bluuebunny/crossref_metadata_2025 huggingface dataset:
A Diagnostic Approach to the Identification of Burkitt-like Lymphoma With 11q Aberration in Aggressive B-Cell Lymphomas
Authors: Horn Heike , Kalmbach Sabrina , Wagener Rabea , Staiger Annette M. , Hüttl Katrin , Mottok Anja , Bens Susanne , Traverse-Glehen Alexandra , Fontaine Juliette , Siebert Reiner , Rosenwald Andreas , Ott German
Published: November 2020

Rare cases of aggressive B-cell lymphomas with a morphology similar to Burkitt lymphoma (BL) present with the BL-typical immunophenotype, but lacked MYC translocation (MYC-negative Burkitt-like lymphoma: mnBLL). A proportion of those with an imbalance pattern in chromosome 11q has been designated Burkitt-like lymphoma with 11q aberration in the recent update of the World Health Organization (WHO) classification. Because of the problems in the identification of Burkitt-like lymphoma with 11q aberration, our goal was to retrospectively analyze their frequency in a cohort of “candidate” aggressive lymphomas (cohort 1, n=35) such as mnBLL (n=16), diffuse large B-cell lymphoma with similarities to Burkitt lymphoma (DLBCL-BL; n=3), high-grade B-cell lymphomas, not otherwise specified (NOS) (n=16), as well as in a cohort of MYC-negative diffuse large B-cell lymphoma NOS (cohort 2, n=62). In total, 17/33 cohort 1 cases (52%) harbored the typical 11q aberration pattern, predominantly those that had been classified as mnBLL (12/16, 75%), but also as DLBCL-BL (2/3, 67%) and high-grade B-cell lymphomas, NOS (3/14; 21%). The specimens with this typical 11q aberration pattern were usually negative for the BCL2 protein. Of interest and as a new finding, samples harboring the 11q aberration pattern were often characterized by strikingly coarse apoptotic debris within starry sky macrophages facilitating their recognition. In contrast, only 1 of 62 garden variety DLBCL, NOS was positive for the 11q aberration pattern. In 2 DLBCL-BL, a dual MYC translocation/11q aberration pattern was detected. As a diagnostic algorithm, we, therefore, propose analysis of 11q status in MYC-negative high-grade lymphomas with features of BL, especially showing BCL2 negativity and a conspicuous coarse apoptotic debris in starry sky macrophages.
Sinonasal Chondrosarcoma Presenting With Isolated Severe Vision Loss
Authors: Nguyen Michael T. B. , Farahvash Armin , Dickson Brendan C. , Lee John M. , Cusimano Michael D. , Tsang Derek S. , Micieli Jonathan A.
Published: November 2020

A 24-year-old man presented with a 2-month history of progressive, painless vision loss in the right eye, with no history of headache, nasal congestion, rhinorrhea, or epistaxis. His visual acuity was counting fingers at 1 ft in the right eye and 20 of 20 in the left eye with a right relative afferent pupillary defect and mild temporal optic disc pallor. MRI of the brain and orbits showed a mass involving bilateral ethmoid and sphenoid sinuses and right nasal cavity. He underwent urgent extended endoscopic endonasal transsphenoidal approach for resection of the sinonasal skull base tumor and photon radiation therapy. Pathology revealed a well-differentiated cartilaginous neoplasm with focal areas of entrapped native bone, consistent with a chondrosarcoma WHO grade I/III. At 6-month follow-up after surgery, he had a visual acuity of 20/40 in the right eye and 20/20 in the left eye. Malignant tumors from the sinonasal area should be kept in the differential diagnosis for compressive optic neuropathies and may present with vision loss even in the absence of nasal or sinus symptoms.
Retinal Microvascular Alterations as the Biomarkers for Alzheimer Disease: Are We There Yet?
Authors: Jiang Hong , Wang Jianhua , Levin Bonnie E. , Baumel Bernard S. , Camargo Christian J. , Signorile Joseph F. , Rundek Tania
Published: November 2020

Background:

Alzheimer disease (AD) is a heterogeneous and multifactorial disorder with an insidious onset and slowly progressive disease course. To date, there are no effective treatments, but biomarkers for early diagnosis and monitoring of disease progression offer a promising first step in developing and testing potential interventions. Cerebral vascular imaging biomarkers to assess the contributions of vascular dysfunction to AD are strongly recommended to be integrated into the current amyloid-β (Aβ) [A], tau [T], and neurodegeneration [(N)]—the “AT(N)” biomarker system for clinical research. However, the methodology is expensive and often requires invasive procedures to document cerebral vascular dysfunction. The retina has been used as a surrogate to study cerebral vascular changes. There is growing interest in the identification of retinal microvascular changes as a safe, easily accessible, low cost, and time-efficient approach to enhancing our understanding of the vascular pathogenesis associated with AD.

Evidence acquisition:

A systemic review of the literature was performed regarding retinal vascular changes in AD and its prodromal stages, focusing on functional and structural changes of large retinal vessels (vessels visible on fundus photographs) and microvasculature (precapillary arterioles, capillary, and postcapillary venules) that are invisible on fundus photographs.

