bluuebunny/crossref_metadata_2025 huggingface dataset:
Branched chain amino acids and risk of breast cancer
Authors: Zeleznik Oana A. , Balasubramanian Raji , Ren Yumeng , Tobias Deirdre K. , Rosner Bernard , Peng Cheng , Bever Alaina M. , Frueh Lisa , Clish Clary B. , Mora Samia , Hu Frank , Eliassen A. Heather
Published: September 2020

Circulating branched chain amino acid (BCAA) levels reflect metabolic health as well as dietary intake and have been linked to some cancers. Associations with breast cancer are unclear.

We evaluated the association between circulating BCAA levels and risk of breast cancer in a prospective nested case-control study (1,997 cases, 1,997 controls) within the Nurses’ Health Study (NHS) and NHSII. Two-thirds of women in NHS (592 cases) donated two blood samples collected 10 years apart. We used conditional logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) of breast cancer risk in multivariable models which included BMI at age 18 and adulthood weight gain, in addition to other risk factors. We conducted an external validation with secondary analyses in the Women’s Health Study (WHS) (1,297 cases).

Among NHSII participants (predominantly premenopausal at blood collection), elevated circulating BCAA levels were associated with suggestively lower breast cancer risk (e.g., isoleucine highest vs. lowest quartile, multivariable OR (95% CI)= 0.86 (0.65-1.13), p-trend=0.20), with significant linear trends among fasting samples (e.g., isoleucine OR (95% CI)=0.74 (0.53-1.05), p-trend=0.05). In contrast, among postmenopausal women, proximate measures (within 10y from blood draw) were associated with increased breast cancer risk (e.g., isoleucine highest vs. lowest quartile multivariable OR (95% CI)=1.63 (1.12-2.39), p-trend=0.01), with slightly stronger associations among fasting samples (OR (95% CI)=1.73 (1.15-2.61), p-trend=0.01). Distant measures (10-20y since blood draw) were not statistically significantly associated with risk (OR (95% CI)=1.15 (0.87-1.52), p-trend=0.35). We did not observe significant heterogeneity by ER status or BMI. In the WHS, a suggestive positive association was observed for distant measures of leucine among postmenopausal women: OR (95% CI)=1.31 (0.97-1.75), p-trend=0.05.

Although elevated circulating BCAA levels were associated with lower breast cancer risk among premenopausal NHSII women and higher risk of postmenopausal breast cancer in NHS when assessed within 10 years of diagnosis, independent of established risk factors, including adiposity, results were not validated in WHS. Additional independent studies are needed to reassess and understand the complex relationship between BCAAs, menopausal status and timing, and risk of breast cancer.

Statement of significance

Elevated circulating BCAA levels were associated with lower breast cancer risk among premenopausal NHSII women and higher risk of postmenopausal breast cancer in NHS when assessed within 10 years of diagnosis, independent of established risk factors, including adiposity.
Extreme stiffness of neuronal synapses and implications for synaptic adhesion and plasticity
Authors: Yang Ju , Mandriota Nicola , Harrellson Steven Glenn , Jones-Molina John Anthony , Yuste Rafael , Lefort Roger , Sahin Ozgur
Published: September 2020

Synapses play a critical role in neural circuits, and they are potential sites for learning and memory. Maintenance of synaptic adhesion is critical for neural circuit function, however, biophysical mechanisms that help maintain synaptic adhesion are not clear. Studies with various cell types demonstrated the important role of stiffness in cellular adhesions. Although synaptic stiffness could also play a role in synaptic adhesion, stiffnesses of synapses are difficult to characterize due to their small size and challenges in verifying synapse identity and function. To address these challenges, we have developed an experimental platform that combines atomic force microscopy, fluorescence microscopy, and transmission electron microscopy. Here, using this platform, we report that functional, mature, excitatory synapses had an average elastic modulus of approximately 200 kPa, two orders of magnitude larger than that of the brain tissue, suggesting stiffness might have a role in synapse function. Similar to various functional and anatomical features of neural circuits, synaptic stiffness had a lognormal-like distribution, hinting a possible regulation of stiffness by processes involved in neural circuit function. In further support of this possibility, we observed that synaptic stiffness was correlated with spine size, a quantity known to correlate with synaptic strength. Using established stages of the long-term potentiation timeline and theoretical models of adhesion cluster dynamics, we developed a biophysical model of the synapse that not only explains extreme stiffness of synapses, their statistical distribution, and correlation with spine size, but also offers an explanation to how early biomolecular and structural changes during functional potentiation could lead to strengthening of synaptic adhesion. According to this model, synaptic stiffness serves as an indispensable physical messenger, feeding information back to synaptic adhesion molecules to facilitate maintenance of synaptic adhesion.
Widespread decline in plant diversity across six decades
Authors: David Eichenberg , Bowler Diana E. , Aletta Bonn , Helge Bruelheide , Volker Grescho , David Harter , Ute Jandt , Rudolf May , Marten Winter , Florian Jansen
Published: September 2020

