bluuebunny/crossref_metadata_2025 huggingface dataset:
Cooling Intervention (MUSTCOOL) for Prevention of Lower Extremity Ulcer Recurrence
Authors: Kelechi Teresa J. , Madisetti Mohan , Prentice Margaret , Mueller Martina
Published: March 2021

PURPOSE:

The purpose of this study was to test our MUSTCOOL cooling patch intervention on the incidence of venous leg (VLU) and diabetic foot ulcer (DFU) recurrence over a previously healed wound.

DESIGN:

A 6-month randomized controlled trial.

SUBJECTS AND SETTING:

The target population was individuals with previously healed ulcers receiving care in outpatient wound centers in the Southeastern region of the United States. The sample comprised 140 individuals with recently healed ulcers; their average age was 62.4 years (SD = 12 years); 86 (61.4%) were male; and 47 (33.6%) were Black or African American.

METHODS:

Participants were randomized to the MUSTCOOL or placebo patch. Both groups received instructions to apply the patch 3 times per week, and engage in standard of care including compression and leg elevation (VLU) or therapeutic footwear and hygiene (DFU). Demographic data were collected at baseline, and incidence measures taken at 1, 3, and 6 months. We also studied whether new ulcers developed on the adjacent leg or foot. Data were reported in frequencies/percentages.

RESULTS:

One hundred seventeen participants (84%) were analyzed who completed 6 months of study participation. Thirteen percent (9/69) and 17% (12/69) developed a recurrent or new VLU, respectively; 29% (14/48) and 13% (6/48) developed a recurrent or new DFU, respectively. One person in the DFU group developed both a recurrent and new ulcer. For 9 recurrent VLUs, 6 (66.7%) recurred in the MUSTCOOL group and 3 (33.3%) receiving the placebo. Of the 15 recurrent DFUs (includes individual who developed both a recurrent and new ulcer), 10 (66.7%) recurred in the MUSTCOOL group and 5 (33.3%) receiving the placebo.

CONCLUSIONS:

While the incidence of ulcer recurrent was slightly higher in the MUSTCOOL group, this finding was not considered clinically relevant. Overall ulcer recurrence during the 6-month study period was lower than reports in the literature, the time frame in which recurrence rates are highest.

TRIAL REGISTRATION:

The study was prospectively registered with ClinicalTrials.gov on December 10, 2015 (Identifier: NCT02626156)—https://clinicaltrials.gov/ct2/show/NCT02626156.
Fertoeibacter niger gen. nov., sp. nov. a novel alkaliphilic bacterium of the family Rhodobacteraceae
Authors: Szuróczki Sára , Abbaszade Gorkhmaz , Buni Dominika , Bóka Károly , Schumann Peter , Neumann-Schaal Meina , Vajna Balázs , Tóth Erika
Published: March 2021

Three Gram-stain-negative, non-motile, oxidase- and catalase-positive, rod-shaped, black, facultative phototrophic bacterial strains, RG-N-1aT, DMA-N-7a and RA-N-9 were isolated from the water sample from Lake Fertő/Neusiedler See (Hungary). Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains form a distinct linage within the family

Rhodobacteraceae

and their closest relatives are

Tabrizicola piscis

K13M18T (96.32%) followed by

Cypionkella psychrotolerans

PAMC 27389T (96.25%). The novel bacterial strains prefer alkaline environments and grow optimally at 23–33 °C in the presence of NaCl (1–2 w/v%). Bacteriochlorophyll a was detected. Cells contained exclusively ubiquinone Q-10. The major cellular fatty acids were C18 : 1ω7c, C19 : 1iso ω5c, C18 : 0 3-OH and C18 : 1ω7c 11-methyl. The polar lipid profile contains diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid and four unidentified lipids. The assembled draft genome of RG-N-1aT had 33 contigs with N50 values 315 027 nt, 96× genome coverage, total length of 4 326 551 bp and a DNA G+C content of 64.9%. Genome-based calculations (genome-to-genome distance and DNA G+C percentage) and pairwise amino acid identity (AAI <73.5%) indicate that RG-N-1aT represents a novel genus. RG-N-1aT (=DSM 108317T=NCAIM B.02647T) is suggested as the type strain of a novel genus and species in the family

Rhodobacteraceae

, for which the name Fertoeibacter niger gen. nov., sp. nov. is proposed.
Profile of specific antibodies to the SARS-CoV-2
Authors: Mou Danlei , Feng Huahua , Cao Ruiyuan , Weng Xing , Zhao Lizhe , Yang Lingling , Jin Ronghua , Chen Weijun
Published: March 2021

In this work, we studied the profile of IgM and IgG antibody responses to SARS-CoV-2 in 32 patients with COVID-19 from day 1 to day 24. IgM remained measurable for a much shorter period than IgG, suggesting that IgG antibody may represent the primary immune response.
Deep learning-based pan-cancer classification model reveals cancer-specific gene expression signatures
Authors: Divate Mayur , Tyagi Aayush , Richard Derek J , Prasad Prathosh A , Gowda Harsha , Nagaraj Shivashankar H
Published: March 2021