Results:

Static and dynamic retinal microvascular alterations such as retinal arterial wall motion, blood flow rate, and microvascular network density were reported in AD, mild cognitive impairment, and even in the preclinical stages of the disease. The data are somewhat controversial and inconsistent among the articles reviewed and were obtained based on cross-sectional studies that used different patient cohorts, equipment, techniques, and analysis methods.

Conclusions:

Retinal microvascular alterations exist across the AD spectrum. Further large scale, within-subject longitudinal studies using standardized imaging and analytical methods may advance our knowledge concerning vascular contributions to the pathogenesis of AD.
A retrospective study evaluating efficacy and safety of compassionate use of tocilizumab in 13 patients with severe-to-critically ill COVID-19: analysis of well-responding cases and rapidly-worsening cases after tocilizumab administration
Authors: Hashimoto Shoji , Kitajima Heita , Arai Tsuyoshi , Tamura Yoshitaka , Nagai Takayuki , Morishita Hiroshi , Matsuoka Hiroto , Han Yuki , Minamoto Seijiro , Hirashima Tomonori , Yamada Tomoki , Kashiwa Yozo , Kameda Makoto , Yamaguchi Seiji , Uno Kazuko , Nakayama Emi , Shioda Tatsuo , Yoshizaki Kazuyuki , Kang Sujin , Kishimoto Tadamitsu , Tanaka Toshio
Published: November 2020

We administered tocilizumab into 13 severe-to-critically ill patients with coronavirus disease 2019 (COVID-19) for compassionate use in combination with potential anti-viral agents in those who required an oxygen supply and showed increased laboratory inflammatory markers such as C-reactive protein (CRP) and ferritin. One injection of tocilizumab led to rapid improvements in clinical features, inflammatory findings, and oxygen supply in seven patients with severe COVID-19 and substantial amelioration in two patients who were critically ill, whereas four patients, who exhibited rapidly worsened respiratory function, required artificial ventilatory support even after tocilizumab treatment. Three of these four patients ultimately recovered from deterioration after methylprednisolone treatment. Administration of tocilizumab did not affect viral elimination nor IgG production specific for the virus. Compared with well-responding patients, rapidly-worsened patients showed a significantly higher ratio of ferritin vs. CRP. These findings suggest that tocilizumab has beneficial effects in severe-to-critically ill patients with COVID-19; however, in some cases, addition of methylprednisolone is required for disease rescue.
rawR - Direct access to raw mass spectrometry data in R
Authors: Kockmann Tobias , Panse Christian
Published: November 2020

The Bioconductor project has shown that theRstatistical environment is a highly valuable tool for genomics data analysis1, but with respect to proteomics we are still missing low level infrastructure to enable performant and robust analysis workflows inR. Fundamentally important are libraries that provide raw data access. OurRpackagerawDiaghas provided the proof-of-principle how access to mass spectromerty raw files can be realized by wrapping vendor-provided APIs, but rather focused on meta data analysis and visualization2. Our novel packagerawRnow provides complete, OS independent access to all spectral data logged in Thermo Fisher Scientific raw files. In this technical note we present implementation details and describe the main functionality provided by therawRpackage. In addition, we report two use cases inspired by real-word research task that demonstrate the application of the package.

Availability

https://github.com/fgcz/rawR
CoDNaS-RNA: a database of Conformational Diversity in the Native State of RNA
Authors: Buitrón Martín González , Tunque Cahui Ronaldo Romario , Ríos Emilio García , Hirsh Layla , Fornasari María Silvina , Parisi Gustavo , Palopoli Nicolas
Published: November 2020

Conformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function.

We have developed CoDNaS-RNA as the first database of conformational diversity in RNA molecules. Known RNA structures are retrieved and clustered to identify alternative conformers of each molecule. Pairwise structural comparisons within each cluster allows to measure the variability of the molecule. Additional data on structural features, molecular interactions and functional annotations are provided. CoDNaS-RNA is implemented as a public resource that can be of much interest for computational and bench scientists alike.

Availability

CoDNaS-RNA is freely accessible athttp://ufq.unq.edu.ar/codnasrna

Contact

npalopoli@unq.edu.ar
An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins
Authors: Kumar Prateek , Kumar Amit , Garg Neha , Giri Rajanish
Published: November 2020

Intraviral protein-protein interactions are crucial for replication, pathogenicity, and viral assembly. Among these, virus assembly is a critical step as it regulates the arrangements of viral structural proteins and helps in the encapsulation of genomic material. SARS-CoV-2 structural proteins play an essential role in the self-rearrangement, RNA encapsulation, and mature virus particle formation. In SARS-CoV, the membrane protein interacts with the envelope and spike protein in Endoplasmic Reticulum Golgi Intermediate Complex (ERGIC) to form an assembly in the lipid bilayer, followed by membrane-ribonucleoprotein (nucleocapsid) interaction. In this study, we tried to understand the interaction of membrane protein’s interaction with envelope, spike, and nucleocapsid proteins using protein-protein docking. Further, simulation studies performed up to 100 ns to examine the stability of protein-protein complexes of Membrane-Envelope, Membrane-Spike, and Membrane-Nucleocapsid. Prime MM-GBSA showed high binding energy calculations than the docked complex. The interactions identified in our study will be of great importance, as it provides valuable insight into the protein-protein complex, which could be the potential drug targets for future studies.
Differential alteration of plant functions by homologous fungal candidate effectors
Authors: dos Santos Karen Cristine Goncalves , Pelletier Gervais , Séguin Armand , Guillemette François , Hawkes Jeffrey , Desgagné-Penix Isabel , Germain Hugo
Published: November 2020