Based on plant occurrence data covering all parts of Germany, we investigated changes in the distribution of 2146 plant species between 1960 and 2017. We analyzed 29 million occurrence records over an area of ∼350.000 km2on a 5 × 5 km grid using temporal and spatio-temporal models and accounting for sampling bias. Since the 1960s, more than 70% of investigated plant species showed significant declines in nation-wide occurrence. Archaeophytes (species introduced before 1492) most strongly declined but also native plant species experienced severe declines. In contrast, neophytes (species introduced after 1492) increased in their nation-wide occurrence but not homogeneously throughout the country. Our analysis suggests that the strongest declines in native species already happened in the 1960s-80s, a time frame in which usually few data exist. Increases in neophytic species were strongest in the 1990s and 2010s. Overall, the increase in neophytes did not compensate for the loss of other species, resulting in a decrease in mean grid-cell species-richness of -1.9% per decade. The decline in plant biodiversity is a widespread phenomenon occurring in different habitats and geographic regions. It is likely that this decline has major repercussions on ecosystem functioning and overall biodiversity, potentially with cascading effects across trophic levels. The approach used in this study is transferable to large-scale trend analyses using heterogeneous occurrence data.
Attenuation of homeostatic signaling from apoptotic thymocytes triggers a global regenerative response in the thymus
Authors: Kinsella Sinéad , Evandy Cindy A. , Cooper Kirsten , Iovino Lorenzo , deRoos Paul C. , Hopwo Kayla S. , Granadier David W. , Smith Colton W. , Rafii Shahin , Dudakov Jarrod A.
Published: September 2020

The molecular triggers of organotypic tissue repair are unknown. The thymus, which is the primary site of T cell development, is a model of tissue damage and regeneration as it is particularly sensitive to insult, but also has a remarkable capacity for repair. However, acute and profound damage, such as that caused by common cytoreductive therapies or age-related decline, lead to involution of the thymus and prolonged T cell deficiency, precipitating life-threatening infections and malignant relapse. Consequently, there is an unmet need to boost thymic function and enhance T cell immunity. Here, we demonstrate an innate trigger of the reparative response in the thymus, centered on the attenuation of signaling directly downstream of apoptotic cell detection as thymocytes are depleted after acute damage. We found that the intracellular pattern recognition receptor NOD2, via induction of microRNA-29c, suppressed the induction of the regenerative factors IL-23 and BMP4, from thymic dendritic cells (DCs) and endothelial cells (ECs), respectively. During steady-state, when a high proportion of thymocytes are undergoing apoptosis (as a consequence of selection events during T cell development), this suppressive pathway is constitutively activated by the detection of exposed phosphatidylserine on apoptotic thymocytes by cell surface TAM receptors on DCs and ECs, with subsequent downstream activation of the Rho GTPase Rac1. However, after damage, when profound cell depletion occurs across the thymus, the TAM-Rac1-NOD2-miR29c pathway is abrogated, therefore triggering the increase in IL-23 and BMP4 levels. Importantly, this pathway could be modulated pharmacologically by inhibiting Rac1 GTPase activation with the small molecule inhibitor EHT1864, leading to increased thymic function and T cell recovery after acute damage. In conclusion, our work not only represents a novel regenerative strategy for restoring immune competence in patients whose thymic function has been compromised due to cytoreductive conditioning, infection, or age; but also, identifies a mechanism by which tissue regenerative responses are triggered.
Selective effects of arousal on population coding of natural sounds in auditory cortex
Authors: Heller Charles R. , Schwartz Zachary P. , Saderi Daniela , David Stephen V.
Published: September 2020

The ability to discriminate between complex natural sounds is critical for survival. Changes in arousal and other aspects of behavioral state can impact the accuracy of sensory coding, affecting both the reliability of single neuron responses and the degree of correlated noise between neurons. However, it is unclear how these effects interact to influence coding of diverse natural stimuli. We recorded the spiking activity of neural populations in primary auditory cortex (A1) evoked by a large library of natural sounds while monitoring changes in pupil size as an index of arousal. Heightened arousal increased response magnitude and reduced noise correlations between neurons, improving coding accuracy on average. Rather than suppressing shared noise along all dimensions of neural activity, the change in noise correlations occurred via coherent, low-dimensional modulation of response variability in A1. The modulation targeted a different group of neurons from those undergoing changes in response magnitude. Thus, changes in response magnitude and correlation are mediated by distinct mechanisms. The degree to which these low-dimensional changes were aligned with the high-dimensional natural sound-evoked activity was variable, resulting in stimulus-dependent improvements in coding accuracy.
Multi-modal pooled Perturb-CITE-Seq screens in patient models define novel mechanisms of cancer immune evasion
Authors: Frangieh Chris J. , Melms Johannes C. , Thakore Pratiksha I. , Geiger-Schuller Kathryn R. , Ho Patricia , Luoma Adrienne M. , Cleary Brian , Malu Shruti , Cuoco Michael S. , Zhao Maryann , Rogava Meri , Hovey Lila , Rotem Asaf , Bernatchez Chantale , Wucherpfennig Kai W. , Johnson Bruce E. , Rozenblatt-Rosen Orit , Schadendorf Dirk , Regev Aviv , Izar Benjamin
Published: September 2020

