only males produce songs while females do not. Female birds are sensitive to inter- and intra-species song variation. Some aspects of female song preference depend on developmental experiences. For example, in Bengalese finches and zebra finches, adult females prefer the song to which they were exposed early in life, such as the father’s song. However, it is unclear whether such song preference in females is sexually motivated. The purpose of our study is to test if female Bengalese finches recognize their father’s song as sexually attractive. We measured copulation solicitation displays during playbacks of the father’s song vs. unfamiliar conspecific songs and found that across individuals, the father’s song elicited more displays than other songs. In addition, we analyzed if a bird’s response to a given song could be predicted by the level of similarity of that song to the father’s song. The results suggest that preference for the father’s song in this species is actually relevant to mate choice. Although more precise control is necessary in future studies to elucidate the process of preference development, our results imply the significance of early-life experience in shaping female song preference.
Evaluation of the sensitivity and specificity of three diagnostic tests for Coxiella burnetii infection in cattle and buffaloes in Punjab (India) using Bayesian latent class analysis
Authors: Meletis E. , Keshavamurthy R. , Singh B.B. , Aulakh R.S. , Dhand N.K. , Kostoulas P.
Published: July 2021

Q Fever is a zoonotic disease of significant animal and public health concern, caused by Coxiella burnetii (C. burnetii), an obligate intracellular bacterium. This study was done to evaluate the sensitivity (Se) and specificity (Sp) of three diagnostic methods to diagnose C. burnetii infection in cattle and buffaloes in Punjab, India: an indirect ELISA method applied in serum samples and a trans-Polymerase Chain Reaction (trans-PCR) technique applied in milk samples and genital swabs. Bayesian Latent Class Models were developed following the STARD-BLCM reporting guidelines. Conditional independence was assumed between the tests, given (i) the different biological principle of ELISA and trans-PCR and (ii) the fact that the trans-PCR was performed on different tissues. The ELISA method in the serum samples showed the highest Se of 0.97 (95% Probability Intervals (PIs): 0.93; 0.99) compared to the trans-PCR method applied in milk samples 0.76 (0.62; 0.87) and genital swabs 0.7 (0.55; 0.82). The Sps of all tests were high, with trans-PCR in genital swabs recording the highest Sp of 0.99 (0.98; 1), while the Sp of trans-PCR in milk samples and ELISA in serum samples were 0.98 (0.96; 0.99) and 0.95 (0.93; 0.97) respectively. The study results show that none of the applied tests are perfect, therefore, a testing regimen based on the diagnostic characteristic of the tests may be considered for diagnosis of C. burnetii.
Vision-based monitoring and measurement of bottlenose dolphins’ daily habitat use and kinematics
Authors: Gabaldon Joaquin , Zhang Ding , Lauderdale Lisa , Miller Lance , Johnson-Roberson Matthew , Barton Kira , Shorter K. Alex
Published: July 2021

This research presents a framework to enable computer-automated observation and monitoring of bottlenose dolphins (Tursiops truncatus) in a professionally managed environment. Results from this work provide insight into the dolphins’ movement patterns, kinematic diversity, and how changes in the environment affect their dynamics. Fixed overhead cameras were used to collect ∼100 hours of observations, recorded over multiple days including time both during and outside of formal training sessions. Animal locations were estimated using convolutional neural network (CNN) object detectors and Kalman filter post-processing. The resulting animal tracks were used to quantify habitat use and animal dynamics. Additionally, Kolmogorov-Smirnov analyses of the swimming kinematics were used for high-level behavioral mode classification. The detectors achieved a minimum Average Precision of 0.76. Performing detections and post-processing yielded 1.24×107estimated dolphin locations. Animal kinematic diversity was found to be lowest in the morning and peaked immediately before noon. Regions of the habitat displaying the highest activity levels correlated to locations associated with animal care specialists, conspecifics, or enrichment. The work presented here demonstrates that CNN object detection is not only viable for large-scale marine mammal tracking, it also enables automated analyses of dynamics that provide new insight into animal movement and behavior.
Virulence and antimicrobial resistance profile of non-typhoidalSalmonella entericaserovars recovered from poultry processing environments at wet markets in Dhaka, Bangladesh
Authors: Siddiky Nure Alam , Sarker Md Samun , Khan Md. Shahidur Rahman , Rahman Md. Tanvir , Kafi Md. Abdul , Samad Mohammed A.
Published: July 2021