Rust fungi are plant pathogens that cause epidemics that threaten the production of important plant species, such as wheat, soy, coffee and poplar.Melampsora larici-populina(Mlp) causes the poplar rust and encodes at least 1 184 candidate effectors (CEs), however their functions are poorly known. In this study, we usedArabidopsisplants constitutively expressing CEs ofMlpto discover processes targeted by these fungal proteins. For this purpose, we sequenced the transcriptome and used mass spectrometry to analyse the metabolome ofArabidopsisplants expressing individually one of the 14 selected CEs and of a control line. We found 2 299 deregulated genes across the experiment. Among the down-regulated genes, the KEGG pathways “MAPK signaling pathway” and “Plant-pathogen interaction” were respectively over-represented in six and five of the 14 transgenic lines. Moreover, genes related to hormone response and defense were down-regulated across all transgenic lines are. We further observed that there were 680 metabolites deregulated in at least one CE-expressing transgenic line, with highly unsaturated and phenolic compounds enriched in up-regulated metabolites and peptides enriched among down-regulated metabolites. Interestingly, we found that transgenic lines expressing unrelated CEs had correlated patterns of gene and metabolite deregulation, while expression of CEs belonging to the same family deregulated different genes and metabolites. Taken together, our results indicate that the sequence of effectors and their belonging to families may not be a good predictor of their impact on the plant.

Importance

Rust fungi are plant pathogens that threaten the production of important crops, including wheat, soy, coffee and poplar. Effectors are used by pathogens to control the host, however in the case ofMelampsora larici-populina, the causal agent of the poplar rust, and other rust fungi these proteins are poorly known. We usedArabidopsisplants expressing candidate effectors (CEs) ofMlpto better understand the interaction between this pathogen and its hosts. We found that expression of unrelated CEs led to similar patterns of gene and metabolite deregulation, while transgenic lines expressing CEs belonging to the same family showed different groups of different genes and metabolites deregulated. Thus, our results suggest that functional annotation of effectors based on sequence similarity may be misleading.
Adenomatous Polyposis Coli Loss Controls Cell Cycle Regulators and Response to Paclitaxel
Authors: Astarita Emily M. , Hoover Camden A. , Maloney Sara M. , Nair T. Murlidharan , Prosperi Jenifer R.
Published: November 2020

Adenomatous Polyposis Coli (APC) is lost in approximately 70% of sporadic breast cancers, with an inclination towards triple negative breast cancer (TNBC). TNBC is treated with traditional chemotherapy, such as paclitaxel (PTX); however, tumors often develop drug resistance. We previously created APC knockdown cells (APC shRNA1) using the human TNBC cells, MDA-MB-157, and showed that APC loss induces PTX resistance. To understand the mechanisms behind APC-mediated PTX response, we performed cell cycle analysis and analyzed cell cycle related proteins. Cell cycle analysis indicated increased G2/M population in PTX-treated APC shRNA1 cells compared to PTX-treated controls, suggesting that APC expression does not alter PTX-induced G2/M arrest. We further studied the subcellular localization of the G2/M transition proteins, cyclin B1 and CDK1. The APC shRNA1 cells had increased CDK1, which was preferentially localized to the cytoplasm, and increased CDK6. RNA-sequencing was performed to gain a global understanding of changes downstream of APC loss and identified a broad mis-regulation of cell cycle-related genes in APC shRNA1 cells. Our studies are the first to show an interaction between APC and taxane response in breast cancer. The implications include designing combination therapy to re-sensitize APC-mutant breast cancers to taxanes using the specific cell cycle alterations.
Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations
Authors: Miersch Shane , Li Zhijie , Saberianfar Reza , Ustav Mart , Case James Brett , Blazer Levi , Chen Chao , Ye Wei , Pavlenco Alevtina , Gorelik Maryna , Perez Julia Garcia , Subramania Suryasree , Singh Serena , Ploder Lynda , Ganaie Safder , Chen Rita E. , Leung Daisy W. , Pandolfi Pier Paolo , Novelli Giuseppe , Matusali Giulia , Colavita Francesca , Capobianchi Maria R. , Jain Suresh , Gupta J.B. , Amarasinghe Gaya K. , Diamond Michael S. , Rini James , Sidhu Sachdev S.
Published: November 2020

Neutralizing antibodies (nAbs) hold promise as effective therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and its tetravalent versions can block entry with a potency that exceeds the bivalent nAbs by an order of magnitude. Structural studies show that both the bivalent and tetravalent nAbs can make multivalent interactions with a single S-protein trimer, observations consistent with the avidity and potency of these molecules. Significantly, we show that the tetravalent nAbs show much increased tolerance to potential virus escape mutants. Bivalent and tetravalent nAbs can be produced at large-scale and are as stable and specific as approved antibody drugs. Our results provide a general framework for developing potent antiviral therapies against COVID-19 and related viral threats, and our strategy can be readily applied to any antibody drug currently in development.
Anopheles coluzziiinfection by the microsporidian,Vavraia culicis: the effect of host age
Authors: Vyas-Patel Nayna
Published: November 2020