Resistance to immune checkpoint inhibitors (ICI) that activate T cell mediated anti-tumor immunity is a key challenge in cancer therapy, yet the underlying mechanisms remain poorly understood. To further elucidate those, we developed a new approach, Perturb-CITE-seq, for pooled CRISPR perturbation screens with multi-modal RNA and protein single-cell profiling readout and applied it to screen patient-derived autologous melanoma and tumor infiltrating lymphocyte (TIL) co-cultures. We profiled RNA and 20 surface proteins in over 218,000 cells under ~750 perturbations, chosen by their membership in an immune evasion program that is associated with immunotherapy resistance in patients. Our screen recovered clinically-relevant resistance mechanisms concordantly reflected in RNA, protein and perturbation effects on susceptibility to T cell mediated killing. These were organized in eight co-functional modules whose perturbation distinctly affect four co-regulated programs associated with immune evasion. Among these were defects in the IFNγ-JAK/STAT pathway and in antigen presentation, and several novel mechanisms, including loss or downregulation ofCD58, a surface protein without known mouse homolog. Leveraging the rich profiles in our screen, we found that loss ofCD58did not compromise MHC protein expression and thatCD58was not transcriptionally induced by the IFNγ pathway, allowing us to distinguish it as a novel mechanism of immune resistance. We further show that loss ofCD58on cancer cells conferred immune evasion across multiple T cell and Natural Killer cell patient co-culture models. Notably, CD58 is downregulated in tumors with resistance to immunotherapy in melanoma patients. Our work identifies novel mechanisms at the nexus of immune evasion and drug resistance and provides a general framework for deciphering complex mechanisms by large-scale perturbation screens with multi-modal singlecell profiles, including in systems consisting of multiple cell types.
Spatially-targeted proteomics of the host-pathogen interface during staphylococcal abscess formation
Authors: Guiberson Emma R. , Weiss Andy , Ryan Daniel J. , Monteith Andrew J. , Sharman Kavya , Gutierrez Danielle B. , Perry William J. , Caprioli Richard M. , Skaar Eric P. , Spraggins Jeffrey M.
Published: September 2020

Staphylococcus aureusis a common cause of invasive and life-threatening infections that are often multi-drug resistant. To develop novel treatment approaches, a detailed understanding of the complex host-pathogen interactions during infection is essential. This is particularly true for the molecular processes that govern the formation of tissue abscesses, as these heterogeneous structures are important contributors to staphylococcal pathogenicity. To fully characterize the developmental process leading to mature abscesses, temporal and spatial analytical approaches are required. Spatially targeted proteomic technologies, such as micro liquid extraction surface analysis, offer insight into complex biological systems including detection of bacterial proteins, and their abundance in the host environment. By analyzing the proteomic constituents of different abscess regions across the course of infection, we defined the immune response and bacterial contribution to abscess development through spatial and temporal proteomic assessment. The information gathered was mapped to biochemical pathways to characterize the metabolic processes and immune strategies employed by the host. These data provide insights into the physiological state of bacteria within abscesses and elucidate pathogenic processes at the host-pathogen interface.
Branching microtubule nucleation is controlled by importin-mediated inhibition of TPX2 phase separation
Authors: Safari Mohammad S. , King Matthew R. , Brangwynne Clifford P. , Petry Sabine
Published: September 2020

The microtubule-based mitotic spindle is responsible for equally partitioning the genome during each cell division, and its assembly is executed by several microtubule nucleation pathways. In the spindle center, Targeting Protein for XKlp2 (TPX2) promotes branching microtubule nucleation, where new microtubules are nucleated from pre-existing ones. Until the onset of spindle assembly, TPX2 is sequestered by importins-α/β, yet the molecular nature of this regulation remains unclear, particularly since TPX2 was recently found to undergo a liquid-liquid phase separation to execute its function. Here we demonstrate that TPX2 interacts with importins-α/β with nanomolar affinity as a 1:1:1 mono-dispersed trimer. We identify a new nuclear localization sequence (NLS) on TPX2, which contributes to its high-affinity interaction with importin-α. Interestingly, importin-β alone can also associate with TPX2, and does so via dispersed, weak interactions. Interactions of both importin-α and importin-β with TPX2 each inhibit its propensity for phase separation, and consequently its ability to orchestrate branching microtubule nucleation. In sum, our study explains how TPX2 is regulated in order to facilitate spindle assembly, and provides novel insight into how a protein phase separation can be inhibited via weak biomolecular interactions.

