bluuebunny/crossref_metadata_2025 huggingface dataset:
Prognostic implications of Global Longitudinal Strain versus Ejection Fraction in End-stage Renal Disease: a systematic review protocol
Authors: da Silva Guedes de Moura Barbara Leticia , dos Santos Mucenieks Anderson Gusthavo , Prajiante Bertolino Enrico , Chiqueto Duarte Giordanna , Dudek Joao Vitor , Daniel da Silva Mariana Amancio , Demarchi Izabel Galhardo , Yamada Sergio Seiji , Passos Okawa Rogerio Toshiro , Teixeira Jorge Juarez
Published: July 2022

Background: In hemodialysis (HD) patients, the presence of Heart failure (HF) at the start of dialysis is a strong and independent predictor of short and long-term mortality, and its prevalence increases with declining kidney function and HD time. Left ventricular (LV) ejection fraction (EF) is widely used as a measure of systolic function. Reduced EF (<50%) is an important prognostic marker, however, less than 15% of End-stage Renal Disease (ESRD) patients have detectable systolic dysfunction and the EF is susceptible to loading conditions, which change dramatically during interdialytic intervals. Global Longitudinal Strain (GLS) derived by 2D Speckle-Tracking Echocardiography (STE) is an emerging technique for measuring more subtle disturbances in LV systolic function. Although ESRD patients have subclinical evidence of impaired strain but preserved EF, there is evidence that GLS is better in ESRD group receiving maintenance HD compared with moderate-advanced CKD patients. This systematic review will evaluate the evidence related to the incremental prognostic value of LV GLS by 2D-STE concerning mortality and cardiovascular (CV) events in ESRD patients. Methods: This protocol is reported according to the PRISMA-P guideline. The databases PubMed, EMBASE, LILACS, Web of Science, and Google Scholar system will be searched and double screening for longitudinal studies that assessed the prospective association of STE-derived parameters with at least one of the pre-specified outcomes in ESRD patients. Discrepancies will be resolved through consensus. A modified version of the Newcastle-Ottawa Quality Assessment Scale of cohort studies will be used. We intend to use the random-effects model, considering at least moderate heterogeneity between studies. If data allow, we will perform meta-regression to explore potential sources of between-study heterogeneity. An adaptation of the GRADE framework for prognostic studies will be employed to judge the quality of evidence for each outcome reported in this systematic review. Discussion: This systematic review will summarize current evidence about STE-derived measures in ESRD patients and clarify the incremental prognostic value of this diagnostic tool versus LVEF in these patients. Evidence about other measures (circumferential and radial strain) or 3D STE-derived indices will also be investigated.
Plasma protein profiling of multiple sclerosis using proximity extension assays
Authors: Huang Jesse , Khademi Mohsen , Piehl Fredrik , Olsson Tomas , Kockum Ingrid
Published: July 2022

Background

Multiple sclerosis (MS) is an inflammatory disease characterized by demyelination and neuro-axonal degeneration in the central nervous system. Except for neurofilament light protein, identification of biomarkers has been difficult to assess in the blood, presumably due partly to sensitivity. To detect traces of disease activities in the periphery and identify low-abundance protein biomarkers, this study conducts an exploratory examination of the plasma proteome of MS using proximity extension technology, a high-sensitivity multiplex PCR-based immunoassay.

Methods

A case-control cohort consisting of 52 MS cases (relapsing-remitting=30, progressive=22) and 17 healthy controls were enrolled at the Karolinska University Hospital. EDTA plasma was analyzed for 1157 unique protein targets across thirteen proximity extension assays. Protein associations to disease outcomes and related clinical measures were assessed using a multivariable linear regression model corrected for sex and age at sampling.

Results

AHCY and CHR levels were higher among MS cases than controls, while FABP2 was lower among those with relapsing-remitting disease than controls (Pdiscovery<0.05, Preplication<0.05), although not significant after multiple test corrections. Furthermore, PTN and CYR61 levels were higher in progressive MS than in relapsing-remitting disease (P<0.0002, PFDR<0.05), and CRNN and CXCL13 were associated with more severe disability at sampling (P<0.0001, PFDR<0.05), independent of disease course. CTSF was positively correlated with disease duration (P=4.1×10−5, PFDR=0.044), while RRM2B level correlated with intrathecal immunoglobulin production (IgG Index) in relapsing-remitting MS (P=1.7×10−5, PFDR=0.018).

Conclusion

We provide several candidates for characterizing MS, particularly progressive disease, which may help monitor disease progression and treatment response in a clinical setting.
Outbreak of Highly Pathogenic Avian Influenza H5N1 in New England Seals
Authors: Puryear Wendy , Sawatzki Kaitlin , Hill Nichola , Foss Alexa , Stone Jonathon J. , Doughty Lynda , Walk Dominique , Gilbert Katie , Murray Maureen , Cox Elena , Patel Priya , Mertz Zak , Ellis Stephanie , Taylor Jennifer , Fauquier Deborah , Smith Ainsley , DiGiovanni Robert A. , van de Guchte Adriana , Gonzalez-Reiche Ana Silvia , Khalil Zain , van Bakel Harm , Torchetti Mia K. , Lenoch Julianna B. , Lantz Kristina , Runstadler Jonathan
Published: July 2022

The recent incursion of Highly Pathogenic Avian Influenza A (H5N1) virus into North America and subsequent dissemination of virus across the continent, has had significant adverse impacts on domestic poultry, and has led to widespread mortality in many wild bird species. Here we report the recent spillover of H5N1 into marine mammals in the northeastern United States, with associated mortality on a regional scale. This spillover is coincident with a second wave of H5N1 in sympatric wild birds also experiencing regional mortality events. Viral sequences derived from both seal and avian hosts reveal distinct viral genetic differences between the two waves of infection. Spillover into seals was closely related to virus from the second wave, and one of eight seal-derived sequences had the mammalian adaptation PB2 E627K.