Host age at infection has important implications for disease development. In mosquitoes, infections with microsporidia and later concurrent infections with malaria parasites, leads to a suppression in the development of malaria parasites. Host age at infection with microsporidia could have implications for disease outcomes when infection occurs subsequently with malaria parasites. Mosquito larvae can take between five to seven days or more depending on the temperature to reach the adult stage, giving the microsporidianVavraia culicis, a theoretical head start in establishing and developing within larvae and possibly resulting in different levels of infection in emergent adult mosquitoes. To determine the effects of early or late infection withV. culicis, equal numbers ofAnopheles coluzziilarvae were infected individually with a high or low dose ofV. culicis, at different ages post hatching.

Significantly fewer spores were produced from mosquitoes infected later, than ones infected earlier with microsporidia and there was an initial delay in the production of spores from later infected mosquitoes. In early infected larvae, there was no such initial delay and spore production took off unchecked. The infectious dose ofV. culicisdid not affect the total spore count per mosquito. Male mosquitoes produced fewer spores than females. Daily mosquito longevity and pupation was not affected significantly by infection, the infectious dose ofV.culicisgiven or by the sex of the mosquito. Considering hourly deaths, early infected hosts died 17 to 18 hours earlier than later infected larvae. The number ofV. culicisspores rose with increasing duration of infection. When equal duration of infection was considered, the findings remained the same. Host age at infection influences disease outcomes and virulence.
A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium
Authors: Warwicker Jim
Published: November 2020

SARS-CoV-2, causative agent of the COVID-19 pandemic, is thought to release its RNA genome at either the cell surface or within endosomes, the balance being dependent on spike protein stability, and the complement of receptors, co-receptors and proteases. To investigate possible mediators of pH-dependence, pKa calculations have been made on a set of structures for spike protein ectodomain and fragments from SARS-CoV-2 and other coronaviruses. Dominating a heat map of the aggregated predictions, 3 histidine residues in S2 are consistently predicted as destabilising in pre-fusion (all 3) and post-fusion (2 of 3) structures. Other predicted features include the more moderate energetics of surface salt-bridge interactions, and sidechain-mainchain interactions. Two aspartic acid residues in partially buried salt-bridges (D290 – R273 and R355 – D398) have pKas that are calculated to be elevated and destabilising in more open forms of the spike trimer. These aspartic acids are most stabilised in a tightly closed conformation that has been observed when linoleic acid is bound, and which also affects the interactions of D614. The D614G mutation is known to modulate the balance of closed to open trimer. It is suggested that D398 in particular contributes to a pH-dependence of the open/closed equilibrium, potentially coupled to the effects of linoleic acid binding and D614G mutation, and possibly also A570D mutation. These observations are discussed in the context of SARS-CoV-2 infection, mutagenesis studies, and other human coronaviruses.
Priority effects alter interaction outcomes in a legume-rhizobium mutualism
Authors: Boyle Julia A. , Simonsen Anna K. , Frederickson Megan E. , Stinchcombe John R.
Published: November 2020

Priority effects occur when the order of species arrival affects final community structure. Mutualists often interact with multiple partners in different orders, but if or how priority effects alter interaction outcomes is an open question. In the field, we paired the legumeMedicago lupulinawith two nodulating strains ofEnsiferbacteria that vary in nitrogen-fixing ability. We inoculated plants with strains in different orders and measured interaction outcomes. The first strain to arrive primarily determined plant performance and final relative abundances of rhizobia on roots. Plants that received effective microbes first and ineffective microbes second grew larger than plants inoculated with the same microbes in opposite order. Our results show that mutualism outcomes can be influenced not just by partner identity, but by interaction order. Furthermore, hosts receiving high-quality mutualists early can better tolerate low-quality symbionts later, indicating priority effects may help explain the persistence of ineffective symbionts.
Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 Main Protease complexes reveal the role of a lateral pocket in enhancing the ligand affinity
Authors: Li Weng Ying , Naik Shiv Rakesh , Dingelstad Nadia , Kalyaanamoorthy Subha , Ganesan Aravindhan
Published: November 2020

