bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Insight into Mitochondrial β-Barrel Outer Membrane Protein Biogenesis
Authors: Diederichs Kathryn A. , Ni Xiaodan , Rollauer Sarah E. , Botos Istvan , Tan Xiaofeng , King Martin S. , Kunji Edmund R.S. , Jiang Jiansen , Buchanan Susan K.
Published: April 2020

In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold β-barrel proteins and insert them into the mitochondrial outer membrane. We report cryoEM structures of the SAM complex fromMyceliophthora thermophila, which show that Sam50 forms a 16-stranded transmembrane β-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analysis shows how the Sam50 β-barrel opens a lateral gate to accommodate its substrates. The SAM complex structure suggests how it interacts with other mitochondrial outer membrane proteins to create supercomplexes.
Cytoplasmic mRNA decay represses RNA polymerase II transcription during early apoptosis
Authors: Duncan-Lewis Christopher , Hartenian Ella , King Valeria , Glaunsinger Britt A.
Published: April 2020

RNA abundance is generally sensitive to perturbations in decay and synthesis rates, but crosstalk between RNA polymerase II transcription and cytoplasmic mRNA degradation often leads to compensatory changes in gene expression. Here, we reveal that widespread mRNA decay during early apoptosis represses RNAPII transcription, indicative of positive (rather than compensatory) feedback. This repression requires active cytoplasmic mRNA degradation, which leads to impaired recruitment of components of the transcription preinitiation complex to promoter DNA. Importin α/β- mediated nuclear import is critical for this feedback signaling, suggesting that proteins translocating between the cytoplasm and nucleus connect mRNA decay to transcription. We also show that an analogous pathway activated by viral nucleases similarly depends on nuclear protein import. Collectively, these data demonstrate that accelerated mRNA decay leads to the repression of mRNA transcription, thereby amplifying the shutdown of gene expression. This highlights a conserved gene regulatory mechanism by which cells respond to threats.

IMPACT STATEMENT

Human cells respond to cytoplasmic mRNA depletion during early apoptosis by inhibiting RNA polymerase II transcription, thereby magnifying the gene expression shutdown during stress.
Deaf intermarriage does not increase the prevalence of deafness alleles
Authors: Braun Derek C. , Jain Samir , Epstein Eric , Greenwald Brian H. , Herold Brienna , Gray Margaret
Published: April 2020

The idea that deaf intermarriage increases deafness was forcefully pushed in the late 19th century by Alexander Graham Bell, in proceedings published by the National Academy of Science. Bell’s hypothesis was not supported by a 19th century study by Edward Allen Fay, which was funded by Bell’s own organization, the Volta Bureau. The Fay study showed through an analysis of 4,471 deaf marriages that the chances of having deaf children did not increase significantly when both parents were deaf. In light of an apparent increase in non-complementary pairings when a recent dataset of Gallaudet alumni was compared with the 19th century Fay dataset, Bell’s argument has been resurrected that residential schools for the deaf, which concentrate signing deaf individuals together, have promoted assortative mating and increased the prevalence of both phenotypic deafness and the commonest recessive deafness allele. Because this hypothesis persists, even though it contradicts classical models introduced by R.A. Fisher and Sewell Wright, it is critically important that this hypothesis be thoroughly re-investigated. In this study, we used an established forward-time genetics simulator with parameters and measurements collected from the published literature. Compared to mathematical equations, simulations allowed for more complex modeling, operated without assumptions of parametricity, and captured ending distributions and variances. Our simulation results affirm predictions from classical equations and show that assortative mating only modestly increases the prevalence of phenotypically deaf individuals, with this effect mostly completed by the third generation. Most importantly, our data show that even intense assortative mating does not increase allelic frequency under reported conditions. These results are not locus-specific and are generalizable to other forms of recessive deafness. We offer alternative explanations for the higher rate of non-complementary pairings measured in the contemporary Gallaudet alumni sample as compared to the Fay dataset.
The Molecular Landscape of Asian Breast Cancers Reveals Clinically Relevant Population-Specific Differences
Authors: Pan Jia-Wern , Ahmad Zabidi Muhammad Mamduh , Ng Pei-Sze , Meng Mei-Yee , Hasan Siti Norhidayu , Sandey Bethan , Sammut Stephen-John , Yip Cheng-Har , Rajadurai Pathmanathan , Rueda Oscar M. , Caldas Carlos , Chin Suet-Feung , Teo Soo-Hwang
Published: April 2020

Molecular profiles of breast cancer have contributed to an improved understanding of the disease, enabled development of molecular prognostic signatures to guide treatment decisions and unveiled new or more accurate therapeutic options for breast cancer patients. However, the extent to which differences in genetic, environmental and lifestyle factors influence molecular profiles in different populations remains poorly characterised, as relatively few large-scale molecular studies of breast tumours in non-Caucasian populations have hitherto been reported. Here, we present the molecular profiles of 560 Asian breast tumours and a comparative analysis of breast cancers arising in Asian and Caucasian women. Compared to the breast tumours in predominantly Caucasian women reported in TCGA and METABRIC, we show an increased prevalence of Her2-enriched molecular subtypes and higher prevalence ofTP53somatic mutations in ER+ Asian breast tumours. Using gene expression and immunohistochemistry, we observed elevated immune scores in Asian breast tumours, suggesting potential clinical response to immune checkpoint inhibitors. Whilst Her2-subtype and enriched immune score are associated with improved survival, presence ofTP53somatic mutations is associated with poorer survival in ER+ tumours. Taken together, these population differences unveil new opportunities to improve the understanding of this disease and lay the foundation for precision medicine in different populations.
A smartphone microscope method for simultaneous detection of (oo)cyst ofCryptosporodiumandGiardia
Authors: Shrestha Retina , Duwal Rojina , Wagle Sajeev , Pokhrel Samiksha , Giri Basant , Neupane Bhanu Bhakta
Published: April 2020