One-Sentence Summary

An outbreak of H5N1 in New England seals is the first known population-scale mammalian mortality event associated with the emerging highly pathogenic avian influenza clade 2.3.4.4b.
Ena/VASP proteins at the crossroads of actin nucleation pathways in dendritic cell migration
Authors: Visweshwaran Sai Prasanna , Nayab Hafiza , Hoffmann Lennart , Gil Marine , Liu Fan , Kühne Ronald , Maritzen Tanja
Published: July 2022

As sentinels of our immune system dendritic cells (DCs) rely on efficient cell migration for patrolling peripheral tissues and delivering sampled antigens to secondary lymphoid organs for the activation of T-cells. Dynamic actin polymerization is key to their macropinocytic and migratory properties. Both major actin nucleation machineries, formins and the Arp2/3 complex, are critical for different aspects of DC functionality, by driving the generation of linear respectively branched actin filaments. However, the importance of a third group of actin nucleators, the Ena/VASP family, has not been addressed yet. Here, we show that the two family members Evl and VASP are expressed in murine DCs and that their loss negatively affects DC macropinocytosis, spreading, and migration. Our interactome analysis reveals Ena/VASP proteins to be ideally positioned for orchestrating the different actin nucleation pathways by binding to the formin mDia1 as well as to the WAVE regulatory complex, a stimulator of Arp2/3. In fact, Evl/VASP deficient murine DCs are more vulnerable to inhibition of Arp2/3 demonstrating that Ena/VASP proteins contribute to the robustness and efficiency of DC migration.
Epidermis Derived Lactate Promotes Sterile Inflammation by Inducing Metabolic Rewiring in Macrophages
Authors: Ayyangar Uttkarsh , Karkhanis Aneesh , Tay Heather , Afandi Aliya Farissa Binte , Bhattacharjee Oindrila , Han Lee Sze , Chan James , Raghavan Srikala
Published: July 2022

Dysregulated macrophage responses and changes in tissue metabolism are hallmarks of chronic, sterile inflammation. However, the metabolic cues that direct and support macrophage functions are poorly understood. Here, we show that during sterile inflammation in skin, the epidermis and macrophages uniquely depend on glycolysis and TCA cycle, respectively. This compartment separation is initiated by HIF1a stabilization and enhanced glycolysis in the epidermis. The end product of glycolysis, lactate is exported and utilized by the dermal macrophages to drive their effector functions. Notably, inhibition of lactate mediated crosstalk between the epidermis and macrophages leads to inhibition of sterile inflammation. Overall, our study identifies an essential role for the metabolite lactate in regulating macrophage response that can be effectively targeted to treat skin disorders such as psoriasis.

One-Sentence Summary

Epidermis derived lactic acid drives sterile inflammation by augmenting pro-remodeling state in dermal macrophages.
Cloning, heterologous expression and characterization of o-phthalyl-CoA decarboxylase from phthalate degrading denitrifying bacterium
Authors: Junghare Madan
Published: July 2022

Phthalic acid esters (phthalates) are used as additives in various plastics and industrial applications. They are produced worldwide in huge amounts causing major pollution in the environment. Biodegradation of phthalates from the environment is an important route for their removal. In our previous work, we showed that Azoarcus sp. strain PA01 catabolizes o-phthalate via the anaerobic benzoyl-CoA pathway that involved two putative enzymes: the succinyl-CoA:o-phthalate CoA-transferase activates o-phthalate to o-phthalyl-CoA which is subsequently decarboxylated to benzoyl-CoA by o-phthalyl-CoA decarboxylase. In this work, we provide the information on the enzymes involved in the promising step of anoxic decarboxylation of o-phthalate to benzoyl-CoA. We have identified that there are two proteins are involved in decarboxylation step, of which only one does the actual decarboxylation but other one is essential. o-Phthalyl-CoA decarboxylase (PhtDa and PhtDb) encoded by the two genes PA01_00217 and PA01_00218 which catalyses the decarboxylation of activated o-phthalate to benzoyl-CoA. Both genes are originally annotated as an UbiD-like/UbiX-like protein. The gene with locus tag PA01_00217 is 1584 bp long coding for protein PhtDa (60 kDa), whereas PA01_00218 is 600 bp long codes for protein PhtDb (22 kDa). Here, we demonstrate that PhtDb is a flavin mononucleotide (FMN)-binding protein which does not function as a decarboxylase alone. Rather, PhtDb is assumed to generate a modified FMN-containing cofactor that is required by the PhtDa for decarboxylase activity. Alone, PhtDa does not function as a decarboxylase either. Recombinantly expressed PhtDa and PhtDb together showed activity for decarboxylation of o-phthalyl-CoA to benzoyl-CoA, only if PhtDb was previously incubated with FMN and dimethylallyl monophosphate. Phylogenetically, the proteins PhtDa and PhtDb are closely related to UbiD-like/UbiX-like enzymes that catalyses the decarboxylation of 4-hydroxy-3-octaprenylbenzoic acid to 2-octaprenylphenol, an intermediate step in ubiquinone biosynthesis. Furthermore, multiple sequence alignment and structural modelling of both proteins suggested that only PthDb possesses the binding site for FMN. These results strongly indicate that the flavin-containing cofactor is essential for decarboxylation of o-phthalyl-CoA to benzoyl-CoA during anaerobic o-phthalate degradation by Azoarcus sp. strain PA01.
Dynamic states of eIF6 and SDS variants modulate interactions with uL14 of the 60S ribosomal subunit
Authors: Elliff Jonah , Biswas Aparna , Kuppa Sahiti , Roshan Poonam , Patterson Angela , Mattice Jenna , Chinnaraj Mathivanan , Burd Ryan , Walker Sarah E. , Pozzi Nicola , Antony Edwin , Bothner Brian , Origanti Sofia
Published: July 2022