The 2019 novel coronavirus pandemic caused by SARS-CoV-2 remains a serious health threat to humans and a number of countries are already in the middle of the second wave of infection. There is an urgent need to develop therapeutics against this deadly virus. Recent scientific evidences have suggested that the main protease (Mpro) enzyme in SARS-CoV-2 can be an ideal drug target due to its crucial role in the viral replication and transcription processes. Therefore, there are ongoing research efforts to identify drug candidates against SARS-CoV-2 Mpro that resulted in hundreds of X-ray crystal structures of ligand bound Mpro complexes in the protein data bank (PDB) that describe structural details of different chemotypes of fragments binding within different sites in Mpro. In this work, we perform rigorous molecular dynamics (MD) simulation of 62 reversible ligand-Mpro complexes in the PDB to gain mechanistic insights about their interactions at atomic level. Using a total of ~2.25 μs long MD trajectories, we identified and characterized different pockets and their conformational dynamics in the apo Mpro structure. Later, using the published PDB structures, we analyzed the dynamic interactions and binding affinity of small ligands within those pockets. Our results identified the key residues that stabilize the ligands in the catalytic sites and other pockets in Mpro. Our analyses unraveled the role of a lateral pocket in the catalytic site in Mpro that is critical for enhancing the ligand binding to the enzyme. We also highlighted the important contribution from HIS163 in this lateral pocket towards ligand binding and affinity against Mpro through computational mutation analyses. Further, we revealed the effects of explicit water molecules and Mpro dimerization in the ligand association with the target. Thus, comprehensive molecular level insights gained from this work can be useful to identify or design potent small molecule inhibitors against SARS-CoV-2 Mpro.
TMPRSS2 and ADAM17 interactions with ACE2 complexed with SARS-CoV-2 and B0AT1 putatively in intestine, cardiomyocytes, and kidney
Authors: Stevens Bruce R.
Published: November 2020

COVID-19 outcomes reflect organ-specific interplay of SARS-CoV-2 and its receptor, ACE2, with TMPRSS2 and ADAM17. Confirmed active tropism of SARS-CoV-2 in epithelial cells of intestine and kidney proximal tubule, and in aging cardiomyocytes, capriciously manifests extra-pulmonary organ-related clinical symptoms in about half of COVID-19 patients, occurring by poorly understood mechanisms. We approached this knowledge gap by recognizing a clue that these three particular cell types share a common denominator kindred of uniquely expressing the SLC6A19 neutral amino acid transporter B0AT1 protein (alternatively called NBB, B, B0) serving glutamine and tryptophan uptake. B0AT1 is a cellular trafficking chaperone partner of ACE2, shown by cryo-EM to form a thermodynamically-favored stabilized 2ACE2:2B0AT1 dimer-of-heterodimers. The gut is the body’s site of greatest magnitude expression depot of both ACE2 and B0AT1. This starkly contrasts with pulmonary pneumocyte expression of monomeric ACE2 with conspicuously undetectable B0AT1. We hypothesized that B0AT1 steers the organ-related interplay amongst ACE2, TMPRSS2, ADAM17, and SARS-CoV-2 RBD. The present study employed molecular docking modeling that indicated active site catalytic pocket residues of TMPRSS2 and ADAM17 each formed bonds ≤ 2 A with monomer ACE2 specific residues within a span R652-D713 involved in cleaving sACE2 soluble ectodomain release. These bonds are consistent with competitive binding interactions of experimental anti-SARS-CoV-2 drug small molecules including Camostat and Nafamostat. Without B0AT1, ACE2 residues K657 and N699 dominated docking bonding with TMPRSS2 or ADAM17 active sites, with ACE2 R710 and R709 contributing electrostatic attractions, but notably ACE2 S708 never closer than 16-44 A. However, in the dimer-of-heterodimers arrangement all ACE2 neck region residues were limited to TMPRSS2 or ADAM17 approaches 35 A, with the interference directly attributed to the presence of a neighboring B0AT1 subunit complexed to the partnering ACE2 subunit of 2ACE2:2B0AT1; ADAM17 failed to dock by bumping its active site pocket oriented dysfunctionally outwardly facing 1800away. Results were the same whether the dimer-of-heterodimers was in either the “closed” or “open” conformation, or whether or not SARS-CoV-2 RBD was complexed to ACE2. The results implicate B0AT1-and in particular the 2ACE2:2B0AT1 complex-as a maJor player in the landscape of COVID-19 pathophysiology engaging TMPRSS2 and ADAM17, consistent with experimental evidence in the literature and in clinical reports. These findings provide a gateway to understanding the roles of B0AT1 relating to COVID-19 manifestations putatively assigned to intestinal and renal epithelial cells and cardiomyocytes, with underpinnings useful for considerations in public hygiene policy and drug development.
Focus-tunable microscope for imaging small neuronal processes in freely moving animals
Authors: Bagramyan Arutyun , Tabourin Loïc , Rastqar Ali , Karimi Narges , Bretzner Frédéric , Galstian Tigran
Published: November 2020

Miniature 1-photon microscopes have been widely used to image neuronal assemblies in the brain of freely moving animals over the last decade. However, these systems have important limitations for imaging in-depth fine neuronal structures. We present a novel subcellular imaging 1-photon device that uses an electrically tunable liquid crystal lens to enable a motion-free depth scan in the search of such structures. Our miniaturized microscope is compact (10 mm × 17 mm × 12 mm), lightweight (≈ 1.4 g), provides fast acquisition rate (30-50 frames/second), high magnification (8.7x) and high resolution (1.4 μm) that allow imaging of calcium activity of fine neuronal processes in deep brain regions during a wide range of behavioural tasks of freely moving mice.
Inflect: Optimizing Computational Workflows for Thermal Proteome Profiling Data Analysis
Authors: McCracken Neil A. , Peck Justice Sarah A. , Wijeratne Aruna B. , Mosley Amber L.
Published: November 2020