Gastrointestinal disorders caused by ingestion of (oo)cysts ofCryptosporodiumandGiardiais one of the major health problems in developing countries. We developed a smartphone based microscopic assay method to screen (oo)cysts ofCryptosporodiumandGiardiacontamination in vegetable and water samples. We used sapphire ball lens as the major imaging element to modify a smartphone as a microscope. Imaging parameters such as field of view and magnification, and image contrast under different staining and illumination conditions were measured. The smartphone microscope method consisting of ball lens of 1 mm diameter, white LED as illumination source and Lugols's iodine staining provided magnification and contrast capable of distinguishing (oo)cysts ofCrypstopsporodiumandGiardiain the same sample. The analytical performance of the method was tested by spike recovery experiments. The spiking recovery experiments performed on cabbage, carrot, cucumber, radish, tomatoes, and water resulted 26.8±10.3, 40.1 ± 8.5, 44.4±7.3, 47.6±11.3, 49.2 ±10.9, and 30.2±7.9% recovery forCryptosporodium, respectively and 10.2±4.0, 14.1±7.3, 24.2±12.1, 23.2±13.7, 17.1±13.9, and 37.6±2.4% recovery for , respectively. These recovery results were found to be similar when compared with the commercial brightfield and fluorescence microscopes. We tested the smartphone microscope system for detecting (oo)cysts on 7 types of vegetable (n=196) and river water (n=18) samples. Forty two percent vegetable and thirty-nine percent water samples were found to be contaminated withCryptosporodiumoocyst. Similarly, thirty one percent vegetable and thirty three percent water samples were contaminated withGiardiacyst. This study showed that the developed method can be a cheaper alternative for simultaneous detection of (oo)cysts in vegetable and water samples.
Improved synthetic lipidation-based protein translocation system for SNAP-tag fusion proteins
Authors: Yoshii Tatsuyuki , Tahara Kai , Suzuki Sachio , Hatano Yuka , Kuwata Keiko , Tsukiji Shinya
Published: April 2020

The ability to artificially attach lipids to specific intracellular protein targets would be a valuable approach for controlling protein localization and function in cells. We recently devised a chemogenetic method in which a SNAP-tag fusion protein can be translocated from the cytoplasm to the plasma membrane by post-translationally and covalently conjugating a synthetic lipopeptide in cells. However, the first-generation system lacked general applicability. Herein, we present an improved synthetic lipidation system that enables efficient plasma membrane translocation of SNAP-tag fusion proteins in cells. This second-generation system is now applicable to the control of various cell-signaling molecules, offering a new and useful research tool in chemical biology and synthetic biology.
Differential protein phosphorylation affects the localisation of two secretedToxoplasmaproteins and is widespread during stage conversion
Authors: Young Joanna , Broncel Malgorzata , Teague Helena , Russell Matt , McGovern Olivia , Renshaw Matt , Frith David , Snijders Bram , Collinson Lucy , Carruthers Vern , Ewald Sarah , Treeck Moritz
Published: April 2020

The intracellular parasiteToxoplasma gondiiresides within a membrane bound parasitophorous vacuole (PV) and secretes an array of proteins to establish this replicative niche. It has been shown previously thatToxoplasmaboth secretes kinases and that numerous proteins are phosphorylated after secretion. Here we assess the role of phosphorylation of SFP1 and the related GRA29, two secreted proteins with unknown function. We show that both proteins form stranded structures in the PV that are independent of the previously described intravacuolar network or actin. GRA29 likely acts as a seed for SFP1 strand formation, and these structures can form independently of otherToxoplasmasecreted proteins. We show that an unstructured region at the C-terminus of SFP1 and GRA29 is required for the formation of strands and that mimicking phosphorylation of this domain negatively regulates strand development. When tachyzoites convert to chronic stage bradyzoites, both proteins show a dispersed localisation throughout the cyst matrix. Many secreted proteins are reported to dynamically redistribute as the cyst forms and secreted kinases are known to play a role in cyst formation. Using quantitative phosphoproteome and proteome analysis comparing tachyzoite and early bradyzoite stages, we reveal widespread differential phosphorylation of secreted proteins. These data support a model in which secreted kinases and phosphatases are important to dynamically regulate parasite secreted proteins during stage conversion.