Assembly of ribosomal subunits into active ribosomal complexes is integral to protein synthesis. Release of eIF6 from the 60S ribosomal subunit primes 60S to associate with the 40S subunit and engage in translation. The dynamics of eIF6 interaction with the uL14 (RPL23) interface of 60S and its regulation by somatic mutations acquired in Shwachman-Diamond Syndrome (SDS) is yet to be clearly understood. Here, by using a modified strategy to obtain high yields of recombinant human eIF6 we have uncovered the critical interface entailing 8 key residues in the C-tail of RPL23 that is essential for physical interactions between 60S and eIF6. Disruption of the complementary binding interface by conformational changes in eIF6 disease variants provide a mechanism for weakened interactions of variants with the 60S. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) analyses uncovered dynamic configurational rearrangements in eIF6 induced by binding to RPL23 and exposed an allosteric interface regulated by the C-tail of eIF6. Disrupting a key residue in the eIF6-60S binding interface markedly limits proliferation of cancer cells, which highlights the significance of therapeutically targeting this interface. Establishing these key interfaces thus provide a therapeutic framework for targeting eIF6 in cancers and SDS.
Interspecies Killing Activity of Pseudomonas syringae Tailocins
Authors: Weaver Savannah L. , Zhu Libin , Ravishankar Sadhana , Clark Meara , Baltrus David A.
Published: July 2022

Tailocins are ribosomally synthesized bacteriocins, encoded by bacterial genomes, but originally derived from bacteriophage tails. As with both bacteriocins and phage, tailocins are largely thought to be species-specific with killing activity often assumed to be directed against closely-related strains. Previous investigations into interactions between tailocin host range and sensitivity across phylogenetically diverse isolates of the phytopathogen Pseudomonas syringae have demonstrated that many strains possess intraspecific tailocin activity and that this activity is highly precise and specific against subsets of strains. However, here we demonstrate that at least one strain of P. syringae, USA011R, defies both expectations and current overarching dogma because tailocins from this strain possess broad killing activity against other agriculturally significant phytopathogens such as Erwinia amylovora and Xanthomonas perforans as well as against the clinical human pathogen Salmonella choleraesuis. Moreover, we show that the full spectrum of this interspecific killing activity is not conserved across closely related strains with data suggesting that even if tailocins can target different species, they do so with different efficiencies. Our results reported herein highlight the potential for and phenotypic divergence of interspecific killing activity of P. syringae tailocins and establish a platform for further investigations into the evolution of tailocin host range and strain specificity.
A molecular mechanism for membrane chaperoning by a late embryogenesis abundant protein
Authors: Li Xiao-Han , Yu Conny W.H. , Gomez-Navarro Natalia , Stancheva Viktoriya , Zhu Hongni , Guibao Cristina , Murthy Andal , Xie Boer , Wozny Michael , Leslie Benjamin , Kaminski Marcin , Malhotra Ketan , Johnson Christopher M. , Blackledge Martin , Santhanam Balaji , Green Douglas R. , Peng Junmin , Liu Wei , Huang Jinqing , Miller Elizabeth A. , Freund Stefan M.V. , Babu M. Madan
Published: July 2022

Environmental stress can result in substantial damage to proteins, membranes, and genetic material, impacting organismal survival1-3. Stress tolerance can be conferred by intrinsically disordered proteins (IDPs)4 that lack stable tertiary structure. IDPs from the large family of late embryogenesis abundant (LEA) proteins confer a fitness advantage when heterologously expressed5,6. Such protection suggests a general molecular function leading to stress tolerance, although the mechanisms remain unclear. Here, we report that a tardigrade LEA protein that confers stress tolerance in yeast acts as a molecular chaperone for the mitochondrial membrane. This protein, named HeLEA1, localizes to the mitochondrial matrix, and harbors conserved LEA sequence motifs that undergo dynamic disorder-to-helical transition upon binding to negatively charged membranes. Yeast expressing HeLEA1 show increased mitochondrial membrane fluidity, increased membrane potential, and enhanced tolerance to hyperosmotic stress under non-fermentative growth without significantly altering mitochondrial lipid composition or triggering a generic stress response. We demonstrate that membrane binding ameliorates excess surface tension, possibly by stabilizing lipid packing defects. Evolutionary analysis suggests that HeLEA1 homologs localize to different membrane-bound organelles and share similar sequence and biophysical features. We suggest that membrane chaperoning by LEA proteins represents a general biophysical solution that can operate across the domains of life.
Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs
Authors: Rathinaswamy Manoj K , Jenkins Meredith L , Zhang Xuxiao , Stariha Jordan TB , Ranga-Prasad Harish , Dalwadi Udit , Fleming Kaelin D. , Yip Calvin K , Williams Roger L , Burke John E
Published: July 2022