The use of CETSA and Thermal Proteome Profiling (TPP) analytical methods are invaluable for the study of protein-ligand interactions and protein stability in a cellular context. These tools have increasingly been leveraged in work ranging from understanding signaling paradigms to drug discovery. Consequently, there is an important need to optimize the data analysis pipeline that is used to calculate protein melt temperatures (Tm) and relative melt shifts from proteomics abundance data. Here we report a user-friendly analysis of the melt shift calculation workflow where we describe the impact of each individual calculation step on the final output list of stabilized and destabilized proteins. This report also includes a description of how key steps in the analysis workflow quantitatively impacts the list of stabilized/destabilized proteins from an experiment. We applied our findings to develop a more optimized analysis workflow that illustrates the dramatic sensitivity of chosen calculation steps on the final list of reported proteins of interest in a study and will make the R based program Inflect available for research community use. Overall, this work provides an essential resource for scientists as they analyze data from TPP and CETSA experiments and implement their own analysis pipelines geared towards specific applications.
Discovery of new genetic determinants controlling the morphological plasticity in rice root and shoot under phosphate starvation using GWAS
Authors: Mai Nga T P , Mai Chung Duc , Van Nguyen Hiep , Le Khang Quoc , Duong Linh Viet , To Huong Thi Mai
Published: November 2020

Phosphorus is an essential nutrient for plants that is often in short supply. In rice (Oryza sativaL.), phosphate (Pi) deficiency leads to various physiological disorders that consequently affect plant productivity. In this study, a large-scale phenotyping experiment of a set of 160 Vietnamese rice landraces was performed under greenhouse conditions by employing an alpha lattice design with three replicates to identify quantitative trait loci (QTLs) associated with plant growth inhibition by Pi deficiency. Rice plantlets were grown for six weeks in the PVC sand column (16 cm diameter × 80 cm height) supplied with Pi-deficient (10 µM P) medium or full Pi Yoshida (320 µM P) medium. The effects of Pi deficiency on the number of crown roots, root length, shoot length, root weight, shoot weight and total weight were studied. From 36 significant markers identified by using Genome-wide association study, a total of 21 QTLs associated with plant growth inhibition under Pi starvation conditions were defined. A list of 158 candidate genes co-located with defined QTLs was found. Interestingly, a QTL namelyqRST9.14were detected found common across three weight-traits. The co-located geneGLYCEROPHOSPHODIESTER PHOSPHODIESTERASE 13was found potentially involved in Pi transport. Understanding the molecular mechanisms of Pi starvation responses, and identifying potential QTLs responsible for low-Pi stress tolerance will provide valuable information for developing new varieties tolerant to low-Pi conditions.
Uncovering the mesendoderm gene regulatory network through multi-omic data integration
Authors: Jansen Camden , Paraiso Kitt D. , Zhou Jeff J. , Blitz Ira L. , Fish Margaret B. , Charney Rebekah M. , Cho Jin Sun , Yasuoka Yuuri , Sudou Norihiro , Bright Ann Rose , Wlizla Marcin , Veenstra Gert Jan C. , Taira Masanori , Zorn Aaron M. , Mortazavi Ali , Cho Ken W.Y.
Published: November 2020

Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low-throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data comprised of more than two data types is challenging. Here, we use linked self-organizing maps to combine ChIP-seq/ATAC-seq with temporal, spatial and perturbation RNA-seq data fromXenopus tropicalismesendoderm development to build a high resolution genome scale mechanistic GRN. We recovered both known and previously unsuspected TF-DNA/TF-TF interactions and validated through reporter assays. Our analysis provides new insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly-dimensional multi-omic data sets.

Highlights

Built a generally applicable pipeline to creating GRNs using highly-dimensional multi-omic data sets

Predicted new TF-DNA/TF-TF interactions during mesendoderm development

Generate the first genome scale GRN for vertebrate mesendoderm and expanded the core mesendodermal developmental network with high fidelity

Developed a resource to visualize hundreds of RNA-seq and ChIP-seq data using 2D SOM metaclusters.
A New Comprehensive Catalog of the Human Virome Reveals Hidden Associations with Chronic Diseases
Authors: Tisza Michael J. , Buck Christopher B.
Published: November 2020

While there have been remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This is despite the fact that many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases and all of them encompass large amounts of viral sequences. The lack of a comprehensive database for human-associated viruses, along with inadequate methods for high-throughput identification of highly divergent viruses in metagenomic data, has historically stymied efforts to characterize virus sequences in a comprehensive way. In this study, a new high-specificity and high-sensitivity bioinformatic tool, Cenote-Taker 2, was applied to thousands of human metagenome datasets, uncovering over 50,000 unique virus operational taxonomic units. Publicly available case-control studies were re-analyzed, and over 1,700 strong virus-disease associations were found.
The Genetic Architecture of Larval Aggregation Behavior in Drosophila
Authors: McKinney Ross M , Ben-Shahar Yehuda
Published: November 2020