The identification of cancer-specific biomarkers and therapeutic targets is one of the primary goals of cancer genomics. Thousands of cancer genomes, exomes, and transcriptomes have been sequenced to date. In this study, we conducted a pan-cancer analysis of transcriptome datasets from 37 cancer types provided by The Cancer Genome Atlas (TCGA) in an effort to identify cancer-specific gene expression signatures. We employed deep neural networks to train a model on the transcriptome profile datasets for all cancer types. The model was validated, and its predictive accuracy was determined using an independent dataset, achieving > 97% prediction accuracy across cancer types. This strongly suggests that there are distinct gene expression signatures associated with various cancer types. We interpreted the model using SHapley Additive exPlanations (SHAP) to identify specific gene signatures that significantly contributed to the classification of cancer types. In addition to known biomarkers, we identified several novel biomarkers in different cancer types. These cancer-specific gene signatures are valuable candidates for future studies of their potential utility as cancer biomarkers and putative therapeutic targets.
SARS-CoV-2 spike protein induces inflammation via TLR2-dependent activation of the NF-κB pathway
Authors: Khan Shahanshah , Shafiei Mahnoush S. , Longoria Christopher , Schoggins John , Savani Rashmin C. , Zaki Hasan
Published: March 2021

Pathogenesis of COVID-19 is associated with a hyperinflammatory response; however, the precise mechanism of SARS-CoV-2-induced inflammation is poorly understood. Here we investigated direct inflammatory functions of major structural proteins of SARS-CoV-2. We observed that spike (S) protein potently induces inflammatory cytokines and chemokines including IL-6, IL-1ß, TNFa, CXCL1, CXCL2, and CCL2, but not IFNs in human and mouse macrophages. No such inflammatory response was observed in response to membrane (M), envelope (E), and neucleocapsid (N) proteins. When stimulated with extracellular S protein, human lung epithelial cells A549 also produce inflammatory cytokines and chemokines. Interestingly, epithelial cells expressing S protein intracellularly are non-inflammatory, but elicit an inflammatory response in macrophages when co-cultured. Biochemical studies revealed that S protein triggers inflammation via activation of the NF-κB pathway in a MyD88-dependent manner. Further, such an activation of the NF-κB pathway is abrogated in Tlr2-deficient macrophages. Consistently, administration of S protein induces IL-6, TNF-a, and IL-1 ß in wild-type, but not Tlr2-deficient mice. Together these data reveal a mechanism for the cytokine storm during SARS-CoV-2 infection and suggest that TLR2 could be a potential therapeutic target for COVID-19.
Epigallocatechin Gallate from Green Tea Effectively Blocks Infection of SARS-CoV-2 and New Variants by Inhibiting Spike Binding to ACE2 Receptor
Authors: Liu Jinbiao , Bodnar Brittany H , Meng Fengzhen , Khan Adil , Wang Xu , Luo Guangxiang , Saribas Sami , Wang Tao , Lohani Saroj Chandra , Wang Peng , Wei Zhengyu , Luo Jinjun , Zhou Lina , Wu Jianguo , Li Qingsheng , Hu Wenhui , Ho Wenzhe
Published: March 2021

As the COVID-19 pandemic rages on, the new SARS-CoV-2 variants have emerged in the different regions of the world. These newly emerged variants have mutations in their spike (S) protein that may confer resistance to vaccine-elicited immunity and existing neutralizing antibody therapeutics. Therefore, there is still an urgent need of safe, effective, and affordable agents for prevention/treatment of SARS-CoV-2 and its variant infection. Here, we demonstrated that green tea beverage (GTB) or its major ingredient, epigallocatechin gallate (EGCG), were highly effective in inhibiting infection of live SARS-CoV-2 and human coronavirus (HCoV OC43). In addition, infection of the pseudoviruses with spikes of the new variants (UK-B.1.1.7, SA-B.1.351, and CA-B.1.429) was efficiently blocked by GTB or EGCG. Among the 4 active green tea catechins at noncytotoxic doses, EGCG was the most potent in the action against the viruses. The highest inhibitory activity was observed when the viruses or the cells were pre-incubated with EGCG prior to the infection. Mechanistic studies revealed that EGCG blocked infection at the entry step through interfering with the engagement of the receptor binding domain (RBD) of the viral spikes to angiotensin-converting enzyme 2 (ACE2) receptor of the host cells. These data support further clinical evaluation and development of EGCG as a novel, safe, and cost-effective natural product for prevention/treatment of SARS-CoV-2 transmission and infection.
Molecular characterization reveals genomic and transcriptomic subtypes of metastatic urothelial carcinoma
Authors: Alberto Nakauma-González J. , Rijnders Maud , van Riet Job , van der Heijden Michiel S. , Voortman Jens , Cuppen Edwin , Mehra Niven , van Wilpe Sandra , Oosting Sjoukje F. , Lucia Rijstenberg L. , Westgeest Hans M. , Zwarthoff Ellen C. , de Wit Ronald , van der Veldt Astrid A.M. , van de Werken Harmen J. G. , Lolkema Martijn P. J. , Boormans Joost L.
Published: March 2021

Background

Molecular characterization of primary urothelial carcinoma (UC) revealed molecular subtypes with different genomic, transcriptomic, and clinicopathological characteristics, which might guide therapeutic decision making. A comprehensive molecular characterization of metastatic UC (mUC), however, is currently lacking in the literature. Because of the lethality of mUC, with few therapeutic options available for patients, a multi-omics characterization of mUC could aid to improve patient selection for new and existing therapies.