Class IB phosphoinositide 3-kinase (PI3Kγ) is activated in immune cells by diverse stimuli and can form two distinct complexes, with the p110γ catalytic subunit binding to either p101 or p84 regulatory subunits. These two complexes are differentially activated by G-protein coupled receptors (GPCRs) and Ras, but the molecular details of this activation are still unclear. Using a combination of X-ray crystallography, HDX-MS, EM, molecular modeling, and biochemical assays we reveal molecular differences between the two p110γ-p84 and p110γ-p101 complexes that explain their differential activation. The structure of p110γ-p84 shows a similar assembly to p110γ-p101 at the p110γ interface, however the interface in p110γ-p84 is dynamic and is evolutionarily conserved to be less stable compared to p110γ-p101. The p110γ-p84 complex is only weakly recruited to membranes by Gβγ subunits alone and requires recruitment by Ras to allow for Gβγ activation through an interaction with the p110γ helical domain. The interfaces of the p101 GBD with Gβγ, and the p110γ helical domain with Gβγ were determined using computational alphafold2 modeling and HDX-MS. There are distinct differences in the C-terminal domain of p84 and p101, which allows p101 to bind Gβγ subunits, while p84 does not. The two Gβγ interfaces in p110γ and p101 are distinct, revealing how unique mutants of Gβγ cause differential disruption of PI3Kγ complex activation. Overall, our work provides key insight into the molecular basis for how different PI3Kγ complexes are activated.
TERRA increases at short telomeres in yeast survivors and regulates survivor associated senescence (SAS)
Authors: Misino Stefano , Busch Anke , Wagner Carolin B. , Luke Brian
Published: July 2022

Cancer cells achieve immortality by employing either homology-directed repair (HDR) or the telomerase enzyme to maintain telomeres. ALT (alternative lengthening of telomeres) refers to the subset of cancer cells that employ HDR. ALT mechanisms are strongly conserved from yeast to human cells, with the yeast equivalent being referred to as survivors. The non-coding RNA, TERRA and its ability to form RNA-DNA hybrids have been implicated in ALT/survivor maintenance by promoting HDR. It is not understood which telomeres in ALT/survivors engage in HDR, nor is it clear which telomeres upregulate TERRA. Using yeast survivors as a model for ALT, we demonstrate that HDR only occurs at telomeres when they become critically short. Moreover, TERRA levels steadily increase as telomeres shorten and decrease again following HDR-mediated recombination. Surprisingly, we observe that survivors undergo cycles of senescence, in a similar manner to non-survivors following telomerase loss, which we refer to as survivor associated senescence (SAS). Similar to “normal” senescence, we observe that RNA-DNA hybrids slow the rate of SAS by decreasing the rate of telomere shortening. In summary, TERRA RNA-DNA hybrids regulate telomere dysfunction-induced senescence in both pre- and post-crisis cells.
Advancing Spectrally-Resolved Single Molecule Localization Microscopy using Deep Learning
Authors: Manko Hanna , Mély Yves , Godet Julien
Published: July 2022

Spectrally-Resolved Single Molecule Localization Microscopy (srSMLM) is a recent multidimensional technique enriching single molecule localization imaging by the simultaneous recording of single emitters spectra. As for SMLM, the localization precision is fundamentally limited by the number of photons collected per emitters. But srSMLM is more impacted because splitting the emission light from single emitters into a spatial and a spectral channel further reduces the number of photons available for each channel and impairs both spatial and spectral precision - or forces the sacrifice of one or the other. Here, we explored the potential of deep learning to overcome this limitation. We report srUnet - a Unet-based image processing that enhances the spectral and spatial signals and compensates for the signal loss inherent in recording the spectral component. We showed that localization and spectral precision of low-emitting species remain as good as those obtained with a high photons budget together with improving the fraction of localizations whose signal is both spatially and spectrally interpretable. srUnet is able to deal with spectral shift and its application to multicolour imaging in biological sample is straight-forward.

srUnet advances spectrally resolved single molecule localization microscopy to achieve performance close to conventional SMLM without complicating its use.
Molecular phylogenetic analysis for Ovis aries with whole mitochondrial genome sequencing
Authors: Pal Aruna , Banerjee Samiddha , Pathak Kanai , Das Manas Kumar , Chatterjee P.N.
Published: July 2022

Domestication of Ovis aries has taken place time immorial across the different geographical regions across the globe. Biodiversity among the sheep population has been interesting to study by a group of researchers based on mitochondrial genes like Cytochrome B, D loop. The current study is a novel attempt to understand the molecular phylogenomics among Ovis aries through all the 37 genes of mitochondria. We have analyzed complete mitochondrial genome sequencing for sheep breeds for West Bengal as Garole, Chotanagpuri, Bonpala and Birbhum sheep. Phylogenetic analysis reveals genetic similarity between Garole and Chotanagpuri brred of sheep, where as Birbhum and Bonpala were found to be genetically distinct. Phylogenomics in a global prospect reveal three lineages, Lineage A comprise of sheep from West Bengal grouped with Tibetan sheep. Lineage B consists of sheep population across the other parts including Europe (France, Denmark), Africa and Syro-Arabian desert, whereas Lineage C emerged as smaller outgroup.
Rescue Stenting in Mechanical Thrombectomy Refractory Occlusions: A Single Center Multiethnic Cohort
Authors: Imam Yahia Z , Akhtar Naveed , Kamran Saadat , Bermejo Pablo , Jerdi Salman Al , Zakaria Ayman , Own Ahmed , Patro Satya
Published: July 2022

Introduction

Refractory large vessel occlusion in acute ischemic stroke carries high morbidity and mortality. Rescue stenting is an emerging modality that is increasingly utilized especially in East Asia. We aim to investigate the safety and efficacy of performing rescue stenting in acute stroke patients who had failed mechanical thrombectomy.