Significance Statement

The discovery that proteins can undergo phase separation is revolutionizing biology. Characterization of dozens of phase separating proteins in vitro over the past several years has mainly focused on how macromolecules undergo liquid-liquid phase separation (LLPS). The next, and possibly bigger challenge is to investigate how LLPS is regulated in the cell, namely how it is inhibited to spatiotemporally control a certain cellular function. Here, we addressed this challenge by identifying how the spindle assembly factor TPX2 is inhibited by importins from undergoing LLPS and thereby turning on spindle assembly.
Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls
Authors: Howard Nicholas P. , Troggio Michela , Durel Charles-Eric , Muranty Hélène , Denancé Caroline , Bianco Luca , Tillman John , van de Weg Eric
Published: September 2020

Background

Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20K and Affymetrix Axiom® 480K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n=3,141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls.

Results

Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8,412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3’ end of the probe.

Conclusions

The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development.
VeTra: a tool for trajectory inference based on RNA velocity
Authors: Weng Guangzheng , Kim Junil , Won Kyoung Jae
Published: September 2020

Trajectory inference (TI) for single cell RNA sequencing (scRNAseq) data is a powerful approach to interpret dynamic cellular processes such as cell cycle and development. Still, however, accurate inference of trajectory is challenging. Recent development of RNA velocity provides an approach to visualize cell state transition without relying on prior knowledge. To perform TI and group cells based on RNA velocity we developed VeTra. By applying cosine similarity and merging weakly connected components, VeTra identifies cell groups from the direction of cell transition. Besides, VeTra suggests key regulators from the inferred trajectory. VeTra is a useful tool for TI and subsequent analysis.
Low-level, prediction-based sensory and motor processes are unimpaired in Autism
Authors: Finnemann Johanna , Plaisted-Grant Kate , Moore James , Teufel Christoph , Fletcher Paul
Published: September 2020

A new promising account of human brain function suggests that sensory cortices try to optimise information processing via predictions that are based on prior experiences. The brain is thus likened to a probabilistic prediction machine. There has been a growing – though inconsistent – literature to suggest that features of autism spectrum conditions (ASCs) are associated with a deficit in modelling the world through such prediction-based inference. However empirical evidence for differences in low-level sensorimotor predictions in autism is still lacking. One approach to examining predictive processing in the sensorimotor domain is in the context of self-generated (predictable) as opposed to externally-generated (less predictable) effects. We employed two complementary tasks – force-matching and intentional binding – which examine self-versus externally-generated action effects in terms of sensory attenuation and attentional binding respectively in adults with and without autism. The results show that autism was associated with normal levels of sensory attenuation of internally-generated force and with unaltered temporal attraction of voluntary actions and their outcomes. Thus, our results do not support a general deficit in predictive processing in autism.
Effects of N, P, K on Yield and Quality of Jujube in the Loess Hilly Region and Its Fertilization Model
Authors: Ye Shenglan , Liu Tiancheng , Wei Yulu
Published: September 2020

The aim of this study is to explore the optimal N, P and K fertilization model suitable for pear-jujube in the mountain of northern Shaanxi in 2016 years. This experiment use 3-factor, saturated optimal design for quadratic fertilization scheme. The effects of different fertilization treatments on the yield and quality of pear-jujube were studied through field experiments. And comprehensive evaluation based on the quality of pear-jujube. The results showed that N1P3K3has the highest yield, which is 48% higher than the control (CK). The effect of nitrogen, phosphorus, and potassium on yield is potassium fertilizer (positive effect)> phosphate fertilizer (positive effect)> nitrogen fertilizer (negative effect). Phosphate and potassium fertilizers have significant effects on increasing the content of soluble solids. Application of potassium fertilizer alone can significantly increase the content of reduced Vitamins c. The combined application of nitrogen, phosphorus, and potassium reduced the content of reduced Vitamins c. N3P3K1treatment can significantly increase the total sugar content in fruits. Single application of phosphate and potassium increases the content of organic acids in fruits. Other fertilization treatments have significant effects on reducing the content of organic acids in fruits. The sugar-acid ratio of N3P3K1is significantly higher than CK, which had an important effect on improving the taste. A high amount of potassium fertilizer has a significant effect on increasing the total flavonoid content in fruits. The interaction of nitrogen and phosphorus will reduce the total flavonoid content. The effect of nitrogen, phosphorus, and potassium on quality is potassium (positive effect)> nitrogen (positive effect)> phosphate (positive effect). Comprehensive analysis, the optimal fertilization amount when the target yield is 23000 ∼ 27000 kg·hm-2and the quality score is above 85 is nitrogen (N) 406.93 ∼ 499.31 kg·hm-2, phosphorus (P2O5) 203.94 ∼ 297.08 kg·hm-2, and potassium (K2O) 285.47 ∼ 322.82 kg·hm-2.
Mature black alder shows intermittent events of high stem methane emissions
Authors: Köhn Daniel , Günther Anke , Schwabe Ines , Jurasinski Gerald
Published: September 2020

Tree stems can be a source of the greenhouse gas methane (CH4). However, assessments of the global importance are complicated by a lack of research and a high variability between ecosystems. Here, we determined the contribution of emissions from tree stems of mature black alder (Alnus glutinosa(L.) Gaertn.) to overall CH4exchange in two temperate peatlands.