Many insect species exhibit basal social behaviors such as aggregation, which play important roles in their feeding and mating ecologies. However, the evolutionary, genetic, and physiological mechanisms that regulate insect aggregation remain unknown for most species. Here, we used natural populations of Drosophila melanogaster to identify the genetic architecture that drives larval aggregation feeding behavior. By using quantitative and reverse genetic approaches, we have identified a complex neurogenetic network that plays a role in regulating the decision of larvae to feed in either solitude or as a group. Results from single gene, RNAi-knockdown experiments show that several of the identified genes represent key nodes in the genetic network that determines the level of aggregation while feeding. Furthermore, we show that a single non-coding SNP in the gene CG14205, a putative acyltransferase, is associated with both decreased mRNA expression and increased aggregate formation, which suggests that it has a specific role in inhibiting aggregation behavior. Our results identify, for the first time, the genetic components which interact to regulate naturally occurring levels of aggregation in D. melanogaster larvae.
Sclerostin depletion induces inflammation in the bone marrow of mice
Authors: Donham Cristine , Chicana Betsabel , Robling Alexander , Mohamed Asmaa , Elizaldi Sonny , Chi Michael , Freeman Brian , Millan Alberto , Murguesh Deepa , Loots Gabriela G. , Manilay Jennifer O.
Published: November 2020

Romosozumab, a humanized monoclonal antibody specific for sclerostin, has been approved for treatment of post-menopausal women with osteoporosis at high risk for fracture. In several Phase III clinical trials, romosozumab decreased the risk of vertebral fractures up to 73% and increased total hip area bone mineral density by 3.2%. Previous work in 12 to 15-week-old sclerostin-knockout (Sost-/-) mice indicated that changes in immune cell development occur in the bone marrow (BM), which could be a possible side effect to follow in human patients. Our overall goal was to define the mechanisms that guide behavior of long-term hematopoietic stem cells (LT-HSCs) after exposure to an irregular BM microenvironment. SOST plays an important role in maintaining bone homeostasis, as demonstrated by the increased ratio of bone volume to total volume observed inSost-/-mice. Here, we examined the effects of short-term sclerostin depletion in the BM on hematopoiesis in young (8 week-old) mice receiving sclerostin-antibody (Scl-Ab) treatment for 6 weeks, and the effects of long-term Sost-deficiency on wild-type (WT) LT-HSCs transplanted into older (16-22 week-old) cohorts ofSost-/-mice. Our analyses revealed an increased frequency of granulocytes and decreased frequency of lymphocytes in the BM of Scl-Ab treated mice and WT→Sost-/-hematopoietic chimeras, indicating myeloid-biased differentiation inSost-deficient BM microenvironments. This myeloid bias extended to extramedullary hematopoiesis in the spleen and was correlated with an increase in inflammatory cytokines TNFα, IL-1α and MCP-1 in the serum of theSost-/-BM. Additionally, we observed alterations in erythrocyte differentiation in the BM and spleen ofSost-/-mice. Taken together, our current study indicates novel roles forSostin the regulation of myelopoiesis and control of inflammation in the BM. Our animal studies strongly recommend tracking of hematopoietic function in patients treated with romosozumab.
CD4+ T cell subsets present stable relationships in their T cell receptor repertoires
Authors: Wang Shiyu , Wang Longlong , Liu Ya
Published: November 2020

CD4+ T cells are key components of adaptive immunity. The cell differentiation equips CD4+ T cells with new functions. However, the effect of cell differentiation on T cell receptor (TCR) repertoire is not investigated. Here, we examined the features of TCR beta (TCRB) repertoire of the top clones within naïve, memory and regular T cell (Treg) subsets: repertoire structure, gene usage, length distribution and sequence composition. First, we found that memory subsets and Treg would be discriminated from naïve by the features of TCRB repertoire. Second, we found that the correlations between the features of memory subsets and naïve were positively related to differentiation levels of memory subsets. Third, we found that public clones presented a reduced proportion and a skewed sequence composition in differentiated subsets. Furthermore, we found that public clones led naïve to recognize a broader spectrum of antigens than other subsets. Our findings suggest that TCRB repertoire of CD4+ T cell subsets is skewed in a differentiation-depended manner. Our findings show that the variations of public clones contribute to these changes. Our findings indicate that the reduce of public clones in differentiation trim the antigen specificity of CD4+ T cells. The study unveils the physiological effect of memory formation and facilitates the selection of proper CD4+ subset for cellular therapy.
Orai1- and Orai2-, but not Orai3-mediated ICRACis regulated by intracellular pH
Authors: Rychkov Grigori Y. , Zhou Fiona H. , Adams Melissa K. , Brierley Stuart M. , Ma Linlin , Barritt Greg J.
Published: November 2020