Methods

This is a retrospective, all-inclusive, observational, descriptive review of the prospectively collected stroke database. Post stenting, an aggressive antiplatelet protocol was followed with glycoprotein IIb/IIIa infusion. Incidence of intracerebral hemorrhage (ICH), recanalization score and favorable prognosis (modified Rankin Score ≤3) at 90 days was used to determine primary outcome. Additionally, comparison was made between patients from the Middle East and North Africa (MENA) region and others.

Results

In total, 55 patients were included with 87.3% being male. Mean age was 51.3±11.8 years. This included 32 patients (58.3%) from South Asia, 12 (21.8%) from the MENA region, 9 (16.4%) from Southeast Asia and 2 (3.6%) from other parts of the world. Optimal recanalization (Thrombolysis in cerebral infarction (TICI) scale=2b-3) was achieved in 43 (78.2%); the incidence of symptomatic ICH was 2 (3.6%) and favorable outcome at 90 days was seen in 23 (41.8%). Apart from significantly older age, mean 62.8±13 years (median 69) vs. 48.1±9.3 (mean 49) and coronary artery disease burden 4 (33.3%) vs.1 (2.3%) (p<0.05). Patients from the MENA cohort had similar risk factor profiles, stroke severity, recanalization rates, ICH rates and 90-day outcomes compared to patients from South and Southeast Asia.

Conclusion

Rescue stenting showed comparably good outcomes and low risk of clinically significant bleeding in a multiethnic cohort of patients from MENA and South and Southeast Asia.
Modelling the role of quarantine escapees on COVID-19 dynamics
Authors: Mushanyu Josiah , Madubueze Chinwendu Emilian , Chukwu Williams , Chazuka Zviiteyi , Mudzingwa Frenick , Ogbogbo Chisara
Published: July 2022

The recent outbreak of the novel coronavirus (COVID-19) pandemic which originated from the Wuhan City of China has devastated many parts of the globe. At present, non-pharmaceutical interventions are the widely available measures being used in combating and controlling this disease. There is great concern over the rampant unaccounted cases of individuals skipping the border during this critical period in time. We develop a deterministic compartmental model to investigate the impact of escapees on the transmission dynamics of COVID-19 in Zimbabwe. A suitable Lyapunov function has been used to show that the disease-free equilibrium is globally asymptotically stable provided ℛ0< 1. We performed global sensitivity analysis using the Latin-hyper cube sampling method and partial rank correlation coefficients to determine the most influential model parameters on the short and long term dynamics of the pandemic, so as to minimize uncertainties associated with our variables and parameters. Results confirm that there is a positive correlation between the number of escapees and the reported number of COVID-19 cases. It is shown that escapees are largely responsible for the rapid increase in local transmissions. Also, the results from sensitivity analysis show that an increase in the governmental role actions and a reduction in immigration rate will help to control and contain the disease spread.
Native language leaves distinctive traces in brain connections
Authors: Goucha T. , Anwander A. , Adamson H. , Friederici A. D.
Published: July 2022

The world’s languages differ substantially in their sounds, grammatical rules, and expression of semantic relations. While starting from a shared neural substrate, the developing brain must therefore have the plasticity to accommodate to the specific processing needs of each language. However, there is little research on how language-specific differences impacts brain function and structure. Here, we show that speaking typologically different languages leaves unique traces in the brain’s white matter connections of monolingual speakers of English (fixed word order language), German (with grammatical marking), and Chinese (tonal language). Using machine learning, we classified with high accuracy the mother tongue based on the participants’ patterns of structural connectivity obtained with probabilistic tractography. More importantly, connectivity differences between groups could be traced back to relevant processing characteristics of each native tongue. Our results show that the life-long use of a certain language leaves distinct traces in a speaker’s neural network.
Single Cell Cortical Bone Transcriptomics Defines Novel Osteolineage Gene Sets Altered in Chronic Kidney Disease
Authors: Agoro Rafiou , Nookaew Intawat , Noonan Megan L. , Marambio Yamil G. , Liu Sheng , Chang Wennan , Gao Hongyu , Hibbard Lainey M. , Metzger Corinne E. , Horan Daniel , Thompson William R. , Xuei Xiaoling , Liu Yunlong , Zhang Chi , Robling Alexander G. , Bonewald Lynda F. , Wan Jun , White Kenneth E.
Published: July 2022

Due to a lack of spatial-temporal resolution at the single cell level, the etiologies of the bone dysfunction caused by diseases such as normal aging, osteoporosis, and the metabolic bone disease associated with chronic kidney disease (CKD) remain largely unknown. To this end, flow cytometry and scRNAseq were performed on long bone cells from Sost-cre/Ai9+mice, and pure osteolineage transcriptomes were identified, including novel osteocyte-specific gene sets. Clustering analysis isolated osteoblast precursors that expressedTnc,Mmp13,andSpp1,and a mature osteoblast population defined bySmpd3,Col1a1, andCol11a1. Osteocytes were demarcated byCd109,Ptprz1, Ramp1, Bambi, Adamts14,Spns2, Bmp2,WasI,andPhex. We validated ourin vivoscRNAseq using integrativein vitropromoter occupancy via ATACseq coupled with transcriptomic analyses of a conditional, temporally differentiated MSC cell line. Further, trajectory analyses predicted osteoblast-to-osteocyte transitions via defined pathways associated with a distinct metabolic shift as determined by single-cell flux estimation analysis (scFEA). Using the adenine mouse model of CKD, at a time point prior to major skeletal alterations, we found that gene expression within all stages of the osteolineage was disturbed. In sum, distinct populations of osteoblasts/osteocytes were defined at the single cell level. Using this roadmap of gene assembly, we demonstrated unrealized molecular defects across multiple bone cell populations in a mouse model of CKD, and our collective results suggest a potentially earlier and more broad bone pathology in this disease than previously recognized.
Characterization, Comparison, and Optimization of Lattice Light Sheets
Authors: Liu Gaoxiang , Ruan Xiongtao , Milkie Daniel E. , Görlitz Frederik , Mueller Matthew , Hercule Wilmene , Kililea Alison , Betzig Eric , Upadhyayula Srigokul
Published: July 2022