We measured emissions from stems and soils using closed chambers in a drained and a wet alder forest over two years. Further, we studied the importance of alder leaves as substrate for methanogenesis in an incubation experiment.

Stem CH4emissions were shortlived and occurred only during times of inundation at the wet site. The drained site did not show stem emissions and the soil acted as a small CH4sink. The contribution of stem emissions to the overall CH4budget was below 0.3% in both sites.

Our results show that also mature black alders intermittently can be a source of CH4. However, the low share of stem-mediated CH4emissions in both forests may indicate that this pathway is only of minor relative importance in temperate peatlands.
Metabolic profiling reveals nutrient preferences during carbon utilization inBacillusspecies
Authors: Chang James D. , Vaughan Ellen E. , Liu Carmen Gu , Jelinski Joseph W. , Terwilliger Austen L. , Maresso Anthony W.
Published: September 2020

Pathogenic bacteria take host nutrients to support their growth, division, survival, and pathogenesis. The genusBacillusincludes species with diverse natural histories, including free-living nonpathogenic heterotrophs such asB. subtilisand host-dependent pathogens such asB. anthracis(the etiological agent of the disease anthrax) andB. cereus, a cause of food poisoning. Although highly similar genotypically, the ecological niches of these three species are mutually exclusive, which raises the untested hypothesis that their metabolism has speciated along a nutritional tract. Here, we employed a quantitative measurement of the number of reducing equivalents as a function of growth on hundreds of different sources of carbon to gauge the “culinary preferences” of three distinctBacillusspecies, and relatedStaphylococcus aureus. We show that each species had widely varying metabolic ability to utilize diverse sources of carbon that correlated to their ecological niches. In addition, carbohydrates are shown to be the preferred sources of carbon when grown under idealin vitroconditions. Rather unexpectedly, these metabolic utilizations did not correspond one-to-one with an increase in biomass, which brings to question what cellular activity should be considered productive when it comes to virulence. Finally, we applied this system to the growth and survival ofB. anthracisin a blood-based environment and find that amino acids become the preferred source of energy while demonstrating the possibility of applying this approach to identifying xenobiotics or host compounds that can promote or interfere with bacterial metabolism during infection.

Author summary

Successful organisms must make nutritional adaptations to thrive in their environment. Bacterial pathogens are no exception, having evolved for survival inside their hosts. The host combats these pathogens by depriving them of potential biochemical resources, termed nutritional immunity. This places pathogens under pressure to utilize their resources efficiently and strategically, and their metabolism must in turn be tailored for this situation. In this study, we examined the carbon metabolism of three human pathogens of varying virulence (Bacillus anthracis, Bacillus cereus, andStaphylococcus aureus) and one nonpathogenicBacillus(Bacillus subtilis) via a phenotype microarray that senses reducing equivalents produced during metabolism. Our analysis shows the existence of distinct preferences by these pathogens towards only a select few carbohydrates and implies reliance on specific metabolic pathways. These metabolic signatures obtained could be distinguished from one bacterial species to another, and we conclude that nutrient preferences offer a new perspective into investigating how pathogens can thrive during infection despite host-induced starvation.
Glibenclamide, ATP and Metformin Increases the Expression of Human Bile Salt Export Pump ABCB11
Authors: Vats Nisha , Dubey Ravi Chandra , Sanal Madhusudana Girija , Taneja Pankaj , Venugopal Senthil Kumar
Published: September 2020

Background

Bile Salt Export Pump (BSEP/ABCB11) is important in the maintenance of the enterohepatic circulation of bile acids and drugs. Drugs such as rifampicin, glibenclamide inhibit BSEP. Progressive Familial Intrahepatic Cholestasis Type-2, a lethal pediatric disease, some forms of intrahepatic cholestasis of pregnancy, and drug-induced cholestasis are associated with BSEP dysfunction.

Methods

We started with a bioinformatic approach to identify the relationship between ABCB11 and other proteins, microRNAs, and drugs. Microarray data set of the liver samples from ABCB11 knockout mice was analyzed by GEO2R tool. Differentially expressed gene pathway enrichment analysis was done by ClueGo v2.5.5 app from Cytoscape. Protein-protein interaction network was constructed by STRING application in Cytoscape. Networks were analyzed using the Cytoscape software v3.7.1. CyTargetLinker v4.1.0 was used to screen the transcription factors, microRNAs and drugs. Predicted drugs were validated on human liver cell line, HepG2. BSEP expression was quantified by Real Time PCR and Western Blot.