IMPORTANCE

Toxoplasma gondiiis a common parasite that infects up to one third of the human population. Initially the parasite grows rapidly, infecting and destroying cells of the host, but subsequently switches to a slow-growing form and establishes chronic infection. In both stages the parasite lives within a membrane bound vacuole within the host cell, but in the chronic stage a durable cyst wall is synthesized that provides protection to the parasite during transmission to a new host.Toxoplasmasecretes proteins into the vacuole to build its replicative niche and previous studies identified many of these proteins as phosphorylated. We investigate two secreted proteins and show that phosphorylation plays an important role in their regulation. We also observed widespread phosphorylation of secreted proteins when parasites convert from acute to chronic stages, providing new insight into how the cyst wall may be dynamically regulated.
Know Your Epidemic, Know Your Response: Covid-19 in the United States
Authors: Ciancio Alberto , Kämpfen Fabrice , Kohler Iliana V. , Bennett Daniel , de Bruin Wändi Bruine , Darling Jill , Kapteyn Arie , Maurer Jürgen , Kohler Hans-Peter
Published: April 2020

We document that during the week of March 10–16, the Covid-19 pandemic fundamentally affected the perceptions of U.S. residents about the health risks and socioeconomic consequences entailed by the pandemic. During this week, it seems, “everything changed.” Not only did the pandemic progress rapidly across the United States, but U.S. residents started to realize that the threat was real: increasing Covid-19 caseloads heightened perceptions of infection risks and excess mortality risks, concerns about the economic implications increased substantially, and behavioral responses became widespread as the pandemic expanded rapidly in the U.S. In early to mid-March 2020, average perceptions about the coronavirus infection risks are broadly consistent with projections about the pandemic, while expectations about dying conditional on infection and expectations about Covid-19-related excess mortality during the next months are possibly too pessimistic. However, some aspects of Covid-19 perceptions are disconcerting from the perspective of implementing and sustaining an effective societal response to the pandemic. For instance, the education gradient in expected infection risks entails the possibility of having different perceptions of the reality of the pandemic between people with and without a college education, potentially resulting in two different levels of behavioral and policy-responses across individuals and regions. Unless addressed by effective health communication that reaches individuals across all social strata, some of the misperceptions about Covid-19 epidemic raise concerns about the ability of the United States to implement and sustain the widespread and harsh policies that are required to curtail the pandemic. Our analyses also reveal perceptions of becoming infected with the virus, and dying from Covid-19, were driven upwards by a rapidly increasing national caseload, and perceptions of the economic consequences and the adaptation of social distancing were affected by both national and state-level cases.
Characterization of Oral bacteriome dysbiosis in type 2 diabetic patients
Authors: Kori Junaid Ahmed , Saleem Faizan , Ullah Saeed , Azim M. Kamran
Published: April 2020

We aimed to characterize the relationship of the oral microbiome with diabetes in Pakistan. Saliva samples were collected from diabetic patients (n = 49) and healthy individuals (n = 55). 16S metagenomics saliva was carried out by NGS technology. We observed that the phylum Firmicutes (p-value = 0.024 at 95% confidence interval) was significantly more abundant among diabetic patients than among the controls. We found that the abundance of phylum Actinobacteria did not significantly vary among both groups in contrast to a similar report from the USA (Long et al., 2017). On genus level, acidogenic bacteria Prevotella (p-value = 0.024) and Leptotrichia (p-value = 1.5 × 10−3); and aciduric bacteria Veillonella (p-value = 0.013) were found to be in higher abundance in diabetic patients. These bacteria are found in dental biofilm and involved in the metabolism of fermentable carbohydrates. Stratified analysis by gender revealed healthy and diabetic females to be more divergent. Abundance of Prevotella (p-value = 4.4 × 10-3) and Leptotrichia (p-value = 0.015) was significantly associated with male patients. A comparison of oral bacteriome between two groups revealed the dominance of acidogenic and aciduric bacteria in diabetics which suggested the involvement of these eubacteria in oral dysbacteriosis in diabetes mellitus.
Population age structure only partially explains the large number of COVID-19 deaths at the oldest ages
Authors: Medford Anthony , Trias-Llimós Sergi
Published: April 2020

To date any attention paid to the age shape of COVID-19 deaths has been mostly in relation to attempts to understand the differences in case fatality rates between countries. The aim of this paper is to explore differences in age distribution of deaths from COVID-19 among European countries which have old age structures. We do this by way of a cross-country comparison and put forward some reasons for potential differences.
Classification of COVID-19 in intensive care patients: towards rational and effective triage
Authors: Lu Xiaofan , Wang Yang , Chen Taige , Li Yongsheng , Wang Jun , Yan Fangrong
Published: April 2020

The number of pertinent researches of COVID-19 has increased rapidly but they mainly focused on the description of general information of patients with confirmed infection. We aimed to bridge the gap between disease classification and clinical outcome in intensive care patients, data of which are scarce and such classification could help in individual evaluation and provide effective triage for treatment and management. Specifically, we collected and filtered out 151 intensive care patients with complete medical records from Tongji hospital in Wuhan, China. We constructed a fully Bayesian latent variable model for integrative clustering of six data categories, including demographic information, symptoms, original comorbidities, vital signs, blood routine tests and inflammatory marker measurements. We identified four prognostic types of COVID-19 in intensive care patients, presenting a stepwise distribution in age, respiratory condition and inflammatory markers, suggesting the prognostic efficacy of these indicators. This report, to our knowledge, is the first attempt of dealing with classification of COVID-19 in intensive care patients. We acknowledge the limitation of ignoring the effect of treatment, but we believe such classification is enlightening for better triage, allowing for a more rational allocation of scarce medical resources in a resource constrained environment.
AutoTriage - An Open Source Edge Computing Raspberry Pi-based Clinical Screening System
Authors: Hegde Chaitra , Jiang Zifan , Suresha Pradyumna Byappanahalli , Zelko Jacob , Seyedi Salman , Smith Monique A. , Wright David W. , Kamaleswaran Rishikesan , Reyna Matt A. , Clifford Gari D.
Published: April 2020