Methods

To define the molecular landscape of mUC and to identify potential targets for therapy, we performed whole genome DNA sequencing on fresh-frozen metastatic tumor biopsies of 116 mUC patients, and mRNA sequencing on 90 matched biopsies.

Results

Hierarchical clustering based on mutational signatures revealed two major genomic subtypes. The most prevalent subtype (67%) consisted almost exclusively of tumors with high APOBEC mutagenesis. APOBEC mutagenesis was detected in 91% of the samples, and appeared to be an ongoing process in mUC based on analysis of eight patients from whom serial biopsies were obtained during treatment. Contrary to the overall distribution of mutations, APOBEC associated mutations occurred throughout the genome, and independently of predicted accessible or transcribed genomic regions, suggesting that these mutations were generated during replication. Transcriptomic analysis revealed five mRNA-based subtypes: two luminal subtypes (40%), a stroma-rich (24%), basal/squamous (23%), and non-specified subtype (12%). The transcriptomic subtypes were different regarding driver gene alterations (e.g. ELF3 and TSC1), gene amplifications (NECTIN4 and PPARG), pathway activity, and immune cell infiltration. By integrating the genomic and transcriptomic data, potential therapeutic options per transcriptomic subtype and individual patient were proposed.

Conclusions

This study expands our knowledge on the molecular landscape of mUC, and serves as a reference for subtype-oriented and patient-specific research on the etiology of mUC, and for novel drug development.

Trial registration

The mUC cohort studied here is part of the Netherlands nationwide study of the center for personalized cancer treatment consortium (CPCT-02 Biopsy Protocol, NCT01855477), and the Drug Rediscovery Protocol (DRUP Trial, NCT02925234).
Programmable pattern formation in cellular systems with local signaling
Authors: Ramalho Tiago , Kremser Stephan , Wu Hao , Gerland Ulrich
Published: March 2021

Diverse complex systems, ranging from developing embryos to systems of locally communicating agents, display an apparent capability of “programmable” pattern formation: They reproducibly form a target pattern, but this target can be readily changed. A distinguishing feature of such systems, as compared to simpler physical pattern forming systems, is that their subunits are capable of information processing. Here, we explore schemes for programmable pattern formation within a theoretical framework, in which subunits process discrete local signals to update their internal state according to logical rules. We study systems with different update rules, different topologies, and different control schemes, to assess their ability to perform programmable pattern formation and their susceptibility to errors. Only a small subset of systems permits local organizer cells to dictate any target pattern. These systems follow a common principle, whereby a temporal pattern is transcribed into a spatial pattern, reminiscent of the clock-and-wavefront mechanism underlying vertebrate somitogenesis. An alternative scheme employing several different rules can only form a fraction of patterns but is robust with respect to the timing of organizer cell inputs. Our results establish a basis for the design of synthetic systems, and for more detailed models of programmable pattern formation closer to real systems.
Antibody repertoire analysis of tumor-infiltrating B cells reveals distinct signatures and distributions across tissues
Authors: Aizik Ligal , Dror Yael , Taussig David , Barzel Adi , Carmi Yaron , Wine Yariv
Published: March 2021

The role of B cells in the tumor microenvironment (TME) has largely been under investigated, and data regarding the antibody repertoire encoded by B cells in the TME and the adjacent lymphoid organs are scarce. Here, we utilized B cell receptor high-throughput sequencing (BCR-Seq) to profile the antibody repertoire signature of tumor-infiltrating lymphocyte B cells (TIL-Bs) in comparison to B cells from three anatomic compartments in a mouse model of triple-negative breast cancer. We found that TIL-Bs exhibit distinct antibody repertoire measures, including high clonal polarization and elevated somatic hypermutation rates, suggesting a local antigen-driven B-cell response. Importantly, TIL-Bs were highly mutated but non-class switched, suggesting that class-switch recombination may be inhibited in the TME. Tracing the distribution of TIL-B clones across various compartments indicated that they migrate to and from the TME. The data thus suggests that antibody repertoire signatures can serve as indicators for identifying tumor-reactive B cells.
Mitochondrial fission is required for proper nucleoid distribution within mitochondrial networks
Authors: Ilamathi Hema Saranya , Ouellet Mathieu , Sabouny Rasha , Desrochers-Goyette Justine , Lines Matthew A. , Pfeffer Gerald , Shutt Timothy E. , Germain Marc
Published: March 2021

Mitochondrial DNA (mtDNA) maintenance is essential to sustain a functionally healthy population of mitochondria within cells. Proper mtDNA replication and distribution within mitochondrial networks are essential to maintain mitochondrial homeostasis. However, the fundamental basis of mtDNA segregation and distribution within mitochondrial networks is still unclear. To address these questions, we developed an algorithm, Mitomate tracker to unravel the global distribution of nucleoids within mitochondria. Using this tool, we decipher the semi-regular spacing of nucleoids across mitochondrial networks. Furthermore, we show that mitochondrial fission actively regulates mtDNA distribution by controlling the distribution of nucleoids within mitochondrial networks. Specifically, we found that primary cells bearing disease-associated mutations in the fission proteins DRP1 and MYH14 show altered nucleoid distribution, and acute enrichment of enlarged nucleoids near the nucleus. Further analysis suggests that the altered nucleoid distribution observed in the fission mutants is the result of both changes in network structure and nucleoid density. Thus, our study provides novel insights into the role of mitochondria fission in nucleoid distribution and the understanding of diseases caused by fission defects.