Lattice light sheet microscopy excels at the non-invasive imaging of three-dimensional (3D) dynamic processes at high spatiotemporal resolution within cells and developing embryos. Recently, several papers have called into question the performance of lattice light sheets relative to the Gaussian sheets most common in light sheet microscopy. Here we undertake a comprehensive theoretical and experimental analysis of various forms of light sheet microscopy which both demonstrates and explains why lattice light sheets provide significant improvements in resolution and photobleaching reduction. The analysis provides a procedure to select the correct light sheet for a desired experiment and specifies the processing that maximizes the use of all fluorescence generated within the light sheet excitation envelope for optimal resolution while minimizing image artifacts and photodamage. Development of a new type of “harmonic balanced” lattice light sheet is shown to improve performance at all spatial frequencies within its 3D resolution limits and maintains this performance over lengthened propagation distances allowing for expanded fields of view.

Significance Statement

Despite its rapidly growing use, several misconceptions remain concerning the physics of image formation and its optimization in light sheet microscopy, particularly in high resolution variants tailored for subcellular imaging. These include the role of excitation sidelobes, the significance of out-of-focus fluorescence, the importance and optimization of deconvolution, and the perceived advantages of Gaussian beams. Here we attempt to shatter these misconceptions by showing that the professed tradeoffs between axial resolution and background haze, photobleaching rate, phototoxicity, and propensity for image artifacts do not exist for well-crafted lattice light sheets whose data is acquired and processed rigorously. The framework we provide should enable others to optimize light sheets and extract the most information at the lowest cost in their experiments.
Propagation dynamics of electrotactic motility in large epithelial cell sheets
Authors: Zhang Yan , Xu Guoqing , Wu Jiandong , Lee Rachel M , Zhu Zijie , Sun Yaohui , Zhu Kan , Losert Wolfgang , Liao Simon , Zhang Gong , Pan Tingrui , Xu Zhengping , Lin Francis , Zhao Min
Published: July 2022

Directional migration initiated at the wound edge leads epithelial sheets to migrate in wound healing. How such coherent migration is achieved is not well understood. Here we used electric fields to induce robust migration of sheets of human keratinocytes and developed an in silico model to characterize initiation and propagation of epithelial collective migration. Electric fields initiate increase in migrations directionality and speed at the leading edge. The increases propagate across the epithelial sheets, resulting in directional migration of cell sheets as coherent units. Both the experimental and in silico models demonstrated vector-like integration of the electric and default directional cues at the free edge in space and time. The resultant collective migration is remarkably consistent in experiments and modeling, both qualitatively and quantitatively. The keratinocyte model thus faithfully reflects key features of epithelial migration as a coherent tissue in vivo, e.g. that leading cells lead, and that epithelium maintains cell- cell junction.
Acinetobacter baumanniirepresses type VI secretion system through an Mn2+-dependent sRNA-mediated regulation
Authors: Bhowmik Somok , Pathak Avik , Devnath Kuldip , Sett Abhiroop , Pandey Shivam , Jyoti Nishant , Bhando Timsy , Akhter Jawed , Chugh Saurabh , Singh Ramandeep , Sharma Tarun Kumar , Pathania Ranjana
Published: July 2022

Type VI secretion system (T6SS) is utilized by many Gram negative bacteria for eliminating competing bacterial species and manipulating host cells.Acinetobacter baumanniiATCC 17978 utilizes T6SS at the expense of losing pAB3 plasmid to induce contact-dependent killing of competitor microbes, resulting in the loss of antibiotic resistance carried by pAB3. However, the regulatory network associated with T6SS inA. baumanniiremains poorly understood. Here, we identified an Mn2+-dependent post-transcriptional regulation of T6SS mediated by a bonafide small RNA, AbsR28.A. baumanniiutilizes MumT (Mn2+-uptake inner membrane transporter) for the uptake of extracellular Mn2+during oxidative stress. We demonstrate that the abundance of intracellular Mn2+enables complementary base-pairing of AbsR28-tssMmRNA (that translated to TssM, one of the vital inner membrane components of T6SS), inducing RNase E-mediated degradation oftssMmRNA and resulting in T6SS repression. Thus, AbsR28 mediates a crosstalk between MumT and T6SS inA. baumannii.