With the recent COVID-19 pandemic, healthcare systems all over the world are struggling to manage the massive increase in emergency department (ED) visits. This has put an enormous demand on medical professionals. Increased wait times in the ED increases the risk of infection transmission. In this work we present an open-source, low cost, off-body system to assist in the automatic triage of patients in the ED based on widely available hardware. The system initially focuses on two symptoms of the infection fever and cyanosis. The use of visible and far-infrared cameras allows for rapid assessment at a 1m distance, thus reducing the load on medical staff and lowering the risk of spreading the infection within hospitals. Its utility can be extended to a general clinical setting in non-emergency times as well to reduce wait time, channel the time and effort of healthcare professionals to more critical tasks and also prioritize severe cases.

Our system consists of a Raspberry Pi 4, a Google Coral USB accelerator, a Raspberry Pi Camera v2 and a FLIR Lepton 3.5 Radiometry Long-Wave Infrared Camera with an associated IO module. Algorithms running in real-time detect the presence and body parts of individual(s) in view, and segments out the forehead and lip regions using PoseNet. The temperature of the forehead-eye area is estimated from the infrared camera image and cyanosis is assessed from the image of the lips in the visible spectrum. In our preliminary experiments, an accuracy of 97% was achieved for detecting fever and 77% for the detection of cyanosis, with a sensitivity of 91% and area under the receiver operating characteristic curve of 0.91. Heart rate and respiratory effort are also estimated from the visible camera.

Although preliminary results are promising, we note that the entire system needs to be optimized before use and assessed for efficacy. The use of low-cost instrumentation will not produce temperature readings and identification of cyanosis that is acceptable in many situations. For this reason, we are releasing the full code stack and system design to allow others to rapidly iterate and improve the system. This may be of particular benefit in low-resource settings, and low-to-middle income countries in particular, which are just beginning to be affected by COVID-19.
A new tool for 3D segmentation of computed tomography data:Drishti Paintand its applications
Authors: Hu Yuzhi , Limaye Ajay , Lu Jing
Published: April 2020

Computational tomography is more and more widely used in many fields for its non-destructive and high-resolution in detecting internal structures of the samples. 3D segmentation of computed tomography data, which sheds light into internal features of target objects, is increasingly gaining in importance. However, how to efficiently and precisely reconstruct computed tomography data and better represent the data remains a hassle. Here, using a set of scan data of a fossil fish as a case study, we present a new release of open-source volume exploration, rendering, and 3D segmentation software,Drishtiv2.6.6, and its protocol for performing 3D segmentation and other advanced applications. We provide new toolsets and workflow to segment computed tomography data thus benefit the scientific community with more accurate and precise digital reconstruction, 3D modelling and 3D printing results. Our procedure is widely applicable not only in palaeontology, but also in biological, medical, and industrial researches, and can be used as a framework to segment computed tomography and other forms of volumetric data from any research field.
Daily mitochondrial dynamics in cone photoreceptors
Authors: Giarmarco Michelle Marie , Brock Daniel C , Robbings Brian M , Cleghorn Whitney M , Tsantilas Kristine A , Kuch Kellie C , Ge William , Rutter Kaitlyn M , Parker Edward D , Brockerhoff Susan E
Published: April 2020

Cone photoreceptors in the retina are exposed to intense daylight, and have higher energy demands in darkness. Cones produce energy using a large cluster of mitochondria. Mitochondria are susceptible to oxidative damage, and healthy mitochondrial populations are maintained by regular turnover. Daily cycles of light exposure and energy consumption suggest that mitochondrial turnover is important for cone health. We investigated the 3-D ultrastructure and metabolic function of zebrafish cone mitochondria throughout the day. At night cones undergo a mitochondrial biogenesis event, corresponding to an increase in the number of smaller, simpler mitochondria and increased metabolic activity. In the daytime, ER and autophagosomes associate more with mitochondria, and mitochondrial size distribution across the cluster changes. We also report dense material shared between cone mitochondria that is extruded from the cell in darkness, sometimes forming extracellular structures. Our findings reveal an elaborate set of daily changes to cone mitochondrial structure and function.
Potential host range of multiple SARS-like coronaviruses and an improved ACE2-Fc variant that is potent against both SARS-CoV-2 and SARS-CoV-1
Authors: Li Yujun , Wang Haimin , Tang Xiaojuan , Ma Danting , Du Chengzhi , Wang Yifei , Pan Hong , Zou Qing , Zheng Jie , Xu Liangde , Farzan Michael , Zhong Guocai
Published: April 2020