Results

ABCB11 knockout in mice was associated with a predominant upregulation and downregulation of genes associated with cellular component movement and sterol metabolism respectively. We further identified the hub genes in the network. Genes related to immune activity, cell signaling and fatty acid metabolism were dysregulated. We further identified drugs (glibenclamide and ATP) and a total of 14 microRNAs targeting the gene. Western Blot and Real Time PCR analysis confirmed the upregulation of BSEP on the treatment of HepG2 cells with glibenclamide, ATP, and metformin.

Conclusion

The differential expression of cell signaling genes and those related to immune activity in ABCB11 KO animals may be secondary to cell injury. We have found glibenclamide, ATP, and metformin upregulates BSEP. The mechanisms involved and the clinical relevance of these findings need to be investigated.
Negeviruses reduce replication of alphaviruses during co-infection
Authors: Patterson Edward I. , Kautz Tiffany F. , Contreras-Gutierrez Maria A. , Guzman Hilda , Tesh Robert B. , Hughes Grant L. , Forrester Naomi L.
Published: September 2020

Negeviruses are a group of insect-specific virus (ISV) that have been found in many arthropods. Their presence in important vector species led us to examine their interactions with arboviruses during co-infections. Wild-type negeviruses reduced the replication of Venezuelan equine encephalitis virus (VEEV) and chikungunya virus (CHIKV) during co-infections in mosquito cells. Negev virus (NEGV) isolates were also used to express GFP and anti-CHIKV antibody fragments during co-infections with CHIKV. NEGV expressing anti-CHIKV antibody fragments was able to further reduce replication of CHIKV during co-infections, while reductions of CHIKV with NEGV expressing GFP were similar to titers with wild-type NEGV alone. These results are the first to show that negeviruses induce superinfection exclusion of arboviruses, and to demonstrate a novel approach to deliver anti-viral antibody fragments with paratransgenic ISVs. The ability to inhibit arbovirus replication and express exogenous proteins in mosquito cells make negeviruses a promising platform for control of arthropod-borne pathogens.
Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing
Authors: Hoffer Eric D. , Hong Samuel , Sunita S. , Maehigashi Tatsuya , Gonzalez Ruben L. , Whitford Paul , Dunham Christine M.
Published: September 2020

Modifications in the tRNA anticodon, adjacent to the three-nucleotide anticodon, influence translation fidelity by stabilizing the tRNA to allow for accurate reading of the mRNA genetic code. One example is the N1-methylguaonosine modification at guanine nucleotide 37 (m1G37) located in the anticodon loop, immediately adjacent to the anticodon nucleotides 34-36. The absence of m1G37 in tRNAProcauses +1 frameshifting on polynucleotide, slippery codons. Here, we report structures of the bacterial ribosome containing tRNAProbound to either cognate or slippery codons to determine how the m1G37 modification prevents mRNA frameshifting. The structures reveal that certain codon-anticodon contexts and m1G37 destabilize interactions of tRNAProwith the peptidyl site, causing large conformational changes typically only seen during EF-G mediated translocation of the mRNA-tRNA pairs. These studies provide molecular insights into how m1G37 stabilizes the interactions of tRNAProwith the ribosome and the influence of slippery codons on the mRNA reading frame.

IMPACT STATEMENT

Chemical modifications near the tRNA anticodon and specific mRNA-tRNA pairs combine to control the ribosomal three-nucleotide mRNA reading frame, essential for the sequential addition of amino acids into polypeptide chains.

Data deposition

Crystallography, atomic coordinates, and structure factors have been deposited in the Protein Data Bank,www.pdb.org(PDB codes 6NTA, 6NSH, 6NUO, 6NWY, 6O3M, 6OSI)
Tree-Aggregated Predictive Modeling of Microbiome Data
Authors: Bien Jacob , Yan Xiaohan , Simpson Léo , Müller Christian L.
Published: September 2020

Modern high-throughput sequencing technologies provide low-cost microbiome survey data across all habitats of life at unprecedented scale. At the most granular level, the primary data consist of sparse counts of amplicon sequence variants or operational taxonomic units that are associated with taxonomic and phylogenetic group information. In this contribution, we leverage the hierarchical structure of amplicon data and propose a data-driven and scalable tree-guided aggregation framework to associate microbial subcompositions with response variables of interest. The excess number of zero or low count measurements at the read level forces traditional microbiome data analysis workflows to remove rare sequencing variants or group them by a fixed taxonomic rank, such as genus or phylum, or by phylogenetic similarity. By contrast, our framework, which we calltrac(tree-aggregation ofcompositional data), learns data-adaptive taxon aggregation levels for predictive modeling, greatly reducing the need for user-defined aggregation in preprocessing while simultaneously integrating seamlessly into the compositional data analysis framework. We illustrate the versatility of our framework in the context of large-scale regression problems in human gut, soil, and marine microbial ecosystems. We posit that the inferred aggregation levels provide highly interpretable taxon groupings that can help microbiome researchers gain insights into the structure and functioning of the underlying ecosystem of interest.
Ca2+and Membrane Potential Transitions During Action Potentials are Self-Similar to Each Other and to Variability of AP Firing Intervals Across the Broad Physiologic Range of AP Intervals During Autonomic Receptor Stimulation
Authors: Yang Dongmei , Morrell Christopher H. , Lyashkov Alexey E. , Tagirova Syevda , Zahanich Ihor , Yaniv Yael , Vinogradova Tatiana M. , Ziman Bruce D. , Maltsev Victor A. , Lakatta Edward G.
Published: September 2020