IMPORTANCE

Small RNAs (sRNAs) are identified as critical components within the bacterial regulatory networks involved in fine regulation of virulence-associated factors. The sRNA-mediated regulation ofAcinetobacter baumannii’s T6SS was unchartered. Our findings reveal a novel underlying mechanism of an Mn2+-dependent sRNA-mediated regulation of T6SS inA. baumannii. We show that binding of Mn2+to AbsR28 aids in the complementary base-pairing of AbsR28-tssMmRNA, resulting in RNase E-mediated processing oftssMand T6SS repression. The findings also shed light onA. baumannii’s preference for antibiotic resistance over contact-dependent killing during infection.
High-resolution crystal structure of a metabolic switch protein in a complex with monomeric c-di-GMP reveals a potential mechanism for c-di-GMP dimerization
Authors: Dubey Badri Nath , Shyp Viktoriya , Fucile Geoffrey , Jenal Urs , Schirmer Tilman
Published: July 2022

Bacterial second messengers c-di-GMP and (p)ppGpp have broad functional repertoires ranging from growth and cell cycle control to the regulation of biofilm formation and virulence. The recent identification of SmbA, an effector protein from Caulobacter crescentus that is jointly targeted by both signaling molecules, has opened up studies on how these global bacterial networks interact. C-di-GMP and (p)ppGpp compete for the same SmbA binding site, with a dimer of the former ligand inducing a conformational change of loop 7 leading to downstream signaling. Here, we report a crystal structure of a partial loop 7 deletion mutant, SmbAΔloop in complex with c-di-GMP determined at 1.4 Å resolution. SmbAΔloop binds monomeric c-di-GMP strengthening the view that loop 7 is required for c-di-GMP dimerization. In the crystal, SmbAΔloop forms a 2-fold symmetric dimer via isologous interactions with the two symmetric halves of c-di-GMP. Structural comparisons of SmbAΔloop with wild-type SmbA in complex with dimeric c-di-GMP or ppGpp support the idea that loop 7 is critical for SmbA function by interacting with downstream partners. These results underscore the flexibility of c-di-GMP in binding to the symmetric interface between protein subunits. It is envisaged that such isologous interactions of c-di-GMP will be observed in hitherto unrecognized targets.
Genetic diversity, population structure and parentage analysis of Brazilian grapevine hybrids after half a century of genetic breeding
Authors: de Oliveira Geovani Luciano , Niederauer Guilherme Francio , de Oliveira Fernanda Ancelmo , Rodrigues Cinthia Souza , Hernandes José Luiz , de Souza Anete Pereira , Moura Mara Fernandes
Published: July 2022

In the 1940s, the Agronomic Institute of Campinas (IAC) started a grapevine breeding program to develop new cultivars adapted to the tropical and subtropical regions of Brazil. More than 2,000 crosses were carried out over 50 years, using 850 varieties as parents. However, among the thousands of hybrids developed by the program, only 130 are still maintained in the IAC grapevine germplasm collection. Little is known about their genetic makeup and usefulness for current breeding programs. In this study, we genotyped 130 Brazilian grape hybrids at 21 polymorphic microsatellite markers to evaluate the genetic diversity and population structure of the hybrids and verified their disclosed pedigrees. The results showed that the hybrid collection is highly diverse, with an expected heterozygosity (HE) of 0.80 and an observed heterozygosity (Ho) of 0.78. Strong structure in three subgroups based mainly on the usage and combination of parental groups was revealed by STRUCTURE software and confirmed by discriminant analysis of principal components (DAPC). Through molecular profiling analysis, fourteen synonyms, one homonym and one duplicate were identified. Parentage analysis confirmed 24 full parentages, as well as 33 half-kinships. In addition, 18 pedigrees were invalidated, and seven mislabeling events were identified. No compatible parent was identified for 33% of the IAC hybrids, highlighting severe genetic erosion in the IAC germplasm. The molecular characterization of the breeding hybrid bank collection contributes to our understanding of the genetic basis of the varieties, guiding the efficient utilization of available genetic diversity. Together, our results could be applied to other breeding programs and assist in the selection of parents, management of the breeding collection, and conservation of grapevine genetic resources.
Cell surface receptors TREM2, CD14 and integrin αMβ2drive sinking engulfment in phosphatidylserine-mediated phagocytosis
Authors: Vorselen Daan , Kamber Roarke A. , Labitigan Ramon Lorenzo D. , van Loon Aaron P. , Peterman Eric , Delgado Melissa K. , Lin Sijie , Rasmussen Jeffrey P. , Bassik Michael C. , Theriot Julie A.
Published: July 2022

Macrophages phagocytose and thereby eliminate a wide array of extracellular threats, ranging from antibody-coated bacteria to apoptotic cells. Precision modulation of phagocytosis has emerged as a therapeutic strategy across a range of diseases, but is limited by our incomplete understanding of how macrophages recognize, engulf, and respond to different phagocytic targets. Here, we undertook a systematic investigation of the morphological, biophysical and regulatory differences between two major types of phagocytosis: an immunostimulatory form of phagocytosis triggered by antibody-coated targets and an immunosuppressive form triggered by phosphatidylserine (PS)-coated targets. We confirmed classic observations that antibody-mediated phagocytosis involves the extension of thin actin-rich protrusions around the target, but find that PS-mediated phagocytosis involves an unexpected combination of filopodial probing, piecemeal phagocytosis and a distinct ‘sinking’ mechanism of uptake. Using a genome-wide screening approach, we identified genes specifically required for each form of phagocytosis, including actin regulators, cell surface receptors and intracellular signaling molecules. Three cell surface receptors - TREM2, CD14 and integrin αMβ2- were revealed as essential for PS-mediated uptake. Strikingly, each receptor exhibited a distinct pattern of localization at the plasma membrane and contributed uniquely to the organization of the PS-dependent phagocytic cup. Overall, this work reveals divergent genetic requirements for the morphologically and mechanically distinct forms of PS-mediated and antibody-mediated phagocytosis, thereby informing therapeutic strategies for substrate-specific phagocytosis modulation.
A genetically encoded photo-proximity labeling approach for mapping protein territories
Authors: Hananya Nir , Ye Xuanjia , Koren Shany , Muir Tom W.
Published: July 2022