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a currently uncontrolled pandemic and the etiological agent of coronavirus disease 2019 (COVID-19). It is important to study the host range of SARS-CoV-2 because some domestic species might harbor the virus and transmit it back to humans. In addition, insight into the ability of SARS-CoV-2 and SARS-like viruses to utilize animal orthologs of the SARS-CoV-2 receptor ACE2 might provide structural insight into improving ACE2-based viral entry inhibitors. Here we show that ACE2 orthologs of a wide range of domestic and wild animals support entry of SARS-CoV-2, as well as that of SARS-CoV-1, bat coronavirus RaTG13, and a coronavirus isolated from pangolins. Some of these species, including camels, cattle, horses, goats, sheep, pigs, cats, and rabbits may serve as potential intermediate hosts for new human transmission, and rabbits in particular may serve as a useful experimental model of COVID-19. We show that SARS-CoV-2 and SARS-CoV-1 entry could be potently blocked by recombinant IgG Fc-fusion proteins of viral spike protein receptor-binding domains (RBD-Fc) and soluble ACE2 (ACE2-Fc). Moreover, an ACE2-Fc variant, which carries a D30E mutation and has ACE2 truncated at its residue 740 but not 615, outperforms all the other ACE2-Fc variants on blocking entry of both viruses. Our data suggest that RBD-Fc and ACE2-Fc could be used to treat and prevent infection of SARS-CoV-2 and any new viral variants that emerge over the course of the pandemic.
Towards a probiotic approach for building plumbing – nutrient-based selection during initial biofilm formation on flexible polymeric materials
Authors: Lisa Neu , Laura Cossu , Hammes Frederik
Published: April 2020

Upon entering building plumbing systems, drinking water bacteria experience considerable changes in environmental conditions. For example, some flexible polymeric materials leach organic carbon, which increases bacterial growth and reduces diversity. Here we show that the carbon supply by a flexible polymeric material drives nutrient-based selection within establishing biofilm communities. We found that migrating carbon from EPDM coupons resulted in considerable growth for different drinking water communities (0.2 – 3.3 × 108cells/cm2). All established biofilm communities showed low diversity (29 – 50 taxa/biofilm), with communities dominated by even viewer taxa (e.g., 5 taxa accounting for 94 ± 5 % relative abundance, n = 15). Interestingly, biofilm communities shared some taxa (e.g.,Methylobacteriumspp.) and families (e.g., Comamonadaceae), despite the difference in starting communities. Moreover, selected biofilm communities performed better than their original communities regarding maximum attachment (91 ± 5 vs. 69 ± 23 %, n = 15) and attachment rate (5.0 ± 1.7 × 104vs. 2.4 ± 1.2 × 104cells/cm2/h, n = 15) when exposed to new EPDM coupons. Our results demonstrate nutrient-based selection during initial biofilm formation on a flexible polymeric material and a resulting benefit to selected communities. We anticipate our findings to help connecting observational microbiological findings with their underlying ecological principles. Regarding initial biofilm formation, attachment dynamics, growth, and selection thereof are important for the management of microbial communities. In fact, managing initial colonization by supplying specific carbon and/or introducing consciously chosen/designed communities potentially paves the way for a probiotic approach for building plumbing materials.
Temporal patterns in electrical nerve stimulation: burst gap code shapes tactile frequency perception
Authors: Ng Kevin K. W. , Olausson Christoffer , Vickery Richard M. , Birznieks Ingvars
Published: April 2020

We have previously described a novel temporal encoding mechanism in the somatosensory system, where mechanical pulses grouped into periodic bursts create a perceived tactile frequency based on the duration of the silent gap between bursts, rather than the mean rate or the periodicity. This coding strategy may offer new opportunities for transmitting information to the brain using various sensory neural prostheses and haptic interfaces. However, it was not known whether the same coding mechanisms apply when using electrical stimulation, which recruits a different spectrum of afferents. Here, we demonstrate that the predictions of the burst gap coding model for frequency perception apply to burst stimuli delivered with electrical pulses, re-emphasising the importance of the temporal structure of spike patterns in neural processing and perception of tactile stimuli. Reciprocally, the electrical stimulation data confirm that the results observed with mechanical stimulation do indeed depend on neural processing mechanisms in the central nervous system, and are not due to skin mechanical factors and resulting patterns of afferent activation.
Development of fluorescence polarization-based competition assay for nicotinamideN-methyltransferase
Authors: Iyamu Iredia D. , Huang Rong
Published: April 2020