Significance statement

Mutation or deletion of mitochondrial DNA (mtDNA) is associated with a large number of human diseases. However, the mechanisms controlling mtDNA replication and segregation are still poorly understood. Here, we have developed a new computational method to quantify the distribution of nucleoids (mtDNA with associated proteins) and define how nucleoid distribution is affected by changes in mitochondrial network structure. We demonstrate that mitochondrial fission is required for the proper distribution of nucleoids across mitochondrial networks, cells from patients with fission defects showing irregular nucleoid distribution and perinuclear accumulation. Nonetheless, each fission mutant behaved in a distinct manner, indicating a complex relationship between mitochondrial dynamics and nucleoid distribution.
A Cdc42-Borg4-Septin 7 axis regulates HSCs polarity and function
Authors: Kandi Ravinder , Senger Katharina , Grigoryan Ani , Soller Karin , Sakk Vadim , Schuster Tanja , Eiwen Karina , Menon Manoj B. , Gaestel Matthias , Zheng Yi , Florian Maria Carolina , Geiger Hartmut
Published: March 2021

Aging of hematopoietic stem cells (HSCs) is caused by an elevated activity of the small RhoGTPase Cdc42 and an apolar distribution of proteins. Mechanisms by which Cdc42 activity controls polarity of HSCs are not known. Binder of RhoGTPases proteins (borgs) are known effector proteins of Cdc42 that are able to regulate the cytoskeletal septin network. Here we show that Cdc42 interacts with borg4, which in turn interacts with septin 7 to regulate the polar distribution of Cdc42, borg4 and septin 7 within HSCs. Genetic deletion of either borg4 or septin 7 in HSCs resulted in a reduced frequency of HSCs polar for Cdc42 or borg4 or septin 7 and a reduced engraftment potential and decreased lymphoid-primed multipotent progenitors (LMPPs) frequency in the bone marrow. In aggregation our data identify a Cdc42-borg4-septin 7 axis to be essential for maintenance of polarity within HSCs and for HSC function and provide rationale for further investigating the role of borgs and septins for the regulation of compartmentalization within stem cells.

Graphical Abstract
Clathrin adaptors mediate two sequential pathways of intra-Golgi recycling
Authors: Casler Jason C. , Krahn Adam H. , Pantazopoulou Areti , Johnson Natalie , Day Kasey J. , Glick Benjamin S.
Published: March 2021

The pathways of membrane traffic within the Golgi apparatus are not fully known. This question was addressed using the yeastSaccharomyces cerevisiae, in which the maturation of individual Golgi cisternae can be visualized. We recently proposed that the AP-1 clathrin adaptor mediates intra-Golgi recycling late in the process of cisternal maturation. Here, we demonstrate that AP-1 cooperates with the Ent5 clathrin adaptor to recycle a set of Golgi transmembrane proteins. This recycling can be detected by removing AP-1 and Ent5, thereby diverting the AP-1/Ent5-dependent Golgi proteins into an alternative recycling loop that involves traffic to the plasma membrane followed by endocytosis. Unexpectedly, various AP-1/Ent5-dependent Golgi proteins show either intermediate or late kinetics of residence in maturing cisternae. We infer that the AP-1/Ent5 pair mediates two sequential intra-Golgi recycling pathways that define two classes of Golgi proteins. This insight can explain the polarized distribution of transmembrane proteins in the Golgi.
Burrowing crabs and physical factors hasten marsh recovery at panne edges
Authors: Beheshti Kathryn M. , Endris Charlie , Goodwin Peter , Pavlak Annabelle , Wasson Kerstin
Published: March 2021

Salt marsh loss is projected to increase as sea-level rise accelerates with global climate change. Salt marsh loss occurs along both lateral creek and channel edges and in the marsh interior, when pannes expand and coalesce. Often, edge loss is attributed to erosive processes whereas dieback in the marsh interior is linked to excessive inundation or deposition of wrack. We conducted a two-year field experiment (2016-2018) in a central California estuary, where, immediately preceding our study, marsh dieback at creek edges and panne expansion occurred during a period of severe drought and an overlapping warm water event. Our study explored how an abundant burrowing crab, shown to have strong negative effects on marsh biomass near creek edges, affects panne dynamics. We also explored which panne attributes best predicted their dynamics. Overall, we found that pannes contracted during the study period, but with variable rates of marsh recovery across pannes. Our model incorporating both physical and biological factors explained 86% of the variation in panne contraction. The model revealed a positive effect of crab activity, sediment accretion, and a composite of depth and elevation on panne contraction, and a negative effect of panne size and distance to nearest panne. The positive crab effects detected in pannes contrast with negative effects we had earlier detected near creek edges, highlighting the context-dependence of top-down and bioturbation effects in marshes. As global change continues and the magnitude and frequency of disturbances increases, understanding the dynamics of marsh loss in the marsh interior as well as creek banks will be critical for the management of these coastal habitats.
Representations of context and context-dependent values in vmPFC compete for guiding behavior
Authors: Moneta Nir , Garvert Mona M. , Heekeren Hauke R. , Schuck Nicolas W.
Published: March 2021