Studying dynamic biological processes requires approaches compatible with the lifetimes of the biochemical transactions under investigation, which can be very short. We describe a genetically encoded system that allows protein interactomes to be captured using visible light. Our approach involves fusing an engineered flavoprotein to a protein of interest. Brief excitation of the fusion protein leads to local generation of reactive radical species within cell-permeable probes. When combined with quantitative proteomics, the system generates ‘snapshots’ of protein interactions with high temporal resolution. The intrinsic fluorescence of the fusion domain permits correlated imaging and proteomics analyses, a capability that is exploited in several contexts, including defining the protein clients of the major vault protein (MVP). The technology should be broadly useful in the biomedical area.
Characterization of norbelladine synthase and noroxomaritidine/norcraugsodine reductase reveals a novel catalytic route for the biosynthesis of Amaryllidaceae alkaloids including the Alzheimer’s drug galanthamine
Authors: Majhi Bharat Bhusan , Gélinas Sarah-Eve , Mérindol Natacha , Desgagné-Penix Isabel
Published: July 2022

Amaryllidaceae alkaloids (AAs) are a large group of pharmacological plant-specialized metabolites. Norbelladine is the entry compound in AAs biosynthesis. Two enzymes are capable of catalyzing this reaction in-vitro, both with low-yield; 1) norbelladine synthase (NBS) condenses tyramine and 3,4-dihydroxybenzaldehyde, while 2) noroxomaritidine/norcraugsodine reductase (NR), catalyzes a reduction reaction. To clarify the mechanisms involved in this controversial step, both NBS and NR were characterized from Narcissus papyraceus and Leucojum aestivum. Assays with each enzyme suggested that NBS and NR function together for norbelladine formation. Using molecular-homology modeling and docking studies, we predicted models for the binding of substrates to NBS and NR. Moreover, NBS and NR physically interact, localize to the cell cytoplasm and nucleus and are expressed at high levels in bulbs. Our study establishes that both NBS and NR participate in the biosynthesis of norbelladine, catalyzing the first key steps involved in the biosynthesis of the Alzheimer’s drug galanthamine.
New motifs in Ndc1 mediating interaction with the Nup84 complex and nuclear membranes
Authors: Amm Ingo , Weberruss Marion , Hellwig Andrea , Schwarz Johannes , Tatarek-Nossol Marianna , Lüchtenborg Christian , Kallas Martina , Brügger Britta , Hurt Ed , Antonin Wolfram
Published: July 2022

The nuclear pore complex (NPC) embedded in the double nuclear membrane is built from ~30 different nucleoporins (Nups) in multiple copies, of which a few are integral nuclear membrane proteins. One of these transmembrane Nups is Ndc1, which is thought to play a role in interphase NPC assembly at the fused inner and outer nuclear membrane. In this study, we discovered a direct interaction of Ndc1’s transmembrane domain with Nup120 and Nup133, members of the Y-complex that coats the nuclear pore membrane. In addition, we identified a so far unrecognized amphipathic helix (AH) in the C-terminal domain of Ndc1, which can bind to high curvature liposomes. When overexpressed in yeast this amphipathic motif is toxic and dramatically alters the intracellular membrane organization. Further genetic investigations revealed that Ndc1-AH functionally interacts with related motifs in the C-terminus of Nups Nup53 and Nup59, known to serve in nuclear pore membrane binding and link between NPC modules. This relationship could explain why the essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane biogenesis dependent on a balanced ratio between amphipathic motifs in diverse nucleoporins is essential for interphase NPC biogenesis.
Observation of in-plane shear stress fields in off-axis SiC wafers by birefringence imaging
Authors: Harada Shunta , Murayama Kenta
Published: July 2022

For the nondestructive characterization of SiC wafers for power device application, birefringence imaging is one of the promising methods. In the present study, it is demonstrated that birefringence image contrast variation in off-axis SiC wafers corresponds to the in-plane shear stress under conditions slightly deviating from crossed Nicols according to both theoretical consideration and experimental observation. The current results indicate that the characterization of defects in SiC wafers is possible to achieve by birefringence imaging.
Brittle fracture studied by ultra-high-speed synchrotron X-ray diffraction imaging
Authors: Petit Antoine , Pokam Sylvia , Mazen Frederic , Tardif Samuel , Landru Didier , Kononchuk Oleg , Ben Mohamed Nadia , Olbinado Margie P. , Rack Alexander , Rieutord Francois
Published: July 2022

In situ investigations of cracks propagating at up to 2.5 km s−1 along an (001) plane of a silicon single crystal are reported, using X-ray diffraction megahertz imaging with intense and time-structured synchrotron radiation. The studied system is based on the Smart Cut process, where a buried layer in a material (typically Si) is weakened by microcracks and then used to drive a macroscopic crack (10−1 m) in a plane parallel to the surface with minimal deviation (10−9 m). A direct confirmation that the shape of the crack front is not affected by the distribution of the microcracks is provided. Instantaneous crack velocities over the centimetre-wide field of view were measured and showed an effect of local heating by the X-ray beam. The post-crack movements of the separated wafer parts could also be observed and explained using pneumatics and elasticity. A comprehensive view of controlled fracture propagation in a crystalline material is provided, paving the way for the in situ measurement of ultra-fast strain field propagation.