Methylation-mediated pathways play an important role in the progression of cancer. Inhibitors of several key methyltransferases including DNA methyltransferases and histone methyltransferases have proven to be instrumental for both understanding the function of the respective enzymes activites and translational applications in cancer epigenetic therapy. NicotinamideN-methyltransferase (NNMT) is a major metabolic enzyme involved in epigenetic regulation through catalysis of methyl transfer from the cofactorS-adenosyl-L-methionine, onto nicotinamide and other pyridines, to form S-adenosyl homocysteine and 1-methyl-nicotinamide or the corresponding pyridinium ions. Accumulating evidence infers that NNMT is a novel therapeutic target for a variety of diseases such as cancer, diabetes, obesity, cardiovascular and neurodegenerative diseases. Therefore, there is an urgent need to discover potent and specific inhibitors for NNMT. Herein, we reported the design and synthesis of a fluorescent probeII138, and established a fluorescence polarization (FP)-based competition assay for evaluation of NNMT inhibitors. Importantly, the unique feature of this FP competition assay is its capability to identify inhibitors that interfere with the interaction of the NNMT active site directly or allosterically. In addition, this assay performane is robust with a Z factor of 0.76, and applicable in high-throughput screening for inhibitors for NNMT.
Monolingual and bilingual infants rely on the same brain networks: Evidence from resting-state functional connectivity
Authors: Blanco Borja , Molnar Monika , Carreiras Manuel , Collins-Jones Liam H. , Vidal Ernesto , Cooper Robert J. , Caballero-Gaudes César
Published: April 2020

This study examines whether bilingual exposure has a profound effect on the functional organization of the developing human brain during infancy. Recent behavioural research attests that monolingual vs. bilingual experience affects cognitive and linguistic processes already during the first months of life. However, to what extent the intrinsic organization of the infant human brain adapts to monolingual vs. bilingual environments is unclear. We measured spontaneous hemodynamic brain activity using functional near-infrared spectroscopy (fNIRS) in a large cohort (N=99) of 4-month-old monolingual and bilingual infants. We implemented well-established analysis approaches of functional brain imaging that enabled us to reveal the functional organization of the infant brain in large-scale cortical networks, and to perform group-level comparisons (i.e., monolingual vs. bilingual groups) in a reliable manner. Our results revealed no differences between the intrinsic functional organization of the developing monolingual and bilingual infant brain at 4 months of age.
Host Adaptation PredisposesPseudomonas aeruginosato Type VI Secretion System-Mediated Predation by theBurkholderia cepaciaComplex
Authors: Perault Andrew I , Chandler Courtney E , Rasko David A , Ernst Robert K , Wolfgang Matthew C , Cotter Peggy A
Published: April 2020

Pseudomonas aeruginosa(Pa) andBurkholderia cepaciacomplex (Bcc) species are opportunistic lung pathogens of individuals with cystic fibrosis (CF). WhilePacan initiate long-term infections in younger CF patients, Bcc infections only arise in teenagers and adults. BothPaand Bcc use type VI secretion systems (T6SS) to mediate interbacterial competition. Here, we show thatPaisolates from teenage/adult CF patients, but not those from young CF patients, are outcompeted by the epidemic Bcc isolateBurkholderia cenocepaciastrain AU1054 (BcAU1054) in a T6SS-dependent manner. The genomes of susceptiblePaisolates harbor T6SS-abrogating mutations, the repair of which, in some cases, rendered the isolates resistant. Moreover, seven of eight Bcc strains outcompetedPastrains isolated from the same patients. Our findings suggest that certain mutations that arise asPaadapts to the CF lung abrogate T6SS activity, makingPaand its human host susceptible to potentially fatal Bcc superinfection.
Pioneer factor Foxa2 enables ligand-dependent activation of LXRα
Authors: Kain Jessica , Wei Xiaolong , Price Andrew J. , Woods Claire , Bochkis Irina M.
Published: April 2020

Type II nuclear hormone receptors, such as FXR, LXR, and PPAR, which function in glucose and lipid metabolism and serve as drug targets for metabolic diseases, are permanently positioned in the nucleus regardless of the ligand status. Ligand activation of these receptors is thought to occur by co-repressor/co-activator exchange, followed by initiation of transcription. However, recent genome-wide location analysis showed that LXRα and PPARα binding in the liver is largely ligand-dependent. We hypothesized that pioneer factor Foxa2 evicts nucleosomes to enable ligand-dependent receptor binding. We show that chromatin accessibility, LXRα occupancy, and LXRα-dependent gene expression upon ligand activation require Foxa2. Unexpectedly, Foxa2 occupancy is drastically increased when LXRα is bound by an agonist. Our results suggest that Foxa2 and LXRα bind DNA as an interdependent complex during ligand activation. Our model requiring pioneering activity for ligand activation challenges the existing co-factor exchange mechanism and expands current understanding of nuclear receptor biology, suggesting that chromatin accessibility needs to be considered in design of drugs targeting nuclear receptors.
Identification of Functional Noncoding RNA-encoded Proteins on Lipid Droplets
Authors: Huang Ting , Bamigbade Adekunle T. , Xu Shimeng , Deng Yaqin , Xie Kang , Ogunsade Ololade O. , Mirza Ahmed Hammad , Wang Jifeng , Liu Pingsheng , Zhang Shuyan
Published: April 2020