Value representations in ventromedial prefrontal-cortex (vmPFC) are known to guide the choice between options. But the value of an option can be different in different task contexts. Goal-directed behavior therefore requires to know the current context and associated values of options, and to flexibly switch between value representations in a task-dependent manner. We tested whether task-relevant and -irrelevant values influence behavior and asked whether both values are represented together with context signals in vmPFC. Thirty-five participants alternated between tasks in which stimulus color or motion predicted rewards. As expected, neural activity in vmPFC and choices were largely driven by task-relevant values. Yet, behavioral and neural analyses indicate that participants also retrieved the values of irrelevant features, and computed which option would have been best in the alternative context. Investigating the probability distributions over values and contexts encoded in multivariate fMRI signals, we find that vmPFC maintains representations of the current context, i.e. task state, the value associated with it, and the hypothetical value of the alternative task state. Crucially, we show that evidence for irrelevant value signals in vmPFC relates to behavior on multiple levels, competes with expected value signals, and interacts with task state representations. Our results thus suggest that different value representations are represented in parallel and imply a link between neural representations of task states, their associated values and their influence on behavior. This sheds new light on vmPFC’s role in decision making, bridging between a hypothesized role in mapping observations onto the task states of a mental map, and computing value expectations for alternative states.
A squalene-hopene cyclase inSchizosaccharomyces japonicusrepresents a eukaryotic adaptation to sterol-independent anaerobic growth
Authors: Bouwknegt Jonna , Wiersma Sanne J. , Ortiz-Merino Raúl A. , Doornenbal Eline S. R. , Buitenhuis Petrik , Giera Martin , Müller Christoph , Pronk Jack T.
Published: March 2021

Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report (Bulder (1971), Antonie Van Leeuwenhoek, 37, 353–358) thatSchizosaccharomyces japonicusis exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grownSch. japonicusshowed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene and hopan-22-ol. A putative gene inSch. japonicusshowed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those ofAcetobacterspecies. No orthologs of the putativeSch. japonicusSHC were found in other yeast species. Expression of theSch. japonicusSHC gene (Sjshc1) inSaccharomyces cerevisiaeenabled hopanoid synthesis and supported ergosterol-independent anaerobic growth, thus confirming that one or more of the hopanoids produced by SjShc1 can act as ergosterol surrogate in anaerobic yeast cultures. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast sterol-independent anaerobic growth ofSch. japonicusis an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.

Significance statement

Biosynthesis of sterols requires oxygen. This study identifies a previously unknown evolutionary adaptation in a eukaryote, which enables anaerobic growth in absence of exogenous sterols. A squalene-hopene cyclase, proposed to have been acquired by horizontal gene transfer from an acetic acid bacterium, is implicated in a unique ability of the yeastSchizosaccharomyces japonicusto synthesize hopanoids and grow in anaerobic, sterol-free media. Expression of this cyclase in S.cerevisiaeconfirmed that at least one of its hopanoid products acts as sterol-surrogate. The involvement of hopanoids in sterol-independent growth of this yeast provides new leads for research into the structure and function of eukaryotic membranes, and into the development of sterol-independent yeast cell factories for application in anaerobic processes.
A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component
Authors: Leong Jia Xuan , Raffeiner Margot , Spinti Daniela , Langin Gautier , Franz-Wachtel Mirita , Guzman Andrew R. , Kim Jung-Gun , Pandey Pooja , Minina Alyona E. , Macek Boris , Hafrén Anders , Bozkurt Tolga O. , Mudgett Mary Beth , Börnke Frederik , Hofius Daniel , Üstün Suayib
Published: March 2021

Beyond its role in cellular homeostasis, autophagy plays anti- and pro-microbial roles in host-microbe interactions, both in animals and plants. One prominent role of anti-microbial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. Here, we provide evidence thatXanthomonas campestrispv.vesicatoria (Xcv)suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in depletion of a bacterial virulence factor and unravels an unprecedented pathogen strategy to counteract defense-related autophagy.
Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies
Authors: Greaney Allison J. , Starr Tyler N. , Barnes Christopher O. , Weisblum Yiska , Schmidt Fabian , Caskey Marina , Gaebler Christian , Cho Alice , Agudelo Marianna , Finkin Shlomo , Wang Zijun , Poston Daniel , Muecksch Frauke , Hatziioannou Theodora , Bieniasz Paul D. , Robbiani Davide F. , Nussenzweig Michel C. , Bjorkman Pamela J. , Bloom Jesse D.
Published: March 2021

Monoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasma, including plasma from individuals from whom some of the antibodies were isolated. The plasma-escape maps most closely resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is dominated by a single class of antibodies targeting an epitope that is already undergoing rapid evolution.
Synthesis of the NarP response regulator of nitrate respiration inEscherichia coliis regulated at multiple levels by Hfq and small RNAs
Authors: Brosse Anaïs , Walburger Anne , Magalon Axel , Guillier Maude
Published: March 2021

Two-component systems (TCS) and small RNAs (sRNA) are widespread regulators that participate in the response and the adaptation of bacteria to their environments. They mostly act at the transcriptional and post-transcriptional levels, respectively, and can be found integrated in regulatory circuits, where TCSs control sRNAs transcription and/or sRNAs post-transcriptionally regulate TCSs synthesis.

In response to nitrate and nitrite, the paralogous NarQ-NarP and NarX-NarL TCSs regulate the expression of genes involved in anaerobic respiration of these alternative electron acceptors. In addition to the previously reported repression of NarP synthesis by the SdsN137sRNA, we show here that RprA, another Hfq-dependent sRNA, also negatively controlsnarP. Interestingly, the repression ofnarPby RprA actually relies on two independent controls. The first isviathe direct pairing of the central region of RprA to thenarPtranslation initiation region and presumably occurs at the translation initiation level. In contrast, the second control requires only the very 5’ end of thenarPmRNA, which is targeted, most likely indirectly, by the full-length or the shorter, processed, form of RprA. In addition, our results raise the possibility of a direct role of Hfq innarPcontrol, further illustrating the diversity of post-transcriptional regulation mechanisms in the synthesis of TCSs.
CRISPR-Targeted CAR Gene Insertion Using Cas9/RNP and AAV6 Enhances Anti-AML Activity of Primary NK Cells
Authors: Kararoudi Meisam Naeimi , Likhite Shibi , Elmas Ezgi , Yamamoto Kenta , Schwartz Maura , Sorathia Kinnari , de Souza Fernandes Pereira Marcelo , Devin Raymond D , Lyberger Justin M , Behbehani Gregory K , Chakravarti Nitin , Moriarity Branden S. , Meyer Kathrin , Lee Dean A.
Published: March 2021

Human peripheral blood natural killer (NK) cells have intense antitumor activity and have been used successfully in several clinical trials. Modifying NK cells with a chimeric antigen receptor (CAR) can improve their targeting and increase specificity. Recently, we described an efficient method for gene targeting in NK cells using Cas9/ribonucleoprotein (RNP) complexes. Here we combined this approach with single-stranded (ss) or self-complementary (sc) Adeno-associated virus (AAV)-mediated gene delivery for gene insertion into a safe-harbor locus using a wide variety of homology arms for homology repair (HR) and non-homologous directed CRISPR-assisted insertion tagging (CRISPaint) approaches. For proof-of-concept, we generated mCherry-expressing primary NK cells and determined that sc vectors with 300bp homology arms had optimal transduction efficiency. Then, we generated CD33-targeting CAR NK cells with differing transmembrane and signaling domains (CD4/4-1BB+CD3ζ and NKG2D/2B4+CD3ζ) and expanded them on CSTX002 feeder cells. Expansion kinetics were unaltered and the expanded NK cells maintained high CAR expression (mean 68% CAR+). The CD33-CAR-NK cells showed increased activation markers and enhanced antileukemic activity with improved killing kinetics against CD33-positive acute myeloid leukemia (AML) cell lines and primary samples. Using targeted sequencing we demonstrated the accuracy of CAR gene insertion in human primary NK cells genome. Site-directed insertion using RNP and scAAV6 is an efficient method for stable genetic transfer into primary NK cells that has broad potential for fundamental discovery and therapeutic applications.
β-Carotene oxidation products - function and safety
Authors: Burton Graham W. , Mogg Trevor J. , Riley William W. , Nickerson James G.
Published: March 2021

β-Carotene oxidation products have newly discovered bioactivity in plants and animals. Synthetic fully oxidized β-carotene (OxBC) has application in supporting livestock health, with potential human applications. The safety of synthetic OxBC has been evaluated. An Ames test showed weak-to-moderate mutagenicity in only one cell line at high concentrations. A mouse micronucleus assay established a non-toxic dose of 1800 mg/kg body weight, and no bone marrow micronuclei were induced. Plant sources of β-carotene inevitably contain varying levels of natural OxBC. Vegetable powders and dried forages can be especially rich. Intakes of natural OxBC for humans and livestock alike have been estimated. The exposure range for humans (1-22 mg/serving) is comparable to the safe intake of β-carotene (<15 mg/d). In livestock, OxBC in alfalfa can contribute ~550-850 mg/head/d for dairy cattle but in forage-deficient poultry feed much less (~1 ppm). Livestock intake of supplemental synthetic OxBC is comparable to OxBC potentially available from traditional plant sources. Human intake of synthetic OxBC in meat from livestock fed OxBC is similar to a single serving of food made with carrot powder. It is concluded that consumption of synthetic OxBC at levels comparable to natural OxBC is safe for humans and animals.
Tight nanoscale clustering of Fcγ-receptors using DNA origami promotes phagocytosis
Authors: Kern Nadja , Dong Rui , Douglas Shawn M. , Vale Ronald D. , Morrissey Meghan A.
Published: March 2021