Three Orai (Orai1, Orai2 and Orai3) and two STIM (STIM1 and STIM2;stromal interactionmolecule) mammalian protein homologues constitute major components of the store-operated Ca2+entry mechanism. When co-expressed with STIM1, Orai1, Orai2 and Orai3 form highly selective Ca2+channels with properties of Ca2+release activated Ca2+(CRAC) channels. Despite the high level of homology between Orai proteins, CRAC channels formed by different Orai isoforms have distinctive properties, particularly with regards to Ca2+dependent inactivation, inhibition/potentiation by 2-APB and sensitivity to reactive oxygen species. This study characterises and compares the regulation of Orai1, Orai2- and Orai3-mediated CRAC current (ICRAC) by intracellular pH. Using whole-cell patch clamping of HEK293T cells heterologously expressing Orai and STIM1 we show that ICRACformed by each Orai homologue has a unique sensitivity to changes in intracellular pH (pHi). Orai1-mediated ICRACexhibits a strong dependence on pHiof both current amplitude and the kinetics of Ca2+dependent inactivation. In contrast, Orai2 amplitude, but not kinetics, depends on pHi, whereas Orai3 shows no dependence on pHiat all. Investigation of different Orai1-Orai3 chimeras suggests that pHidependence of Orai1 resides in both, the N-terminus and intracellular loop 2, and may also involve pH-dependent interactions with STIM1.
Dephosphorylation of Plasmid DNA
Authors: Green Michael R. , Sambrook Joseph
Published: November 2020

This protocol presents a method to remove 5′-phosphate residues from protruding or blunt termini of linearized plasmids. This suppresses the recircularization of plasmid DNA during subsequent ligation procedures.
In Vivo Assessment of Drug-Induced Hepatotoxicity Using Xenopus Embryos
Authors: Saide Katy , Wheeler Grant N.
Published: November 2020

Failure to predict drug-induced toxicity reactions is a major problem contributing to a high attrition rate and tremendous cost in drug development. Drug screening in X. laevis embryos is high-throughput relative to screening in rodents, potentially making them ideal for this use. Xenopus embryos have been used as a toxicity model in the frog embryo teratogenesis assay on Xenopus (FETAX) for the early stages of drug safety evaluation. We previously developed compound-screening methods using Xenopus embryos and believe they could be used for in vitro drug-induced toxicity safety assessment before expensive preclinical trials in mammals. Specifically, Xenopus embryos could help predict drug-induced hepatotoxicity and consequently aid lead candidate prioritization. Here we present methods, which we have modified for use on Xenopus embryos, to help measure the potential for a drug to induce liver toxicity. One such method examines the release of the liver-specific microRNA (miRNA) miR-122 from the liver into the vasculature as a result of hepatocellular damage, which could be due to drug-induced acute liver injury. Paracetamol, a known hepatotoxin at high doses, can be used as a positive control. We previously showed that some of the phenotypes of mammalian paracetamol overdose are reflected in Xenopus embryos. Consequently, we have also included here a method that measures the concentration of free glutathione (GSH), which is an indicator of paracetamol-induced liver injury. These methods can be used as part of a panel of protocols to help predict the hepatoxicity of a drug at an early stage in drug development.
Managing student and faculty expectations and the unexpected during the COVID-19 lockdown: role transformation
Authors: Othman Radiah
Published: November 2020

Purpose

The purpose of this paper is to reflect teaching and learning practices, to highlight an educator’s new roles in the transformation when teaching online during the COVID-19 lockdown.

Design/methodology/approach

The paper takes a transformative reflection approach, based on competencies and activity system analysis to connect theory and practical experience in managing the students, the teaching delivery and the assessments.

Findings

The transition to online teaching and assessments requires various considerations of the curriculum and instructional approaches and necessitates the transformation of the role of the subject-matter expert to that of designer and co-learner. Empathy and understanding of students’ conditions enable this role transformation.

Practical implications

The paper highlights the importance of preparedness among faculty members and universities in dealing with uncertainties and the willingness to expand traditional roles and to upgrade the required skills, knowledge and attitudes to engender sustainable teaching and learning practices in response to future disruptions.

Originality/value

The paper reflects on the experience of a faculty who had adopted blended learning prior to the lockdown and how the teaching practice and roles transformed when fully transitioning to online delivery during the lockdown in New Zealand.
Immigrants’ disadvantage online: understanding the effects of immigration status, gender and country of origin on the e-government use in Israel
Authors: Rosenberg Dennis
Published: November 2020

Purpose

Digital inequality studies claim that social inequalities tend to be replicated online. However, studies have not attempted so far to deeper understand such stratification in immigrant societies regarding the e-government use. This study aims to understand the role of immigration status, gender and country of origin in the e-government use, thereby reflecting what the literature on the sociology of migration refers to as immigrants’ “double” and “triple” disadvantage.

Design/methodology/approach

Israel was chosen as a case study because it is an immigration society in which immigrants’ socioeconomic status is usually inferior to that of the native population. The data were attained from the 2017 Israel Social Survey. The population of the study included internet users from the Jewish sector (N = 4,222). Logistic regression was used as the multivariate technique.

Findings

The results indicated that immigrant women are disadvantaged in terms of e-government use regardless of their year of immigration. Yet, when the data are segmented by country of origin, only female immigrants from the former Soviet Union show evidence of a triple disadvantage.

Research limitations/implications

The conclusion is that immigrants’ disadvantages in the offline sphere also exist in the online sphere.

Practical implications

Particular categories, which use e-government to a small extent, were identified, serving a call for action for the public officials. They should develop plans to make e-government more accessible to individuals belonging to these categories.

Originality/value

This study incorporates digital and immigrant sociology for the explanation of immigrants’ (online) social inclusion.