The rapid emergence of virulent and multidrug-resistant (MDR) non-typhoidalSalmonella(NTS)entericaserovars are a growing public health concern globally. The present study focused on the assessment of the pathogenicity and antimicrobial resistance (AMR) profiling of NTSentericaserovars isolated from chicken processing environments at wet markets in Dhaka, Bangladesh. A total number of 870 samples consisting of carcass dressing water (CDW), chopping board swabs (CBS), and knife swabs (KS) were collected from 29 wet markets. The prevalence ofSalmonellawas found to be 20% in CDW, 19.31% in CBS and 17.58% in KS, respectively. Meanwhile, the MDRSalmonellawas found to be 72.41%, 73.21% and 68.62% in CDW, CBS, and KS, respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namelyinvA,agfA,IpfA,hilA,sivH,sefA,sopE, andspvC. TheS. Enteritidis and untypedSalmonellaisolate harbored all virulence genes whileS. Typhimurium isolates carried six virulence genes exceptsefA andspvC. Phenotypic resistance revealed decreased susceptibility to ciprofloxacin, streptomycin, ampicillin, tetracycline, gentamycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanic acid and azithromycin. Genotypic resistance showed higher prevalence of plasmid mediatedblaTEM followed bytetA,sul1,sul2,sul3, andstrA/B genes. Harmonic and symmetrical trend was observed among the phenotypic and genotypic resistance patterns of the isolates. The research findings anticipate that MDR and virulent NTSentericaserovars are prevailing in the wet market environments which can easily enter into the human food chain. There was a resilient and significant correlation existent among the phenotypic and genotypic resistance patterns and virulence genes ofSalmonellaisolate recovered from carcass dressing water, chopping board swabs, and knife swabs (p< 0.05), respectively.
Identification of a distal RXFP1 gene enhancer with differential activity in fibrotic lung fibroblasts involving AP-1
Authors: Chen Ting-Yun , Li Xiaoyun , Goobie Gillian C. , Hung Ching-Hsia , Hamilton Kyle , Bahudhanapati Harinath , Tan Jiangning , Kass Daniel J. , Zhang Yingze
Published: July 2021

Relaxin/insulin-like family peptide receptor 1 (RXFP1) mediates relaxin’s antifibrotic effects and has reduced expression in the lung and skin of patients with fibrotic interstitial lung disease (fILD) including idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc). This may explain the failure of relaxin-based anti-fibrotic treatments in SSc, but the regulatory mechanisms controlling RXFP1 expression remain largely unknown. This study aimed to identify regulatory elements of RXFP1 that may function differentially in fibrotic fibroblasts.

We identified and evaluated a distal regulatory region of RXFP1 in lung fibroblasts using a luciferase reporter system. Using serial deletions, an enhancer upregulating pGL3-promoter activity was localized to the distal region between -584 to -242bp from the distal transcription start site (TSS). This enhancer exhibited reduced activity in IPF and SSc lung fibroblasts. Bioinformatic analysis identified two clusters of activator protein 1 (AP-1) transcription factor binding sites within the enhancer. Site-directed mutagenesis of the binding sites confirmed that only one cluster reduced activity (−358 to -353 relative to distal TSS). Co-expression of FOS in lung fibroblasts further increased enhancer activity. In vitro complex formation with a labeled probe spanning the functional AP-1 site using nuclear proteins isolated from lung fibroblasts confirmed a specific DNA/protein complex formation. Application of antibodies against JUN and FOS resulted in the complex alteration, while antibodies to JUNB and FOSL1 did not. Analysis of AP-1 binding in 5 pairs of control and IPF lung fibroblasts detected positive binding more frequently in control fibroblasts. Expression of JUN and FOS was reduced and correlated positively with RXFP1 expression in IPF lungs.

In conclusion, we identified a distal enhancer of RXFP1 with differential activity in fibrotic lung fibroblasts involving AP-1 transcription factors. Our study provides insight into RXFP1 downregulation in fILD and may support efforts to reevaluate relaxin-based therapeutics alongside upregulation of RXFP1 transcription.
Correlational networking guides the discovery of cryptic natural product biosynthetic enzymes
Authors: Xue Dan , Older Ethan A. , Zhong Zheng , Shang Zhuo , Chen Nanzhu , Dittenhauser Nolan , Hou Lukuan , Walla Michael D. , Dong Shi-Hui , Tang Xiaoyu , Nagarkatti Prakash , Nagarkatti Mitzi , Li Yong-Xin , Li Jie
Published: July 2021

Bacterial natural product biosynthetic genes, canonically clustered, have been increasingly found to rely on cryptic enzymes encoded elsewhere in the genome for completion of biosynthesis. The study and application of lanthipeptides are frequently hindered by cryptic proteases required for final maturation. Here, we establish a global correlation network bridging the gap between lanthipeptide precursors and cryptic proteases. Applying our analysis to 161,954 bacterial genomes, we establish 5,209 correlations between precursors and cryptic proteases, with 91 prioritized. We use network predictions and co-expression analysis to reveal a previously missing protease for the maturation of class I lanthipeptide paenilan. We further discover widely distributed bacterial M16B metallopeptidases of previously unclear biological function as a new family of lanthipeptide proteases. We show the involvement of a pair of bifunctional M16B proteases in the production of novel class III lanthipeptides with high substrate specificity. Together, these results demonstrate the strength of our correlational networking approach to the discovery of cryptic lanthipeptide proteases and potentially other missing enzymes for natural products biosynthesis.