Macrophages destroy pathogens and diseased cells through Fcγ receptor (FcγR)-driven phagocytosis of antibody-opsonized targets. Phagocytosis requires activation of multiple FcγRs, but the mechanism controlling the threshold for response is unclear. We developed a DNA origami-based engulfment system that allows precise nanoscale control of the number and spacing of ligands. When the number of ligands remains constant, reducing ligand spacing from 17.5 nm to 7 nm potently enhances engulfment, primarily by increasing efficiency of the engulfment-initiation process. Tighter ligand clustering increases receptor phosphorylation, as well as proximal downstream signals. Increasing the number of signaling domains recruited to a single ligand-receptor complex was not sufficient to recapitulate this effect, indicating that clustering of multiple receptors is required. Our results suggest that macrophages use information about local ligand densities to make critical engulfment decisions, which has implications for the mechanism of antibody-mediated phagocytosis and the design of immunotherapies.
Identification and characterization of conserved noncoding cis-regulatory elements that impact Mecp2 expression and neurological functions
Authors: Shao Yingyao , Bajikar Sameer S. , Tirumala Harini P. , Gutierrez Manuel Cantu , Wythe Joshua D. , Zoghbi Huda Y.
Published: March 2021

While changes in MeCP2 dosage cause Rett syndrome (RTT) and MECP2 duplication syndrome (MDS), its transcriptional regulation is poorly understood. Here, we identified six putative noncoding regulatory elements of Mecp2, two of which are conserved in humans. Upon deletion in mice and human iPSC-derived neurons, these elements altered RNA and protein levels in opposite directions and resulted in a subset of RTT- and MDS-like behavioral deficits in mice. Our discovery provides insight into transcriptional regulation of Mecp2/MECP2 and highlights genomic sites that could serve as diagnostic and therapeutic targets in RTT or MDS.
MATSAS: a small-angle scattering computing tool for porous systems
Authors: Rezaeyan Amirsaman , Pipich Vitaliy , Busch Andreas
Published: March 2021

MATSAS is a script-based MATLAB program for analysis of X-ray and neutron small-angle scattering (SAS) data obtained from various facilities. The program has primarily been developed for sedimentary rock samples but is equally applicable to other porous media. MATSAS imports raw SAS data from .xls(x) or .csv files, combines small-angle and very small angle scattering data, subtracts the sample background, and displays the processed scattering curves in log–log plots. MATSAS uses the polydisperse spherical (PDSP) model to obtain structural information on the scatterers (scattering objects); for a porous system, the results include specific surface area (SSA), porosity (Φ), and differential and logarithmic differential pore area/volume distributions. In addition, pore and surface fractal dimensions (D
p and D
s, respectively) are obtained from the scattering profiles. The program package allows simultaneous and rapid analysis of a batch of samples, and the results are then exported to .xlsx and .csv files with separate spreadsheets for individual samples. MATSAS is the first SAS program that delivers a full suite of pore characterizations for sedimentary rocks. MATSAS is an open-source package and is freely available at GitHub (https://github.com/matsas-software/MATSAS).
In situ X-ray diffraction investigation of electric-field-induced switching in a hybrid improper ferroelectric
Authors: Clarke Gabriel , Ablitt Chris , Daniels John , Checchia Stefano , Senn Mark S.
Published: March 2021

Improper ferroelectric mechanisms are increasingly under investigation for their potential to expand the current catalogue of functional materials whilst promoting couplings between ferroelectricity and other technologically desirable properties such as ferromagnetism. This work presents the results of an in situ synchrotron X-ray diffraction experiment performed on samples of Ca2.15Sr0.85Ti2O7 in an effort to elucidate the mechanism of hybrid improper ferroelectric switching in this compound. By simultaneously applying an electric field and recording diffraction patterns, shifts in the intensity of superstructure peaks consistent with one of the switching mechanisms proposed by Nowadnick & Fennie [Phys. Rev. B, (2016), 94, 104105] are observed. While the experiment only achieves a partial response, comparison with simulated data demonstrates a preference for a one-step switching mechanism involving an unwinding of the octahedral rotation mode in the initial stages of switching. These results represent some of the first reported experimental diffraction-based evidence for a switching mechanism in an improper ferroelectric.
Is public healthcare healthy? The role of emotional exhaustion
Authors: López-Cabarcos M. Ángeles , López-Carballeira Analía , Ferro-Soto Carlos
Published: March 2021

Purpose

This study analyzes the mediating effect of emotional exhaustion between certain job demands (workload, role conflict, and influence at work) and employees' work attitudes (affective commitment and turnover intention) in public healthcare. Furthermore, it analyzes the moderating effect of possibilities for development and the degree of freedom at work between the above-mentioned job demands and emotional exhaustion.

Design/methodology/approach

A total of 512 healthcare professionals participated in the study. The data were analyzed using structural equation modeling and a hierarchical multiple regression analysis.