Over the past decade, great progress in sequencing technologies and computational biology has revealed that the majority of the mammalian genome considered to be noncoding is rich in functional elements able to produce proteins. Many RNA molecules, mis-annotated as noncoding, actually harbor small open reading frames that are predicted to code for proteins. Some of those proteins have been verified to play critical roles in multiple biological processes. The lipid droplet (LD) is a unique cellular organelle, conserved from bacteria to humans, and is closely associated with cellular lipid metabolism and metabolic disorders. No noncoding RNA-coded proteins have been identified on LDs. Here, for the first time, we searched the organelle for their presence. After the enrichment of small proteins of LDs isolated from myoblasts, we used mass spectrometry coupled with our lab made protein database to identify LD-associated noncoding RNA-encoded proteins (LDANPs). A total of 15 new proteins were identified. One of them was studied further and termed LDANP1. LDANP1 was localized on LDs by imaging, cell fractionation, and immunogold labeling. Like LD resident proteins, LDANP1 was degraded by the proteasome. Using the CRISPR/Cas9-mediated genome editing technique, the endogenous expression of LDANP1 was validated. The stable expression of LDANP1 suppressed the accumulation of triacylglycerol in oleic acid treated myoblasts and inhibited the rescue of palmitate-inhibited insulin sensitivity by oleic acid. In summary, we report for the first time that translatable, nominally noncoding RNA-derived proteins, which are new and cannot be identified using current research methods, were associated with LDs and that among these, LDANP1 modulated lipid metabolism and insulin sensitivity. The discovery of noncoding RNA-encoded proteins on LDs paves a new way for the research of LDs and lipid metabolism.
Morphological integration between seeds and seedlings ofHymenaea courbaril
Authors: Regnier Leonardo de Lima Pereira
Published: April 2020

Morphological integrations are unknown to forestry seeds. Understanding if seed measurements could predict its future seedlings features is a central question in seedling production.Hymenaea courbarilis an important species in this context and to the applied forestry. Thus, this study aimed to understand how some seedling features, could be related to the seed weight, and be affected by the population origin. The measurements consisted of seedling collar diameter, weight, protophilus area, central and lateral vein. Seed weight consistently varied between the populations in the study. Both populations had higher weight ranges than mentioned in the literature. There was no strong evidence that greater seed weight requires lesser time to germinate, conflicting with previous information. All the measurements presented enough shreds of evidence to be considered different when comparing the populations, except for the protophilus area and lateral vein length. All the studied measurements presented low correlation indexes to seed weight, except for seedling collar diameter, and seedling weight, which presented a moderate correlation. Protophilus elongation pattern was strongly associated with the leaf width when compared to midvein.
Immune factor of bacterial origin protects ticks against host skin microbes
Authors: Hayes Beth M. , Radkov Atanas D. , Yarza Fauna , Flores Sebastian , Kim Jungyun , Zhao Ziyi , Lexa Katrina W. , Marnin Liron , Biboy Jacob , Bowcut Victoria , Vollmer Waldemar , Pedra Joao H. F. , Chou Seemay
Published: April 2020

Hard ticks are blood-feeding arthropods that carry and transmit microbes to their vertebrate hosts1. Tick-borne disease cases have been on the rise over the last several decades, drawing much-needed attention to the molecular interplay between transmitted pathogens and their human hosts. However, far less is known about how ticks control their own microbes, which is critical for understanding how zoonotic transmission cycles persist. We previously found that ticks horizontally acquired an antimicrobial toxin gene from bacteria known asdomesticatedamidaseeffector 2(dae2)2. Here we show that this effector from the tick vectorIxodes scapularis(Dae2Is) has structurally and biochemically diverged from ancestral bacterial representatives, expanding its antibacterial targeting range to include host skin microbes. Disruption ofdae2Isincreases the burden of skin-associated staphylococci withinI. scapularisand adversely affects tick fitness, suggesting resistance of host microbes may be important for the parasitic blood-feeding lifestyle. In contrast, Dae2Ishas no intrinsic ability to killBorrelia burgdorferi, the tick-borne bacterium of Lyme disease. Our observations suggest that ticks have evolved to tolerate their own symbionts while resisting host skin commensals, which we discover are natural opportunistic pathogens of ticks. This work moves our understanding of vector biology beyond a human-centric view: just as tick commensals are pathogenic to humans, so too do our commensals pose a threat to ticks. These observations illuminate how a complex and mirrored set of interkingdom interactions between blood-feeding vectors, their hosts, and associated microbes can ultimately lead to disease.
Changes to the resistome ofPseudomonas aeruginosaclone ST308 associated with corneal infection over time
Authors: Khan Mahjabeen , Willcox Mark D P , Rice Scott A , Sharma Savitri , Stapleton Fiona
Published: April 2020

Objectives

This study compared the resistomes of isolates ofPseudomonas aeruginosaclone ST308 from 2018 and 1997 from India.

Methods

Two ocular clonal type ST308 isolates ofPseudomonas aeruginosa(198 and 219) isolated in 2018 and five historical isolates (31, 32, 33, 35 and 37) isolated in 1997 at the LV Prasad Eye Institute in India were analysed for their susceptibilities to ciprofloxacin, levofloxacin, gentamicin, tobramycin, piperacillin, imipenem, ceftazidime and polymyxin B. DNA was extracted using the DNeasy® Blood and Tissue. Paired-end library was prepared using Nextera XT DNA library preparation kit. Libraries were sequenced on Illumina® MiSeq bench top sequencer generating 300 bp paired-end reads. Spades v3.12.0 was used for assembly, Resfinder v3.1. for acquired resistance genes and Snippy V2 for variants calling. Integron finder v1.5.1 was used to identify the integrons present in the genomes.