Graphical abstract
Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines
Authors: Gilliland Theron , Liu Yanan , Li Rong , Dunn Matthew , Cottle Emily , Terada Yutaka , Ryckman Zachary , Alcorn Maria , Vasilatos Shauna , Lundy Jeneveve , Larson Deanna , Wu Hua , Luke Thomas , Bausch Christoph , Egland Kristi , Sullivan Eddie , Wang Zhongde , Klimstra William B.
Published: July 2021

Pandemic SARS CoV-2 has been undergoing rapid evolution during spread throughout the world resulting in the emergence of many Spike protein variants, some of which appear to either evade antibody neutralization, transmit more efficiently, or potentially exhibit increased virulence. This raises significant concerns regarding the long-term efficacy of protection elicited after primary infection and/or from vaccines derived from single virus Spike (S) genotypes, as well as the efficacy of anti-S monoclonal antibody based therapeutics. Here, we used fully human polyclonal human IgG (SAB-185), derived from hyperimmunization of transchromosomic bovines with DNA plasmids encoding the SARS-CoV-2 Wa-1 strain S protein or purified ectodomain of S protein, to examine the neutralizing capacity of SAB-185 in vitro and the protective efficacy of passive SAB-185 antibody (Ab) transfer in vivo. The Ab preparation was tested for neutralization against five variant SARS-CoV-2 strains: Munich (Spike D614G), UK (B.1.1.7), Brazil (P.1) and SA (B.1.3.5) variants, and a variant isolated from a chronically infected immunocompromised patient (Spike Δ144-146). For the in vivo studies, we used a new human ACE2 (hACE2) transgenic Syrian hamster model that exhibits lethality after SARS-Cov-2 challenge and the Munich, UK, SA and Δ144-146 variants. SAB-185 neutralized each of the SARS-CoV-2 strains equivalently on Vero E6 cells, however, a control convalescent human serum sample was less effective at neutralizing the SA variant. In the hamster model, prophylactic SAB-185 treatment protected the hamsters from fatal disease and minimized clinical signs of infection. These results suggest that SAB-185 may be an effective treatment for patients infected with SARS CoV-2 variants.
A new perspective on sales outcome controls: an inside sales perspective
Authors: Conde Richard , Prybutok Victor , Thompson Kenneth
Published: July 2021

Purpose

Previous sales control research has limited the definition of outcome controls exclusively to sales outcomes in an outside sales context. In addition to sales outcome controls, inside sales managers use phone operational outcomes to influence inside sales agent performance, supporting the need to expand the broader definition of outcome controls. Hence, the purpose of this paper is to explore the need to bifurcate outcome controls into two distinct variables: sales and phone operational controls. Researchers know little about the application of sales outcome controls beyond sales-only outcomes, which, in turn, limits the definition of outcome controls.

Design/methodology/approach

Through the utilization of survey, secondary operational data and sales manager’s feedback, this paper demonstrates that the definition of outcome controls needs to be divided into two distinct areas, sales and phone operational controls for inside sales agents, which, in turn, acts collectively to impact an inside sales agent’s job performance and satisfaction.

Findings

This research demonstrates that inside sales managers depend on both sales and phone operational outcome controls to drive sales agent performance, varying in degrees by industry. Even as inside sales managers focus on creating an employee-centric autonomous motivational work culture, the overarching controlling factors associated with phone operational outcomes dampen an inside sales agent’s performance and job satisfaction.

Research limitations/implications

To the best of the authors’ knowledge, as the first sales control research to examine an inside sales context, this study provides support to further study sales controls in an inside sales context. This research can be enhanced by examining business-to-consumer inside sales environments, behavior controls, greater sample size and additional work outcomes such as turnover and tenure.

Practical implications

The findings have important implications because they can help practitioners understand the effect that both sales and phone operational outcomes have on sales agent performance. It also illuminates the need for inside sales managers to be less controlling in their focus on phone operational outcomes, as such a practice has a negative influence on key sales agent job outcomes.

Originality/value

To the best of the authors’ knowledge, this study is the first to triangulate multiple data sources to illustrate the need to evaluate both sales and phone operational outcomes as broader components of sales outcome controls. The study of sales controls in a different sales context suggests that sales management controls may differ by sales context, opening the door to extend the vast sales control literature beyond its current context of outside sales.