Findings

The results show that emotional exhaustion fully mediates the relationship between job demands (workload and role conflict) and work attitudes (affective commitment and turnover intention). Moreover, the possibilities for development and degree of freedom at work moderate the relationship between role conflict and emotional exhaustion.

Practical implications

Strategies should be designed to prevent employees from becoming emotionally exhausted and lead them to feel more motivated, which results in a more effective public healthcare service.

Originality/value

This study stresses the importance of analyzing the role of emotional exhaustion in the public healthcare context. It demonstrates the mediating role of this variable between several antecedents and consequences, and it analyzes whether other relevant variables can moderate the negative effects of emotional exhaustion.
Hermite polynomial normal transformation for structural reliability analysis
Authors: Wang Jinsheng , Aldosary Muhannad , Cen Song , Li Chenfeng
Published: March 2021

Purpose

Normal transformation is often required in structural reliability analysis to convert the non-normal random variables into independent standard normal variables. The existing normal transformation techniques, for example, Rosenblatt transformation and Nataf transformation, usually require the joint probability density function (PDF) and/or marginal PDFs of non-normal random variables. In practical problems, however, the joint PDF and marginal PDFs are often unknown due to the lack of data while the statistical information is much easier to be expressed in terms of statistical moments and correlation coefficients. This study aims to address this issue, by presenting an alternative normal transformation method that does not require PDFs of the input random variables.

Design/methodology/approach

The new approach, namely, the Hermite polynomial normal transformation, expresses the normal transformation function in terms of Hermite polynomials and it works with both uncorrelated and correlated random variables. Its application in structural reliability analysis using different methods is thoroughly investigated via a number of carefully designed comparison studies.

Findings

Comprehensive comparisons are conducted to examine the performance of the proposed Hermite polynomial normal transformation scheme. The results show that the presented approach has comparable accuracy to previous methods and can be obtained in closed-form. Moreover, the new scheme only requires the first four statistical moments and/or the correlation coefficients between random variables, which greatly widen the applicability of normal transformations in practical problems.

Originality/value

This study interprets the classical polynomial normal transformation method in terms of Hermite polynomials, namely, Hermite polynomial normal transformation, to convert uncorrelated/correlated random variables into standard normal random variables. The new scheme only requires the first four statistical moments to operate, making it particularly suitable for problems that are constraint by limited data. Besides, the extension to correlated cases can easily be achieved with the introducing of the Hermite polynomials. Compared to existing methods, the new scheme is cheap to compute and delivers comparable accuracy.
The interplay between financial rules, trust and power in strategic partnerships in the construction industry
Authors: Koolwijk Jelle , van Oel Clarine , Bel Mirjam
Published: March 2021

Purpose

To explore how and why the social structures of strategic partnerships are shaped by actors and how these interrelate with a team's interpersonal relationships over time. Grasping the complexity of this interplay is essential if we want to comprehend what actually goes on in these partnerships and understand why actors often disengage from them.

Design/methodology/approach

In three cases, 14 in-depth interviews were held with knowledgeable actors about important events and activities that influenced the relationships between partners. Interview data were triangulated with journals kept by the lead author, who participated as an engaged scholar in the three cases. Because this study took an interdisciplinary approach, new insights could evolve from the multi-level analysis.

Findings

Trust has a moderating effect on the relation between open-book accounting and the degree of control a dominant party wants to exercise. When the level of control is raised, this can signal distrust to the other partners, which can harm the relationship. When partners feel more dependent on each other's capabilities to reach their long-term goals, the parties seem to be less likely to put the blame on one of the partners in the case of undesirable events.

Practical implications

Managers should be aware of their power position and acknowledge the effects of power on their relationships. If long-term and close collaboration does not emerge in their partnership, it may be due to how they use their power position.

Originality/value

Thanks to the interdisciplinary approach, this is the first study that shows the significance of trust and power in maintaining strategic partnerships in the construction industry, and how trust can affect the financial rules of actors.
Using issue logs to improve construction project performance
Authors: Shalwani Amirali , Lines Brian
Published: March 2021

Purpose

The Project Management Body of Knowledge recommends the use of issue logs as a best practice to minimize the potential project cost and schedule growth. Although the broader topic of project control has been widely studied in the construction literature, the specific application of issue logs has remained relatively understudied. This study aims to analyze the extent and consistency with which construction teams utilize issue logs and the corresponding project performance outcomes.

Design/methodology/approach

A dataset of 5,635 individual issues was gathered from the final issue logs of 881 small building projects delivered via the design–bid–build method. Differences between groups were determined using the Kruskal–Wallis H test with post hoc testing via the Mann–Whitney U test with pairwise comparison.

Findings

The results showed that, on average, project teams who used issue logs to a greater extent achieved a 3.1 to 4.3% reduction in cost growth and a 5.3 to 12.3% reduction in schedule growth. This result shows that issue logs can be used to improve construction project performance in the areas of cost and schedule.

Originality/value

This result provides a contribution to practitioners, wherein project teams should be encouraged to establish their issue management practices early in the project schedule to encourage greater issue log usage for the remainder of the project.