Results

The recent isolate 219 was resistant to all tested antibiotics except polymyxin while isolate 198 was resistant to ciprofloxacin, levofloxacin, gentamicin and tobramycin. Among historical isolates five were resistant to gentamicin, tobramycin and ciprofloxacin, four were resistant to levofloxacin while two were resistant to polymyxin. Twenty-four acquired resistance genes were present in the 2018 isolates compared to 11 in the historical isolates. All isolates contained the following genes encoding for aminoglycosideaph(6)-Id,aph(3′)-lIb, aph(3″)-Ib), beta-lactam (blaPAO), tetracycline (tet(G)), fosfomycin(fosA), chloramphenicol (catB7), sulphonamide (sul1), quaternary ammonium (qacEdelta1)and fluoroquinolone (crpP)resistance. Isolate 198 possessedaph(3′)-VI,rmtD2, qnrVC1, blaOXA-488, blaPME-1, while 219 possessedaadA1, rmtB, aac(6′)-Ib-cr, blaTEM-1B, blaVIM-2, mph(E), mph(A), msr(E). In the isolate 219 genesblaTEM-1b,blaVIM-2,sul1,qnrvc1,rmtBandaadA1were carried on class 1 integron. While an incomplete class 1 integron was also found in isolate 198 which was located on the genome where genermtB,blaPME-1,qnrVC1andsul1genes were positioned. There were no notable differences in the number of single nucleotide polymorphisms, but recent isolates carried more insertions and deletions in their genes.

Conclusion

P. aeruginosaocular clonal isolates have changed over time, with strains acquiring genes and having more insertions and deletions in their chromosomal genes that confirm resistance to antibiotics.

Highlights

Recent clonal ocular isolates ofPseudomonas aeruginosafrom India have acquired a number of resistance genes compared to historical clones

Consequently, resistance to antibiotics particularly fluoroquinolones in recent clones ofP. aeruginosaappears to have increased.

The acquired resistance genes found in the recentP. aeruginosaisolates were related to mobile genetic elements.
Homologous protein domains in SARS-CoV-2 and measles, mumps and rubella viruses: preliminary evidence that MMR vaccine might provide protection against COVID-19
Authors: Young Adam , Neumann Bjoern , Mendez Rocio Fernandez , Reyahi Amir , Joannides Alexis , Modis Yorgo , Franklin Robin JM
Published: April 2020

The COVID-19 disease is one of worst pandemics to sweep the globe in recent times. It is noteworthy that the disease has its greatest impact on the elderly. Herein, we investigated the potential of childhood vaccination, specifically against measles, mumps and rubella (MMR), to identify if this could potentially confer acquired protection over SARS-CoV-2. We identified sequence homology between the fusion proteins of SARS-CoV-2 and measles and mumps viruses. Moreover, we also identified a 29% amino acid sequence homology between the Macro (ADP-ribose-1’’-phosphatase) domains of SARS-CoV-2 and rubella virus. The rubella Macro domain has surface-exposed conserved residues and is present in the attenuated rubella virus in MMR. Hence, we hypothesize that MMR could protect against poor outcome in COVID-19 infection. As an initial test of this hypothesis, we identified that 1) age groups that most likely lack of MMR vaccine-induced immunity had the poorest outcome in COVID-19, and 2) COVID-19 disease burden correlates with rubella antibody titres, potentially induced by SARS-CoV2 homologous sequences. We therefore propose that vaccination of ‘at risk’ age groups with an MMR vaccination merits further consideration as a time appropriate and safe intervention.
Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
Authors: Barré Benjamin P. , Hallin Johan , Yue Jia-Xing , Persson Karl , Mikhalev Ekaterina , Irizar Agurtzane , Holt Sylvester , Thompson Dawn , Molin Mikael , Warringer Jonas , Liti Gianni
Published: April 2020

Aging varies among individuals due to both genetics and environment, but the underlying molecular mechanisms remain largely unknown. Using a highly recombined Saccharomyces cerevisiae population, we found 30 distinct quantitative trait loci (QTLs) that control chronological life span (CLS) in calorie-rich and calorie-restricted environments and under rapamycin exposure. Calorie restriction and rapamycin extended life span in virtually all genotypes but through different genetic variants. We tracked the two major QTLs to the cell wall glycoprotein genes FLO11 and HPF1. We found that massive expansion of intragenic tandem repeats within the N-terminal domain of HPF1 was sufficient to cause pronounced life span shortening. Life span impairment by HPF1 was buffered by rapamycin but not by calorie restriction. The HPF1 repeat expansion shifted yeast cells from a sedentary to a buoyant state, thereby increasing their exposure to surrounding oxygen. The higher oxygenation altered methionine, lipid, and purine metabolism, and inhibited quiescence, which explains the life span shortening. We conclude that fast-evolving intragenic repeat expansions can fundamentally change the relationship between cells and their environment with profound effects on cellular lifestyle and longevity.
Functional Features of TREHALOSE-6-PHOSPHATE SYNTHASE1, an Essential Enzyme in Arabidopsis[OPEN]
Authors: Fichtner Franziska , Olas Justyna J. , Feil Regina , Watanabe Mutsumi , Krause Ursula , Hoefgen Rainer , Stitt Mark , Lunn John E.
Published: April 2020

In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.