Ca2+and Vmtransitions occurring throughout AP cycles in sinoatrial nodal (SAN) cells arecuesthat: (1)not only regulateactivation states of molecules operating within criticality (Ca2+domain) and limit-cycle (Vmdomain) mechanisms of a coupled-clock system that underlies SAN cell automaticity; (2) but are alsoregulated bythe activation states of the clock molecules they regulate. In other terms, these cues arebothcauses and effects of clock molecular activation (recursion). Recently, we demonstrated that Ca2+and Vmtransitions during AP cycles in single SAN cells isolated from mice, guinea pigs, rabbits and humans are self-similar (obey a power law) and are also self-similar to trans-species AP firing intervals of these cells invitro, to heart rate invivo, and to body mass.

Neurotransmitter stimulation of β adrenergic receptor or cholinergic receptor initiated signaling in SAN cells modulates their AP firing rate and rhythm by impacting on the degree to which SAN clocks couple to each other, creating the broad physiologic range of SAN cell mean AP firing intervals and firing interval variabilities. Here we show that Ca2+and Vmdomain kinetic transitions (time to AP ignition in diastole and 90% AP recovery) occurring within given AP, the mean AP firing intervals, and AP firing interval variabilities within time-series of APs in 230 individual SAN cells are self-similar (obey power laws). In other terms, these long-range correlations inform on self-similar distributions of order among SAN cells across the entire broad physiologic range of SAN AP firing intervals, regardless of whether autonomic receptors of these cells are stimulated or not, and regardless of the type (adrenergic or cholinergic) of autonomic receptor stimulation. These long-range correlations among distributions of Ca2+and Vmkinetic functions that regulate SAN cell clock coupling during each AP cycle in differentindividual, isolated SAN cells not in contact with each other. Our numerical model simulations further extended our perspectives to the molecular scale and demonstrated that many ion currents also behave self-similar across autonomic states.

Thus, to ensure rapid flexibility of AP firing rates in response to different types and degrees of autonomic input, nature “did not reinvent molecular wheels within the coupled-clock system of pacemaker cells”, but differentially engaged or scaled the kinetics of gears that regulate the rate and rhythm at which the “wheels spin” in a given autonomic input context.
Local Bilayer Hydrophobicity Modulates Membrane Protein Stability
Authors: Marx Dagan C. , Fleming Karen G.
Published: September 2020

Through the insertion of nonpolar side chains into the bilayer, the hydrophobic effect has long been accepted as a driving force for membrane protein folding. However, how the changing chemical composition of the bilayer affects the magnitude side chain transfer free energieshas historically not been well understood. A particularly challenging region for experimental interrogation is the bilayer interfacial region that is characterized by a steep polarity gradient. In this study we have determined thefor nonpolar side chains as a function of bilayer position using a combination of experiment and simulation. We discovered an empirical correlation between the surface area of nonpolar side chain, the transfer free energies, and the local water concentration in the membrane that allows forto be accurately estimated at any location in the bilayer. Using these water-to-bilayervalues, we calculated the interface-to-bilayer transfer free energy. We find that theare similar to the “biological”, translocon-based transfer free energies, indicating that the translocon energetically mimics the bilayer interface. Together these findings can be applied to increase the accuracy of computational workflows used to identify and design membrane proteins, as well as bring greater insight into our understanding of how disease-causing mutations affect membrane protein folding and function.
Calcium-dependent protein acyltransferase DHHC21 controls activation of CD4+T cells
Authors: Shayahati Bieerkehazhi , Fan Ying , West Savannah , Tewari Ritika , Ko Junsuk , Mills Tingting , Boehning Darren , Akimzhanov Askar M.
Published: September 2020

Despite the recognized significance of reversible protein lipidation (S-acylation) for T cell receptor signal transduction, the enzymatic control of this post-translational modification in T cells remains poorly understood. Here, we demonstrate that DHHC21, a member of the DHHC family of mammalian protein acyltransferases, mediates agonist-induced S-acylation of proximal T cell signaling proteins. Using Zdhhc21depmice expressing a functionally deficient version of DHHC21, we show that DHHC21 is a calcium/calmodulin-dependent enzyme critical for activation of naïve CD4+T cells in response to T cell receptor stimulation. We found that disruption of the calcium/calmodulin binding domain of DHHC21 does not affect thymic T cell development but prevents differentiation of peripheral CD4+T cells into Th1, Th2, and Th17 effector T helper lineages. Our findings identify DHHC21 as an essential component of the T cell receptor signaling machinery and define a new role for protein acyltransferases in regulation of T cell-mediated immunity.

Significance

This study identifies DHHC21, a member of the DHHC family of mammalian protein acyltransferases, as a novel component of the TCR signaling pathway and demonstrates that this enzyme critically regulates activation and differentiation of CD4+T cells by mediating rapid TCR-induced S-acylation of signaling proteins. This finding shows that protein acyltransferases can play a vital function in regulation of T cell-mediated immunity and thus serve as potential drug targets in diseases associated with altered immune system homeostasis.
Automated Deep Learning-based Multi-class Fluid Segmentation in Swept-Source Optical Coherence Tomography Images
Authors: Oakley Jonathan D. , Sodhi Simrat K. , Russakoff Daniel B. , Choudhry Netan
Published: September 2020

Purpose

To evaluate the performance of a deep learning-based, fully automated, multi-class, macular fluid segmentation algorithm relative to expert annotations in a heterogeneous population of confirmed wet age-related macular degeneration (wAMD) subjects.

Methods

Twenty-two swept-source optical coherence tomography (SS-OCT) volumes of the macula from 22 from different individuals with wAMD were manually annotated by two expert graders. These results were compared using cross-validation (CV) to automated segmentations using a deep learning-based algorithm encoding spatial information about retinal tissue as an additional input to the network. The algorithm detects and delineates fluid regions in the OCT data, differentiating between intra- and sub-retinal fluid (IRF, SRF), as well as fluid resulting from in serous pigment epithelial detachments (PED). Standard metrics for fluid detection and quantification were used to evaluate performance.

Results

The per slice receiver operating characteristic (ROC) area under the curves (AUCs) for each of these fluid types were 0.90, 0.94 and 0.94 for IRF, SRF and PED, respectively. Per volume results were 0.94 and 0.88 for IRF and PED (SRF being present in all cases). The correlation of fluid volume between the expert graders and the algorithm were 0.99 for IRF, 0.99 for SRF and 0.82 for PED.

Conclusions

Automated, deep learning-based segmentation is able to accurately detect and quantify different macular fluid types in SS-OCT data on par with expert graders.
Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders
Authors: Gómez-Carballa Alberto , Bello Xabier , Pardo-Seco Jacobo , Martinón-Torres Federico , Salas Antonio
Published: September 2020

The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extent.
Sterile Spikelets Contribute to Yield in Sorghum and Related Grasses
Authors: AuBuchon-Elder Taylor , Coneva Viktoriya , Goad David M. , Jenkins Lauren M. , Yu Yunqing , Allen Doug K. , Kellogg Elizabeth A.
Published: September 2020

Sorghum (Sorghum bicolor) and its relatives in the grass tribe Andropogoneae bear their flowers in pairs of spikelets in which one spikelet (seed-bearing or sessile spikelet [SS]) of the pair produces a seed and the other is sterile or male (staminate). This division of function does not occur in other major cereals such as wheat (Triticum aestivum) or rice (Oryza sativa). Additionally, one bract of the SS spikelet often produces a long extension, the awn, that is in the same position as, but independently derived from, that of wheat and rice. The function of the sterile spikelet is unknown and that of the awn has not been tested in Andropogoneae. We used radioactive and stable isotopes of carbon, RNA sequencing of metabolically important enzymes, and immunolocalization of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to show that the sterile spikelet assimilates carbon, which is translocated to the largely heterotrophic SS. The awn shows no evidence of photosynthesis. These results apply to distantly related species of Andropogoneae. Removal of sterile spikelets in sorghum significantly decreases seed weight (yield) by ∼9%. Thus, the sterile spikelet, but not the awn, affects yield in the cultivated species and fitness in the wild species.
Introducing an innovation promotion model for construction projects
Authors: Fernando Sam , Panuwatwanich Kriengsak , Thorpe David
Published: September 2020

Purpose

This study aims to investigate and model the complex dynamics of innovation enablers in construction projects aiming to develop a framework identifying actions for clients to promote innovation.

Design/methodology/approach

Through a comprehensive literature review, a conceptual model was previously derived to explain the client-driven enablers in promoting innovation. This was tested using the data from 131 Australian construction projects. Statistical analysis was conducted on the data using factor analysis and correlation analysis to test the model, which was validated using the case study approach. The testing and validating aspects are explained in this paper.

Findings

The constructs of the recommended model are idea harnessing, relationship enhancement, incentivization and project team fitness.

Research limitations/implications

The difficulty of analyzing the complex dynamics happening within projects in relation to innovation has been a barrier to progress research in this area. The introduction of this model would pave the way for researchers to explore this area with ease.

Originality/value

As revealed in the detailed literature review undertaken, this is the first time that a comprehensive study has been conducted to identify client-led innovation enablers for construction projects. The results would benefit industry practitioners to achieve enhanced project outcomes in construction projects through innovation.